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Biology

Watch Jennifer Franks '12 Discuss Her Research

Watch Kristen Lindbergh '12 Discuss Her Research

Evidence of multiple algal replacement in the Hydra viridissima-Chlorella symbiosis

Alexya Aguilera ('12); Kun WeiSong ('12); Abril Iniguez ('08); Diana Chen ('09); Richard Campbell*; Mentor: Daniel Martinez
*Cell & Developmental Biology; UC Irvine, Irvine, CA

Abstract: The phylogenetic relationships among species within the genus Hydra are unclear. A recent paper published by the lab supports that the species cluster into four groups. Further analyses indicate that the viridissima group (green hydra with intracellular algae) diverged first and brown hydra groups share a common ancestor. The complete internal transcribed spacer 1 (ITS1), 5.8S rDNA, and ITS2 nuclear rDNA region, and the rRNA (18S) gene were sequenced for viridissima strains from over 50 worldwide locations. The molecular phylogeny based on these sequences reveals that there are several distinct clades of Hydra viridissima, with closely related hydra sharing similar Chlorella. Furthermore, the algal endosymbionts of different hydra strains are diverse and appear in five distinct clades with unclear affinities to free-living Chlorella. These results direct future analyses on the evolution of Chlorella-hydra symbiosis. A working hypothesis suggests that sporadic replacements of the algae have occurred since the original symbiosis.
Funding provided by The Fletcher Jones Foundation (AA), National Science Foundation (DM)

The Role of Birds in the Regeneration of Native Forests: A Case Study from the Mariana Islands

Eleanor Caves ('11); Summer B. Jennings ('12 Butte CC); Haldre S. Rogers*; Eliza K. Hooshiar* Mentor: Josh Tewksbury*
*Biology Dept., University of Washington, Seattle, WA

Abstract: Approximately 35% of Earth's lands have been heavily influenced by humans, though only a small fraction are undergoing restoration efforts; the remainder are left to natural processes. In this study, we evaluate the importance of frugivorous birds in the regeneration of native forest on the island of Guam, which has experienced the functional extinction of its native forest birds, and Saipan, a nearby island with birds. We compared seed rain in non-native Leucaena forest adjacent to native forest on Guam and Saipan by establishing transects of seed traps extending from native forest 100m into Leucaena forest. Seed rain from 270 traps at six sites was sorted after 26 days. We found zero bird-handled seeds in traps on Guam, and an average of 0.86 seeds/m2 on Saipan. Our results imply a key role for birds in forest regeneration, suggesting slow to nonexistent regeneration of native forest from Leucaena forest on Guam.
Funding provided by The Fletcher Jones Foundation, National Science Foundation, Research Experience for Undergraduates

Loss of Sensory Hair Cells in Adult Zebrafish using Gentamicin and a Non-Invasive Procedure to Test Hearing in Zebrafish

Chien-Wei Chen ('11); Sarah Rubenstein ('11 SCR); Julia Gleichman ('10); Dennis Higgs*; Mentor: Jonathan Matsui
*University of Windsor, Ontario, Canada

Abstract: Sensory hair cells are mechanoreceptors found in the inner ear that mediate hearing. Certain pharmaceutical drugs (e.g. aminoglycoside antibiotics) can kill these receptors, causing permanent hearing loss in humans. Varying concentrations of gentamicin were intraperitoneally (IP) injected into adult zebrafish to examine hair cell death. Following the injections, fish were euthanized and fixed. Hair cells were stained with phalloidin, while nuclei were stained with Hoechst 33342 and viewed using fluorescent and confocal microscopy. In a separate study, we evaluated normal zebrafish hearing through auditory brainstem responses(ABR), which is a non-invasive procedure regularly used to test hearing in infants. Future studies will involve correlating hair cell loss with hearing loss in gentamicin-treated zebrafish.
Funding provided by Rose Hills Foundation, National Institutes of Health Grant R15DC010998-1 (JM)

Murrelets on the Move?: A study on the effects of the El Niño Southern Oscillation weather pattern on the distribution of Xantus's Murrelets around Santa Barbara Island

Alyssa Corley ('11); Nicholas Tyack ('11); Mentor: Nina Karnovsky

Abstract: The purpose of this study was to examine the effects of the El Niño Southern Oscillation (ENSO) on the distribution of Xantus's murrelets around Santa Barbara Island (SBI) of the Channel Islands. We examined the distribution of the murrelets in relation to oceanographic conditions, in particular water temperature and depth of thermocline, as well as the distributions of zooplankton prey. We collected data for this study during March, April and May 2010. Zooplankton was collected in net tows in the upper 50 meters of the water column and we measured temperature and salinity in the top 100 meters. Surveys for murrelets were also conducted along transect lines radiating from the island. This study will not only provide insight about the effects of ENSO on murrelet populations near SBI, but could also serve to help with the continued conservation of the murrelet, which has recently been named a threatened species.
Funding provided by Montrose Settlement Restoration Program

Investigating a Trifunctional Enzyme of Tetrahymena thermophila

Thomas Dixon ('11); Mentors: Andre Cavalcanti, Tina Negritto

Abstract: Tetrahymena thermophila are freeliving protozoa, and are often used as a model organism in experimental biology. Tetrahymena possess unusual versions of many metabolic pathways, including the methionine salvage pathway, which recycles scarce methionine and regulates polyamines. Polyamines are organic molecules that control cell growth and death in most eukaryotes. Our study focuses on a particular gene in the methionine salvage pathway in Tetrahymena that performs the function of three separate genes in yeast. The objective of this study is to determine how the two conserved domains in the Tetrahymena gene catalyze the same reaction as three genes in yeast. To accomplish this, we seek to perform complementation testing in yeast cells, a process which involves cloning of PCR products and creation of yeast double mutants. Our hypothesis is that dioxygenase domain of the Tetrahymena gene will catalyze the combined reaction of the latter two yeast genes.
Funding provided by National Science Foundation ARRA #MCB920697 (AC)

Genes that control vesicular transport in Drosophilia

Nydia Ekasumara ('11); Mentor: Clarissa Cheney

Abstract removed upon request.

Ciliate Nuclear Evolution

Kristen Lindbergh ('12); Mentor: Andre Cavalcanti

Abstract: Ciliates are unique among eukaryotes because each ciliate cell has two kinds of nuclei: a germline nucleus (micronucleus) used to exchange genetic material during sexual reproduction, and a somatic nucleus (macronucleus) used for transcription. The ciliate macronucleus has a very unique chromosomal organization, in some cases containing thousands of copies of up to 20,000 small, gene-sized chromosomes. To investigate how these ciliates reached this state, we created a simulation that models the growth of a ciliate population. Starting with cells possessing more typical eukaryotic chromosome levels, we allowed the population to evolve, carefully tracking the chromosome fragmentation and copy number amplification. There are many unknown parameters for this model, but for a wide range of parameters, the simulation resulted in copy and chromosome numbers similar to those observed in nature. This demonstrates that evolutionary pressures can explain ciliate macronuclear organization.
Funding provided by Howard Hughes Medical Institute

Physiological Divergence in Two Species of the Hawaiian Silversword Alliance and Their Hybrids

Drew McKinney ('12); Mentor: David Becker

Abstract removed upon request.

Foraging Behavior of Cassin's Auklets in the Gulf of Farallones

Kristina McOmber ('12); Eleanor Caves ('11); Russ Bradley*; Pete Warzybok*; Mentor: Nina Karnovsky
*PRBO Conservation Science, Petaluma, CA

Abstract: The purpose of this study was to investigate linkages between Cassin's Auklet (Ptychoramphus aleuticus) foraging, prey abundance, and ocean conditions in the Gulf of the Farallones. We hypothesized that as the density of krill near the Cassin's Auklet colony increased, the birds’ foraging behavior would reflect this change by making fewer dives, diving to shallower depths, and shortening their dive bouts, We hypothesized that the density of krill would decrease during 2010, an El Nino year, as compared to 2008 and 2009, non El Nino years. We tested this hypothesis in May and July of 2010 by affixing Time Depth Recorders (TDRs) to foraging auklets. We assessed the distribution and abundance of krill in relation to ocean conditions in the Gulf of Farallones during oceanographic cruises concurrent with TDR deployment. We recovered 13 deployments of TDRs in 2010. We found no differences in chick growth between instrumented and non-instrumented birds.
Funding provided by The Fletcher Jones Foundation (KM, EC), PRBO Conservation Science

Biochemical Characterization of Homing Endonucleases

Zachary Mirman ('11); Mentor: Len Seligman

Abstract: Homing Endonucleases (HEs) recognize 14-40 base pair sequences in DNA and induce double-stranded breaks. I-CfrI and I-CpaII, two HEs encoded by genes located in introns of the chloroplast DNA of different Chlamydomonas species, have each shown some activity in vivo in E.coli. I engineered a 6-histidine C-terminus tag on I-CfrI and I-CpaII to purify each protein. In preliminary experiments, I-CfrI shows some activity in vitro. I have also cloned two archael intein encoded HEs, from Pyrococcus abyssi (Pab) and P. furiosus (Pfu), into expression plasmids for future biochemical characterization.
Funding provided by The Fletcher Jones Foundation

Correlating DNA damage in older generations of Saccharomyces cerevisiae with the Sir2 gene

Sameera Mokkarala ('12); Mentor: Laura Hoopes

Abstract: Recent research suggests that extrachromosomal ribosomal DNA circles (ERCs) play a significant role in how Saccharomyces cerevisiae yeast age. The asymmetric aging process of yeast causes these ERCs to accumulate in the mother cells, which shortens cell lifespan. The Sir2 gene has been found to have possible ties to yeast aging as well, with a lack of the gene causing a shortened lifespan and an extra copy of the gene causing an extended lifespan. This project seeks to discover whether there is a relationship between DNA damage with age and the Sir2 gene. Yeast strains used were sir2", which has the Sir2 gene deleted, and the wild type. Experiments were conducted using Biotin age sorts and TUNEL fluorescent labeling assays. Results thus far confirm the relationship established by previous research. Future research should look to investigate the relationship between sir2", the wild type, and SIR2EX.
Funding provided by The Fletcher Jones Foundation

Ammonia excretion patterns in the intertidal isopod, Ligia occidentalis

Maya Nakamura ('11); Rebecca Abbey ('07); Mentor: Jonathan Wright

Abstract: Water conservation strategies are an important adaptation for the majority of terrestrial and intertidal crustaceans, since they rely on ammonotelic excretion. Some adaptations include diurnal patterns of gaseous excretion in terrestrial isopods and tidal patterns of aqueous excretion in marine crabs, where both selectively exploit high humidity or water availability. We hypothesized the intertidal isopod, Ligia occidentalis, like marine crabs, would also have a tidal excretion pattern. Ammonia excretion was assayed by comparing acid dissolved ammonia concentrations between animals with and without access to water. Glutamine, a primary form of sequestered nitrogen, was also measured by comparing in vivo concentrations in animals collected 2 hours before and after high tide as evidence for a tidal excretion pattern. Ammonia excretion was found to be significantly higher when water was available, while glutamine assays indicated greater accumulation during low tide, as predicted. Both provide support for the tidal hypothesis of ammonia excretion.
Funding provided by The Elgin Fund for Summer Student Research

Bacterial-Bacterial interactions: studying the effect of Pseudomonas aeruginosa on Burkholderia cenocepacia

Craig Ramirez ('11); Steve Bernier*; Mentor: George O'Toole*
*Microbiology/Immunology Dept, Dartmouth Medical School, Hanover, NH

Abstract: Burkholderia cenocepacia, and Pseudomonas aeruginosa are two opportunistic pathogens that are commonly found in CF patients with pulmonary infections. They are able to co-infect patients' lungs, causing more severe symptoms. In this study we aim to obtain a better understanding and appreciation for microbial community dynamics. Based off the observation that B. cenocepacia increases its binding ability of congo red dye when in the presence of P. aeruginosa, we ask two main questions: what is the molecule secreted by P. aeruginosa causing a change in B. cenocepacia's phenotype, and, what is the molecular response by B. cenocepacia? We report that the molecule secreted by P. aeruginosa is a diffusible molecule that is linked to the rhl quorem-sensing system, and propose a basic model for our observations. We have also shown that clinical strains of both P. aeruginosa and B. cenocepacia show the same effect as their wild-types.
Funding provided by Department of Defense ASSURE Program (NIH)

Hand Jive: Digit Ratio, Hormones & Gender Identity

Kristin Raphel ('11); Jennifer Franks ('12); Anna Fiastro ('11 SCR); Jennie Sweda ('11); Katie Cettie ('11); Ian Hannigan ('08); Mentor: Rachel Levin

Abstract removed upon request.

A mutation in the active site of Palmitoyl Protein Thioesterase 1 in Drosophila melanogaster alters synaptic transmission

Amalia Roth ('11); Elizabeth Aby ('11); Christopher Korey*; Mentor: Karen Parfitt
*Biology Dept, College of Charleston, Charleston, SC

Abstract: Infantile Neuronal Ceroid Lipofuscinosis (INCL) is a neurodegenerative disease caused by a mutation in palmitoyl protein thioesterase (PPT1), and may result in impaired synaptic transmission. To examine possible defects in synaptic transmission in a Drosophila model of INCL, we recorded spontaneous miniature excitatory junction potentials (mEJPs) and evoked EJPSs at the neuromuscular junction of wild-type (W1118) and PPT1-mutant (A179T) Drosophila larvae. No differences were seen in average mEJP frequency or amplitude, suggesting that this point mutation is not significantly affecting spontaneous pre- or post-synaptic exocytosis. The rate of vesicle depletion and recovery is not significantly different between the wild-type and mutant in normal or low (.5 mM) extracellular calcium. However, at low calcium there was a significant difference in baseline evoked EJP amplitude. Taken together, these data suggest that this point mutation in PPT1 does not affect endocytosis or spontaneous neurotransmitter re-lease, but does affect calcium-mediated exocytosis.
Funding provided by The Fletcher Jones Foundation (AR); The Paul K. Richter and Evalyn E. Cook Richter Award (EA); The Hirsch Foundation (KP)

Comparing the effectiveness of insect visitors to Eriastrum sapphirinum

Allison Sherris ('13); Mentor: Frances Hanzawa

Abstract: Pollen limitation, reduction in plant fitness due to inadequate pollination, is known to occur in habitats affected by fragmentation and the invasion of non-native species. In this study we analyzed insect visitors to the pollen-limited wildflower E. sapphirinum to determine which are the most effective pollinators. To do this, we counted the number of pollen grains adhering to insects‚ Äô bodies and calculated what percent of the pollen was conspecific (from E. sapphirinum flowers). We found that bees carried significantly more pollen than flies or beetles and had pollen loads with the highest proportion of conspecific pollen, indicating that they are the most effective pollinators. Non-native honey bees carry the most heterospecific pollen (which can "clog" the stigma of a flower and reduce plant fitness) making them less favorable floral visitors than native bees.
Funding provided by The Schenck Fund

Genes that control vesicular transport in Drosophilia

Tim Stutz ('12); Mentor: Clarissa Cheney

Abstract removed upon request.

The Hydra viridissima-Chlorella Symbiosis

Joseph Tseng ('12); David Pichardo ('13); Kun-Wei Song ('12); Alexya Aguilera ('12); Abril Iniguez; Diana Chen; Richard Campbell; Mentor: Daniel Martinez

Abstract: Work done by our lab has shown that green hydra may be grouped into five different clades, each carrying a unique endosymbiotic alga. Given that endosymbiotic Chlorella can be infected by highly specific viruses, we hypothesize that the five distinct groups of hydra endosymbionts may be infected by five distinct viral strains. Our goal is to isolate the chlorella endosymbionts from each of the five groups of green hydra and use these cells for the isolation of viruses from the wild. Algae were isolated from green hydra collected from various locations in the world and were cultured in solid and liquid media. DNA sequencing was done on the algal cultures to verify their identities. All of our cultures indicated contamination by various strains of algae and we are currently continuing this verification process along with a more detailed analysis of the existing cultures.
Funding provided by Rose Hills Foundation (JT); Howard Hughes Medical Institute (DP); The Fletcher Jones Foundation (AA)

Research at Pomona