University of California_ Berkeley

University of California,

Berkeley



College of Natural Resources



SPRING SEMESTER 2008



Honors Research Program



PROJECT ABSTRACTS









Susan Kishi, Program Manager

Prof. Tasios Melis, Symposium Organizer and Host

CNR HONORS RESEARCH ABSTRACTS; BY PAGE LISTED

3. Allen Lucy.doc

4. Ananth Aditi.doc

5. Ben-Zekry Barruch.doc

6. Blosse Pierre.doc

7. Castillo Jessica.doc

8. Chadwick Katherine.doc

9. Chan Sharon.doc

10. Cocking Amanda.doc

11. Corral Jr Ismael.doc

12. Creed Elizabeth.doc

13. Early Desirae.doc

14. Engleman Marissa.doc

15. Feder Tay.doc

16. Fox Emily.doc

17. Gonzalez Joel.doc

18. Halliday Fletcher.doc

19. Hanna Zachary.doc

20. Henriquez Claudia.doc

21. Hung Yuen Wai.doc

22. Ikeda John.doc

23. Jen Maxwell.doc

24. Kim Min.doc

25. Kolahi Kourosh.doc

26. Kwong Stanley.doc

27. Lagomarsino Laura.doc

28. Lara Lesley.doc

29. Lau Alex.doc

30. Lee Angie.doc

31. Lee Kevin.doc

32. Lin Daniel.doc

33. Lindsey Spencer.doc

34. Liu William.doc

35. Martinez-Romo Miguel.doc

36. McGown Kathryn.doc

37. McKenney Michelle.doc

38. Montes Eva.doc

39. Padilla Miguel.doc

40. Saad Katherine.doc

41. Schulte Peter.doc

42. Silva Radolfo.doc

43. Sweeney Colin.doc

44. Tan Han-Qi.doc

45. Thomson Madison .doc

46. Totsuka Mayuko.doc

47. Truong Linda.doc

48. Ward Anna.doc

49. Yang April.doc

50. Yu Angela.doc

51. Yu Dawn.doc







2

SOIL ORGANIC CARBON DYNAMICS ACROSS A GRADIENT OF EARTHWORM

INVASION IN A NORTHERN MICHIGAN HARDWOOD FOREST

Lucy H. Allen, (Gordon Frankie, Margaret Torn)

Conservation and Resource Studies, (ESPM)



Many previously earthworm-free regions of northern North America are now being

invaded by European worm species. Previous studies on the impacts of earthworms on soil

organic C and N have shown that they can cause significant changes. Understanding the effects

of earthworms on northern forest soils will be critical for effectively managing these forests, and

will increase our overall understanding of soil organic C cycling and storage.

We looked at soils sampled at 3 depths (0-10cm, 10-20cm and 20-50cm), plus organic

horizons, in 3 sites along a gradient of worm invasion in the Huron Mountains, Michigan. Using

a density separation method, soils were separated into four organic C pools which turnover at

different rates: organic matter that is not mineral associated or protected within aggregates (free

light fraction, free LF), organic matter protected within aggregates (occluded light fraction,

occluded LF), organic matter associated with minerals with a density of less than 2.4g/cm3

(intermediate fraction, IF), and organic matter associated with minerals with a density greater

than 2.4g/cm3 (dense fraction, DF). Bulk soils and soil fractions were analyzed for C, N, and 14C

content, and data for the low worm density site (LW site) and high worm density site (HW site)

were compared in order to understand the effects of earthworms on C cycling dynamics. Here

we report only C and 14C results. 14C is used to estimate the rate of C turnover, with higher 14C

values indicating faster turnover relative to soil C with lower 14C values.

Increased worm density resulted in 1) redistribution and reduction in mass of total C

within the entire soil profile through incorporation of organic soil horizons into the mineral soil,

and 2) decreased stability of C in the mineral soil. The entire soil profile in the HW site

contained 4% less gC/m2 than the LW site; however, the mineral soil (excluding organic

horizons) of the HW site contained 26% more gC/m2. Analysis of ∆14C values in the soil

fractions gives greater resolution to the overall trends apparent in the bulk soil. Our data suggest

major pathways of C redistribution in the HW site that differ with depth; the upper soil is

dominated by a decrease in size of the free LF C pool and incorporation of organic horizons

primarily into the occluded LF and IF, whereas the lowest depth is dominated by redistribution

of the previously stable occluded LF C pool to the IF and DF in addition to loss of the free LF.

Occluded LF ∆14C values were 27 to 100‰ greater in the HW than the LW site, indicating that

worms caused destabilization of aggregates and incorporation of C from the organic horizons,

which had high ∆14C values, into new aggregates. In the top two depths, ∆14C values for IF and

DF were higher in the HW site as well, indicating more rapid turnover and incorporation of

organic horizons into these fractions. In the bottom depth, ∆14C values for IF and DF decreased,

but as a percentage of total C these pools increased. Thus, these fractions must be incorporating

C with low ∆14C, most likely from the previously stable occluded LF pool. This mechanism is

probably occurring across depths but is most evident in the bottom depth where C inputs and

overall activity are lower. The introduction of earthworms to this forest soil has fundamentally

changed the storage, distribution, and turnover of soil organic C.

This program gave me the valuable experience of engaging in the entire scientific process

from formulation of questions to data analysis, while learning from and collaborating with field

experts. It also provided me with a better understanding of what graduate school might be like as

well as a glimpse into the professional academic world.





3

PHOSPHORYLATION AND ACETYLATION OF USF-1 FUNCTIONS AS A SENSOR

FOR NUTRITIONAL STATUS.

Aditi Lalitha Ananth, (Dr. Hei Sook Sul)

Nutritional Sciences: Physiology and Metabolism, (Dept. of Nutritional Sciences & Toxicology)



Diabetes is a major concern with the increased prevalence in obesity worldwide.

Lipogenesis is exquisitely regulated by nutritional/hormonal states. To understand the regulation

of fatty acid synthesis between fasting/feeding we have studied the transcriptional regulation of

Fatty Acid Synthase (FAS) as a model. This enzyme plays a central role in fatty acid

biosynthesis during feeding and is regulated transcriptionally, therefore indicating the nutritional

status of the organism. FAS is transcriptionally regulated by USF which is constitutively bound

to the E-box and plays a critical role in mediating the transcriptional activation of lipogenesis in

response to feeding/insulin. Here, we show phosphorylation of USF by Kinase X at a specific

site, and acetylation of USF at a specific site during feeding. This phosphorylation and

acetylation of USF functions as a molecular switch for the FAS promoter activation. To further

confirm these molecular events in animals, we determined USF phosphorylation by feeding in

Kinase X deficient mice (KXD). Our studies reveal a novel signaling pathway involving USF as

a molecular sensor for nutritional status. During the program, I learned to work independently

yet also cooperate with other undergraduates to attain a common goal. Applying the concepts

I’ve learned in classes to real research has also trained me to critically analyze other scientific

studies, a skill I know I will need in the future.









4

EFFECT ON SALES OF POPCORN FROM A “SEAL OF APPROVAL” MADE ON ITS

NUTRITION CLAIMS

Barruch Ben-Zekry, (Sofia Berto Villas-Boas)

Environmental Economics and Policy



Since the inception of the National Label and Education Act (NLEA) numerous studies

have shown that consumers respond favorably to higher levels of transparency with regard to

nutrition information on the food they consume (Burton & Biswas, Moorman & DuMela,

Krutchfield, Kuchler & Variyam etc.). However, there still remains a subset of consumers who

do not use nutrition labels when making their food purchasing decisions (Nayga). My research

appeals to this group of unresponsive consumers. Using a seal of approval on nutrition claims, I

attempt to find a way of adding additional credibility to those claims in the hopes of increasing

their overall use. My research was done in conjunction with a larger study that investigates

empirically whether consumers respond to point of purchase changes in nutritional information

in general. I examine if consumers respond to a seal of approval regarding that nutrition

information.

The food product used in our study was popcorn and the venue for our research was a

major food retailer. Five treatment stores were randomly selected and a four-week treatment

cycle was exercised on each of the five stores. During the treatment cycle our research team

added additional labels to specific popcorn products at each of the stores consisting of nutrition

information that corresponded directly to those products. My research focuses on two labels

placed on a variety of corresponding products. The first label read “low fat” while the second

read “low fat” and below that “According to FDA Nutrient Content Claims”. The two labels

were placed on the same products but at different stores.

There are two main results of my study. In the first, I find that low fat popcorn products

tend to sell less on average than non-low fat popcorn products with or without an additional

label. This result was highly statistically significant. Popcorn tends to be a food of indulgence

and low fat does is not typically a characteristic sought after in such foods. In the second, adding

a seal of approval to low-fat claims further depreciates sales of low fat popcorn products. This

result was statistically significant at the ten percent level. The second result seams to indicate

that the seal of approval adds additional credibility to the nutrition claim thusly exacerbating the

effect of the label itself. If seals of approval were widely used they could both increase the

quality of food purchases for consumers and increase sales of healthier foods for producers. If a

seal was used on a food whose health attributes consumers valued it could lead to increased sales

of the healthier food. This would give way to additional health benefits for consumers and higher

revenues for producers.

Being a part of the CNR honors thesis program taught me a great deal about independent

research. Prior to participating in this program I had never performed a real empirical study on

my own research topic. Through the program I was able to learn how to properly form a research

question, to some extent administer an empirical study and think critically about empirical

results. As an exercise I feel that the program was highly beneficial overall. Not only will it help

me in pursuing a graduate education in economics should I decide to but it was a critical element

in obtaining employment set to begin after graduation.









5

TOWARD DEVELOPMENT OF A GENE-TARGETING TOOL IN WHEAT USING

MAIZE AC/DS

Pierre-Alain Blosse, (Peggy G. Lemaux)

Genetics and Plant Biology, (Sponsoring CNR Department)



Cereal crops account for two-thirds of the world’s food supply. For thousands of years

improvements were made using conventional breeding techniques, in particular cross-

hybridization. With advances in biotechnology and genetic engineering in recent years, new

methods to improve cereal crops have surfaced, allowing for faster and more precise

enhancements. However, it is difficult to effectively engineer a cereal without knowing more

about its genome and the genes it contains, which is why there has been a push to sequence

entire genomes of important crop species, such as rice. Unfortunately the wheat genome is too

large to sequence today – about forty times the size of the rice genome. Thus, we have to resort

to other methods to learn about wheat’s genes and what they do. One such method utilizes the

Ac/Ds transposon system, which through controlled movement around the genome can insert

into genes (it has a preference to move into genes). By doing so it turns expression of genes off

and enables us to find genes – in the sea of noncoding sequences – and to determine what

happens to the plant when the gene is turned off. The Ac/Ds transposon system comes from

maize, and has successfully been inserted and used in a number of heterologous systems,

including barley in my host laboratory. In my project, efforts will be initiated to introduce into

wheat genome the mobile element, Ds, and the gene for the enzyme, AcTPase, that is responsible

for the movement of Ds.

Seven transformations were performed between November 2007 and April 2008. The

first one was a particle bombardment of 159 embryos on November 1st 2007, using Ds and hpt

(hygromycin resistance) as a selectable marker. These embryos were selected on increasing

concentrations of hygromycin, and four survived and are being grown on soil. PCR and Southern

Blotting will be done shortly to assess if they do have the Ds transgene. The second

transformation was an Agrobacterium-mediated transformation of 179 embryos with AcTPase

and hpt as a selectable marker, on November 19 2007. None made it through the selection phase.

The third and fourth transformations were done with bombardment of Ds with PMI as a

selectable marker, and AcTPase with PMI as a selectable marker, both with about 100 embryos

on February 8 2008. These were unfortunately contaminated with bacteria, and no embryos

survived. The fifth transformation was done with bombardment of AcTPase with PMI as a

selectable marker on March 7 2008, using 36 embryos. These are being selected with increasing

concentrations of mannose, and so far a few are rigorously growing and are probably transgenic.

Further tests (PCR, Southern Blots) when these are bigger will be performed. The sixth and

seventh transformations were bombardments of Ds and Ac with PMI as a selectable marker, on

April 4 2008, with 62 and 74 embryos respectively. These have just been put on selection media

containing mannose. When the selection process is finished, any surviving embryos will be

tested with PCR and Southern blotting for the transgenes.

This program has been very important and rewarding to me. I have been working in the

lab for 2 years, and finally getting my own project was very satisfying. I was able to not only

learn many important laboratory techniques, but also had to learn when and how to plan

experiments. I learned that science takes time, experiments can take months or years and many

things can go wrong with them in the meantime, but you just have to accept it. This program

showed me the life of a scientist much better than any of the classes I have taken at Cal.





6

ENDANGERED FECES: AN ANALYSIS OF PREDATOR DIET AT CARRIZO PLAIN

NATIONAL MONUMENT, CALIFORNIA

Jessica A. Castillo, (Justin Brashares)

Conservation and Resource Studies, (Environmental Science Policy and Management)



The partitioning of prey among co-occurring predator species is an important strategy for

minimizing interspecific competition over limited resources. Many studies have focused on this

niche partitioning; however, few studies have looked empirically at dietary overlap among

multiple, sympatric predator species. I quantified the diet of three major predators; coyote (Canis

latrans), San Joaquin kit fox (Vulpes macrotis mutica), and Great Horned Owl (B u b o

virginianus) at the Carrizo Plain National Monument in Central California. The Carrizo Plain is

the largest remaining fragment of the San Joaquin Valley biogeographic province and home to

several state and federally listed flora and fauna, including the San Joaquin kit fox and the giant

kangaroo rat (Dipodomys ingens). In this study, I investigated the relative diversity of predator

diets as well as overlap in food niche among my three focal species. I also examined seasonal

changes in diet composition within and between these focal species. I particularly focused

throughout this study on the giant kangaroo rat as an important prey item because it is both an

endangered species and a keystone species in this ecosystem.

I identified 30 food item categories from owl pellets (n=55), coyote scat (n=48), and kit

fox scat (n=65). Food items included mammals, birds, lizards, arthropods, and plants. Mammals

were the most common prey, with rodents comprising 51% of all food items. Food niche breadth

(FNB) was calculated for each predator species using an inverse Simpson index. Coyote diet was

the most diverse with 21 different food items and FNB of 9.3. Kit fox diet was the least diverse,

consisting of only 10 food categories and a FNB of 4.77. Owls were intermediate with 16 food

categories and FNB of 8.38. There was relatively little overlap in food niche among predator

species; with coyotes and kit foxes exhibiting the least amount of overlap. Kit foxes were diet

specialists that preyed primarily on kangaroo rats (Dipodomys sp.) and arthropods (51% and 44%

of diet, respectively). In contrast, owls and Coyotes were generalists, with no single prey

category comprising more than 22% of their diets. Diet composition for predator species varied

between the fall and spring. Although few of these differences were statistically significant,

orthoptera (grasshoppers, Jerusalem crickets, etc.) were a significantly more common prey item

in the fall, and coyotes consumed significantly more juniper berries in the fall than in the spring.

Coyotes, kit foxes, and owls appear to avoid competition through food niche partitioning.

Coyotes prey more often on large mammals such as pocket gophers (Thomomys bottae) and

leporids (rabbits and hares), and owls prey more often on small mammals such as pocket mice

(Chaetodipus californicus). However, both species also frequently prey on kangaroo rats,

particularly D. ingens. Giant kangaroo rats are a keystone species in this ecosystem. They alter

the plant community through seed caching and preferential seed predation, and are a major food

source for predators. Dipodomys ingens accounted for more than 20% of all the prey items in this

study. This high frequency of predation has important implications for management strategies,

especially when you find one endangered species in another endangered species’ feces.

Participating in this research project allowed me to pursue a question and field of study in

which I was very interested, but had little experience. I was able to make use of the skills I

acquired through my career as a student and I gained valuable knowledge and experience that

cannot be taught in a classroom. Working one-on-one with my faculty mentor was inspiring and,

overall, I feel more prepared for my future endeavors.





7

MARKET STRUCTURE AND CONSUMER PREFERENCES FOR LIVESTOCK

PRODUCTS IN LAO PDR

Katherine Chadwick, (David Roland-Holst)

Environmental Economics and Policy



Rural populations in developing countries are highly dependent on livestock for nutrition,

agricultural services, and direct income. In the last context, demand for animal products rises

rapidly with income, offering otherwise isolated poor farmers a way to participate in urban

growth through food markets. This market participation is seriously complicated, however, but

information failures across informal supply chains that link rural household producers to urban

consumers. Because middlemen often transfer animals to wholesale and retail markets,

smallholder products are pooled and adverse selection results, i.e. there is no incentive for small

holders to invest in improving product quality. This puts a serious constraint on the economic

benefits producers can reap, an also poses a threat to animal health status, an essential quality

characteristic from a public health perspective. Fortunately, there are policies available that

would facilitate the flow of product information and help correct these market failure, such as

branding by origin and/or government certification. To evaluate the feasibility and benefits of

these policy options, however, market structure and factors influencing consumer demand must

be more clearly understood. This paper examines such market characteristics in the capital of

Lao PDR, Vientiane, as a first step to more effective evaluating policy options for improving

livestock quality and smallholder livelihoods.









8

LAND USES, PLANNING AND THEIR ENVIRONMENTAL IMPLICATIONS: THE

CASE OF HONG KONG, CHINA

Man Sharon Chan, (Professor, Sofia Villas Boas)

Environmental Economics and Policy, (EEP)



This paper develops a general review on the different land use patterns in Hong Kong

which reflects their correlation with pollution.

The question that leads the analysis in this paper is whether Hong Kong needs “more” conserved

land or “better” planning on the allocation of land to different uses. According to the Population

Reference Bureau, Hong Kong has one of the highest percentages of conserved land area in the

world. In spite of the high proportion of conserved land relative to total land area, the pollution

problems, especially air pollution addressed in this paper, have not shown significant

improvement. Thus, this project will discuss the effectiveness of land management from two

perspectives, local and regional.

From the local perspective, the paper has summarized the major friction that slows down

pollution reduction despite the huge investments in these areas. The main reason is the hilly and

rugged topography. This has created the extremely high population density in the limited flat-

land and urban areas. It is also observed that the distribution of land to different end uses has

remained rather steady. Hence, it favors the reasoning which says the rising intensity of

industrial activities, transportation and the increasing height of buildings for residential and

commercial use resulted from the high population density are found to be the major obstacle to

conservation investment and implementation.

In addition to urban development as major source of pollution at local level, some

deficiencies in the current institutional set-up and city planning are also responsible for the

pollution problems. The paper has focused on two factors, the lack of clear regulations in

building density, which contributed to trapping pollutants, and the lack of a clear objective, an

implementation, enforcement and monitoring system in long term to cooperate with the Pearl

River Delta region in pollution control. This leads us to the second perspective of the research,

the regional perspective, in approaching the fundamental question stated in the beginning.

The paper briefly described the interaction and exchange of emission of pollutants

between Hong Kong and the major Pearl River Delta region. A framework is developed for the

economic values of industries and output that correlates with the emission characteristics. It is

found that due to the heavy industrialization in the Guangdong area, the number of days with

smog in Hong Kong has continued to rise. By comparing the difference in industrial, price and

income level between both areas, the research projects the difficulty in achieving cross-border

consensus.

In conclusion, this paper serves as an introduction to the association between land uses

and pollution in the case of Hong Kong, which explores the inefficiency in land use planning and

the resulting environmental consequences.









9

ESTABLISHING AN SUSTAINABLE AFTER SCHOOL GARDEN CLUB IN AN

URBAN ELEMENTARY SCHOOL

Amanda Cocking, (Dr. Gordon Frankie)

Conservation and Resource Studies, (CRS)



My research began as an interest in the connection between children and the natural

world in urban areas and how that applied to context based science education. Growing up in

rural northern California gave me ample context for understanding the importance of as well as

the excitement of science education. When I began tutoring at Civic Core Elementary in Oakland

I was teaching science to fourth and fifth graders. Realizing they had no context for why they

should want to learn about different ecosystems, I became interested in context based education

in urban areas. I began to research "Place Based" education, the idea of using the community

and natural settings around the students own neighborhoods to teach science. I decided my

educational medium would be school gardens, later I discovered the habitat garden and how it

could be used as a hands on means to introduce ecological interactions.

The main goal of my research project was to start and facilitate an after school garden

club in a school that previously did not have one that was: approved by school administrators,

introduced complex ecological concepts through habitat gardening for bees and butterflies,

reconnected students to where their food came from through planting and eating out of a small

vegetable garden, test out selected curriculum from the North American Pollinator Protection

Campaign and create a enjoyable hands on learning environment for students. I researched

schools in the Bay area and decided to work with Civic Core Elementary, who I had tutored for

in years prior. The first part of my research involved finding information to help communicate

the psychological and academic benefit of an after school gardening program in hopes of being

allowed to start the program. This research took place through interviews of a multitude of

outdoors educators, science teachers and professors for inspiration, ideas and key reasons why

context based education is essential to teaching science. I went to environmental education

conferences, read school garden curriculum and literature and visited as community and school

gardens in Berkeley and Oakland. I developed a portfolio of my own ideas and curriculum as

well as curriculum and ideas that fit into my program. Before getting accepted as the after school

garden coordinator I established connection to the school through tutoring a science class once a

week and talking to different teachers about what they would like to see as a garden, and what

science concepts they are having difficulty expressing. The goal of this reconnaissance study

being that teachers were prepared for and approved of my take on outdoor science education as

well as to understand where the school stands on hands on education. A connection with staff

was essential in establishing the program and its sustainability. I began connecting with different

nurseries in the bay area and receiving plant donations as well as donations of soil, tools and

plants from the U.C Berkeley California Native Bee Garden. After presenting my research on

school gardens through an interview I was allowed a three month trial run where I worked with

many different students and tested out many different ideas in a raised bed in the playground. I

was evaluated by the after school program coordinator and given my list of students grades

kindergarten through fifth grade for the rest of the year.

Through teacher and student evaluations of my programs I was able to receive positive

and negative feedback. The garden club will continue next year, students learned difficult

concepts of habitat ecology through hands on experiences as well as ate out of the garden. The

program was an overall success as well as a learning experience.





10

SEARCH FOR NEW ALTERNATIVE ANTI-EPILEPTIC DRUGS USING THE

SEIZURE MODEL DROSOPHILA

Ismael Corral Jr., Dr. Mark Tanouye

Molecular Environmental Biology, Environmental Science, Policy and Management



Epileptic seizures caused by excessive neuronal activity in the brain are a relatively

common neurological condition affecting 1% of the global population. Approximately 1/3 of

epilepsy sufferers do not respond to conventional drugs or experience severe side-effects,

necessitating the need for novel anti-epileptic drugs (AEDs). Previous studies have shown that

‘bang-sensitive’ mutant strains of the fruit fly Drosophila melanogaster that undergo epileptic-

like seizures respond favorably to treatment with current AEDs such as valproate (Kuebler and

Tanouye 2002). Thus, we can use Drosophila as a disease model for epilepsy. Using this model,

we have developed a rapid screening protocol by which novel drugs that have seizure suppressor

activity can be identified. The bang senseless (bss) mutant strain of Drosophila was utilized

because of its prolonged recovery time which allows small decreases in recovery period to be

easily detected. bss flies are fed drugs in a sucrose solution along with a metabolic inhibitor

(Piperonyl butoxide) that reduces degradation of the drug. After 24 hours of feeding, the flies are

subjected to an intense physical ‘bang’ that induces seizures in control flies. After the initial

seizure, flies experience paralysis as a result of synaptic failure. As neurons recover function, the

flies undergo a second seizure, followed by recovery. This stereotyped behavior is termed the

recovery period. Flies treated with current AEDs show a significant decrease in average recovery

period compared to control flies. The drug screen relies on detection of novel AEDs by

observing a reduction in the recovery period of bang senseless flies after drug feeding.

Currently, we have screened approximately 400 novel compounds for anti-epileptic

properties. We have identified more than 10 compounds that have a positive effect in two

successive trials. One such compound is a barbiturate-derivative very similar in structure to

Phenobarbital, one of the most widely used anticonvulsant drugs. This result validates our

screening protocol and indicates that the other compounds we have isolated as having AED

activity could potentially prove to be valuable tools in treating patients who do not respond to

current treatments.

Drosophila has proven to be a very useful model for the effective design and

implementation of a protocol aimed at screening new anti-epileptic drugs. Our goal is to

successfully screen 2000 compounds in hopes of alleviating the current shortage of AEDs.

Throughout the course of this year I have been able to explore a subject matter that not

only interests me but also affects my family. With in the past year my niece has had several

seizures which her physician has diagnosed as epilepsy. I am fortunate, though, to have lent a

hand toward the development of new screening methods that can possibly lead to the discovery

of new effective drugs. I have also gained an abundant amount of lab experience, which I know

will be an invaluable tool in professional school. Discipline, patience, and commitment are

attributes that are a must in not only in the laboratory but in life. I feel that my past year of

experience in the Tanouye Lab I have been exposed to these attributes and truly believe I have

acquired them. Finally I would like to thank all those in the Tanouye Lab for their support and

guidance, especially Dr. Tanouye and Louise Parker.









11

CLIMATE CHANGE & AIR CONDITIONING USE IN SAN FRANCISCO: CLIMATE

CHANGE IMPACTS AND ADAPTATION

Elizabeth Creed, (Sofia Villas-Boas)

Environmental Economics and Policy, (College of Natural Resources)



This case study examines the impact that climate change will have on air conditioning

(A/C) demand in San Francisco and considers adaptation strategies to minimize a resultant

increase in energy use. Since many of the users of cooling systems in San Francisco are

commercial and office spaces, the study is written primarily for commercial property landlords,

facility managers and policy makers involved in setting building standards.





The approach was to (a) calculate the magnitude of warming expected in San Francisco

due to climate change, (b) estimate the resultant change in demand for heating and cooling

systems and (c) estimate the energy benefits that increased A/C base temperatures offer San

Francisco businesses given the magnitude of future warming expected in the city.





The main results were that (a) reduced demand for heating services due to climate change

does not offset increased demand for cooling services and that (b) reductions in energy demand

are gained at each incremental increase in A/C base temperature. The results are particularly

interesting due to San Francisco’s temperature characteristics; the city’s historic temperature

range hovers so close to conventional heating and cooling system trigger points that a small

change in temperature results in a large change in heating and cooling demand and that slight

increases to A/C settings offer considerable energy savings to the city’s businesses.









12

CONSUMER DEMAND FOR DISH DETERGENTS: T HE INFLUENCE OF ECO-

LABELS, REGIONAL, AND HOUSEHOLD CHARACTERISTICS

Desirae Early, (Sofia Villas-Boas)

Environmental Economics and Policy, (Agricultural and Resource Economics)



The demand for green products has substantially increased in recent years, though most

environmental products still comprise a very small share of the market. There is an absence of

empirical studies that measure how consumer demand shifts in response to eco-labeling for

nonfood products. This study evaluates a consumer demand model for dish detergents using

price and product information in Safeway stores in six divisions across the United States, which

was gathered from their website.



In this study, price is considered a proxy of demand since a product’s price is

representative of a consumers’ willingness to pay for the bundle of attributes that constitute the

product. We created a consumer demand model for all of the detergent products that evaluates

the following factors: (1) fluid ounces, (2) presence of an environmental label, (3) brand, (4)

division in which the product is sold, (5) availability of products, and (6) interactions between

the division and presence of an environmental label. We also analyzed the influences of

household characteristics including income, race, household size, and population size. None of

the household characteristics are statistically significant once the division is taken into account,

suggesting that household characteristics are captured in regional differences.



The fluid ounces, brand, and division are all significant factors on the product price. The

chart below summarizes the effects of each division:

Division States Division Premium (95% CI) Environmental Premium (95% CI) Mean Income

Eastern MD, VA, DC base base $68,354

Genuardi NJ, PA -.32 to - .24 .10 to .40 $67,890

NorCal CA -.10 to - .03 - .10 to .19 $66,060

OrWa OR, WA -.36 to - .29 .13 to .44 $57,000

Vons CA -.10 to - .03 .01to .29 $49,145

Phoenix AZ -.27 to - .20 .06 to .37 $49,900



The base environmental premium is $1.45 to $2.35. The additional premium for each

division, except for the Northern California division, is statistically significant and higher than

the Eastern division. These results show that there is not a ubiquitous environmental premium,

but rather, the price premium and therefore the demand for environmental products varies across

regions.



This project has given me insight into the process of economic research. Designing and

conducting experiments that generate useful data can be very difficult, yet successful empirical

research projects are also very rewarding. Studying the microeconomics of environmental

products is critical since they are undergoing remarkable growth in their demand and supply.

Empirical research in this area can measure the potential of new product introductions, eco-

labeling, and information availability to change markets. As a result of this project, I have

confirmed my interest in pursuing a graduate degree and continuing research in environmental

economics.





13

HYDROELECTRIC DAMS:

CONFLICTING INTERESTS ALONG THE TANA RIVER, KENYA

Marissa Engleman, (Associate Professor, Claudia J. Carr, Ph.D.)

Conservation and Resource Studies, (Environmental Science and Policy Management)



The Tana River’s Seven Forks hydroelectric scheme is comprised of five dams. The

project was established to provide a stable water supply for irrigation projects and to provide

energy and water for Nairobi’s booming population. However, the project has fallen short of

expectations. This paper examines the environmental and social impacts of the Seven Forks

hydroelectric scheme. Attention is placed on the conflict between hydroelectric and

development needs, ecosystem health, and the survival strategies of the two dominant

communities along the Tana River, the Pokomo and the Orma. Research was conducted on the

general effects of damming, the demand for energy and development in Kenya, and the affects of

dams on vegetation and local livelihoods on the Lower Tana.

Vegetation along the Tana is highly dependent on a minimum level of flooding.

Diminishing floodplain forests have resulted from a reduction of water released by upstream

dams. Additionally, reduced flooding has led to infertile land and less water access for both the

Pokomo and Orma. The Pokomo are sedentary agriculturalists who cultivate along the river.

Attempts have been made to relocate Pokomo living within designated conservation areas,

further stressing their resource availability. The Orma are pastoralists dependent on the Tana

and adjacent common land for livestock grazing. Government land adjudication programmes

and irrigation projects have privatized land traditionally used by the Orma. Development and

conservation projects along the Tana have greatly affected the availability of resources for local

communities. Degradation and restricted access to resources has led to violence between the two

groups. The Pokomo and Orma are being forced to survive with only a fraction of the water and

land they historically had access to, resulting in a struggle to ensure their livelihoods in an

increasingly devastated environment.

The lack of attention paid to environmental and social issues in the planning of large

dams has resulted in increased environmental degradation along the Tana River. This

degradation has stressed local communities and endemic species, resulting in conflicts over

resource access. I recommend, that prior to any dam construction, a collaborative and extensive

study be conducted on all possible downstream effects. National governments and international

financing institutions need to evaluate the affects of development on local survival strategies and

work with communities on issues of displacement and compensation prior to construction.

Additionally, conservation efforts along the Tana River need to consider the livelihoods of the

Pokomo Orma and provide continual resources and incentives for communities to cooperate,

while protecting their traditional land and land management practices.

In my research of the Tana River I have had the opportunity to explore in depth the

interconnectedness of an entire ecosystem. Working for a year on this research has allowed me

to gain an understanding of the various dimensions of an independent research project. I also

have had the opportunity to work closely with Professor Carr and benefit from her experience

and knowledge. This program has also allowed me to further explore my personal and

professional interests for the future.









14

AN EMPIRICAL COMPARISON OF NET ENERGY METERING AND FEED-IN

TARIFFS FOR RESIDENTIAL SOLAR PHOTOVOLTAIC USERS

Tay Feder, (Alex Farrell; Larry Karp)

Environmental Economics and Policy, (Agricultural and Resource Economics)



California’s Solar Initiative (CSI), also known as the “million solar roofs” program,

offers large cash subsidies towards installation of solar photovoltaic (PV) systems that operate in

parallel with the electric system grid. In combination with state and federal tax incentives,

aggregate government programs currently constitute approximately half of the retail price of a

residential solar PV system. For example, a two-kilowatt (kW) solar PV system is priced near

$16,000 installed, but will cost only $8,000 after a $5,000 CSI cash-rebate and $3,000 in tax

incentives. Customers plan to recover these remaining costs from a reduced electricity bill with a

Since 1992,

discount rate and payback time similar to that of a home mortgage. the California

Public Utilities Commission has required investor-owned-utilities (IOUs) such as PG&E to offer

a net energy-metering (NEM) program to households with distributed generation (DG) such as

solar PV. The NEM programs in California use a bi-directional electricity meter to measure and

bill the difference between the amount of electricity consumed and the amount generated.

Therefore, the instantaneous value to consumers of residential solar PV electricity generation is

equal to their marginal cost of electricity. When a household is generating more electricity than

used within the home, ‘the meter flows backwards,’ electricity is fed back into the grid, and

consumers are given a bill credit priced equal to their marginal cost.

Opponents against NEM programs generally argue for co-metering distributed generation

such that one meter separately measures the usage of electricity by a household and another

meter measures generation of electricity from the DG system. This enables policy makers to set a

value for particular modes of distributed generation – be it solar PV, wind turbines, or natural gas

micro-turbines – and require investor-owned utilities to buy that power at a regulated rate. Policy

makers who are against the subsidization of expensive distributed generation such as solar PV

can price this rate at a low level. Those in favor of subsidizing DG technologies such as solar PV

and fuel cells can set the co-metered buy-back for solar PV at a high level in substitution or

complementation of other incentives such as cash rebates and tax incentives. This practice is

commonly referred to as a feed-in tariff (FiT), is very popular in Europe as a means to subsidize

renewable electricity generation and was recently enacted in California as of January 31st, 2008.

Feed-in tariffs are known for a highly subsidized buy-back rate that is guaranteed to new

investors for a long period (10, 15, or 20 years in California).

This study compares the distributional impacts of feed-in tariffs with the status quo NEM

programs offered by Pacific Gas & Electric, Southern California Edison, and San Diego Gas &

Electric. With empirical load data from 442 random Californian households whom do not have

solar PV, monthly bills are modeled under NEM as if each household has purely inelastic

demand for electricity and is given a south facing 2kilowatt solar PV system with 25 degrees of

tilt. First, monthly bills under NEM are compared to alternative flat buy-back rates of 10 to 70

cents per kilowatt-hour in 10 cent increments. Second, a feed-in tariff that is revenue neutral for

the average customer over a year is estimated and the distributional impacts are evaluated using a

simple regression analysis. Lastly, the optimum scale of a residential PV system in proportion to

its household load is estimated using linear programming and compared to empirical data

measuring the decisions consumers have actually made when determining the size of their solar

PV systems.





15

FUNCTIONAL ANALYSIS OF THE ARABIDOPSIS POLLEN RECEPTOR KINASE3

(PRK3) FAMILY DURING POLLEN TUBE GROWTH

Emily Fox1, Yan Zhang2,3, Colleen Lau4, Sheila McCormick2,3

1

Department of Environmental Science, Policy and Management, University of California,

Berkeley, CA 94720

2

Plant Gene Expression Center, United States Department of Agriculture/Agricultural Research

Service, Albany, CA 94710

3

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720

4

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720



Directional growth of pollen tubes is directed by molecular signals received from the

pistil. Three pollen-specific receptor kinases (PRKs) that mediate signal transduction during

pollen tube growth have been identified in tomato and Arabidopsis. Of these, PRK1 and PRK2

have been more fully characterized than PRK3. In this study, overexpression of the three

members (a, b, and c) of the PRK3 family in Arabidopsis were used to determine the function of

PRK3s in pollen tube growth. Expression of PRK3 promoter-PRK3 protein-fluorescent protein

gene constructs indicated that PRK3s are expressed specifically in mature pollen grains and are

localized to the plasma membrane as well as to the cytoplasm. Overexpression of these PRK3a

and PRK3b constructs resulted in distorted, depolarized pollen tube growth during in vitro pollen

germination, while overexpression of the PRK3c construct had no pollen tube phenotype.

Overexpression of each PRK3 construct also reduced the proportion of germinated pollen grains.

These results indicate that PRK3 a and b play an important role in initiation and maintenance of

polarized pollen tube growth and that PRK3c may play a distinct role from PRK3a and b, despite

having high sequence similarity. PRK3a and PRK3b interacted with RopGEF12 in a yeast

reporter system, which indicates that these PRK3s may relay extracellular signals to activate

RopGTPase, an important regulator of actin polymerization during pollen tube growth.









16

EXPRESSION PATTERN OF EMF2-3XFLAG in Arabidopsis Thaliana

Joel R. Gonzalez, (Dr. Z Renee Sung)

Molecular Environmental Biology (Environmental Science, Policy, and Management)



EMF2, one of the major repressors of floral development, encodes a Polycomb group

(PcG) homolog in Arabidopsis. The functional EMF genes and PcG protein complex are

responsible for floral repression in vegetative development. The PcG protein complex is a group

of proteins that act as a transcription factor to prevent the transcription of AGAMOUS (AG), a

gene responsible for controlling floral organ development. The emf mutants are loss-of-function

mutants that result in transcription of MADS-box genes, ultimately bypassing vegetative growth

and flower upon germination. EMF2 is a gene that encodes a protein that is part of the PcG

protein complex. To study the expression pattern of EMF2, a cDNA was tagged with 3 repeats of

a FLAG sequence and was expressed under the control of a portion of the EMF2 promoter.

A transgene with construct EMF2 promoterB::EMF2cDNA-3X FLAG was introduced

into plants with an emf2-1 mutant background.  Two generations after the insertion of the

construct, plants were scored to determine whether the insertion of the construct into the mutant

background plants was successful. The potential rescued mutants displayed a wild-type

phenotype and hygromycin resistance on MS agar+hygromycin Petri dishes. The wild-type

phenotype plants contained seedlings with round cotyledons and petiole, a long hypocotyl, long

roots, green pigment, and leaf development after 7-10 days of germination.

After 13 lines of rescued mutants were found, 5 lines with the homozygous emf2-1

background (3-7-7, 3-7-20, 9-2-6, 9-2-13, 9-2-14) were confirmed by PCR-based genotyping.

Genomic DNA was extracted from hygromycin-resistant wild-type-like plants and then PCR was

performed to amplify the region that contains the emf2-1 mutation in the EMF2 locus. The

resulting fragments were digested with restriction enzyme Hpy188III. Rescued mutants showed

the restriction pattern characteristic of the emf2-1 mutants (210- and 230-bp fragments), while

genotyped wild-type transgenic plants showed the restriction pattern for the wild-type allele

(440-bp) fragments. Protein gel blots probed with monoclonal anti-flag antibody detected

EMF2-FLAG protein in nuclear extracts from rescued mutants but not from wild-type plants that

did not harbor the construct.

In conclusion, the transgene EMF2 promoterB::EMF2cDNA-3X FLAG is functional in

vivo because it rescues the emf2-1 mutant by showing a wild-type phenotype on hygromycin

plates and confirms the homozygous emf2-1 background by PCR-based genotyping. As of right

now, detection of EMF2-3XFLAG protein of two rescued mutant plant lines (3-7-7, and 9-2-6)

have been confirmed in rosette leaves. Very soon, I plan to finish studying the temporal

expression of EMF2 protein by detection of different levels of nuclear protein from the flower

buds, stems, opened flowers, rosette leaves, roots, and apices from all five mutant background

lines, which will help us determine different levels of expression of the EMF2 protein in A.

thaliana.

From my experience in the CNR Honors Program, I have improved my scientific

composition and writing skills, as well as communication skills by explaining my project to

members inside and outside the scientific community. I have also further understood the culture

of biology research and the overall subject of plant molecular genetics.









17

COMPLEX WETLAND INTERACTIONS: HOW BIRD MIGRATION AND HABITAT

DEGRADATION MEDIATE PARASITE DYNAMICS IN THE MARINE SNAIL

CERITHIDEA CALIFORNICA

Fletcher Halliday, (Professors Wayne Sousa and Mark Tanouye)

Molecular Environmental Biology, (Environmental Science Policy and Management)



Host-parasite interactions play an important role in shaping natural communities,

particularly in wetland habitats (Sousa 1991, Hudson et al 2006). Habitat degradation also likely

alters these interactions (Huspeni and Lafferty 2004), but little long-term data on these dynamics

exists. In Bolinas Lagoon, Marin Co. California, there are a 15 trematode species that use the

snail, Cerithidea californica, as the first intermediate host in their lifecycle; most use shorebirds

or waterfowl as definitive hosts for adult stages. In previous studies conducted from 1981-1988,

Sousa (1993) demonstrated that interspecific competition exists between parasites for their host

snails. However, snail habitat heterogeneity as well as spatial and temporal variation in avian

host abundance may have a larger influence on snail population structures. Since the 1970’s, the

Point Reyes Bird Observatory has conducted yearly winter censuses of migratory birds in

Bolinas lagoon. The purpose of this project was to use both data sets from 1980-88,

supplemented with my own data from a 2007-08 sampling, in order to demonstrate how habitat

degradation as well as bird distribution and abundance mediate parasite dynamics in Cerithidea.

Since 1988, snail populations have been dramatically altered in distribution by the

expansion of pickleweed, Salicornia virginica, the increased abundance of the ghost shrimp,

Callianasa californiensis, and the appearance of the invasive Japanese snail, Batillaria

attramentaria, though the latter is rare. The percent of single trematode species infections in

snails dramatically increased at both sites despite a decrease in overall bird abundance,

suggesting that other factors (such as snail size or density) may increase snail susceptibility to

parasites. Two moderately abundant species of trematode were not present in 2008, despite the

presence of known definitive hosts of these parasites, while two species dramatically increased in

prevalence at both sites, particularly at Kent Island. Bird and trematode diversity were positively

correlated both temporally and spatially between sites, however they were not correlated among

snail subpopulations in a single year, likely due to bird mobility. This reinforces the importance

of scale in interpreting multi-host dynamics in wetland communities.

Examining the 109 species of winter-foraging birds for individual associations with

parasites revealed surprising results. Several species were significantly correlated at both sites in

multiple tests, suggesting that bird behavior may play a role in parasite dispersal. Besides

finding new associations between migratory birds and parasites, this project presents important

evidence that changes in global bird trends may play an important role on local parasite

communities, laying the groundwork for future studies in the role of migration at a variety of

scales.

Through my participation in this program, I learned how to conduct independent field and

laboratory research, and was able to broaden my horizons by conducting a multifaceted

experiment. In addition, I gained experience in the intensive and complicated processes of data

analysis and scientific writing. Finally, I had the opportunity to synthesize the broad array of

information I absorbed while at Berkeley, in a unique way, drawing on a variety of subjects,

including ecology, geography, genetics, and mathematics.









18

PHYLOGEOGRAPHY OF THE ORANGE-CROWNED WARBLER (VERMIVORA

CELATA)

Zachary Hanna, (Dr. Rosemary Gillespie)

Molecular Environmental Biology, (Dept. of Environmental Sciences, Policy, and Management)



Objectives

The Orange-crowned Warbler (Vermivora celata) is separated into four subspecies that differ

in plumage color, size, molt patterns, habitat, and timing of migration and breeding. Three

subspecies (celata, orestra, and lutescens) have wide-ranging breeding distributions throughout

western and northern North America, while sordida is restricted primarily to islands off the coast

of southern California and northwestern Baja California. Previous studies have generated testable

hypotheses concerning population relationships within this species. However, molecular data

have yet to inform our knowledge of the degree of divergence of Orange-crowned Warbler

populations on a species-wide level. The objectives of our study were to analyze divergences

between populations to examine whether subspecies boundaries are congruent with genetic data

and to test hypotheses about population colonization. To address these questions, we analyzed

two mtDNA genes (ND2, ATP6) and 3 polymorphic microsatellite markers, which were

developed from V. celata. The data set included 120 individuals from 7 populations representing

all four subspecies.

Major Results

Analyses of genetic data revealed that population divergences are relatively recent, but

structured. Samples from the Channel Islands (sordida) mostly cluster together, but there is no

differentiation between island populations within this subspecies (northern Santa Cruz Island

versus southern Santa Catalina Island). The data do not support Johnson’s (1972) hypothesis that

sordida is most closely related to the Rocky Mountain form orestera. Rather, sordida appears to

be most closely related to the Pacific Coast subspecies lutescens. Samples of lutescens and

orestera also mostly group together, as does the northern subspecies celata, although lineage

sorting is incomplete and some individuals of those subspecies are scattered throughout the tree.

Analyses of nuclear microsatellite data reveal low levels of overall population differentiation.

The contrast between the microsatellite and mitochondrial DNA data suggests that male-biased

gene flow may be occurring. Analysis of additional microsatellite loci is needed and will provide

further evidence for the relation between genetic differentiation and subspecies boundaries. The

combination of these data will determine whether the sharing of haplotypes between different

subspecies or geographic regions is ancestral or the result of ongoing gene flow, and will be used

to examine patterns of colonization.

The genetic data suggest that the phenotypic differences between subspecies are recently-

derived. This is a first attempt to assess whether V. celata subspecies boundaries are congruent

with molecular data, and to test prior hypotheses about population colonization and

differentiation. The planned next phase for this project is the addition of song and morphologic

characters to the analysis.

Personal Benefits from Experience and Acknowledgements

This research experience has afforded me the opportunity to greatly expand my knowledge of

genetics laboratory and analysis techniques. I acquired and honed valuable organizational and

project management skills. I would like to extend my extreme gratitude and appreciation to my

supportive and inspiring advisers: Dr. Rauri Bowie, Dr. Carla Cicero, and Dr. Rosemary

Gillespie.





19

MOLECULAR AND MORPHOLOGICAL ANALYSIS OF THE MEXICAN MILLA

COMPLEX

Claudia Henriquez, (Chelsea Specht, PhD.)

Genetics and Plant Biology, (Department of Plant and Microbial Biology)



The plant family Themidaceae contains ~62 species divided into 12 genera. Within this

family resides the Milla complex that includes 5 genera centered in Mexico. Although recent

studies have confirmed the monophyly of the Milla complex, taxon sampling was limited making

existing taxonomic classifications provisional at best. Here I present a morphological and

phylogenetic analysis of the Mexican Milla complex in an attempt to clarify at a finer scale the

evolutionary relationships among members of this group. Cladistic analysis of DNA sequences

from three plastid regions (rpl16, ndhF and trnL-F), focused on increasing sampling within

Milla, were incorporated into the existing phylogenetic tree. Results from the combined analysis

provide the highest degree of resolution and show support for the monophyly of the complex,

however, constituent clades within the group are paraphyletic. These results suggest the

necessity for new generic circumscription of members of the Milla complex. Further

morphological and phylogenetic analysis of all species comprising the five genera of the clade

will be needed to produce a more robust history of the evolutionary events that lead to

diversification within the Mexican Milla complex of Themidaceae.



The opportunity to have been able to work in a professional laboratory, addressing

currently relevant scientific questions as an undergraduate researcher, is one I will treasure for

the rest of my life. The education available through required course material is exceptional in

itself here at UC Berkeley, but to become incorporated in the ongoing research at one of the best

research institutions in the world enhances the learning experience exponentially. I feel that I

can now approach any scientific environment with a certain degree of confidence. I am

immeasurably grateful to the department of Plant and Microbial Biology, my Professor Chelsea

Specht, PhD., and my graduate student mentor Chodon Sass for giving me the chance to fulfill

my aspirations.









20

DEVELOPMENT OF A REAL-TIME PCR ASSAY TO QUANTITATIVELY DETECT

SCHISTOSOMA JAPONICUM CERCARIAE IN WATER

Yuen Wai Hung, (Prof. Robert Spear, co-sponsor: Prof. Steven Lindow)

Molecular Environmental Biology, (SPH, co-sponsor department: ESPM)



Schistosoma japonicum is among the three human-disease causing schistosomes that cause

schistosomiasis, a parasitic disease second only to malaria in public health importance. In the

mountainous regions of Sichuan Province, China, re-emergence of the disease in previously

controlled areas has been observed, and high spatial variability of the parasite in the environment

has been shown using traditional detection methods. Current detection of the larval stage of the

parasite in water relies on the use of a sentinel mouse method, which has limited spatial and

temporal resolution, as the mice must be raised in the laboratory for 6 weeks before being

dissected to count the worms inside. In order to improve the detection capabilities of public

health officials, a molecular assay using PCR was developed for S. japonicum cercariae in

laboratory samples.

My project focused on the development of a real-time PCR assay which enables quantitative

detection of the parasite in environmental samples. Preliminary PCR and real-time PCR using

SyberGreen were used to test the effectiveness of different primers sets to amplify various target

sequences in S. japonicum. A set of primers and TaqMan probe specific to S. japonicum was

selected to quantify S. japonicum cercariae based on the results of the preliminary tests. A

BLAST search of the primers and probe produced no other hits but the target sequence of the

parasite. No positive results were obtained when tested for cercariae of S. mansoni and S.

haematobium. Samples containing various concentrations of S. japonicum cercariae showed that

real-time PCR detection had a strong linear correlation (R2 = 0.912, n=25) with number of

cercariae counted using light microscopy. The assay was sensitive, able to detect as few as 1

cercaria in replicated laboratory samples.

In order to determine the potential application of the real-time PCR assay in water samples,

cercariae were spiked in water and analyzed with real-time PCR. Known amounts of S.

japonicum cercariae determined by light microscopy counts were spiked in 1 liter of water

collected from Strawberry Creek Canyon on campus. Samples were processed by filtration and

DNA extraction was performed directly from the filter membrane. Positive detection was

obtained from 93% of the total 32 samples analyzed. The number of cercariae estimated in creek

water by real-time PCR by had a larger variance than laboratory samples. Hence, the absolute

number of cercariae estimated by qPCR should be interpreted with caution. With further

investigation in optimizing the assay, this method has the potential to be modified for application

to environmental water samples so as to produce a rapid, reliable assay for determining the

location and concentration of cercariae in endemic environments.

Through the honors program, I have the opportunity to participate in a research project that

can potentially contribute to field data collection. With the guidance from my supervising

professor, I was able to conduct an independent research project closely related to my academic

interest. The research project has given me hands on experience in designing laboratory

experiments that most coursework could not have provided. This program provided invaluable

experience in understanding and having hands on experience in the research process, meanwhile

enriching my insight in the academic field.









21

EFFECTS OF A HIGH SALT DIET ON THE GUT, VISCERAL ADIPOSITY, AND

INSULIN RESISTANCE

John Ikeda, (Mark Shigenaga, Mentor) (Nancy Amy, Sponsor)

Nutritional Science, (Nutritional Science and Toxicology)



The sodium Adequate Intake set for adults is 1.5 g/day, much lower than the 3-4.5 g/day

taken in on average by an adult in the U.S. consuming a Western Diet high in added salt (sodium

chloride). Consuming high levels of salt is associated with hypertension, obesity, diabetes, heart

and kidney failure, gastric cancer, osteoporosis, and other morbidities. To clarify some of these

associations, I investigated in an animal model the effects of high salt feeding on weight gain,

visceral adiposity, and insulin resistance. I hypothesize that high salt feeding accelerates these

morbidities through its irritating effect in the gut, leading to increased gut bacterial antigen

translocation, chronic inflammation, insulin resistance, and subsequently a compensatory fat

expansion.

I used 11 week old male C57BL/6J mice provided ad libitum for 20 weeks on either a

Western Diet (45% Kcal fat; 22% wt sucrose, no fiber; control) or a similar diet supplemented

with 4% sodium chloride (high salt). Despite comparable food intake the high salt group was

unexpectedly lighter than the control group (p

$100k (7.8%) groups, for T1DM patients. The HbA1c were significantly higher for the lower

income group (<$40k) then higher income levels (p = 0.026) for T2DM. Language had no

significance on HbA1c or BMI%ile for either group. A.As had a significantly higher HbA1c

compared to all the other ethnicities (p<0.05) for T1DM only. The BMI %ile among T2DM was

significantly greater for both A.A.s and Latinos compared to Asians (p=0.010 & p=0.009).

Results for the mail in surveys are still pending.

Findings/Conclusions: The results showed that disparities in glycemic control existed in

the diabetic population at Children’s Hospital Oakland in terms of different socio-economic

conditions, among them income levels and ethnicity. A.As and Latinos have higher BMI%iles

than Asians with T2DM. Also, T1DM patients with a lower socio-economic status and of certain

ethnicity are at risk for poorer glycemic control, while the greatest risk factor for poor glycemic

control in T2DM was an income of <$40k. The reasons for these disparities should be the

subjects of further studies.

Benefits from Program: I was able to familiarize myself with clinical research in general,

but more importantly, the program taught me first hand how clinical/epidemiological research is

important in finding disparities in health. I was able to make the connection that finding those

inequalities in health are the first steps to changing public health policy to make healthcare

management more equal for people afflicted with a number of diseases. Furthermore, the

research experience sparked my interest in Public Health, specifically in Epidemiology. The

experience has inspired me to pursue graduate school in order to receive an M.P.H in

Epidemiology. I hope to be performing epidemiological research as a career in order to discover

disparities in health across different socio-economic conditions and to help make healthcare

management equal for all.









7

The effect of intensive treatment of diabetes on the development and progression of long-term complications in insulin-

dependent diabetes mellitus. The Diabetes Control and Complications Trial Research Group. New England Journal of Medicine

Vol. 329, No. 14 :977-86, 1993





35

ESSENCE OF PLACE: THE LENS THROUGH WHICH YOU LOOK DETERMINES

WHAT YOU WILL SEE

Kathryn McGown, (Jeff Romm)

Forestry and Natural Resources, (Society and the Environment)



As a rural, forestland community experiences shifts in its resource based economy, the

essence of place becomes threatened by proposed development and economic polices.

Implementation decisions are often made without full comprehension or analysis of the potential

impacts on the existing social structure, resulting in unintended consequences. I believe it is

essential for decision makers to have a basic understanding of the structure of community and

the way in which it functions to inform the locals’ worldview. This research documents a

personal attempt to illuminate the essence of a community. My constantly evolving

methodology reflects, in my view, the limitations and incompleteness of many traditional

community studies approaches.

When I began this process I was interested in learning which community study methods

would reveal the essence of community. Sitting my analysis in Quincy, CA, I looked at the

requirements and results of three different methods: economic base, social networks, and sacred

places. These three different approaches highlight different elements of place and required

different observational and data analysis methods. The economic base method reduces the

community down to numbers and figures that describe the makeup of residents and industry.

With my analysis focused on census data and General Plan documents the human element of a

community was lost and the particularness of Quincy became hidden behind summary statistics.

A social network approach highlights the personal relations that tie community residents

to each other. Using a combination of ego-centric and snowball methods, I set out to map a

single subcultural group. Interviewing Holly Nordit, a highly visible and centrally located

individual within the network, I became aware of the difficulty of acquiring data about personal

relations. I found this method for illuminating the social structure and function conceptually

interesting but prohibitively time and labor intensive. Also limiting is the usability of the data

once collected. Theoretically social network analysis provides readers with a description of how

people relate to one another and the pathways by which information is dispersed though a

community, but it is difficult to use this data to analyze potential policy affects.

The sacred places method attempts to identify and map the unique and sacred physical

elements of the community. These structures and sites are deemed sacred through daily and

ritual use by the town’s residents. A sacred landscape emerges only though the direct

observation of residents’ behavior, the community may not even be aware of the importance of

certain sites. These elements can be used to quantify the essence of place by pointing to the

unique characteristics of Quincy.

The central elements of Quincy identified by the economic analysis were the major

industries, Sierra Pacific Industries, USDA Forest Service, and Plumas County Government. The

sacred places methodology included restaurants, open spaces and churches in this list and gave

no indication of their economic relevance. I hoped that the social network analysis would allow

me to unite these two descriptions of Quincy, by describing how the residents organized

themselves around these elements of place, but limited time, money and data prohibited such

integration.









36

DETECTION AND QUANTIFICATION OF SHIGA TOXINS FROM

ESCHERICHIA COLI O157:H7

Michelle S. McKenney, (Beatriz Quiñones, USDA & Steven E. Lindow, PMB)

Microbial Biology, (Plant and Microbial Biology Department)



Escherichia coli O157:H7 (EcO157) has been recognized as a leading cause of foodborne

illness. This human pathogen produces Shiga toxins (Stx), which inhibit protein synthesis in

human cells. There are two major groups of Stx, Stx1 and Stx2, and recent evidence suggests

that Stx2 may be more virulent than Stx1. Within the Stx2 group, five variants have been

identified, including StxII, Stx2c, Stx2d, Stx2e and Stx2f. Over the past decade, multiple

EcO157 outbreaks have been traced to leafy vegetables grown in the Salinas Valley region of

California. In 2006, a multi-state EcO157 outbreak associated with the consumption of pre-

packaged spinach grown in Salinas, resulted in 205 confirmed cases of illness and 3 deaths. To

investigate potential sources of contamination, the USDA-ARS identified over 200 strains from

various sources and locations in the Salinas Valley by using multi-locus variable-number-

tandem-repeat Analysis (MLVA). All spinach-outbreak strains belonged to the MLVA 163

genogroup. Furthermore, a PCR-restriction fragment length polymorphism (RFLP) analysis

showed that these strains possessed two stx2 genes, stxII and stx2c. To investigate the prevalence

of the stxII/stx2c genotype among potential sources of contamination, the first objective of this

project was to identify the stx2-variant genotype in EcO157 strains from various sources and

locations in the Salinas valley. The results from the PCR-RFLP analysis demonstrated that there

was no correlation between potential sources and stx2-variant genotype. Interestingly, EcO157

strains that were closely related by MLVA types were found to have the same stx2-variant gene

profiles. In particular, EcO157 strains that clustered with MLVA 163 strains also possessed the

stxII /stx2c genotype.

Given that current methods used to measure Stx activity are very laborious and time

consuming, the second objective of this project was to develop a simple and quantitative method

to assay Stx activity from EcO157 cells. To compare the inhibition of protein synthesis by Stx1-

and Stx2-expressing EcO157 strains, Vero cells, a mammalian cell line highly sensitive to Stx,

were generated to constitutively express a destabilized variant (t1/2=2h) of the enhanced green

fluorescent protein (EGFP). To develop the use of Vero-d2EGFP cells to measure Stx activity

from EcO157 strains, bacterial culture supernatants were grown aerobically at 37°C for 24 hr and

then added to Vero-d2EGFP cells. EGFP fluorescence was measured by using a fluorescence

microplate reader, and the inhibition of protein synthesis was determined by measuring a

decrease in EGFP fluorescence. The results demonstrated that Vero-d2EGFP cells incubated

with supernatants from Stx2-expressing strains with different MLVA types had a lower EGFP

fluorescence than Stx1-expressing strains. Also, strains expressing both Stx1 and Stx2 showed

the greatest reduction of EGFP fluorescence. These findings suggest that strains expressing Stx2

or both Stx1 and Stx2 may have a higher virulence "potential”, resulting in a greater inhibition of

protein synthesis in mammalian cells. Further studies are aimed at quantifying the amounts of

Stx expressed by these EcO157 strains, and at identifying environmental conditions that may

promote Stx production. This program provided an invaluable opportunity for obtaining hands-

on experience in a dynamic lab setting and the development of analytical skills necessary to

successfully design and implement an experimental research project. This has been an insightful

experience that I would recommend to anyone with a strong interest in pursuing a postgraduate

education in the biological sciences.





37

LEARNING SCIENTIFIC INQUIRY THROUGH ROLE PLAYING

Eva Montes, (Dr. Barbara Y. White, Graduate School of Education)

Molecular Environmental Biology, (Dr. Mark Tanouye, Environmental Science Policy &

Management)



Our group, headed by Barbara Y. White, Professor of Education at UC Berkeley, has

been working with a fifth grade classroom at an urban school. The students in this class were

engaged in a curriculum, designed by our research team, in which they played roles as they tried

to understand a work of historical fiction, which they were reading and discussing in groups, and

then as they undertook a scientific inquiry project, which was also done in groups. The roles

included cognitive, social, and metacognitive roles, such as the Theory Manager, Evidence

Manager, Collaboration Manager, Planning Manager, and Reflection Manager. The aim of the

roles and the curriculum is to (1) help fifth graders acquire and understand widely useful

cognitive capabilities, like theorizing and synthesizing, (2) develop their collaborative skills

through a focus on group processes, (3) enable them to improve metacognitive awareness and

self-regulation, and (4) help students to develop theories of their own cognitive, social, and

metacognitive processes with the aim of improving them.

In my investigation, I addressed three key questions: (1) Are the students playing the

roles? (2) How many roles do the students play (assimilate)? and (3) Which roles are the students

playing? It was concluded that students played each type of role (cognitive, social, and

metacognitive) at an average rate of 16% of their total talk. The mean number of roles played

when the students (as a group) have been introduced to all twelve roles (on the last phase of

group work, where they have been introduced to the metacognitive roles) is 5.8 roles. This shows

that students play more roles than they are assigned (87% of the time, the students in the final

phase of group work were assigned two roles), and that they can make use of nearly six roles in a

single group conversation. Finally, it was concluded that students play roles they have never

been assigned 64% of the time! They play roles they have previously played 7.3% of the time

and play roles they were assigned 29.2% of the time. Students are clearly choosing to use roles in

their group conversations even when they have not been assigned to use those roles. This

indicates that students were able to play multiple role-managers as they progressed through the

curriculum and were able to play other role managers by learning them from their group

members. This displays the possibility for internalization of the roles and sophisticated role use.

This has allowed us to determine that the students were able to learn the roles effectively,

understand the roles, and understand their purpose. Ultimately, this has allowed us to determine

that the curriculum was effective.

I have gained a rich experience by participating in a research group and investigating my

own research questions. I have learned how to analyze data in a qualitative research setting, think

critically, and have derived many new skills. Thank you Barbara for this wonderful research

opportunity!









38

MOLECULAR IDENTIFICATION OF THE DROSOPHILA BANGSENSELESS (BSS)

GENE

Miguel Padilla, (Dr. Mark Tanouye)

Molecular Environmental Biology, (ESPM)



With the guidance of Dr. Tanouye and post-doctoral fellow Louise. Parker, I undertook a

project investigating the basic mechanisms of epilepsy. bangsenseless (bss) mutant flies are

seizure-sensitive or ‘bang sensitive’, and can be induced to seize by physical or electrical shock.

The bss mutation was identified three decades ago (Jan and Jan 1978) but the gene affected has

yet to be characterized. In order to further our understanding of the genetic basis of epilepsy, I

am attempting to identify this gene using various techniques. Previous recombination mapping

had located the bss gene to the left of a known gene (eas). The low level of resolution in this

mapping left significant uncertainty as to the exact location, placing bss in a ~300kb region

approximately, containing about 45 genes. By the end of Fall 2007 I had completed a higher

resolution recombination mapping using known P element insertions, which locates bss in

between the paraJS1 and EY00852 insertions (0.025 cM to the left of insertion paraJS1 and 0.05cM

to the right of EY00852). paraJS1 lies within the 3’ UTR of para, a gene encoding a sodium

channel. The EY00852 insertion lies in the first intron of Rbp2, itself lying immediately 3’ of

para. Rbp2 encodes a putative RNA binding protein. Given that para encodes a sodium channel,

and that multiple sodium channel mutations have been associated with epilepsy in humans, it is

of great interest to us to determine whether or not bss is a mutation in this gene. Rbp2 is an

equally intrigueing candidate as the RNA binding domains most closely resemble those of Elav,

a pan-neural RNA binding protein known to regulate neuronal translation. The next phase in my

project will focus on the use of bss1, paraJS1 and EY852 bss1 flies generated in my mapping in a P

element imprecise excision mutagenesis screen. I will assay flies for loss of bang sensitivity –

this should correspond to disruption of the gene that encodes bss. I will then sequence the

genomic DNA of any flies that show loss of bang sensitivity to establish which gene has been

disrupted.









39

DETERMING PHOTOSYNTHESIS LEVELS OF WETLAND VEGETATION USING

HIGH-RESOLUTION SPECTRAL RELFECTANCE DATA

Katherine Saad, (Dr. Dennis Baldocchi)

Environmental Sciences, (ESPM)



The xanthophyll cycle of a plant is part of nonphotochemical quenching (NPQ), a defense

mechanism that occurs when excess light or other stresses might damage the plant. Demonstrated

by a change in reflectance in a narrow range of PAR centered at 531nm, changes in the

xanthophyll cycle are detected via the photochemical reflectance index (PRI), which is a value

calculated as the percent change in reflections at 531 and 570nm. Changes in PRI have been

correlated to Radiation Use Efficiency (RUE), which has the potential to measure photosynthesis

more accurately. However, because most current literature relating PRI to RUE using spectral

reflectance incorporates data collected from satellite platforms, several gaps exist: first, a lack of

narrowness of wavelengths due to low resolution reduces the accuracy and usefulness of the

data; secondly, usually satellite data does not measure at-surface reflectance and thus the PRI

and RUE values cannot be corrected for atmospheric interference; thirdly, large gaps in the

canopy where soil appears distorts PRI; and lastly, vertical canopy structures affect light

scattering, and thus PRI values, so measurements taken above the canopy usually do not

represent true changes in the xanthophyll cycle.

In this study, I used a high-resolution laser absorption spectrometer, which overcame

most of these drawbacks because the solar spectrum is measured to the accuracy of tenths of

wavelengths and measurements are taken near the land surface, and thus do not produce values

that need to be corrected for atmospheric interference or the canopy structure. The appearance of

soil still distorts PRI values, but by choosing one control site, the values can be corrected for.

Spectral reflectance data was collected from April 2007 to April 2008 at between 9 and 17 field

sites per visit, and from this data PRI was calculated. The data demonstrates seasonal variability

that correlates to plant productivity, thereby indicating a relationship between spectral response

and plant productivity.

Through this project I was able to carry out high-level field work and data analysis while

contributing to a larger, long-term study. This study was conducted as part of a larger

biometeorology project in the Sacramento-San Joaquin Delta, in which methane and carbon

dioxide land-atmosphere fluxes were measured. The data I acquired, when used in conjunction

with the methane and carbon dioxide flux data, can be used to determine a relationship between

PRI and these atmospheric gases.









40

EXAMINING AQUACULTURE AS A RESTORATION TOOL FOR DECLINING

CAPTURE FISHERIES IN GHANA

Peter Schulte, (Justin Brashares)

Conservation and Resource Studies, (Environmental Science, Policy, and Management)



Over-fishing, pollution, and global warming are decimating global fish populations,

resulting in heightened food security problems for humans and extensive damage to aquatic

ecosystems, both freshwater and marine. This is especially important in African nations such as

Ghana, where fish production contributes roughly 5% of the nation’s GDP, fish accounts for

about 60% of the animal protein consumed, and the per capita food supply from fish is 31 kg as

opposed to an average of 16 kg for the world. Declining fisheries and damaged aquatic

ecosystems pose problems for traditional livelihoods, employment, protein supply, and the fight

against poverty in Ghana; finding a solution is of critical importance for the country.

Aquaculture has been proposed as one way to supplement capture fishery production and

provides jobs and has recently seen a great rise in popularity in Ghana in the last decade. The

international development community has also often referred to aquaculture’s potential to

function as a conserve and restoration tool for the declining fisheries, however the specific

mechanism through which this might occur has not been developed or tested.

This research is meant to help determine whether aquaculture is currently having

restoration effects for Ghanaian inland fisheries, and/or if it has potential to do so in the future.

In order to conduct this study, I traveled to Ghana for seven weeks as a recipient of the Rosberg-

Geist Research Fellowship provided by the Center for African Studies at UC Berkeley. While in

Ghana I collected surveys of 26 Lake Volta fishers and 53 Volta Region fish farmers, as well as

several government officials. I determined that to act as a restoration tool, aquaculture would

have to either 1) produce enough fish to effectively compete with capture fisheries as a source of

fish, in order to lower the economic importance of capture fisheries, or 2) convert fishers to

aquaculture and therefore reduce the amount of effort exerted on capture fisheries.

The research concluded that aquaculture in Ghana is currently not having a

conservation/restoration effect in Lake Volta due to the insignificant amount of aquaculture

production in Ghana coupled with the large discrepancy between fish supply and demand.

Furthermore, aquaculture has limited potential to restore capture fisheries in the future due to this

growing gap between supply and demand and also because of the lack of a practical and

appealing mechanism to efficiently transition fishers to aquaculture. Such a transition is unlikely

due to high costs in starting a fish pond, the lack of funding opportunities available to fishers, the

lack of technical aquaculture and agriculture skills, geographical distance between capture

fisheries and the majority of potential fish ponds, and the close relationship and association of

fish farming with agriculture activities rather than fishing activities. Also among the core

reasons for this lack of a restoration function is that government agencies and potential fish

farmers alike do not intend aquaculture to have such a function, and therefore it is not being

implemented or managed as such.

This project has allowed me to gain considerable experience in research as well as the

opportunity to spend time in and learn the realities of the non-Western, “developing” world.

Furthermore, it has been an ideal way to work closely with a professor and pursue a topic to a

degree beyond what undergraduate courses typically allow, providing me with unique

preparation for graduate studies.







41

3, 3-DIINDOLYLMETHANE UPREGULATES INTERFERON GAMMA RECEPTOR

EXPRESSION IN MCF-7 BREAST CANCER CELLS THROUGH THE PRODUCTION

OF REACTIVE OXYGEN SPECIES

Rodolfo Silva, Leonard Bjeldanes

Molecular Toxicology, Department of Nutritional Sciences and Toxicology



3,3-Diindolylmethane (DIM) is a metabolic compound derived from the consumption of

Brassica vegetables such as broccoli and cauliflower. Previous studies have shown that DIM

possesses potent anticancer properties, which, in part, may result from activation of the

interferon-_ (IFN- _) pathway in cancer cells. IFN- _ prevents the development of tumors by

increasing the cell surface expression of MHC-I, and thus making the cancer cells more

susceptible to apoptosis by immune cells. It is known that DIM mediates activation of the

interferon-_ pathway through the production of IFN-_ and an increased expression of the

interferon-_ receptor (IFN-_R), however, the mechanism for increased IFN-_R expression is

largely unknown. To determine whether DIM triggers IFN-_R expression through the generation

of reactive oxygen species, we performed a western blot analysis for IFN-_R expression in

MCF-7 cells treated with DIM (15µM) in the presence or absence of the mitochondrial

antioxidant N-t-Butyl hydroxylamine (NtBHA). The results indicate that NtBHA was able to

reduce DIM-induced IFN-_R expression in a concentration dependent manner. Furthermore,

MCF-7 cells treated with H2O2 (0.003%) alone were seen to express a high level of IFN-_R.

Measurement of reactive oxygen species production by flow cytometry showed that the relative

amount of reactive oxygen species produced after each treatment corresponded to the relative

levels of IFN-_R protein expression, with DIM-treated cells showing approximately a three-fold

increase in reactive oxygen species, and H2O2-treated cells showing almost a five-fold increase in

reactive oxygen species over the DMSO control. These results establish reactive oxygen species

as the major trigger for DIM-induced expression of IFN-_R in MCF-7 cancer cells.

The opportunity to conduct research through the CNR Honors Program has been my most

rewarding college experience. Through this program I have developed a great deal of admiration

for those who conduct research because research is certainly not easy, and it can often be

frustrating. Nevertheless, my involvement in research has been a very positive experience, and it

helped me look at science as a process rather than just collections of facts presented in textbooks.

I want to give a special thanks to Professor Bjeldanes for letting me work in his lab and for being

such a great mentor. Thanks also go out to Jacques Riby and Holly Hantz who frequently

provided troubleshooting advice.









42

THE RESOURCE CURSE IN BRAZIL

Colin M. Sweeney, (Elisabeth Sadoulet, sponsor)

Environmental Economics & Policy, (Department of Agriculture and Resource Economics)



Natural resource endowments have long played an ambivalent role in economic

development. This is primarily because of the boom and bust cycles that have come to define

minerals markets. In an environment of rising prices, economies with large resource sectors

enjoy windfall profits for their resource exporters as well as welcome revenues in their

treasuries. However, the boom in demand for their endowments increases demand for their

currency. So while resources are thriving, other domestic industries competing on the global

market suffer. When global prices are falling, governments can find themselves short on

revenues and unable to meet certain obligations just as a key sector is contracting. Resource-

based economies thus are seen to pose significant challenges to the governments which oversee

their maintenance. This study looks at the resource dilemma popularly known as the “Resource

Curse” in the Brazilian context.

Econometric analysis plays a central role as this study uses state-level panel data gathered

from records over the last 20 years to measure the relationship of the extractive sector as a share

of an individual state’s economy with the average wage and the income distribution in Brazil. In

doing this, we can measure the welfare affects of resource booms and in particular, to see to what

segments of the income ladder those benefits accrue. The findings reinforce the ambivalent

perceptions of the minerals sector. As a state’s resource sector grows faster relative to the growth

of the rest of the economy, this study found statistically significant evidence that the average

wage can be expected to fall. Despite this, each 10 percent of the poorest 40 percent of the

population would see their percent-share of total wealth increase during resource sector

expansion. This points to the fact that in Brazil, the resource sector booms mainly support low-

skill and, as a result, low-wage employment. This is beneficial in that it creates wealth and

employment for the most in need in the population. But it does so at a wage much lower than the

rest of the economy. We discuss how this is a problem because, as other studies have shown,

resource sector employment provides little in the way of skill accumulation and labor

productivity growth for those it employs. As a result, the labor productivity of the work force is

diminished over the long-term. This argument is borne out in data presented in this study that

shows how higher literacy rates in a state correlate positively and significantly with the share of

new investment into the mineral sector that is directed toward higher value, downstream

production processes such as refining. Meaning that states with less educated and less skilled

workers receive less investment into high value production processes and more into physical

extraction which varies in value as a result of volatile commodity prices. Thus as a conclusion, it

is important not to demonize resources themselves, but recognize that states and governments

play a large role in facilitating and encouraging the training of its work force. It must be noted

however that a large, prosperous, and booming resource sector as exists in contemporary Brazil

can undermine these efforts in that it attracts many young low-skill workers who might benefit

from job training or continued education, yet are nonetheless drawn in to the primary sector with

its accompanying low wage and low productivity growth.

In closing, I’d like to say that this experience has exposed me to the rigor of academic

pursuits like nothing I have ever done before. The process of researching, testing and honing my

arguments is one that has given me confidence in my ability to make a sustained academic

argument. Looking back, I am proud of the work that I have done.





43

IMPROVING THE NUTRITIONAL VALUE OF SORGHUM

Han-Qi Tan, (Dr. Prof. Peggy G. Lemaux)

Genetics and Plant Biology, (Plant Microbial Biology)



Sorghum grows on the most marginal lands and feeds over 300 million of the world’s

poorest people. Unfortunately, sorghum is not a complete food, containing inadequate levels of

certain amino acids, e.g., lysine, threonine and tryptophan. To address the deficiency of lysine, a

modified barley high lysine gene, bhl9, is being introduced and overexpressed in sorghum.

To optimize transformation of sorghum via Agrobacterium, immature embryos were

infected with Agrobacterium tumefaciens containing a dual- marker plasmid with a selectable

marker gene, pmi (phosphomannose isomerase), which allows cells to grow on mannose, and the

reporter gene sgfp (green fluorescent protein). The conditions for transfection of immature

embryos were adjusted through many trials of different conditions, like temperature and

centrifugation of embryos prior to transfection. Then, transformed embryos were identified by

selecting callus derived from the embryos on mannose-containing medium. Callus that does not

contain the transgene cannot utilize mannose as a carbon source because the cells do not have the

pmi gene and therefore cannot grow on selection media containing mannose. Calluses surviving

selection were screened for presence of the second transgene by GFP expression using

fluorescence microscopy. Callus from putative transformants were cultured on media to

regenerated plants and DNA was isolated from leaves of putative transgenic plants and screened

with Polymerase Chain Reaction (PCR), using primers to amplify pmi. Integration of the genes

into the genome was confirmed by DNA hybridization (Southern) blot analysis using radioactive

probes containing DNA sequences complementary to the GFP gene and by western blots using

antibody to GFP protein to demonstrate GFP expression. Based on results obtained, conditions

for optimal transformation frequency via Agrobacterium involved heat treatment of embryos and

resulted in a transformation frequency of ~8%, higher than that reported in published literature.

I also made efforts on bombardment-mediated transformation of sorghum embryos based

on the experiments using Agrobacterium, described above. The plasmid vector I used also

included the dual-marker plasmid containing pmi and gfp and the gene to increase amino acid

content, bhl9. The technical process of these experiments are nearly the same as above with the

exception of using bombardment to introduce DNA, rather than Agrobacterium infection.

Embryos were selected on mannose medium and screened for fluorescence. Currently tissues

that express GFP are being regenerated on medium containing mannose to make sure that there

are no escaped nontransgenic tissues that survived selection. Further work to confirm the

transgenic nature of the embryos can be done about one month after leaves regenerate from the

potentially transgenic embryos. Molecular tools, like PCR, Southern and western analysis, will

be done to confirm presence and expression of the genes. Lastly, to truly address the problem of

inadequate levels of amino acids in sorghum, an amino acid analysis of lysine, tryptophan and

threonine content will be done to determine if the levels of these amino acids are increased in the

transgenic plants compared to wild type plants.

My involvement in this project through the Honors program gave me the exposure of

working in the lab. I gained hands-on experience with lab techniques, conducting my own

experiments and even coordinating experiments with other undergraduate students. These skills

can not be obtained in class and are very valuable to me. This experience has given me the

opportunity to broaden my views of what research in a biological field is and further strengthens

my intention of continuing my studies and continuing my efforts in scientific research.





44

VEGETATIVE BIOMASS, ROAD SURFACE DEFORMATION, AND DOUGLAS-FIR

SAPLING GROWTH ON DECOMMISSIONED HAUL ROADS IN MENDOCINO

COUNTY

Madison Thomson, (Kevin O’Hara)

Forestry and Natural Resources, (Environmental Science, Policy, and Management)



The creation of roads on forested landscapes has been shown to have a variety of impacts

on hydrological and biological processes, including soil erosion/disturbance, stream

sedimentation, habitat fragmentation, and invasive species dispersal. There were two main

objectives in this study pertaining to the effects of forest roads. The first was to examine how

accumulation of above ground grass and herbaceous biomass and deformation of the road

surface on decommissioned secondary haul roads are related. The second was to determine how

the biomass and height growth of Douglas-fir (Pseudotsuga menziesii) saplings within the road

cut of these same secondary haul roads are influenced by physical site characteristics, namely

soil compaction and distance from the road center. For the purposes of this study several roads

were examined in part of the Navarro River watershed 25-33 kilometers east of Ukiah, California

on Mendocino Redwood Company timberlands.

In the biomass and deformation section of the study, three roads were examined: One

decommissioned in 2003, one in 2004, and one in 2006. Three surface types were examined on

the 2004 road (bare, rocked, and straw mulched) while the 2003 and 2006 roads only had bare

surfaces. No significant difference was found in the above ground vegetative biomass amounts

on the three surface types of the 2004 road. The greatest amount of road surface deformation on

the 2004 road was seen on the bare samples, while the least was seen on the rocked samples, and

the straw mulched samples were in between. The amount of vegetative biomass found on the

2003 and 2004 bare road surfaces was similar (19.068 g/m^2 compared to 19.196 g/m^2

respectively), while the amount of vegetative biomass found on the 2006 bare road surface was

much less (0.746 g/m^2). Road deformation values were greatest for the road decommissioned in

2004 and least on the road decommissioned in 2006 with the 2003 road somewhere in between.

However, greater vehicle use on the 2004 road may have led to discrepancies.

In the study of Douglas-fir sapling growth, all samples were taken from the road

decommissioned in 2004. The results showed weak or no relationship between Douglas-fir

sapling average annual height growth and soil compaction, average annual biomass growth and

soil compaction, average annual height growth and canopy cover, and average annual biomass

growth and canopy cover. However, there was a strong correlation between Douglas-fir average

annual height growth and the distance of the tree from the road center and average annual

biomass growth and distance of the tree from the road center with average annual increment

increasing with increasing distance from the road center.

My goal going into this program was to develop an understanding of what it takes to

design and implement a research project and I feel like I have been successful in this. Through

my struggles to find suitable sample sites and a suitable sample method within a limited time

frame I have gained significant insight as to how to best approach similar situations should they

arise in the future.









45

ENVIRONMENTAL POLICY OF JAPANESE AID:

TOWARDS SUSTAINABLE AGROECOSYSTEMS IN BANGLADESH

Mayuko Totsuka (Prof. Kate O’Neill and Prof. Claudia Carr)

Conservation and Resource Studies (Environmental Science, Policy and Management)



Since 1974, Japan’s official development assistance (ODA) has contributed to

Bangladesh’s food self sufficiency by expanding modern agricultural practices developed during

the 1970’s Green Revolution. Accordingly, Bangladesh drastically increased the production of

high-yielding varieties of rice and wheat and the use of agricultural inputs such as fertilizers,

pesticides, and irrigated water. While this modern agriculture has contributed to increased food

grain production in Bangladesh, it has also degraded soil fertility on agricultural land and now

threatens future agricultural productivity.

The current Japanese aid policy does not incorporate a holistic understanding of

environmental issues with respect to its agricultural aid projects. For example, Japanese ODA

loans have financed chemical fertilizer production in Bangladesh. Consequently, it has promoted

the wide-spread application of chemical fertilizers and other modern agricultural practices

without regard for the long-term sustainability of Bangladesh’s agricultural ecosystems. At

present, there are two forms of environmental policy in Japanese aid. First, Japan’s two ODA

implementing agencies adopted the Guidelines for Environmental and Social Considerations to

mitigate the direct negative environmental impacts from aid projects. Second, sustainable

agricultural practices have been implemented through Japan’s environmental aid projects.

However, these guidelines do not sufficiently address the indirect environmental consequences

of the agriculture aid projects. Also, promoting conservation efforts through “environmental” aid

separately from “agricultural and rural development” projects undermines the importance of

improving environmental sustainability in agricultural development. In addition to the lack of a

holistic approach in these two forms of environmental policy, the recent institutional change in

Japan’s ODA demands new policy innovation. Now is the opportunity for Japan’s ODA to

implement a holistic environmental policy in all its project schemes, including loans, grants, and

technical cooperation.

This thesis attempts to provide some constructive critiques of Japan’s ODA in order to

stimulate a more holistic approach to agricultural development in aid recipient countries. Shifting

from conventional to agroecological farming is essential for restoring the productivity of

degraded agricultural land in Bangladesh. This environmental enhancement through establishing

functioning agroecological systems will also improve the livelihood of Bangladeshi people.

Thus, Japan’s ODA needs to incorporate agroecological principles into its agricultural

development policies. Lastly, the key for its successful policy implementation is a collaborative

effort with the governments and civil societies of recipient countries.



Benefits of the Honors Program:

My honors research gave me the opportunity to pursue an in-depth study of my most

interested academic field with one-on-one guidance of my professors. I also acquired my first

independent field research experience. I conducted interviews with various practitioners in

Bangladesh and Japan, including Japanese aid agency staff, Bangladeshi and Japanese NGO

staff, Bangladeshi farmers, and Japanese engineers at the Chittagong Urea Fertilizer Factory.

These experiences ultimately helped me discover how I want to contribute to solving global

environmental problems after my undergraduate education.





46

BODY PERCEPTION AMONG KOREAN COLLEGE FEMALES

Linda Truong, Nancy K Amy

Nutritional Science-Physiology and Metabolism



Weight and body image can greatly influence negative body dissatisfactions and extreme

actions such as disordered eating. Body image perception plays an important role that influences

behaviors such as dieting and self-esteem. An ideal body image is a desirable body shape that

one would like to achieve. The Contour Drawing Rating Scale, devised by Thompson and Gray

(1995), is one method used that can help determine body perception among different groups of

people. Using the rating scale, past research analyzed the discrepancy between current and ideal

selections of body images of females. Other research also explored the desire of females to

achieve the ideal thin body image that are displayed and advertised by mass media. In addition,

cross-cultural studies have compared females in the United States to females from other cultures.

This research focuses primarily on Korean females that recently came from Korea and

are living in the US (1st generation) and Korean females who were born and are living in the US

(2nd generation). The purpose of this study is to compare differences in body preference between

these two groups of college Korean females and whether the desire to be thin is influenced by

culture or by length of residence in the US. This will enable more knowledge on dieting

behaviors and desired body images of females in the Korean culture. More information on

factors that might cause differences in body perception of females from the same culture can also

further expand our knowledge about certain dieting behaviors. Being able to understand reasons

for dieting to achieve ideal body images will enable development of educational programs that

can reduce unhealthy eating/dieting or not recommended body ideal goals.

Korean females from UC Berkeley were asked to circle body silhouette models from the

Contour Drawing Rating Scale that best represent their current as well as their ideal body image.

They also wrote down their age, height, and weight. Those who were not born in the US also

indicated the year they came to the US.

Average BMI of the 1st and 2nd generation Korean females were the same at 21.3 with

standard deviation of 1.9 and 1.8, respectively. Average weights for the 2nd generation, 125 lbs,

were higher than that of the 1st generation, 120 lbs, by 5 lbs. Average heights for both were the

same at 5’4”. Although both groups chose body silhouette 3 as their ideal body image, females

in the 2nd generation saw themselves on average as slightly bigger. The discrepancy between

body image of self and ideal indicates, however, that 1st generation Korean females had a larger

difference of 1.77 while the 2nd generation had a difference of 1.66. This indicates that although

1st generation Korean females on average weigh less than their 2nd generation counterparts, they

also desire an ideal body image that is thinner than how they view themselves presently.

Females in the 1st generation are also on average about 3 years older than the 2nd generation.

First generation Korean females also spent on average 11 to 12 years acculturating in the US.

The honors program enabled me to work closely with my faculty advisor to research,

devise, and conduct my own experiment and question. I learned the processes required to start a

project and to access approval from the Committee of Protection of Human Subjects. I also

learned more about the Korean culture and how they perceive their own body image. It was a

fun and memorable experience that allowed me to learn more about a topic of my interest.









47

BLOCKADE OF ENDOCANNABINOID METABOLISM LEADS TO ACTIVATION OF

THE ENDOCANNABINOID SYSTEM AND MODULATION OF ARACHIDONIC ACID

LEVELS

Anna Ward, (Professor Casida), Molecular Toxicology



The endogenous cannabinoid (‘endocannabinoid’) system consists of G-protein coupled

receptors (CB1 and CB2) that bind two principal endogenous ligands, 2-arachidonoylglycerol (2-

AG) and anandamide (AEA). Endocannabinoids regulate a diverse array of neurological (e.g.

memory and motility) and metabolic (e.g. feeding and lipolysis) functions. The signaling activity

of endocannabinoids is terminated by enzymatic hydrolysis. Degradation of anandamide is

principally mediated by fatty acid amide hydrolase (FAAH) in vivo. In contrast, the enzymes that

regulate 2-AG signaling in vivo remain largely unknown, although studies with cell and tissue

extracts indicate monoacylglycerol lipase (MAGL) as the principal hydrolase involved in 2-AG

metabolism. Cannabinoid receptors not only recognize endogenous lipid ligands but are also

targets of exogenous agonists, the best known of which is _9-tetrahydrocannabinol (THC), the

psychoactive ingredient in marijuana. THC and other CB1 agonists produce an array of intense

behavioral effects, some of which, such as pain relief, have possible therapeutic utility.

Augmentation of endocannabinoid signaling by blockade of 2-AG and/or anandamide

degradation may offer a more selective pharmacological approach compared to direct CB1

agonists. Also, organophosphorous nerve agents produce their primary neurotoxicity though

inactivation of acetylcholinesterase (AChE). However, many of the pharmacological effects of

OP agents cannot be explained by the disruption of cholinergic transmission. Indeed, the

behavioral effects induced by the sarin homolog, isopropyl dodecylfluorophosphonate (IDFP),

are generally reminiscent of CB1 agonists. Our findings raise the possibility that the non-

cholinergic activities of some OP agents, including commercially used insecticides, could be due

in part to augmentation of endocannabinoid signaling.

We found that blockade of MAGL, the 2-AG-degrading enzyme, by selected

organophosphorus and organosulfur agents leads to 10-fold elevations in brain levels of 2-AG

and robust CB1-dependent behavioral effects that rival in magnitude those observed with direct

CB1 agonists. 2-AG levels are also elevated in most peripheral tissues and arachidonic acid

levels are decreased by the organophosphorus agents in amounts equivalent to elevations in 2-

AG, indicating that endocannabinoid and eicosanoid signaling pathways may be coordinately

regulated in the brain as well as other peripheral tissues. Inhibiting MAGL could yield analgesic

and anti-inflammatory properties making MAGL inhibitors attractive therapeutic agents for pain

and inflammatory diseases through stimulatory action on CB1 and suppression of eicosanoid

signaling.

With the help of the Honors Research Program I have developed technical proficiency,

scientific creativity and independent thought. Working in a team environment has taught me to

communicate effectively and interact with others while performing hands-on work in the

laboratory. This experience has given me the knowledge and qualifications to enter a profession

in the scientific community.



Daniel K. Nomura, Jacqueline L. Blankman, Gabriel M. Simon, Kazutoshi Fujioka, Roger S.

Issa, Anna M. Ward, Benjamin F. Cravatt and John E. Casida. Activation of the

endocannabinoid system by organophosphorus nerve agents. Nature Chemical Biology

advanced online publication, 27 April 2008 (doi: 10.1038/nchembio.86).





48

DEVELOPMENT OF RAPID BEHAVIOURAL SCREEN FOR NOVEL ANTI-

EPILEPTIC DRUGS

April Yang, (Dr. Mark Tanouye)

Molecular Environmental Biology, (ESPM)



Epilepsy is a neurological disorder, which afflicts over two million individuals in the US.

Unfortunately, one-third of the affected population does not respond or suffer from severe side

effects to conventional anti-epileptic drugs (AEDs). In order to address the need for new

anticonvulsants, we have developed a rapid AED screening approach in Drosophila. A number

of ‘bang sensitive’ (BS) mutations have been identified, including bangsenseless (bss), that

render flies susceptible to epileptic-like seizures following electrical or physical stimulation.

Feeding these mutants flies with AEDs used to treat humans (sodium valproate, potassium

bromide and phenytoin) results in suppression or amelioration of seizures. However, visualizing

the suppression in recovery time is labor-intensive, requiring one to measure the individual

recovery time for ~100 animals. In order to screen a large number of compounds rapidly we have

tested a number of different optimization techniques using current AEDs as positive controls. We

have found that aging bss1 homozygous flies increases recovery period, making small reductions

more easily detected. In addition we have shown that feeding flies a metabolic inhibitor

(Piperonyl butoxide) increases the efficacy of AEDs. Our results have allowed us to design a

rapid behavioural screen in which seizures are induced in a population of 20 flies that have been

aged for 24 hours, starved for 24 hours and then fed drug in sucrose solution for 24 hours. The

time at which 10 flies (50%) have recovered is recorded. This is repeated such that 100 flies for

each drug are tested. Current AEDs show a significant decrease in recovery period using this

protocol. We are currently using this technique in a pilot screen of 2000 compounds to test for

anti-epileptic activity in Drosophila. We have already isolated several compounds that

ameliorate seizures in flies and we anticipate that this approach will allow us to identify novel

AEDs with alternative modes of action and/or fewer deleterious side effects than those currently

available.









The entire cycle extending from the initial

hyperactivity to the restoration of normal

behaviour is called the recovery period.

Reproduced from Tan et. al 2004









Being part of the research process has allowed me to refine my experimental technique. I

also learned the importance of being both adaptable and creative when approaching a scientific

obstacle. This program has given me the opportunity to grow into being a more balanced

researcher capable of asking interesting, hypothesis-based questions, performing independent

research to get at the answer, and also conveying my results to others.





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PREVENTION OF PANCREATIC ß-CELL LIPOTOXICITY BY INHIBITION OF

FATTY ACID TRANSPORT PROTEINS

Angela Yu, (Andreas Stahl, Melissa Kazantzis)

Molecular Environmental Biology, (ESPM)



Incidence of type 2 diabetes mellitus (T2DM) is strongly associated with obesity and has

reached worldwide epidemic proportions impacting the well-being and life expectancy of

hundreds of millions of people. The later stages of type 2 diabetes are characterized by ß-cell

failure mainly due to apoptosis (programmed cell death) which has been linked to acutely high

levels of intracellular free fatty acids (FFA) a process termed “lipotoxicity”. Fatty acid transport

proteins (FATPs) are integral transmembrane proteins, which facilitate uptake of FFAs into cells.

Our main hypothesis is that high levels of FFA associated ß-cell failure is due to lipotoxicity and

that this process depends on the protein mediated uptake of fatty acids via FATPs. Inhibition of

FFA transport by FATPs may play a protective role in ß-cell death by preventing lipotoxicity.

1. Identification of MiN6 FATPs and expression: The mouse genome

contains 6 different FATPs and the Stahl lab has raised specific antibodies

against all of them. Preliminary experiments have indicated that FATP3 is

expressed by MiN6 cells. Using immunofluorescence, FATP3 proteins (red)

were found on the MiN6 plasma membrane which also overlapped with

GLUT2 (green), a main glucose transporter also found on the plasma membrane. We also

detected FATP3 proteins present in MiN6 ß-cells via western blots in comparison to FATP3

protein levels in tissues known to be positive for FATP3 such as lung.

2. Expose MiN6 cells to high levels of palmitate: ß-cell line (MiN6 model) was used to

establish a lipid induced apoptotic assay. Palmitate markedly induced MiN6 apoptosis (91%

apoptotic cells) at 500 mM while BSA induced apoptosis in 85.74% of the cells at the same

concentration.

3. Detection of apoptosis: We used annexin, propidium iodine and caspase based assays to

asses and quantitate apoptosis. Apoptosis reduces flippase activity which transports from the

outer to the inner plasma membrane. FITC –coupled annexin was used to measure the presence

of phosphatidylserine on the outer membrane leaflet and thus detect apoptosis. Propidium iodine

staining of nuclei was used to detect loss of plasma membrane integrity to identify necrosis or

late stage apoptosis. Levels of caspase, cysteine proteases essential in cells for apoptosis, were

also measured using a fluorescent caspase assay.

4. Generation of FATP3 specific siRNA constructs: The next step will be to suppress the

expression of these ß-cell FATPs using RNA interferences. This will determine whether loss of

FATP function will reduce fatty acid uptake and confer protection from palmitate induced cell

stress and death and protection from lipotoxicity. Software algorithms were used to design 5

different target sequences for the knockdown of ß-cell FATP3 using pSUPERIOR plasmids, an

expression vector. This will be tested by co-transfection experiments followed by western blot or

uptake assays. We will generate stable knockdown and control MiN6 cells. Ultimately, this

approach could lead to the development of novel treatments for T2DM based on the principle of

ß-cell specific FATP inhibitors.

Benefits: The Honors program was able to provide me with the opportunity to receive credit for

the project I am working on. Not only was I able to learn invaluable lab techniques I could never

learn in class, but I was also able to gain experience in a real world lab setting. I am forever

grateful to Dr. Kazantzis and Dr. Stahl for mentoring me.





50

CYTOKINE PRODUCTION IN RAW 264.7 MACROPHAGES UNDER PRESENCE OF

3,3’-DIINDOLYLMETHANE

Dawn X. Yu, Leonard F. Bjeldanes (Supervisor), Steven E. Lindow (Sponsor)

Microbial Biology, Department of Plant and Microbial Biology



3,3’-Diindolylmethane (DIM) is a phytochemical made from a precursor, indole-3-

carbinol (I3C), found in dietary vegetables of the Brassica genus, such as broccoli, bok choy,

and cabbage. A diet rich in I3C significantly lowers the risk of hormone-dependent cancers.

Studies have confirmed that DIM activates and strengthens the innate immune system in rodent

models. Discovery of the underlying mechanism for DIM’s effect is desirable, as it has potential

for preventing cancer with low toxicity and complementing existing cancer therapeutic agents.



DIM stimulates the innate immune system by activating cytokine production in murine

splenocytes. DIM was orally administered or injected into the intraperitoneal cavity to male

mice. Blood samples were collected at various time intervals, and the amount of serum

cytokines were analyzed using RayBio Mouse Cytokine Array 1. Of the cytokines detected,

interferon-gamma (IFN-_), interleukin 12 (IL-12), interleukin 6 (IL-6) and granulocyte-colony

stimulating factor (G-CSF) were expressed at elevated levels in mice with oral administration of

DIM. Mice with intraperitoneal injection of DIM did not exhibit changes in the level of

cytokines produced. This suggests that DIM metabolites play an important role in activating the

innate immune system. The current study seeks to analyze additional influences DIM has on the

innate immune system. We hypothesize that DIM and/or its metabolites stimulate the production

of IL-6 and G-CSF cytokines in RAW 264.7 macrophages. These cytokines play an essential

role in the innate immunity response, as IL-6 has anti-bacterial properties, and G-CSF promotes

white blood cell formation.



After a 36-hour proliferation study on RAW 264.7 macrophages treated with various

concentrations of DIM, we determined that 10 _M DIM was the highest non-toxic concentration

of DIM that can be used. Macrophages treated in vitro with 10 _M DIM had elevated secretion

of IL-6 as determined by Enzyme-Linked ImmunoSorbent Assay. However, there was no

change in the amount of G-CSF secreted under the same treatment. Recent studies have shown

that co-treatment of Lipopolysaccharide (LPS) and 10 _M DIM yields an elevated level of IL-6

production that is 2-fold of LPS alone, and 45-fold of untreated RAW cells. However, these

results are preliminary and further trials must be performed. DIM metabolites did not change the

secretion levels of IL-6 and G-CSF in RAW 264.7 macrophages. Future studies should focus on

isolating components of DIM metabolites in order to discover the key molecular product(s) that

can activate the innate immunity response.



In this study, DIM produces a weak induction of IL-6 by itself, but it has a synergistic effect on

IL-6 secretion along with LPS. Thus, these are promising results for future research of DIM’s

efficacy in activating the innate immune system.

This experience has reawakened my sense of curiosity and my love for learning. I would

highly recommend the College of Natural Resources Honors Program to anyone who is willing

to tackle challenges and grow intellectually.









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Congratulations Class of 2008!









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