Cal Poly Biology Department

Attend Annual Meeting of the American Society of Cell Biology - Angela Holbrook

By receiving this money, I will travel to San Francisco to attend the annual American Society of Cell Biology meeting. This meeting will allow me to view the most recent research being completed in cell biology. I will attend two days of the conference to hear talks and view posters prepared by cell biologists. I hope this will give me a better idea of the direction I would like to take in my own career while increasing my understanding of the scientific community that I could then pass on to other students.

Participating in the ASCB conference gave me new insight into cell biology. I now have a fuller understanding of what research is being completed in cell biology. I also am more aware of the diversity of the field. I believe this was a great experience to help prepare me for the future. I hope to become a professor in biology at the cellular level and this meeting gave me a peek into what is available currently in cell biology. After attending the American Society of Cell Biology meeting, it is apparent to me that cell biology of cancer fascinates me the most.

The conference was much less intimidating than I expected. The other attendees were helpful and friendly. My exposure to these scientists will help me encourage other students to participate in similar activities. I will be able to relay the laid back atmosphere to fellow classmates to hopefully increase student participation in scientific meetings.

Attend Annual Meeting of the American Society for Cell Biology - Aubrey Isbell

On December 14th through December 18"', 1 will attend the 42 nd Annual Meeting of the American Society for Cell Biology in San Francisco. This trip is valuable to me as a student because it gives me a chance to learn much more about cell biology than the small sampling that is taught to us in class. I plan on continuing my education and this will hopefully help me focus on what I want to concentrate on in grad school. In reading the meeting program, there have been many interesting symposia that I wish to attend, unfortunately most conflict with each other. Regardless, no matter which symposia I attend, I will gain valuable information about the science I have grown to love.

Attended Western Society of Naturalists meeting in Monterey, CA - Jessica Kershner

My reason for attending this meeting was to get a better understanding and knowledge in the field of marine sciences. This conference was specifically designed to accommodate Marine Sciences majors, and I was hoping to make connections with graduate students, professors, and people in the related fields of marine ecology, invertebrate zoology, paleontology, biology, etc. By going to the WSN meeting, I was able to meet people my age who are participating in projects that I have an interest in. This better prepares me for my Senior Project, not to mention helping to make my decision as to which graduate school I would like to attend and what they have to offer. I have always known marine biology was the field I wanted to pursue, but was unsure of which aspect. Until recently, I was leaning toward marine invertebrate ecology (subtidal to intertidal), but after attending the conference I would like to focus more on invertebrate ecology in the coral reefs or mammology—depending on which one I can get more experience in before graduate school. This conference helped to redirect my education goals.

The High Mountain Lookout station currently used for the official research facility of California Condor Radio Telemetry will also serve as a research base station for my study of the small mammals.

Three vegetation types have been identified and described so that some hypothetical comparisons about how small mammals use the differing landscapes can be made. These communities are woodland, chaparral, and riparian. From these communities a small mammal species list will be generated by trapping results, followed by an attempt for abundance estimation using a linear regression method.

GIS software will be used to randomly select 5 one-hectare plots for each of the 3 vegetation communities, resulting in a total of 15 plots. The three communities will be determined by going out and visually confirming the vegetation types. The use of GPS devices will aid in locating the plots on USGS topographical maps. Marking plot centers both at the plot sights and on the maps will be done via GPS. The use of Sherman traps will be the primary data collection device, where identification of the mammal will be done visually. These stations will be set up in the evening and checked the following morning for two consecutive nights. A typical plot will have 16 traps total.. Signs such as tracks, tail drags and scat will be noted for incidental data collection to supplement the trapping data.

Three data collecting sessions will be done, including two nights per session. Each session will focus on one of 3 communities for the winter of 2002-2003.

Having recently undergone a renovation, the Hi Mountain lookout aspires to be a collaborative field station in conjunction with the U.S. Forest Service, U.S. Fish and Wildlife, The Condor Recovery Program, and Cal Poly. My contribution, as a Cal Poly student, will include studies of the mammalian organisms within the surrounding communities of riparian, woodland, and chaparral.

My concern is determining what effects the three aforementioned communities have in relation to the distributions of the mammalian fauna of the region. My study will include a species list with an indication of the abundance of each species within the community type.

This project has the potential to provide the foundation for many future studies. However, this project requires equipment, supplies, and a reliable mode of transportation. The use of the college fee funds would provide for suitable trapping mechanisms, bait for the traps, animal handling tools, necessary camping supplies, anti-poison oak clothing, batteries, headlamps, maps, film, and gasoline.

My hope is for this project to provide a general view of the mammalian diversity surrounding Hi Mountain; and serve as the foundation for future projects of this magnificent area.

Hi Mountain resides on the Pozo Forest Service land, which gives us a wide range to collect data from. I am working with several other Cal Poly students who are studying different aspects of the area, which include vegetation, birds, mammals, and herps. At the same time, we are all being trained in condor telemetry, which is basically what the lookout was designed for. The question I am asking for this project is the following: what is the abundance and distribution of insects and related arthropods in relation to each vegetation community.

Since the main aspect of this project deals with vegetation, I wanted to devise a way to compare insects between the oak woodland, riparian, and chaparral communities. Because of limited time and expense, the easiest and most efficient method of collection is the type and amount of insects found in ground litter, as well as in a net sweep of the surrounding area.

The materials I need to effectively collect insect specimens include a net, an insect kill jar, etc. I also need to create a Berlese funnel to extract the collected arthropods from the soil. Since the senior project includes camping out on Hi Mountain, I need effective camping gear. Including miscellaneous fees, I would need about $400 to cover my senior project cost.

Wildlife Biology at Hi Mountain Lookout: An Educator’s Field Guide - A Krisch

This field guide is written and structured for use by educators teaching advanced high school biology students or non-major college biology/ecology classes. It employs a “learn by doing” approach that is meant to enhance the students’ grasp of systematics and the relationships of various native flora and fauna. This knowledge is then applied in two typical California plant communities in which environmental awareness and ecological comprehension is attained.

Requested funds for this project will be used for the following:

Assessment of Plant Communities in the Santa Lucia Wilderness as Bird Habitat - Holly Messer

The Santa Lucia Wilderness located in Central California, supports three dominant plant communities of mixed chaparral, oak woodland, and riparian. Research plots will be selected within the communities using a Geo Positioning Satellite System. Research data will be compiled using Geographic Information Systems. Twenty-five plots per community will be randomly selected resulting in 75 study sites. By guaranteeing random selection, each plant community is equally represented through unbiased data. Within the three communities, aspects of the ecosystem including plants, mammals, reptiles, amphibians, insects, and birds will be researched. Data will be collected during the wet and dry seasons.

Ornithology research will document ecological significance of each plant community and how communities support bird habitat. A diversity index compiled from surveyed plot data will be developed. Methods used for studying or monitoring breeding land birds include point counts and area searches. Point counts are conducted from plot centers and completed once per plot. Observers will record avian species seen or heard for a radius of fifty meters within a 5-minute time limit. Area searches differ form point counts in that area searches cover the length of one-hectare plots. Each plot will be searched for 6.66 minutes. Data sheets modeled after the Point Reyes Bird Observatory (PRBO) Data Sheets will be used for recording area searches and point counts.

Data analysis composed of simple statistics including the mean and standard deviation of diversity and abundance will document trends among birds within the study area. Linear regression will establish a correlation between habitat quality and abundance or absence of avian species.

Our study is within the Los Padres National Forest, 15 miles east of the city of San Luis Obispo, California. Point counts and area searches will be conducted in both the wet and dry seasons to census avifauna within 75 randomly selected plots within oak woodland, chaparral, and riparian communities surrounding the Hi Mountain Condor Lookout. We will be accessing various factors of the vegetative communities and the effects of these factors on bird species diversity and abundance within each of our study plots. In doing this we hope to relate specific habitat features which are desirable to various avian species within these communities. Conducting our census during both the wet and dry season will allow us to determine birds that are resident, wintering, locally breeding, or migratory. Data will be analyzed using simple statistical methods and a diversity index will be created. The design of this study allows for it to be continued into the future indefinitely. In doing so it will give a picture of the avian population dynamics occurring in the above named vegetative communities over time. The four hundred dollars requested for this senior project will be used to defray costs of travel to the study sites, food, and various supplies both already incurred and pending.

Steelhead Habitat in San Luis Obispo Creek - Ulysses Ablen, Tina Chouinard, and Cecelia Boudreau

In September of 2002, a concrete dam was demolished on the upper San Luis Obispo Creek watershed. These small dams have historically been an impediment to successful steelhead migration and spawning. The purpose of this study is to determine the improvements of instream steelhead habitat with the removal of these dams. We are currently measuring stream morphology (pools and riffles), Nitrates and Phosphates, Dissolved Oxygen, Temperature, as well as indigenous plants and animals.

The funds from this grant will allow us to determine the total suspended solids (sediment loads) within the upper reaches of San Luis Obispo Creek. Excessive sediment loads are of critical interest since they smothers steelhead eggs.

I am applying for senior project funds to continue research that was begun this summer 2002. The research pertains to two moth populations of the species Hyalophora euryalus. One moth population is located in Los Osos, and the other is located in Santa Maria. Both moth populations feed on different substrates, and emerge at different times of the year. The Los Osos moths have been found to feed on Ceonothus bush, and California coffee-berry, and the moths in Santa Maria feed on Pepper- tree. The fact that the moths feed on different substrates is a quirk, and the fact that each population (possibly) emerges at different times of the year is also strange. (tests are being done right now to determine if light or temperature act as cues for eclosion). Therefore, as a biologist, I think both moth populations need to be studied.

I’ve decided to use a molecular- based approach in analyzing the two moth populations: By comparing gene sequences of the mitochondrial control region, and period gene (present in both groups of organisms), and possibly ribosomal RNA. The mitochondrial control region (mtDNA region) is highly variable, and is good for use in intraspecific (within species) comparisons. The period gene is involved in the insect’s circadian rhythm (or biological clock), and seems to also be a prime candidate for this study.

Population dynamics and cluster formation of overwintering monarch butterflies - Charis Claassen

I will research several elements of habitat use, including cluster placement on the trees, behavior relative to temperature, sunlight and wind speed and cluster dispersal and formation differences over time. I plan to find a method to study how the last sunlight of the day effects cluster placement and orientation on the branches. My primary study site is in San Luis Obispo, but I also am carrying out a comparative study with three northern sites in Monterey, Santa Cruz, and Marin Counties. I am requesting money for mileage for a trip to Monterey County (Esalen Institute monarch habitat; November 11, 2002), as well as mileage and lodging expenses for a trip on January 1-4, 2003 to collect data for my project in Marin and Santa Cruz Counties.

Effects of a protozoan parasite (Ophryocystis elektroscirrha) on the migration of monarch butterflies (Danaus plexippus L.) in part of the range of the wintering generation - Janelle Parson

My project is a part of a study called Monarch Alert, which is a large-scale tagging project jointly being done by Dr. Dennis Frey (Cal Poly Biological Sciences Department) and biologists from the Ventana Wilderness Society. I am studying populations found in four counties (San Luis Obispo, Monterey, Santa Cruz, and Marin). I am helping tag nearly 24,000 butterflies. The tags have unique ID numbers on them along with a Toll-free phone number so the public can report finding them in the spring. Approximately 40% of these butterflies will be sampled for their level of infection by the parasite using a non-invasive technique. I touch a small piece of transparent tape to their abdomen during the tagging which removes a small number of scales. Spores of the parasite occur on the scales. In the lab, I screen the tape swatches for presence/absence of spores and rate the infected ones on a scale developed by Sonia Altizer (Emory University monarch expert). As part of this project, I accompany Dr. Frey on trips to each of the four counties during the wintering season (Nov, Dec., and Jan). While the overall project, Monarch Alert, pays for part of my travel costs, each undergrad is expected to pay for their transportation and lodging for at least one of the trips. I am requesting money for mileage for a trip on November 11, 2002 to Monterey County (Esalen Institute monarch habitat), as well as mileage and lodging expenses for a trip on January 24-26, 2003 to collect data for my project in Marin and Santa Cruz Counties.

Effects of a protozoan parasite (Ophryocystis elektroscirrha) on the migration of monarch butterflies (Danaus plexippus L.) in part of the range of the wintering generation - Emily Amaral.

My project is part of a study called Monarch Alert, a large-scale tagging project jointly executed by Dr. Dennis Frey (Cal Poly Biological Sciences Department) and biologists from the Ventana Wilderness Society. The study includes populations found in four counties (San Luis Obispo, Monterey, Santa Cruz, and Marin) and will tag nearly 24,000 butterflies. The tags have unique ID numbers on them along with a Toll-free phone number so the public can report finding them in the spring. Approximately 40% of these butterflies will be sampled for their level of infection by the parasite using a non-invasive technique. By touching a small piece of transparent tape to their abdomen during the tagging a small number of scales are removed. Spores of the parasite occur on the scales. In the lab, I screen the tape swatches for the presence/absence of spores and rate the infected ones on a scale developed by Sonia Altizer (Emory University monarch expert). As part of this project, I accompany Dr. Frey on trips to each of the four counties during the wintering season (Nov, Dec., and Jan). While the overall project, Monarch Alert, pays for part of my travel costs, each undergrad is expected to pay for their transportation and lodging for at least one of the trips. I am requesting money for mileage for two trips to Monterey County (Esalen Institute monarch habitat; December 18, 2002 & January 20, 2003), as well as mileage and lodging expenses for a trip on November 22-24, 2002 to collect data for my project in Marin and Santa Cruz Counties.

Effects of a protozoan parasite (Ophryocystis elektroscirrha) on the migration of monarch butterflies (Danaus plexippus L.) in part of the range of the wintering generation - Erin Nakada

My project is a part of a study called Monarch Alert, which is a large-scale tagging project jointly being done by Dr. Dennis Frey (Cal Poly Biological Sciences Department) and biologists from the Ventana Wilderness Society. I am studying populations found in four counties (San Luis Obispo, Monterey, Santa Cruz, and Marin). I am helping tag nearly 24,000 butterflies. The tags have unique ID numbers on them along with a Toll-free phone number so the public can report finding them in the spring. Approximately 40% of these butterflies will be sampled for their level of infection by the parasite using a non-invasive technique. I touch a small piece of transparent tape to their abdomen during the tagging which removes a small number of scales. Spores of the parasite occur on the scales. In the lab, I screen the tape swatches for presence/absence of spores and rate the infected ones on a scale developed by Sonia Altizer (Emory University monarch expert). As part of this project, I accompany Dr. Frey on trips to some of the four counties during the wintering season (Nov, Dec., and Jan). While the overall project, Monarch Alert, pays for part of my travel costs, each undergrad is expected to pay for their transportation and lodging for some of the trips. I am requesting money for mileage for two trips to Monterey County (Esalen Institute monarch habitat; Dec. 18, 2002 & Jan. 20, 2003).

Comparison of Detection methods for Plasmodium mexicanum in Sceloporus occidentalis populations in San Luis Obispo County - Milania Dela Cruz

Lizards and birds worldwide are infected with numerous vector-borne apicomplexan blood parasites (hemoparasites). In Northern California, one such host-parasite system has been well-studied in Western fence lizards, Sceloporus occidentalis, infected with Plasmodium mexicanum. Although other members of the Plasmodium genus cause malaria in humans, P. mexicanum is transmitted exclusively to lizards via sand flies, and serves as an interesting basis for study of parasite-host ecological relationships. The prevalence of P. mexicanum infection in local S. occidentalis populations has never been examined in this region of California. Previous studies have indicated that standard methods of detection, such as thin blood film smear examinations, may underestimate the prevalence of infections with this parasite if parasitemias are low. Recent studies using a nested PCR procedure and Plasmodium-specific primers have allowed more accurate detection of this parasite, particularly when infections are subpatent by microscopic examination. This study will be conducted to estimate the prevalence of P. mexicanum in S. occidentalis by comparison of microscopic examination of stained blood smears for parasites inside erythrocytes versus the nested PCR technique. Major supplies needed for the project include PCR primers, DNA extraction kits, PCR reagents and microscope slides.

For my senior project I would like to investigate the possibility of the purple sea urchin, Strongylocentrotus purpuratus, expressing the low-affinity neurotrophin receptor p75NTR. This neurotrophin receptor has been found in mammals and is believed to be linked with the signaling sequence that causes apoptosis in cells. It would be interesting to see if echinoderms, such as the purple sea urchin, have the gene for this receptor. If so, then studies could be done to determine when or if the p75NTR receptor is expressed.

In order to be able to look for the p75NTR gene in the purple sea urchin’s genome, PCR will be used. To be able to do this, supplies are needed to try to detect the gene. The typical supplies for PCR are needed. Some will be supplied by using common lab stock for PCR tubes, racks, MgCl2, BSA, DEPC water, as well as cloning and sequencing supplies, including Luria Broth media, MiniPrep Kits, and BigDye Sequencing Kits. The other items that are more specialized or that will be in large demand by this project include: primers sets for the p75 gene, Taq enzyme for PCR, buffer and dNTPs; these are the items for which funding is being requested. I would like to be able to design four different primers for the p75 gene, which cost about thirty dollars each depending on the length of the oligomer. I would also like to order two vials of Taq enzyme which is approximately forty-five dollars per vial. Each Taq vial comes with the buffer for those enzymes. Also, I would like to have one vial of dNTP's to use for polymerization. This will cost approximately ninety dollars. These values are all approximate because exact values were not able to be obtained from the vendors. So, I am requesting funding for a total of three hundred dollars to fund the purchase of Taq polymerase enzyme, dNTPs and p75 primers. It cannot be foreseen how many rounds of PCR and how much of these reagent will be utilized will be needed in order to say confidently that the purple sea urchin has or does not have the p75 receptor gene. This will depend on the optimization of the PCR reaction with its components, so this request may be too little or may be too large for the aim of this project.

Senior Project Money Request ($400)

The goal of this project is to attain secreted expression of a glycosylated bovine beta-casein gene in the fungal expression system Pichia pastoris. This will be achieved by construction of a fusion gene containing a yeast secretion signal (S. cerevisiae alpha-factor prepro peptide) to the bovine gene in the vector pPIC9K. New primers need to be developed to PCR of the gene from the plasmid pAML01, that will add new directional restriction sites to the gene. Once successful, Pichia pastoris will be transformed with the pPIC9K/beta-casein construct to obtain strains capable of secreted expression of the protein product. Funds will be spent on cloning tools such as the new directional primers and restriction enzymes, competent cells, Taq, etc.

Mechanism of Round-up Resistance in a Population of Lolium - Yadi Sandoval, Jake Shaul, and Noelle Lapcevi

The pathway leading to the synthesis of aromatic amino acids and other important trans-cinamic acid derivatives begins with the enzyme 5-enolpyruvylshikimate 3-phosphate synthase (EPSP-S). Round-up is a powerful herbicide that acts by inhibiting this enzyme. Significantly, Monsanto has developed Round-up Ready crops like cotton, soybean, and corn. These Round-up resistant crops produce an EPSP-S enzyme that is resistant to Round-up. Recently, however, several weed populations with resistance to Round-up have emerged. The focus of this project is to determine the mechanism that confers Round-up resistance to the “Chico” population of Lolium. To this end, the EPSP-S gene sequences from the Round-up resistant and Round-up sensitive varieties of the weed Lolium will be compared. The first major step involves DNA isolation, obtaining polymerase chain reaction (PCR) products (the primers were designed and tested through a previous senior project), cloning the PCR product, and then sequencing the cloned PCR products. The second major step will involve sequencing regions that flank this portion of the EPSPS gene. In order to obtain repeated data suitable for publication, three students are currently involved, and each will start will their own samples of sensitive and resistant Lolium plants.

I am currently working on my senior project, which involves the cloning of a genetically modified bovine b-casein gene (obtained from Dr. Rafael Jimenez-Flores of the Cal Poly Dairy Science Department) into the yeast Yarrowia lipolitica in order to gain expression of the gene and secretion of the resulting protein. The modification to the gene results in site-specific posttranslational glycosylation of the protein when expressed in a eukaryotic system such as the yeast Yarrowia. If successful, this project will create an efficient means of production for glycosylated bovine b-casein, which can be used for analysis of suspected improvement to functional properties of the protein resulting from glycosylation.

In order to complete this project, I will need a number of products and supplies including: PCR reagents, competent E. coli cells, growth media, reagents for yeast transformation, restriction endonucleases and oligonucleotide primers; the last three of which are very specific to this project and are not available in the lab. For transformation of Yarrowia using the LiAc procedure, PEG 4000 must be purchased. For recombination, the following restriction enzymes are needed: SfiI, PmlI, NotI, and ApaI, all of which range from $50 to $60 each. For amplification of the b-casein gene and cycle sequencing, a total of eight custom oligonucleotide sequences will be ordered, which depending on the length of each sequence, will total about $160. These three, and possibly some of the other aforementioned supplies will be purchased to complete the project.

Phytoremediation through the use of Poplar sp. in order to degrade hydrocarbons - Eric Brothwell

Transgenic tobacco (Nicotiana tabacum var. Xanthi), containing a plasmid constructed by Monica Britton (Horticulture, graduated 2001), may theoretically degrade hydrocarbons (alkanes) through the use of two genes found on the plasmid: cytochrome P450 reductase and corresponding monooxygenase. As to date, Monica’s plasmid has been inserted via Agrobacterium tumefaciens 4404 into Xanthi discs, cocultivated, and are currently being micropropagated. Next, I would need to being testing the presence and expression of the two genes. There are three major ways by which one may test this: first, through direct isolation of DNA and subsequent sequencing for those two genes using preexisting primers and/or PCR the genes and run a gel with the original plasmid’s genes; second, through the use of a florescent dye specific for the endoplasmic reticulum and compare “percent abundance” of ER within transgenic and non-transgenic Xanthi; and third, to test whether or not the Xanthi may survive on oil-based agar (with or without the presence of light). In order to strengthen any positive results, it would be preferential for me to use all three methods. If proven to work, this would be the first known example of a plant being capable of degrading, and possibly living off of, hydro-carbons.

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