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Biology

The Relationship of MSN2/4 to PNC1, CTT1 and SOD1

Carter, Sally ('10);  Hoopes, Laura L. Mays

The transcription factors Msn2 and Msn4 regulate a variety of stress response genes. Microarray data suggested that possible targets of Msn2/Msn4 include PNC1, CTT1, and SOD1. The expression of these genes in 1 generation and 8 generation wild-type yeast and msn2msn4 mutants was tested via qRT-PCR, which, along with earlier microarray data, suggested that Msn2 and Msn4 promote transcription of PNC1 and CTT1. ADD conclusions.
Funding provided by: Pomona College SURP

Why Mountain Men Are Better Than Valley Boys

Cettie, Kristin Kaye ('11);  Cerny-Chipman, Elizabeth (‘09);  Gleichman, Julia (‘10);  McGill, Jade (‘09);  Levin, Rachel N.;  King, Caroline ('07);  King, Jacqueline (‘07);  Whittlesey, Elicia (‘07);  Bailey, Allison (‘07)

House wren males, Troglodytes aedon, vary in the degree to which they provide parental care. It has been proposed that altitudinal variation, and, indirectly, variation in food supply and/or predator pressure might explain differing degrees of male involvement, but this remains unresolved. We directly tested male parental investment by placing a rubber snake on nest boxes containing young (6 days old) and old (12+ days old) nestlings and observing male and female response at both low elevation (Marshall Canyon, 34° N, 480 m) and high elevation (Sierra Nevada Aquatic Research Lab (SNARL), 38° N, 2164 m) sites. Female response to simulated nest predators was strong and did not vary over time or between sites. Male response in Marshall Canyon declined as nestlings matured, whereas the response of SNARL males remained high. This result is consistent with life history theory which predicts greater male investment at higher elevations under harsher conditions.
Funding provided by: Pomona College SURP (KC, EC, JG)

Genes that control vesicular transport in Drosophila

Chau, Kimberly M. ('10);  Cheney, Clarissa

Abstract removed upon request.

Comparison of Growth Rates of Early and Late Hatching Little Auks in the High Arctic

Gleichman, Julia ('10);  Young, Derek ('09);  Karnovsky, Nina;  McFadden, Laurel ('06)

Due to the short Arctic breeding season, little auk (Alle alle) chicks must develop within 25 days before fledging and flying out to sea. During chick rearing both parents make foraging trips to sea to bring back zooplankton to feed their rapidly growing chick. This season we found that the chicks hatched within a range of 13 days. We hypothesized that growth rates of the chicks that hatched later would be slower. Earlier hatching chicks may grow at a faster rate because their parents have better body condition, better nesting sites, or more experience raising chicks. In addition, the timing of egg laying may have been determined by late snow cover over some nest sites. To test our hypothesis, at approximately three day intervals we took morphometric measurements on 53 chicks and compared the growth of early hatching versus late hatching chicks.
Funding provided by: Pomona College SURP (JG);  National Science Foundation Grant (NK)

The Song Does Not Remain the Same...So What Does It Mean?

Gleichman, Julia ('10);  Cettie, Kristin Kaye (‘11);  Cerny-Chipman, Elizabeth (‘09);  McGill, Jade (‘09);  Levin, Rachel N.;  Cavalcanti, Andre

Most studies of bird song focus on species in which birds sing repertoires of stereotyped songs. We are studying the structure and function of variable song using the house wren, Troglodytes aedon. We recorded morning songs from birds at low and high elevation temperate zone sites. Each bird was recorded for two days and then recorded while responding to playback of songs from an unfamiliar house wren. We spectrographically analyzed 1,476 songs of three birds and compiled a dictionary of song phrases used. We are now using a clustering program to look for individual syntax consistency across days and change in syntax in response to song playback. Initial analyses suggest that morning song sequences are not fixed, and that rates of song switching increase radically when birds are responding to simulated intruders. Future comparisons across birds and sites should reveal how syntax is used to communicate song function.
Funding provided by: Pomona College SURP (JG, KC, EC)

Investigating Purine Concentrations and Trends in Oniscidea

Howe, Caitlin ('09);  Wright, Jonathan

The purpose of this study was to determine if the urate deposits found in Oniscidean isopods have adaptive roles for life on land or if they are present in terrestrial species because of phylogenetic constraint. High Performance Liquid Chromatography (HPLC) was used to measure purine concentrations in six species from intertidal and terrestrial habitats (Figure 1). No functional roles have yet been discovered for these purine deposits. Mean concentrations for all purines were determined for each species and sufficient data were collected for five of the six species to perform an ANOVA test. The highest levels of urate were found in species with low cuticle permeabilities, regardless of genetic relatedness or habitat. The reasons for this trend remain unknown and will be investigated further in the fall. Specifically, isotopic labeling will be used to determine if dietary nitrogen is converted to urate and later mobilized for protein synthesis.
Funding provided by: The Paul K. Richter and Evalyn E. Cook Richter Award

Appearance of Numerous Foci in Saccharomyces Cerevisiae Following UV Damage Indicating the Presence of a Unique Pathway in Nucleotide Excision Repair (NER) as Compared to That of Recombinational Repair

Khan, Afshin Alaf ('11);  Hoopes, Laura L.;  Simning, Adam ('05)

Nucleotide excision repair (NER) requires the Rad1-Rad10 endonuclease. We sought to ascertain whether NER takes place at either specific foci or “randomly” throughout the nucleus. In this study, Green Fluorescent Protein (GFP) was fused to the Rad1 gene in two yeast strains, YLH 315 (Rad1-GFP, Sik1-RFP) and YLH 316 (Rad1-GFP, Nic96-RFP). Growth of yeast colonies was then measured when the strains were irradiated with different UV doses. Both YLH315 and YLH316 have similar UV response curves to wt. Nuclei looked intact (RFP images) and the Rad1-GFP was “randomly” distributed after 0 or 20 Joules;  numerous foci appeared after 55 or 80 J, and the nuclei were disorganized and possibly fragmented after 100 J. We concluded that foci did form and that there were many more foci (4±1) than we predicted by comparison with the recombinational repair (RR) pathway. Some or all of these foci could be specific to NER rather than shared with recombinational repair.
Funding provided by: Pomona College SURP

Alleopathic Effects of Coastal Sage Scrub Plants on Invasive Star-Thistle

Noto, Akana ('09);  Hanzawa, Fran

Disturbed areas are often more prone to invasion by non-native plants than intact communities. This may be due to increased resource availability in disturbed areas, reduced seed predation, or fewer allelochemicals from natives suppressing growth of invasives. In this study, allelopathy’s role in preventing the spread of the invasive star-thistle, Centaurea melitensis, in coastal sage scrub (CSS) communities was examined. Star-thistle seeds were treated with extracts of three native shrubs, sagebrush, California buckwheat and yerba santa, to determine whether they prevent establishment of this invasive. It was hypothesized that only sagebrush, which is known to produce allelochemicals, would inhibit star-thistle germination, but in fact, all three extracts did. Sagebrush had the strongest effect, limiting germination more severely and at lower concentrations than the others. This suggests that allelopathy plays a role in reducing invasibility of CSS communities with sagebrush, the most dominant shrub, having the strongest effect against star-thistle.

Funding provided by: The Schenck Fund

Awareness of Breast Cancer Detection Methods Among Indigenous

Platter, Erin ('10); Gareiss, Shelly (UIUC '10)*;  Parfitt, Karen
*University of Illinois Urbana-Champaign, Urbana IL

This study focused on six indigenous communities of Costa Rica: Guaymi, Boruca, Chorotegas, Maleku, Afro-Caribbean, and Bribri, and assessed statistically their awareness of breast cancer and methods of breast cancer detection. As rural communities with varied access to television and medical facilities, these communities offered the perfect opportunity to assess the effect of these sources on awareness. It was hypothesized that if 1) proximity to medical facilities increased and 2) amount of television access increased, then awareness would increase. Our hypotheses were supported by our findings;  people with TVs were significantly more aware of breast cancer and breast cancer self-examinations (BSE) and there was a significant, negative correlation between distance to major cities and awareness of BSE. We therefore found that access to televisions and medical facilities play a significant role in awareness, and the use of both tools is an effective way to spread awareness.
Funding provided by: Ogelsby Grant of Pomona College Biology Department; Pomona College SURP

Gene Fuser Defuser: Identifying Candidate Fusion Genes with an Automated Search Algorithm

Salim, Hannah ('09);  Cavalcanti, Andre;  Stover, Nicholas*
*Biology Department, Bradley University, Peoria IL

Researchers often struggle with creating and rooting phylogenetic trees, but the identification of fused genes in the genomes being studied can facilitate this process. A fusion gene is formed when two separate genes are genetically merged, resulting in a gene that codes for one hybrid protein. Gene fusion events are rare, and it is extremely unlikely that they would occur convergently. They can therefore serve as important markers of evolution. However, few fusion genes have been identified in eukaryotes. We created an automated search algorithm that finds candidate fusion genes. Using this tool, we searched the complete Tetrahymena thermophila genome and have identified one very strong candidate fusion gene that is involved in the methionine salvage pathway. We are currently performing experimental work to verify the existence and the function of this gene as well as continuing to search for potential fusion genes in other eukaryote genomes.
Funding provided by: Rose Hills Foundation Summer Science and Engineering Research Fellowship

Ion Regulation in the Marsupium of Brooding Isopods

Yoshizawa, Anne ('09);  Wright, Jonathan

Although isopods have evolutionarily adapted from an aquatic to a terrestrial existence, the developing eggs still require an aqueous environment, the marsupium. The marsupial fluid of different species is filled either externally from the environment or internally, but ion regulation of the marsupial fluid is largely unstudied. I compared ion concentrations (potassium, chloride, pH, sodium, and calcium) of the marsupium with the hemolymph of several genuses of brooding isopods: Ligia, Alloniscus, and Armadillidium. Alloniscus and Armadillidium supply their marsupium internally;  as predicted, there is no significant difference between the hemolymph and the marsupium for most ions. In contrast, Ligia, an intertidal species, acquires its marsupial fluid externally from the seawater;  the marsupium had similar concentrations to both the seawater and the hemolymph for most ions. Interestingly, Ligia’s calcium levels were markedly different, and potassium is higher in the marsupium than the hemolymph of all three genuses. Thus, there is indication of ion regulation that requires further study.
Funding provided by: Pomona College SURP

Honey, I'm Home: Parental Coordination of Chick Rearing in Little Auks

Young, Derek ('09);  Gleichman, Julia ('10);  Karnovsky, Nina;  McFadden, Laurel ('06)

We determined how little auk (Alle alle) parents coordinate their patterns of nest attendance. In this Arctic species, both parents incubate the egg and then care for the chick. Little auks have a bimodal foraging strategy whereby they take short (<5 h) foraging trips to collect prey for their chick and long (>5 h) foraging trips to collect food for themselves as well as for their chick. We hypothesized that parents would alternate incubation shifts to allow one parent to forage while the other incubates the egg. During development of the chick, we hypothesized that parents would display a similar coordination with one parent making a long trip while the other makes multiple short trips. We used PIT tags to detect the beginning and duration of each nest visit. Preliminary results confirmed our hypothesis;  however, as the chick developed, coordination became less strict.
Funding provided by: Pomona College SURP (JG);  National Science Foundation Grant (NK)

Yeast Aging Clock is Reset Very Early in Meiosis

Zhao, Ann ('09);  Young, Jocelyn ('11);  Joo, Janice ('11);  Allen, Rachel ('10);  Hoopes, Laura;  DeSantiago, S.('05);  Cope, A. ('06);  Cahoon, L.;  Wu, M.;  Lancaster, K. ('05);  McFarlane, M.;  Rockmill, B.*
*Yale University, New Haven CT

Saccharomyces cerevisiae can be induced into meiosis by nutrient starvation and then restored to mitotic growth when returned to rich media. Our lab has found that when aged 8 generation cells are induced into meiosis to form four ascospores, which are returned to mitotic growth, their life spans resemble those of non-sporulating young cells. This suggests that the aging clocks of the 8g cells are meiotically reset. Without the transcription factor Ndt80, cells stall at pachytene. Life spans of 8g ndt80/ndt80 cells show meiotic resetting;  therefore, meiotic resetting occurs before pachytene. Life spans of WT cells returned to mitotic growth at various time points after induction into meiosis, suggests that the mechanism for this resetting occurs very early in meiosis, most likely between two and three hours after the yeast cells have been induced into meiosis, possibly during meiotic DNA replication.
Funding provided by: Merck Institute for Science Education and AAAS (AZ);  Pomona College SURP (JY);  NIH AREA (LH;  LC) ;  NSF RUI (LH;  MW)

Exploring the Effect of SIR2 on Yeast Meiotic Resetting Mechanism

Young, Jocelyn ('11);  Zhao, Ann ('09);  Hoopes, Laura Mays

Saccharomyces cerevisiae are induced into meiosis through the deprivation of nutrients. Our lab has found that the aging clocks of 8 generation cells are reset to zero when induced into meiosis for 1 to 4 hours and then returned to mitotic growth. To further narrow the time frame and observe the effects of life span extending Sir2 on the resetting mechanism, life span dissections of both wild-type background cells and Sir2 delete diploid cells were performed. Resetting of wild-type cells appears to occur between 2 and 3 hours while no conclusions could be drawn about the Sir2 delete diploid cells.
Funding provided by: Merck Institute for Science Education and AAAS (AZ);  Sontag Grant (LMH)

Research at Pomona