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- Creator:
- Bailey, Melinda
- Description:
- Place-based education is an instructional approach that engages students with their local environment, which can enrich the educational experience and improve scientific literacy. This project is a place-based secondary-level life science curriculum incorporating important ecological concepts using select forest types of the North Coast of California, USA. The North Coast has a rich natural history and many schools are situated near forests. This curriculum is multidimensional and includes structured units for middle school and high school students presented in three thematic modules: general forest ecology, coast redwoods, and oak woodlands. Units are preceded by a companion piece for each module that embeds some of the latest scientific research intended to broaden a teachers’ previous knowledge. Information is approached from different spatial and temporal scales and designed for flexibility in order to fit the needs of local educators. Information was routinely sourced from primary scientific literature and professional reports, which often can be difficult to obtain and comprehend by the non-specialist. Components include figures and select data, which are integrated into student lessons that offer a unique conduit between scientists, science teachers, and science students. Evidence reveals students learn best when actively engaged and presented with relevant information. By developing a challenging place-based curriculum aligned to new standards that incorporate scientific skills and interdisciplinary connections, both formal and informal science educators will have a useful, informative resource pertaining to local forest types that can enrich the learning experience of their students while connecting them to the place in which they live.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- Tout, Jeremy
- Description:
- A sampling design that can provide estimates of abundance with low variance is very valuable to biologists working with limited budgets and time. Estimates that are precise even with low sampling efforts allow researchers to cheaply and confidently monitor rare populations. Adaptive cluster sampling has the potential to be much more efficient at sampling rare populations than conventional sampling designs, but it has also been shown to be highly inappropriate for some populations. Applications of adaptive cluster sampling (ACS) have had inconsistent results in real-world settings, leading to increasing scrutiny of the factors that influence the efficiency of this design. Much more work still needs to be done in order to provide samplers with the knowledge of when ACS is appropriate and how to maximize its effectiveness through constructing an optimal design. This study develops a procedure in a GIS environment for rigorously examining the effects of design parameters on the variance of ACS estimates, and applies this procedure to some real-world point populations. The relative efficiency of adaptive cluster sampling to simple random sampling is shown to be dramatically influenced by design parameters. This highlights the need for further investigation and a better understanding of how these parameters interact with point distributions through the use of procedures and tools such as those introduced here.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- Frimodig, Adam J.
- Description:
- Seagrass beds are productive, structurally complex ecosystems that support an abundant and diverse assemblage of animals. Although light is clearly important to seagrass productivity, grazers also alter this aspect of plant communities. Grazers may indirectly affect the associated animal community but this perspective has not been rigorously examined in temperate western North American seagrass beds. My thesis objective was to experimentally examine the effects of Pacific black brant geese (Branta bernicla nigricans) grazing and fecal addition on the abundances and sizes of the animals within an eelgrass (Zostera marina) bed of Humboldt Bay, CA (40º 43.1’ N, 124º 13.3’ W). In situ brant simulations were used to investigate the effects of different treatments (clipping, fecal addition, the combination of both at “intermediate” and “intense” levels, and brant exclusion) on the abundances and sizes of the animals within the Z. marina community. Animal treatment responses were only compared when Z. marina vegetation structure (shoot density, shoot length) significantly differed among treatments. By including covariates like climate and water quality variables, as well as distance of a treatment from channels, this study also identified the recruitment and environmental conditions that favor the development of a positive or negative relationship between animal abundance and size versus Z. marina complexity. For example, large interannual variation in juvenile Dungeness crab (Cancer magister) abundance was attributed to warmer water current structure changes during 2005, and may have therefore delivered fewer megalopae to Humboldt Bay. Similarly, the effects of fish predation may have equalized the abundance and distribution of small Z. marina invertebrates, such as caprellid and gammarid amphipods and bay isopod (Idotea resecata), and thus prevented a relationship with vegetation structure from developing. Following the effects of climate on recruitment and fish predation, brant induced changes to the vegetation structure did affect animal abundances and sizes, but responses were species-specific. The abundance of Taylor’s sea hare (Phyllaplysia taylori) increased when a maximum number of shoots were created by intermediate levels of brant grazing, and both the abundance and size of P. taylori decreased in response to shorter shoots created by intense levels of brant grazing. Other animal responses responded negatively to brant induced changes to the vegetation structure. For example, I. resecata were smaller when shoots were more dense and longer, and they were larger when shoots were less dense and shorter. Lastly, the abundances and sizes of some animals were significantly different among brant simulation treatments, but animal differences did not parallel the brant induced changes to the vegetation. Therefore, brant induced changes to the structural complexity of Z. marina affect both the abundance and size of the associated animal community under a limited set of circumstances.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- McDonald, Steven
- Description:
- The development of industry, mining activity, irrigation of waste water, and the application of sewage sludge to agricultural lands have increased the release of metals into our ecosystems causing serious environmental problems and posing threats to human health. Phytoremediation has become one possible remediation strategy to address lead toxicity. The heavy-metal tolerance of Typha latifolia (broadleaf cattail) has made it a potential candidate for chemically enhanced lead phytoremediation.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- Barrett, Jeffery A.
- Description:
- The Early Devonian epoch (419.2 ±3.2-393.3 ±1.2 Ma) (Gradstein 2012) marked the commencement of a rapid evolutionary radiation and increase in the diversity and complexity of basal tracheophytes and other groups of land plants. While the importance of the Early Devonian to the radiation of early land plants cannot be overstated, a comprehensive database compiling the most current knowledge of this flora has been lacking. Using a newly revised taxonomic system of Early Devonian land plants, this study seeks to assemble all Early Devonian records of tracheophytes and related land plants into one database in order to assess the geographic and stratigraphic patterns of plant diversity during this interval. Records were cross-referenced with previous analyses and other databases to ensure that the nomenclature, ages, locations, and other data reported for each record are as accurate and current as possible. The locations of fossil assemblages were plotted on both present-day and Early Devonian maps. The Early Devonian paleoflora was characterized by high levels of endemism among Incertae sedis taxa, zosterophyllopsids, and rhyniopsids, and a varied flora spread across six or possibly seven floristic provinces. Taxonomic richness was lowest during the Lochkovian which was dominated by Incertae sedis taxa and rhyniopsids, especially in Laurussia. Both genus and species richness peaked during the Pragian when zosterophyllopsids dominated the floras of most provinces. Overall taxonomic richness declined considerably during the Emsian, although taxonomic richness peaked in Laurussia and Siberia during this stage, largely as a result of the dominance of euphyllophytes. The database created for this study contains a total of 1325 records of 185 genera and 305 species distributed within 357 assemblages and forms the most comprehensive compilation of Early Devonian land plant records to date. The results of this study will provide a basis for future studies aimed at better understanding the patterns of evolutionary radiation in early land plants.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- Whittemore, Alan
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
707. A mark-recapture study of the wandering salamander, Aneides vagrans, in a redwood rain forest canopy
- Creator:
- Spickler, James C.
- Description:
- I investigated seasonal activity, movement patterns, and habitat use of the wandering salamander, Aneides vagrans, in an old-growth forest canopy. During the fall and winter months from September 2000 to January 2003, a mark—recapture study of salamanders was conducted in the crowns of five large redwoods (Sequoia sempervirens) in Prairie Creek Redwoods State Park, Humboldt County, California. This represents a first attempt to describe the arboreal behavior of A. vagrans. A cover object approach limited damage to fragile canopy habitats. Litter bags were placed on 65 randomly selected fern mats, covering 10% of the total surface area of epiphytic fern (Polypodium scouleri) mats in each tree. Crack boards were also placed on one fern mat in each of two trees. These cover objects were then checked 2-4 times per month during the field season. Captured salamanders were marked by injecting tags near the base of the tail. A total of 52 captures were made of 40 individuals, including 15 recaptures. One salamander was captured on 4 occasions over the 3-year study period. Only one recaptured salamander moved (vertically 7 m) from its original point of capture. There was no evidence of territorial behavior by A. vagrans in the canopy. Salamander captures were compared to tree-level and fern mat-level variables with correlation analysis and stepwise regression. At the tree-level, the best predictor of salamander abundance was the total mass of fern mats in crotches. At the fern mat-level, the presence of crack boards accounted for 85% of the variability observed in captures, while the mass and height of the fern mat accounted for the remaining 6% explained by the model. Population estimates were made by applying the Lincoln-Peterson method to the capture data. This analysis revealed that individual redwoods can support at least 28 individual salamanders associated with fern mats. By virtue of their high water-holding capacities, large fern mats likely enable year-round occupation of the redwood forest canopy by A. vagrans. Anecdotal observations of A. vagrans and its close relative A. ferreus by scientists and forest activists strongly suggest that these salamanders also occupy additional habitats in forest canopies, especially rotting wood and fire cavities.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- Morago, Shannon
- Description:
- Historically human olfaction has been underestimated. There is considerable recent evidence that olfaction is biologically important in social and emotional contexts, including mate selection and kin recognition. Observations of humans in social contexts show that some humans sniff while clenching their teeth. This study documented the prevalence of this behavior in a surveyed population and investigated the physiological aspects of this behavior in a distinct population. The airflow, duration and volume of a sniff were measured while sniffing and teeth clenching and during sniffing alone. In the surveyed population 13% reported clenching their teeth while sniffing others in social contexts, 18% in familial contexts and 14% in sexual contexts. Physiologically, sniffing while teeth clenching resulted in an increase in airflow for 52% of the population, while 43% experienced an increase when sniffing alone. It appears some humans display this behavior, which may enhance olfactory perception by increasing the airflow of the sniff.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- McGary, Cara L.
- Description:
- Long term comparisons are important for understanding intertidal community dynamics and documenting response to environmental pressures. This study compares the historical abundance of high intertidal sessile organisms at two rocky intertidal sites within Redwood National and State Parks shortly after the park was established (“historical”:1974-1976) to the present community (2004-2005) at the same locations. Percent cover of ephemeral, early successional species was higher in historical assessments, whereas percent cover and magnitude of seasonal variation in perennial, late successional organisms increased in assessments of the present community. The long term successional shift is likely a result of decreased disturbance severity between the mid 1970’s to present. Severe historical disturbance is linked to increased sedimentation and frequent driftwood battering associated with logging. Conservation and rehabilitation strategies in the adjacent terrestrial landscape since 1978 may have resulted in spatial dominance by mid to late successional species at these two sites. Several alternative causal hypotheses regarding long term climate change, El Niño Southern Oscillation, upwelling intensity, and species interactions are evaluated, but not supported by the results of this study.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- Haggard, Judy Ann Ganz
- Description:
- The movement ecology of the adult northern red-legged frog (Rana aurora aurora) is essentially unknown throughout its range. Systematic studies, particularly those that investigate terrestrial movements of these animals, are urgently needed since this species has been listed federally and by the state of California as a Species of Special Concern. I conducted a radio-telemetry study to determine the extent of the terrestrial movements and habitat use of 12 adult R. a. aurora, 11 females and 1 male, at Freshwater Lagoon, Humboldt County, California, from March through July 1999. The beaded-chain belt method of attaching radio transmitters was tested to evaluate its efficacy on adult R. a. aurora. There was considerable variability in the movements and movement patterns of the frogs. A majority of the frogs moved away from the periphery of the lagoon, the assumed breeding site, some to considerable distances (range of furthest distances = 30-270 m). Most of the distances moved per day were 5 m or less (range = 0-87.5 m). Observed range length (the map distance between the two relocation points farthest from each other in an individual's observed range) varied from 5 to 221 m. Those frogs who made long-distance moves did not, for the most part, do so synchronously, and there was no apparent pattern to these movements on a seasonal basis or in response to daily weather conditions. The frogs, except for one individual, were detected on land during 90% of the survey period, and they tended to stay 5 m or less from water (lagoon, stream, ditch, or seep). Overall distances from water did not appear to decrease as precipitation and soil moisture decreased. Although there was considerable individual variability, the frogs were found much more often in the closed canopy thicket/forest habitat than in the other habitat types, which, in descending order of use, were forb patch, emergent vegetation, grassland, and man-made objects. Sword ferns may be important at the microhabitat level in providing cover for R. aurora. Six of the frogs appeared to use intermittent streams, especially those upslope from the lagoon, within the study area as corridors for at least part of their travels. Conservation efforts should take into consideration that R. a. aurora uses upland habitats. Any terrestrial buffer zones should maintain key vegetative components such as dense patches of shrub and herbaceous vegetation. Movement surveys of R. aurora should be conducted year-round and for subsequent years. The beaded-chain belt method of attaching transmitters proved to be a relatively safe and effective technique for use on large adult R. a. aurora.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- Kennedy, Jean-Paul
- Description:
- Throughout their global distribution, bats vary in their use of microhabitats along the vertical strata of forests. Ground-based detection techniques typically cannot sample canopy strata in taller forests as it falls beyond detection and netting range. High-flying bats, those that exploit the canopy and above-canopy edge, may avoid capture or be under-represented in assessments using these methods. To improve our understanding of how bats use forests, I assessed bat activity and species stratification along the vertical gradient near Bull Creek in Humboldt Redwoods State Park, Humboldt County, northern California. Humboldt Redwoods State Park is the tallest forest in the world, containing 70 percent of known trees over 107 m. Two coast redwood, Sequoia sempervirens, trees were equipped with full spectrum automated bat detector units at treetop (108 m), middle crown (50 m), and ground level (5 m) from April 2008 to November 2009, excluding December and January. I sampled 1,365 detector nights and recorded 3,796 echolocation sequences containing one or more calls. I identified the presence of 12 species: Corynorhinus townsendii, Eptesicus fuscus, Lasionycteris noctivagans, Lasiurus blossevillii, L. cinereus, Myotis californicus, M. evotis, M. lucifugus, M. volans, M. thysanodes, M. yumanensis, and Tadarida brasiliensis. Two species, L. blossevillii, and T. brasiliensis, were undocumented in previously published surveys from redwood forests. I recorded the highest amount of activity at the treetop and least at the middle crown for both trees (65% and 43% at treetop, 7% and 23% at middle crown and 28% and 33% at ground level). I observed a greater number of species present at ground level compared to middle crown and treetop detectors at both trees. However, the data revealed a difference in the species composition of calls recorded at each level. Non-Myotis species composed 95% of the calls at the treetop, 87.5% at middle crown, and 21% at ground level. Calls from all Myotis species averaged 71% of all calls recorded from the ground level compared to less than 4% at both middle crown and treetop detectors. There was a marked decline, but not an absence of activity, during late fall through early spring. The combination of a temperate climate and observations of larger, migratory species during November, February, and March suggests the potential for resident populations or inland migrants overwintering in these forests. My findings illustrate the need to consider the full vertical habitat when designing bat habitat use studies, as species composition varies across the vertical gradient in forests.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
712. Reproductive isolation in five hybridizing species of western gooseberries (Ribes: Grossulariaceae)
- Creator:
- Kalt, Jennifer L.
- Description:
- Five species of western gooseberries (Ribes: Grossulariaceae) hybridize to varying degrees in northwestern California and southwestern Oregon. Pollinator surveys and hand-pollination experiments were conducted to identify reproductive barriers between the species pairs. I found little evidence of isolation due to pollinator behavior, since the five species tended to attract the same pollinators. My attempts to assess the level of post-pollination isolation were hindered by high rates of fruit abortion. Nevertheless, it appears that R. roezlii and R. menziesii are fully interfertile, and that unilateral barriers operate when R. lobbii, which has the longest styles of the set, is the maternal parent in crosses with the other species. Since the level of post-pollination isolation is not correlated with the observed frequency of hybridization in the field, ecological and/or geographical differences may play the most important role in isolating the species.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- Fritz, Gisela B.
- Description:
- Improved understanding of the importance of estuarine wetlands to the function of coastal ecosystems has lead to increased restoration efforts of degraded wetlands. The South Slough National Estuarine Research Reserve (SSNERR) in Coos Bay, Oregon, has taken active steps to restore previously diked tidal wetlands. In addition, they have established monitoring programs that focus on the faunal and floral recovery of restored sites within Kunz Marsh. The overall objective of the present study was to determine the degree of community recovery in restored salt marsh sites relative to control sites. Vascular plants, diatoms, invertebrates, and fish were sampled in spring, summer, and fall of 1998 and 1999. Vegetation cover decreased from high to low elevations, was higher in control than restored sites, and increased between 1998 and 1999. Diatom abundances showed seasonality in most sites and were higher in the restored than the control sites. Relative abundance of invertebrates in the first year was higher in control than in restored sites. More of these animals were found in vegetated than open areas. Fish abundance increased with decreasing elevation and Kunz Marsh sites showed a species composition similar to the adjoining Winchester Creek. In general, community recovery, particularly for plants and invertebrates, occurred more quickly in the higher restored sites. This may be due to the aggressive restoration method used, as well as successional processes that are known to occur more rapidly in the high marsh.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- Succuro, Jerry S.
- Description:
- In this study, two ways of accumulating Pb were investigated: natural accumulation and chemically enhanced accumulation with the chelating agent ethylenediaminetetraacetic acid (EDTA). Young cattails (Typha latifolia) were removed from the Arcata Community Pond in Northern California and transplanted into two-quart mason jars containing four different levels of Pb contamination: 0, 2000, 4000, and 6000 mg Pb/kg soil. Three cattails per jar were grown for a three-week period with half of the plants receiving 10 mmol EDTA on the 15th day of the experiment and allowed to continue growth for the remaining 6 days of treatment. Cattails were harvested, separated into shoots, rhizomes and roots, and then analyzed for Pb concentration in these tissues using Atomic Absorption Spectrophotometry (AAS). For the natural accumulation of Pb, no significant differences among the 2000, 4000, and 6000 mg Pb/kg groups for shoots (p = 0.1063), rhizomes (p = 0.1096) or roots (p = 0.2526) were detected. When EDTA was added to the soil, there was a significant difference among the various levels of soil contamination (p = 0.0002). In this particular case, the largest accumulation of Pb occurred at the 4000 mg Pb/kg soil contamination level with shoots accumulating a combined average of 4744.03 mg Pb/kg. These results show that three cattails can remove Pb from the environment in larger quantities if a chelating agent is present in a short period of time. In addition, it appears that the 6000 mg Pb/kg soil contamination is a threshold of toxicity as all aspects of the experiment showed a decrease in the health, natural accumulation of Pb, and the accumulation of Pb with the addition of EDTA. Typha latifolia has a wide tolerance to many different environments and produces a large amount of biomass, which make it a good candidate for use in phytoremediation. Further research should consider increasing the quantity of cattails to optimize Pb removal from the soil.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Humboldt
- Department:
- Biology
- Creator:
- Marentes, Adam
- Description:
- ∆9-tetrahydrocannabinol (THC), marijuana’s principal psychoactive component, is known to suppress resistance to bacterial, viral and protozoan infections. However, the effect of THC on resistance to fungal infections is unclear. Recently, we found that chronic THC treatment decreased resistance to the yeast Candida albicans (C. albicans) in immune competent mice. However, nothing is known about how THC affects resistance to a fungal infection in an immunocompromised mouse. Our objective was to assess how chronic THC affects an immunocompromised mouse’s ability to ward off systemic candidiasis in an acute and secondary model of infection. 5-fluorouracil (5-F) is a commonly prescribed anti-cancer drug and is also a potent immunosuppressor, increasing susceptibility to C. albicans infection. We found that 5-F treatment severely decreased survival, white blood cell count, splenic IL-12p40 production and increased kidney fungal load. To investigate the effect of THC on resistance to C. albicans in immunosuppressed mice, c57BL/6 female mice were treated via an intraperitoneal (IP) injection with vehicle (ethanol, cremophor, saline (1:1:18)) or THC in vehicle (16mg/kg) 4 days a week, for three weeks (experimental days 1-18). For the secondary infection model, on day 2, the mice received a priming dose (0.75x105 cells) of C. albicans. On day 16, mice received an intravenous (IV) injection of 5-F (0.1ml of 50mg/ml). On day 19, mice were infected with an IV injection of 5x105 C. albicans cells. For the acute infection model, the mice only received an IV injection of C. albicans on day 19 without a priming dose. On day 22, tissues were harvested from some mice to assess tissue fungal load. In addition, splenocytes were cultured and treated with either Concanavalin A (Con A, 5µg/ml) or heat killed (HK) C. albicans (6.25x106 yeast cells/ml) to assess cytokine production responses. Remaining mice were observed for up to 2 weeks for survival and morbidity. We found that in both infection models, mice treated with 5-F and THC succumbed a day earlier to the yeast infection compared to 5-F and vehicle treated mice. In both infection models, 5-F decreased Con A stimulated splenocyte INF-γ secretion from vehicle and THC groups, with no significant difference between the groups. However, the decrease by 5-F was much more pronounced in the acute infection model compared to the secondary infection model. In both infection models, C. albicans-stimulated IFN-γ levels were significantly lower in the THC group compared to the vehicle group. These results strongly suggest that THC has an effect on splenic immune response, and they also suggest that although THC does make the 5-F treated mice slightly more susceptible to the infection, it is not significant enough to conclude that chronic THC treatment is detrimental to immunocompromised mice.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Biology
- Creator:
- DeBevoise, Devon
- Description:
- Fouquieria splendens (ocotillo) is a large, basally branching, shallow-rooted, drought deciduous shrub native to the Chihuahuan and Sonoran Deserts. Ocotillos, like all Fouquieriaceae, have gelatinous fibers (g-fibers), which typically occur in tension wood (TW) of eudicotyledons and can reorient stems and roots. The goal of the research was to determine whether the presence of g-fibers in TW in branches was a response to mechanical stress and whether g-fibers in roots functioned in pulling ocotillos towards the soil. It was hypothesized that TW in the branches aided in resisting gravitational stresses and bending from high winds and that TW in the roots would pull the shoots downward to prevent them from falling over, or provide tension to prevent uprooting. To address the hypotheses, the anatomy of shoots that were displaced or fixed in place was compared to those in their native state in the field. To study the g-fiber function in roots, young ocotillos were planted at different depths and with their caudices (stem/root axis) at different angles from vertical. Shoots had far greater TW coverage in cross-section in sides of the branches experiencing tension than in sides experiencing compression for all treatments. There was also greater TW coverage in the basal regions of branches than in more distal regions, suggesting that they were resisting bending due to static loads as well as possibly dynamic loads (wind). Coverage of TW in taproots differed between sides experiencing tension and compression for plants with half-exposed caudices planted 45 from normal. Further, there was no evidence of contraction in ocotillo roots. However, because g-fibers occurred in lateral roots, all roots may function in resisting tensile stresses. In addition to g-fibers, several other fiber types occurred in ocotillos, indicating an unusual amount of fiber diversity.
- Resource Type:
- Thesis
- Campus Tesim:
- Pomona
- Department:
- Biology
- Creator:
- Deatherage, Nicole Anne
- Description:
- Human population growth and rapid urbanization have created new, attractive environments for opportunistic animals including some species of wild canids. San Joaquin kit foxes (Vulpes macrotis mutica) are a federally listed endangered and California listed threatened canid that persists in the city of Bakersfield, California, where they form a unique ecological guild with three other canid competitors: coyotes (Canis latrans), red foxes (Vulpes vulpes), and gray foxes (Urocyon cinereoargenteus). These four canids typically exhibit avoidance and/or resource partitioning due to overlapping niches, with smaller fox species avoiding attacks from more dominant foxes and coyotes by selecting alternative resources, finding refuge, occupying different habitat types, or adjusting behavior. Recent carnivore sympatry in urban areas may be due to behavioral adjustments and adaptations to complex urban environments, including heterogeneous landscape matrices and new, abundant resources. I investigated carnivore sympatry in urban environments using 5 y of remote camera survey data collected throughout the city of Bakersfield to first determine how landscape attributes within heterogeneous urban landscapes influence San Joaquin kit fox occupancy patterns, and if canid competitors (i.e., coyotes, red foxes, and gray foxes) affect San Joaquin kit fox distributions with the use of occupancy modeling. Second, I investigated how the presence of canid competitors or domestic dogs (Canis familiaris) in the same 1-km2 area affects San Joaquin kit fox spatiotemporal activity with the use of Two-way Contingency Tables, One-way Analysis of Variance, and Kruskal-Wallis tests. I found the most supported occupancy model for San Joaquin kit foxes to be an additive effect of two urban landscape attributes, percentages of paved roads and campuses (e.g., schools, churches, and medical centers) in cells. The percentage of paved roads was a negative predictor of San Joaquin kit fox occupancy while the percentage of campuses was a positive predictor. The percentage of paved roads was ultimately the most supported covariate for predicting San Joaquin kit fox occupancy (or lack thereof) in my study system. Roads are the main source of mortality for urban San Joaquin kit foxes and have greater noise pollution, development, disturbance, and human activity, which may discourage San Joaquin kit foxes from incorporating roads into their urban home ranges. Conversely, campuses have landscaping, sports yards, quadrangles, and walkways that offer open space, which San Joaquin kit foxes select for in natural habitats. These sites also afford security from excess human disturbance and larger predators due to fences and other security measures employed by campuses, as well as anthropogenic food sources from cafeterias and people directly feeding San Joaquin kit foxes. I concluded that San Joaquin kit foxes were avoiding paved roads while selecting for campuses in the urban environment. The presence of coyotes, red foxes, and gray foxes was not a contributing factor of urban San Joaquin kit fox occupancy patterns, though this may have been a result of low sample sizes of other canids compared to San Joaquin kit foxes. Apart from one association between the number of days in which San Joaquin kit foxes occurred alone and the number of days in which they occur with other canids in 2018, I found no other associations between San Joaquin kit fox and other canid occurrences in cells or on given days. I also found differences between the number of days San Joaquin kit foxes occurred alone and the number of days they occurred with another canid for all years collectively and each year individually. I concluded that urban San Joaquin kit foxes rarely occur with coyotes, red foxes, gray foxes, and domestic dogs in the same 1-km2 area within the same day, same year, or 5-y span, suggesting spatiotemporal avoidance of canid competitors. In instances when San Joaquin kit foxes and other canids did occur on the same camera on the same survey night, I found San Joaquin kit foxes delay their time to appearance following sunset by about 3 h at camera stations where another canid species appeared. Furthermore, variances in mean consecutive min that San Joaquin kit foxes spent at stations showed that they had the least predictability in the potential window of time spent at the station if another canid visited the camera station on the same night but did not appear first. San Joaquin kit foxes had the most predictability in the potential window of time spent at the station if another canid appeared first. These results indicate that San Joaquin kit foxes may require a more immediate predator presence cue than scent to perceive imminent risk from nearby competitors. Finally, my results show that if multiple canid species did occur there were never more than three, though primarily only two canids occurred in any given cell or on any given day, with a majority of co-occurrences between kit foxes and domestic dogs. Because domestic dogs are abundant in urban areas, they may not be novel or threatening to kit foxes, allowing domestic dogs and kit foxes to co-occur at higher frequencies than kit foxes and other wild canids. Additionally, where coexistence does occur, canids may only be willing to exist with one other canid species at any given time. In both analyses, I confirm that San Joaquin kit foxes occur in higher abundances than any other wild canid species in Bakersfield. San Joaquin kit foxes may be more receptive and adaptive to highly developed urban areas than other canids and are frequently observed denning in inner city landscapes; whereas past studies show that coyotes require larger, connected ranges and natural habitat, that red foxes avoid coyotes in intermediate human-modified habitats (i.e., suburbs with house densities of < 20 houses/ha), and that gray foxes select for urban edges or more natural, tree covered areas. My results also demonstrated a sizeable decrease in kit fox abundance over the years, with a 69% decrease in San Joaquin kit fox abundance at camera stations and a 40% decrease in probability of San Joaquin kit fox occupancy from 2015 to 2019. This is explained by the recent outbreak of sarcoptic mange (Sarcoptes scabiei) skin disease in San Joaquin kit foxes in Bakersfield, which is highly infectious and 100% fatal in untreated kit foxes. Overall, I conclude that while San Joaquin kit foxes rarely occur with other canid species within a 1-km2 urban area, they may require immediate predator presence cues to perceive risk from competition, while avoidance of paved roads and selection for campuses as urban landscape characteristics may be of greater importance in explaining occupancy dynamics in urban San Joaquin kit foxes. Understanding how top predators adapt to developing landscapes provides insight towards species conservation and management in urban areas, which is particularly important for the San Joaquin kit fox. Conserving the unique urban population in Bakersfield may be significant for the overall health, survival, and recovery of this species as human development is projected to continue, and upcoming conservation efforts may be particularly critical considering the current mange epidemic within this population.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Bakersfield
- Department:
- Biology
- Creator:
- Buchbinder, Margot Valerie
- Description:
- With the predicted acceleration of sea level rise in the mid-21st century, salt marsh restoration efforts are faced with the challenge of building and maintaining sufficient sediment to elevations that support vegetation. The highly subsided Sears Point restoration site uses a novel technique involving the construction of earthen mounds to support sediment accretion; however, the mounds are rapidly eroding. I planted mounds using native Spartina foliosa, and I hypothesized that S. foliosa would stabilize sediments and lead to sediment accretion, while changes to soil due to S. foliosa presence would foster development of soil invertebrate communities. Results show that S. foliosa is able to stabilize sediments and reduce erosion compared to controls over time, with the highest-density plantings providing the most protection. Further, significant increases in macro-organic matter and trends in some invertebrate measures suggest active revegetation will facilitate marsh community development.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Richardson, Nainoa
- Description:
- In Schizosaccharomyces pombe, Cdc24 is required for the completion of S-phase. Many studies implicate Cdc24 in lagging strand DNA replication and in DNA repair. Interestingly, the DNA replication checkpoint kinase, Cdsl (hChk2), and the kinase-dead allele, Cdsl-kd, causes a dosage growth defect in cdc24 truncation mutants (cdc24-M38 and cdc24-Gl) when overexpressed from a medium strength nmt promoter. This defect has also been reported in mutant alleles of mcll+, which encodes the DNA polymerase-a accessory factor. We hypothesize that the defect in cdc24 is due to the endonuclease Mus81, which is regulated by Cdsl to prevent unscheduled DNA cleavage. Alternatively, the defect is due to the Rad2 (hFenl) endonuclease. I used a genetic approach to investigate the dosage growth defect in order to understand the the function of Cdc24 with respect to Cdsl. To test for the involvement of Mus81, Rad2, and other replication factors such as Pol3, the catalytic subunit of DNA polymerase-6, I overexpressed Cdsl, Cdsl-kd, or an empty plasmid in cdc24 mutants that contain a background mutation at the mus81+, rad2+, pol3+, or other loci. Consistent with my hypothesis, my spot assay analyses show that the Cdsl or Cdsl-kd dosage growth defect in cdc24 is Rad2- dependent, but not Mus81-dependent. Intriguingly, we also found that Cdsl or Cdsl-kd caused a dosage growth defect in pol3 single mutant cells. These results suggest that Cdc24, Pol-6, and Mcll have overlapping functions in DNA replication and DNA repair, possibly to promote activation of Cdsl during a replication fork stall.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Shay, Jacqueline Elizabeth
- Description:
- Prior to this monographic treatment, limited research on the genus Marasmius (Basidiomycota, Agaricales) had been conducted in Madagascar. Based on field work in January 2013 and January-February 2014, which generated 45 specimens of Marasmius sensu stricto, supplemented by herbarium exsiccatae and published literature, 35 species of Marasmius are documented from Madagascar. Of these, 5 species are recognized herein as new to science, viz., Marasmius madagascariensis, M. rubrobrunneus, M. dendrosetae, M. sokola and M. tanaensis; an additional 11 species represent new distribution records for Madagascar. Comprehensive descriptions based on morphological and molecular sequences (ITS) data, illustrations and color photographs, comparisons with allied taxa, a key to aid in identification, and phylogenetic inferences are provided.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Description:
- Substratum geology is fundamental in shaping rocky shore morphology. Specific lithologies have various responses to wave action, tectonic features (e.g. fractures, faults) and sedimentary structures (e.g. bedding), creating distinctive multi-scale weathering profiles. By digitally capturing substrata surface morphology, it becomes possible to fingerprint individual rock types. This study presents results of multi-scale terrestrial laser scanning surveys from 10 rocky intertidal outcrops from central to northern California, representing the most common igneous, sedimentary, and metamorphic units along the coast. Analysis of surface morphology from 3D data using two surface roughness parameters and geological measurements made in situ support the hypothesis that surface properties can change significantly with changing scale, each rock type having distinct surface characteristics which are similar to comparable lithologies exposed at different locations. These distinct characteristics act as signatures within the rock, making the morphology predictable for outcrops along the California coast.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Clancy, Darragh Lillian
- Description:
- A two-part study was carried out examining population genetics and fusion behavior of an invasive colonial ascidian, Didemnum vexillum. A barcoding mitochondrial gene, COI, was used in previous studies at global and regional levels to assess the native region (Japan) by comparing diversity and to begin to examine how fusion may affect invasions. The study here uses higher-resolution multi-locus genotyping to assess population differences within the western North American region. Results show that a small isolated population in Alaska was bottlenecked to a degree beyond the decreased diversity of western North America in comparison with native Japan, and that Tomales Bay, off Point Reyes National Seashore, in central California, is surprisingly more genetically diverse than the nearby invasion hotspot of San Francisco Bay. The study also paired live colonies in field fusion assays and analyzed the effect pairwise relatedness had on fusion probability. Results show a correlation between higher estimated relatedness between paired colonies and the likelihood that those colonies fused. The results of this study have implications regarding Didemnum vexillum’s possible transport vectors and establishment success, which could aid in future management policies that are compatible with aquaculture.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Gonzalez, Julie Anne
- Description:
- There is an atypical distribution of the non-native crab Carcinus maenas, rarely found at high elevations in the intertidal zone elsewhere but mainly located in high elevation habitats in San Francisco Bay. Perceived threat from subtidal predators at low tidal elevations may cause C. maenas to seek refuge in higher tidal elevations, potentially in recently restored cordgrass (Spartina foliosa) habitat where their foraging activity may cause damage. Distribution of and predation on C. maenas were quantified using trapping and tethering experiments across tidal elevations, and also among high elevation habitat types. I found that use of S. foliosa by C. maenas may be context dependent; influenced by types of available refuge and whether competitors are present. I evaluated the effects of crab activity within cordgrass patches using a field enclosure experiment. Results show deleterious effects on cordgrass caged with C. maenas. Additionally, there was a trend in positive effects of native crab Hemigrapsus oregonensis on S. foliosa health and survivorship; potentially due to higher levels of nitrogen in the sediment. These results directly inform S. foliosa restoration efforts in the Bay, and give us new insight in to invasive species impacts on restoration efforts.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Duffy, Laura Margaret
- Description:
- This research takes an innovative approach to modeling distribution of a marine predator explicitly in the temporal domain. Harbor porpoise (Phocoena phocoena) are a small cetacean seen in San Francisco Bay year round. Porpoise presence at the entrance of the Bay varies from zero sightings to over 100 in an hour. The solitary social and foraging behavior of this non-migratory species makes it an especially useful indicator of habitat patchiness along the west coast and of tide-dependent ecological processes in central Bay. Bathymetry data of the Golden Gate channel show steep shelf breaks and complex outcroppings that effect water flow and create spatially stable areas where tidal fronts occur. Oceanographic features associated with tidal fronts are recognized by marine predators as areas in which prey biomass accumulates. Sighting frequencies were hypothesized to vary according to changes in the same spatially consistent, but temporally variable, tidal factors that correlate to lower trophic level congregating mechanisms. Circular statistics were used to describe sightings data over a 24 hour tidal period. Sightings were fit to circular models based on tidal segments that correlated to tidal state: ebb or flood, and changes in current velocity. One year of data show a greater number of porpoises are present during a flood tide, but there are more sightings during an ebb tide. Porpoise sighting frequency showed multimodal distribution and best fit a model with a specific mean direction at the 95% confidence interval with [F=0.34, p = 0.001]. Most sightings occurred within three hours after maximum inflow current velocity on the north side of the channel. The time at which the most sightings occurred over a 24 hour tidal period correlated to the time at which the most defined shear zones occur in central Bay with a circular correlation coefficient of -0.15 (p=0.0006). A three tiered, nested ANOVA found significant variation in porpoise foraging behavior correlated to tidal phase or tidal front presence. Foraging behavior varied significantly according to tidal state with [F=9.96, p = 9.38 x 1 O'08]. The data show that it is the patch in tidal progression, rather than geographic space, which is significant to variations in porpoise sightings and foraging behavior in the Golden Gate. The results produce a temporal habitat model for a federally protected, upper trophic level predator in the Bay. Models like this are an efficient way to inform management in a highly anthropogenic influenced area.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Mancera, Jeffrey Pascual
- Description:
- The Astronieae represent one of the earliest diverging clades of the pantropical family Melastomataceae and are endemic to the rainforests of southeast Asia and the Pacific islands. They comprise about 150 species of trees and shrubs in four currently accepted genera: Astrocalyx, Astronia, Astronidium, and Beccarianthus. A prior phylogenetic analysis focused on the Astronieae but sampling was insufficient to draw conclusions about generic circumscriptions or species-level relationships. Moreover, family-wide molecular phylogenetic analysis revealed that Tessmannianthus from tropical America has a closer relationship with the Astronieae than the Neotropical Merianieae, where it was originally placed. This study presents the first phylogenetic analysis of the tribe based on morphological data. Parsimony analyses of 57 ingroup taxa with 205 morphological characters were conducted to test support for the monophyly of each constituent genus and to verify the placement of Tessmannianthus within the Astronieae. Characters were partitioned into discrete and continuous datasets to assess potential areas of incongruence; the latter was coded with the differential gap-weighting method. The global analysis yielded two equally most parsimonious trees, the strict consensus of which shows that Astrocalyx, Astronia, and Astronidium are each monophyletic. Beccarianthus is biphyletic, consisting of one clade with oblong anthers and another with linear anthers, the latter being restricted to New Guinea. Likewise, Astronia section Astigmata was found to be polyphyletic. Intergeneric relationships within the tribe are well-resolved but these need further confirmation and support. Tessmannianthus forms a monophyletic genus that groups within the Merianieae. However, the partitioned analysis of discrete dataset suggests that Astronia sect. Astigmata is monophyletic with a single reversal and that the Astronieae are sister to Tessmannianthus except T. cereifolius. The phylogeny of the Astronieae sensu stricto supports the evolutionary change from axile to ascending and bilobed basal-axile placentae, and ultimately into collapsed ones. The resurrection of Bamlera to accommodate the Papuasian Beccarianthus clade is proposed.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Wingert, Charles Johann
- Description:
- A northern California strain of Pseudo-nitzschia australis was examined using nonaxenic, batch cultures to examine the effects of more acidic conditions (reduced pH due to increased pCO2) on the growth, photosynthesis, and domoic acid production of this toxigenic diatom. Specific growth rates at the lowest pH tested (7.8) were 30 percent lower than the other three pH treatments (8.1, 8.0, 7.9). Macronutrient drawdown ratios of Si:N and Si:P decreased linearly with declining pH. Maximum rates of photosynthesis per cell were significantly elevated in the two lowest pH treatments relative to the control pH of 8.1. Domoic acid (DA) was detected in all pH treatments during both the nutrient-replete exponential growth phase and the nutrient-deplete stationary growth phase. Total cellular DA did not significantly differ among pH treatments during exponential growth, but increased with decreasing pH and reached a maximum of 3.61 pg DA • cell"1 during the stationary phase of growth.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Markello, Kelly McNeal
- Description:
- Sea urchins (Echinoidea) comprise a group exhibiting enormous diversity in shape and size. At the lowest end of the size scale is Echinocyamus, a poorly known genus of highly miniaturized relatives of the sand dollars sometimes called “sea peas.” There are sixteen known extant species of Echinocyamus and two species in the sister genus, Mortonia. Using elliptical Fourier analysis to compare these species, 13 of them with sufficiently large sample sizes (> ten specimens) were significantly distinct based on test shape alone. A morphological phylogeny indicates that two species, E. planissimus and E. platytatus, should be removed not only from the genus, but from the family to which they belonged, Fibulariidae. With the removal of these two species, Echinocyamus and Mortonia are monophyletic and sister to Fibularia. Mortonia was nested well within Echinocyamus and should be sunk into that genus.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Hartnett, Ryan Jason
- Description:
- Pelagic ecosystem links are typically studied separately with predator response often invoked from climate change, while intermediary alteration in nutrients and plankton production are inferred as the root cause. More specifically, we explored how Pacific climate forces regional upwelling, drives oceanography, nutrients, plankton production and translated into observed predator abundances in the Gulf of the Farallones. We determined key pathways of those drivers with using a spatiotemporal approach to path analysis for a suite of mid and upper trophic level consumers. We found offshore ocean conditions predicted abundance of boreal/cold water copepods and these conditions also support krill abundance. We modeled three krill-predators in the offshore region: blue whales, Chinook salmon, and Cassin’s auklet. We found blue whales and salmon associated with krill biomass, however Cassin’s auklets associated with environmental conditions that influenced krill availability. Although these predators depend on the same prey, they responded differently to environmental drivers and biological resources, highlighting the need to study individual species responses to environmental change. Understanding how these drivers influence responses of upper trophic level species is important in supporting adaptive ecosystem management in the face of rapidly changing climate.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Rezaeihaghighi, Yasha
- Description:
- The alphaproteobacterium Sinorhizobium meliloti colonizes the roots of host plants, such as Medicago species, and induces the formation of nodules, where it fixes molecular nitrogen in exchange for carbon compounds. A previous suppressor analysis had identified two genes, SMc00067 and SMc03872, involved in the synthesis of exopolysaccharide-I (EPS-I), critical for symbiosis. A loss-of-function mutation in either gene resulted in lower production of EPS-I. We used epistasis analysis to investigate the relationship between SMc00067 and SMc03872 and other EPS-I synthesis genes (exoY, exoS, exoR and, expR+). I confirmed lower EPS-I levels in the ASMc00067 and ASMc03872 mutants by direct measurement via anthrone assays. I also found reduced expression of exoY, encoding an enzyme required for EPS-I synthesis, in the mutants. We expected the EPS-I under-production to affect the ability of these two mutant strains to infect and form nodules on alfalfa roots. ASMc00067 and ASMc03872 mutants, although defective in EPS-I production, did not show any defects in stimulating nodules compared to the wild type strain. Further study will uncover the roles of these genes and the regulatory pathways that influences EPS-I production and symbiosis.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Faye, Lindsay Elizabeth
- Description:
- Phyllaplysia taylori, a sea hare found in eelgrass beds along the Pacific coast, is an integral part of eelgrass ecosystems. Temperatures and salinities in San Francisco Bay are highly variable and expected to shift with continued climate change. Phyllaplysia taylori exposure to elevated temperatures and reduced salinities was hypothesized to reduce survival and increase metabolic and epiphyte grazing rates, indicating the energetic costs of temperature and salinity stress. Low survival was observed at the lowest exposure salinities, and metabolic and grazing rates indicated higher levels of stress and increased energy requirements at low salinities. An orthogonal experimental design was used to determine the interactive effects of temperature and salinity stress. The highest metabolic and feeding rates were measured at a combination of higher temperature and lower salinity, and the lowest metabolic and feeding rates were at a combination of lower temperature and higher salinity. An effect of P. taylori body size and sexual maturity on metabolic and grazing rates was also observed, with higher metabolic rates occurring in smaller pre-reproductive individuals, and higher feeding rates occurring in larger reproductive individuals. The results of this study will help inform eelgrass ecological studies throughout San Francisco Bay by indicating the impacts of shifting temperature and salinity on modulating the relationship between P. taylori and eelgrass performance in response to environmental change.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Hood, Kelly Mae
- Description:
- The purpose of this investigation was to assess the day-to-day and week-to-week reliability of body fat (BF%) measurements using three different methods [air displacement plethysmography (Bod Pod), bioelectrical impedance analysis (Fitbit Aria®), and hydrostatic weighing (HW)] in the San Francisco State University Exercise Physiology Laboratory. Additionally, the validity of BF% measurements using the Bod Pod and Fitbit Aria® were compared to the industry “gold standard” of HW. Twenty-two males and 21 females (age: 27.9 ± 5.6 years) participated in the three-day investigation. Each day, participants completed BF% measurements via Bod Pod, Aria® scale [‘Lean’ (Al) and ‘Regular’ (Ar) modes], and HW. The Bod Pod was found to be a valid method for measuring BF% in all participants (0.4±4.3%; SEE=2.2%); however when analyzed by sex, it was valid for females (-0.3±4.0%; SEE=2.0%) but significantly over estimated males (1.0±4.3%; SEE=2.2%). Ar agreed with HW when analyzing BF% for all participants (-0.8±9.3%; SEE=4.4%) and females (0.4±10.8%; SEE=4.4%), but significantly underestimated males (-2.0±7.1%; SEE=3.7%). Al underestimated BF% by -5±9.1% (SEE=4.2%) for all participants (males: -7.9±6.9%; females: -2.6±8.0%; p<0.05), and this discrepancy was more pronounced in males. Overall, the “mode” chosen on the Aria® scale greatly impacts validity of female participants, but was not valid for males using Al or Ar. All methods were reliable when comparing day-to-day and week-to-week BF% measurements for all groups, suggesting the Fitbit Aria® can be a reliable at-home body composition analysis scale.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Tooley, Aaron Seth
- Description:
- Nitrogen is an essential nutrient that is inaccessible to many organisms in its abundant atmospheric form. Rhizobia, a group of bacteria capable of fixing molecular dinitrogen into more useful forms, symbiotically colonize the root nodules of leguminous plants and provide these hosts with nitrogenous compounds. The exploitation of nitrogen-fixing bacteria has many applications in agriculture, since synthetic fertilizers have adverse effects on the natural environment. Sinorhizobium meliloti is an alpha-proteobacterium that engages in symbiosis with the model legume, Medicago truncatula. The S. meliloti polar organelle development protein (PodJ) is an important factor for symbiosis. Originally identified in Caulobacter crescentus, PodJ is required for the production of holdfast, which is an adhesive organelle synthesized at the bacterial cell pole that enhances attachment to surfaces. A nonsense mutation was identified in the podJ gene in the domesticated S. meliloti Rm1021 lab strain. When the mutation was corrected, the new Rm 1021 -derived podJ+ strain effectively outcompeted Rm 1021 for root nodule invasion in M. truncatula, suggesting that PodJ enhances attachment of S. meliloti to the host plant. To investigate this, competition experiments between Rm1021 and podJ+ strains were conducted. Confocal microscopy analysis showed that the p o d f strain attaches more robustly to the root compared to the Rm1021 strain. Quantitative polymerase chain reaction experiments were used to assess the relative abundance of the Rm1021 and podJ+ strain on root hair. Collectively, the data indicate that PodJ is a conserved polarity factor that contributes to effective symbiosis. Identification of additional molecular factors that may make these types of symbioses more efficient will ideally aid in the development of sustainable substitutes for synthetic fertilizer.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Kim, Richard
- Description:
- Introduced species often disrupt established food webs, but some native predators can come to rely on introduced prey. Understanding the net effects of the non-natives on imperiled predators is crucial for planning conservation measures. The invasive American bullfrog (.Lithobates catesbeianus) can be prey, predators, and competitors for the critically endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia). I examined the seasonal prey use and selection of a T. s. tetrataenia population that cooccurs with L. catesbeianus in San Mateo County, California. I quantified the snakes’ diet from analyzing their fecal DNA and also quantified anuran abundance as available prey. Prey selection varied by snake body size, although 95% credible intervals overlapped zero. If all prey types are equally available, T. s. tetrataenia selected California Red-legged frogs more than Sierran chorus frogs and L. catesbeianus. The degree of seasonal diet overlap between T. s. tetrataenia and L. catesbeianus was high. The strongest interaction between these species is likely competition rather than symmetric predation. Eradication of L. catesbeianus would likely benefit T. s. tetrataenia populations by reducing predation pressure on their shared amphibian prey.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Hulett, Ryan Edward
- Description:
- The family Tritoniidae (Nudibranchia, Cladobranchia, Dendronotidae) is a cryptic group of nudibranchs known to feed on a variety of octocorals (Mcdonald and Nybakken, 1999). The family has a muddled evolutionary history and previously has had limited morphological and molecular work performed to resolve these relationships. This study examines the evolutionary history of the two largest genera, Marionia and Tritonia, by sequencing a 328bp fragment of the nuclear histone 3 gene (H3), a 658bp fragment of the mitochondrial protein coding gene cytochrome c oxidase subunit I (COI), a 454bp fragment of the mitochondrial ribosomal subunit gene (16S), and a 860bp fragment of the nuclear 28S gene. Molecular data were used for likelihood and Bayesian inference analyses to reconstruct the evolutionary history and an ancestral area reconstruction was performed to gather insight into geographic origins. Based on molecular data, Marionia and Tritonia are well-supported, monophyletic groups with ancestral origins in the Indo- Pacific.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Holmes, Ann Elisabeth
- Description:
- Selective feeding by copepods has important ecological implications such as food web length, nutrient limitation, and control of algal blooms. Traditional methods for investigating copepod feeding in natural waters (e.g. stable isotope and fatty acid tracers or microdissection) have low taxonomic specificity or significant biases. We used highthroughput genetic sequencing (HTS) to identify in situ the phytoplankton prey of Pseudodiaptomus forbesi (Copepoda: Calanoida) in the San Francisco Estuary. Amplicons of the 16s rRNA gene were sequenced on an Illumina MiSeq. Cyanobacteria were the most frequently detected prey taxon, a result not predicted due to expected low nutritional value. In contrast, prey taxa expected to have high nutritional value for copepods (diatoms and cryptophytes) were not detected as frequently as anticipated based on the expectations generated using traditional approaches. Although our data is unable to resolve this unexpected result, the apparent feeding outcome could reflect unexpected feeding patterns, trophic upgrading, or poorly understood artifacts of the method. HTS analysis of copepod predation will become an increasingly valuable method as it is further developed and integrated with traditional approaches.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Kowalski, Beatriz Angela
- Description:
- Salmonella, consisting of more than 2000 serovars, is the second most common cause of foodborne illness in the US that can survival intracellularly and lead to gastrointestinal illness. Phosphorothioation (PT) is a post-replicative modification that replaces the non-bridging oxygen in the DNA backbone with sulfur molecule to form a phosphorothioate linkage. PT, a result from dnd gene cluster (dndBCDE), instigates DNA degradation (Dnd) phenotype during gel electrophoresis in the present of Tris buffer. This study examined the functional role of the dnd gene cluster present in Salmonella clinical isolates on microbial pathogenesis and the effect it has on the invasion process. Results showed the dnd gene cluster does not confer additional resistance to hydrogen peroxide or to UV irradiation. Scanning electron microscopy showed the presence of the dnd gene cluster had no visual effect on the morphology of the cell. Primers successfully amplified individual dnd genes in PT+ Salmonella, and unexpectedly the dndD gene was also present in PT- isolates, suggesting occurrence of one or more horizontal gene transfer events. Gene expression analysis showed increased gene expression of the dndCD genes when grown in conditions that mimicked in vivo environments simulating invasion of a host cell. The results suggest that dnd genes participate in coping with environmental stress and in invasion of host cells. This study verifies the functional role of the dnd gene cluster and supports a potential role the dnd gene cluster (especially dndCD) may have in the pathogenicity of PT modified Salmonella.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Harwood, Dashiell Blair
- Description:
- The geographical history of the Gulf of Guinea Islands has played a significant role in shaping the diversity and distributional patterns of the Hemidactylus geckos in the African- Atlantic clade. This study elucidates the phylogenetic relationships between five closely related members of the African-Atlantic clade from the Gulf of Guinea, and presents evidence to recognize a new taxon, Hemidactylus principensis. Previous studies have proposed that H. principensis and H. greeffi are two distinct species, classified both as H. greeffi. A more recent study that included extensive morphological analyses and molecular data recognize H. principensis. In this study I take a molecular approach, employing both mitochondrial and nuclear genes (ND2, a-Enolase, RAG1) to create a more comprehensive phylogeny outlining the African-Atlantic clade, and propose that there is evidence to support H. principensis as an independent and taxonomically coherent species.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Barretto, Kathryn Megan
- Description:
- Microbial mats are found globally in dynamic aquatic environments. Visually different morphotypes (orange-red and black-green) also show different rates of nitrogen fixation and biogeochemical activity. Glacial meltwater communities in the McMurdo Dry Valleys (MDV) of Antarctica present unique opportunities to study microbial mats, due to limited grazing effects and their sensitivity to climate change. Microscopy has yielded a poor understanding of species composition and diversity. I sought to address this limited understanding through deep sequencing of photosynthetic genes such as cbbL, and the 16S rRNA V4 hypervariable region. A total of 15 transects from five valleys were used, with samples representing stream-associated (submerged) or transiently wetted (hyporheic) transect points. While stream position is a clear driver of mat morphotype, morphotype was not associated with microbial community composition. Microbial mat communities exhibit temporal shifts in relative abundance, but not diversity of microorganisms present. We propose that unique mat morphotypes are not distinct communities, but rather a continuum of the same overall community ranging from submerged to hyporheic habitats. As such, microalgal mats have the potential for morphotypic and biogeochemical functional plasticity with changing hydrogeological conditions.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Lee, Calvin Yin-Tat
- Description:
- Chemical contaminants in estuaries may interfere with an organism’s ability to ward against parasites and disease which can shape patterns of genetic diversity in populations, including at the Major Histocompatibility Complex (MHC) which helps recognize foreign pathogens. Here, we examine genetic variation in the MHC, in microsatellite repeats, and in mitochondrial control region (D-Loop) sequences to assess relationships between a tumor-causing pathogen known as X-cell disease, juvenile English sole (Parophrys vetulus), and contaminants in the San Francisco Estuary (SFE), CA. Functional molecular analysis was used to compare fish regionally and by infection status. Supertypes analysis showed no difference in supertype distributions regionally or by infection status, nor was there evidence of differentiation at microsatellite loci and Dloop. These results suggest contaminant distributions may be more fine-grained than patterns of English sole movement in SF Bay, possibly explaining the incidence of tumorous individuals throughout the bay.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Broughton, Jennifer Anne
- Description:
- Phytoplankton form the base of the global marine carbon cycle. Measurements of primary production are integral to understanding fluxes between the atmosphere and both organic and inorganic carbon pools in the ocean. Virtually all measurements today are made using the carbon-14 (l4C) uptake method, yet numerous uncertainties and procedural problems remain unresolved (Karl et al. 1998, Marra 2002). One source of error in the 14C method results from the metabolic activity of grazers, and could potentially be 100% of the measured production rate (Welschmeyer 2010). The purpose of this project was to directly test 14C methodology against an independent carbon-based method of photosynthesis which is also free of grazer-induced biases in order to examine the relationship between grazer metabolism and the observed 14C error. 14C uptake measurements were compared to measurements of gross primary production using the light-dark bottle technique and measuring the change in total inorganic carbon, TCO2, with a coulometer. The 14C technique was found to underestimate primary production by 41%, and a positive relationship between microzooplankton metabolic parameters and a l4C recycling error was observed. The results of this study imply that total global ocean primary production is significantly higher than currently estimated.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Li, Suling
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Johnson, Allison Nicole
- Description:
- Increases in water temperature and salinity that are predicted to occur with climate change are hypothesized to alter phytoplankton communities, expand cyanobacteria blooms, and alter food web structure in estuaries. For example, since 1999 blooms of the toxigenic cyanobacterium Microcystis aeruginosa have been observed in the California Delta (Delta), and appear to be linked to increased water temperature. The goal of this study was to understand how variations in water temperature and salinity influence the community composition of estuarine phytoplankton using a series of bottle experiments conducted with field-collected phytoplankton from the Delta. Based upon analysis of phytoplankton accessory pigments diagnostic of major algal groups (i.e., diatoms, cryptophytes, chlorophytes and cyanobacteria), all phytoplankton-group growth responded positively to elevated water temperature with cyanobacteria showing the largest positive response. Salinity optima were apparent at salinities 6 -8ppt for diatoms and <8ppt for cryptophytes while cyanobacteria showed little response to the salinities tested. Warm temperatures will promote cyanobacteria in fresh waters and coupled with its relative tolerance for salty conditions means that their distribution may spread into brackish water.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Brett, Catherine Helen
- Description:
- Echinoids comprise a diverse group of Echinoderms composed of around 1000 extant species. The sea urchin family, Trigonocidaridae exemplifies echinoid diversity, being found in almost every marine ecoregion from the intertidal zone to depths over 3,000 m. Some of the Trigonocidaridae are also known wood-eaters, an unusual behavior previously recorded in only three sea urchin species. The family is also characterized by miniature body size and sculpturing of the test. This study is the first phylogeny of the Trigonocidaridae inferred from morphological and molecular evidence. All morphological analyses support the monophyly of the family Trigonocidaridae as well as the monophyly of the clades Trigonocidaris + Genocidaris + Desmechinus, and Hypsiechinus + Prionechinus + Asterechinus (which is monotypic). The molecular analysis does not contradict the morphological analyses and shows strong support for a relationship between Asterechinus and Prionechinus. The evolution of wood-eating and the biogeography of the Trigonocidaridae are explored using this phylogeny.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Lee, Jamie
- Description:
- This study demonstrated that Delta Microcystis can utilize different forms o f inorganic and organic N, with the greatest capacity for NH4+ uptake and the least for glutamic acid uptake, though N uptake did not always follow the classic Michaelis-Menten hyperbolic relationship at substrate concentrations up to 31 |imol N L '1. Current ambient N concentrations in the Delta are often at sub-saturating levels for N uptake, indicating that if N loading (especially N H /) were to increase, Delta Microcystis assemblages have the potential for increased N uptake rates, and increased growth, assuming steady-state and balanced growth conditions. In culture, N uptake by non-toxigenic and toxigenic M. aeruginosa strains followed similar trends to those found in the field, and both strains did not show severe inhibition o f N0 3 ~ uptake by NH4 + or inhibition o f NHt+ uptake on NO3”, but did show some inhibition o f urea uptake by N H / ; however severity o f responses to N inhibition phenomena may be strain-specific.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Drake, Michelle Kim
- Description:
- The 2009 Integrated Ocean Drilling Program Expedition 323 (Exp 323) to the Bering Sea recovered the first continuous sediment cores of the Pleistocene glacial cycles from sites throughout the marginal sea. Sediments in this region are dominated by diatom ooze showing different degrees of preservation and secondarily clay minerals and coarser siliciclastic material. Down core lithologic variability is prominent at both glacial/interglacial and millennial scales, which is reflected by variability in physical properties (e.g. bulk density). This thesis will characterize the lithologic expressions of the various scales of climate events from sediment cores from both the open ocean and ocean margin environments in the Bering Sea. The sedimentologic analysis uses an improved smear slide method combined with other independent methods to characterize the sediment (e.g., laser particle size analysis, scanning electron microscopy, physical properties). This novel methodological approach offers new insights on the links between changes in sedimentation and oceanography at different scales of climate variability in the Bering Sea and potentially in other similar high latitude basins.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Denney, Christian Thomas Charles
- Description:
- Increasing use of ecosystem-based management strategies, which are often applied to broad geographic areas and preclude extractive activities, are creating a need for rapid, cost-effective monitoring of large areas. Visual surveys are increasingly being used to meet this need. In this thesis, I examine a new tool for surveying fish assemblages in deep-water habitat: a stereo-video lander. In Chapter 1, I evaluate methodological choices and their impact on the data collected. In Chapter 2 ,I compare the video lander with a Remotely Operated Vehicle (ROV). In characterizing the new stereo-video lander, I found a negligible effect of bait on the number offish observed or on the number of species observed. The rotating camera system yielded density estimates slightly lower than those determined by a stationary camera but the rotating camera system produced less variance with the same number of surveys. In comparing the lander and the ROV, both measured similar densities for most species. Furthermore, I found that estimates of the variance in fish density were similar for the two tools given a comparable sampling effort (i.e., number of sites surveyed). Differences in community assemblage were found to be significant between the two tools. Because of the similarity in results and ability to quickly perform surveys and move on to new areas, the lander represents a new option when considering visual tools for deep-water research. I certify that the Abstract is a correct representation of the content of this dissertation.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
747. Multiple paternity : a life-history strategy for porcelain crabs in the face of rising temperatures
- Creator:
- Yockachonis, Thomas Joseph
- Description:
- Multiple paternity is widespread across many taxa including birds, insects and marine species. Despite multiple paternity being rare among studied crustaceans, a study found that -93% of female porcelain crabs, Petrolisthes cinctipes, mate with more than one male and produce broods of mixed paternity. No explanation has been given to the reason of why multiple paternity is prolific in P. cinctipes, or what function polyandry may serve for crabs in general to my knowledge. In order to identify potential advantages of multiple paternity in P. cinctipes, brood survival differentials were measured under ambient conditions and after a heat-shock. Microsatellite profiling was used to distinguish multiple from single paternity and compared to brood survival, in the presence or absence of a heatshock. When exposed to a heat-shock, single-sired broods experience a significant drop in mean brood hatching %, compared to multiply-sired broods. Multiply sired broods also show a substantial, but non-statistically significant, mean difference in mean hatching % between conditions, compared to single-sired broods. Results suggest that multiple paternity reduces embryo survival variance between ambient and heat-shock conditions and that multiple mating could be an advantage for P. cinctipes in the high-intertidal zone.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology and Marine Sciences
- Creator:
- Pinnell, Cassie Maria
- Description:
- This research was conducted to monitor the response of aquatic macroinvertebrate communities to the restoration of intertidal habitat, including eelgrass (Zostera marina) and native oyster reefs (Ostrea lurida) in the San Francisco Estuary. Plots of each habitat-forming species, alone and interspersed, were established in 2012 and quarterly invertebrate monitoring was conducted for one year prior to restoration (fall 2011 — summer 2012), and post restoration (fall 2012 - summer 2014) using trapping, vacuum sampling, and eelgrass shoot collection. Results were intended to inform the degree to which restored eelgrass and oyster reef habitat, alone and together, promote colonization and use by invertebrates, and if epiphytic invertebrate assemblages vary significantly between natural and restored eelgrass beds. Within two years, correspondence analysis revealed that eelgrass and oyster reefs supported unique invertebrate assemblage composition as compared to pre-treatment and control plots, and that the composition was intermediate in combined eelgrass/oyster plots. Restored eelgrass did not establish an assemblage equivalent to natural beds; several invertebrates beneficial to eelgrass growth, including Phyllaplysia taylori and Pentidotea resecata, remained absent or very rare.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Desmet, Danielle Nicole
- Description:
- Population bottlenecks, and subsequent loss of genetic diversity, are a common occurrence for introduced species. The MHC Class IIDB locus must constantly adapt to detect shifting pathogen communities and is used in this study to assess functional diversity in 2 regions with introduced populations of Rainwater killifish, Lucania parva. L. parva was likely introduced to San Francisco Bay from the Pecos River, New Mexico through a series of sport fish stockings to southern then northern California during the 1940’s and 1950’s. Demographic patterns of San Francisco and New Mexico populations were assessed using microsatellite, D-loop and MHCIIDB diversity. A single D-loop allele was found in all populations and three of four microsatellite loci were fixed at shared alleles, suggesting a strong bottleneck and common ancestry between all populations sampled. MHC diversity was lowest in New Mexico and one very similar allele was shared between the regions sampled. Inferred functional diversity was also assessed using physiochemical properties of MHC codons under positive selection and alleles were grouped into supertypes. Supertype usage and allelic diversity was relatively uniform between San Francisco and New Mexico. Despite low allelic diversity, functional diversity was spread across duplicated MHCIIDB loci. Two supertypes (out of four) were found to dominate in all populations. This reduced MHC diversity may be a result of relaxed parasite mediated selection as decreased immune response, assortative mating or new parasite pressures.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Strong, Shannon Elizabeth
- Description:
- A two-year study of nutrient and chlorophyll-a (chl-a) dynamics within and proximal to a 28 ha restored wetland was evaluated. The net mass flux of dissolved inorganic nitrogen (DIN) and chl-a at the restored site, Blacklock Tidal Marsh (BTM) was also determined by relating constituent concentrations of water samples to flow through breaches in the levee surrounding the wetland. In general, ammonium, nitrate, and chl-a concentrations in BTM were similar to those found at an historic wetland in Suisun Marsh. Variability of constituent concentrations within BTM was high, changing with rising and falling tidal stage and seasons. Though the flux of all constituents varied in magnitude and direction between monitored tidal cycles, BTM appeared to be a net sink of DIN and a source for chl-a.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Gao, Ivan Thomas
- Description:
- For efficient plant growth, legumes form symbiosis with a group of nitrogen-fixing bacteria, Rhizobia. Recent results in Sinorhizobium meliloti Rml 021 have shown that jspA, IppA, and podJ are involved in the production of succinoglycan (EPS-I), an essential exopolysaccharide for symbiosis. However, Rml021 contains a mutant expR allele, which down-regulates galactoglucan (EPS-II), another exopolysaccharide that contributes to symbiosis. To confirm the results seen in Rml021,1 evaluated the functions of orthologous genes in a related rhizobium, S. medicae WSM419, which does not contain a mutant expR allele. EPS-II is known to rescue EPS-I mutants during symbiosis, but jspA or IppA mutations in WSM419 still cause less efficient symbiosis during co-infections. Here I demonstrate that jspA and IppA in WSM419 are important in EPS-I production. EPS-II production in WSM419 does not rescue the symbiosis defect of jspA and IppA mutants. Surprisingly, WSM419 requires podJ for survival in low-nutrient media. Confirming the roles of these genes in S. medicae WSM419 moves us closer to determining the overall effects of these genes on symbiosis in Rhizobia and the possibility of conserved gene functions in other related Alphaproteobacteria.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Carlen, Elizabeth Jane
- Description:
- Giant sengis (genus Rhynchocyon), also known as giant elephant-shrews, are approximately 500 g forest floor mammals that range from Central to East Africa. Previous work on giant sengi taxonomy has focused primarily on pelage color, pelage pattern, and the geographic distributions of the groups. Because there is complex phenotypic variation and large geographic ranges within some species, I chose to use genetic work to evaluate the phylogeny and classification of the genus. Genetic data were used to investigate the four currently recognized species (R. chrysopygus, R. cirnei, R. petersi, and R. udzungwensis) and seven of the eight currently recognized subspecies (R. cirnei cirnei, R. cirnei macrurus, R. cirnei reichardi, R. cirnei shirensis, R. cirnei stuhlmanni, R. p. petersi, and R. p. adersi). I used DNA extracted from fresh and historical museum samples to analyze approximately 4,700 nucleotides (2,685 bases of mitochondrial DNA and 2,019 bases o f nuclear DNA) and reconstruct a molecular phylogeny. I also investigated and genetically confirmed the identity of Rhynchocyon sp. sequences published on GenBank, and suggest that the captive Rhynchocyon populations of North American zoos are R. p. adersi. My analyses confirm the current morphological classification, with each currently recognized species forming a monophyletic clade. My phylogeny suggests that hybridization among taxa is not widespread in Rhynchocyon, that the recently reported sengi from the Boni forest of Northern Kenya is genetically similar to R. chrysopygus, and that the subspecies R. c. stuhlmanni should be elevated to full species.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Abegaz, Metadel Fisseha
- Description:
- Species redistribution is a well-documented response to global change. Understanding the resulting physiological responses of organisms is critical for predicting community composition changes that may occur under future conditions. The porcelain crab Petrolisthes cinctipes resides in the upper to mid intertidal zone and is expected to behaviorally respond to rising temperatures by shifting its distribution lower in the intertidal zone where they will experience higher densities and likely interact more often with a congeneric competitor, Petrolisthes manimaculis. In this study, I addressed how increased density and inter- and intra- species interaction impacts injury, heat shock protein (hsp) expression and reproduction, indexed by circulating levels of the yolk protein vitellogenin (Vg) and expression. To address these questions, female crabs were randomly exposed to high density (787 crabs/m2) or low-density (250 crabs/m2) treatments with and without the presence of a competitor species for 14 days. We found that density and species interactions did not affect injury but significant hsp and Vg differences were detected in P. manimaculis. Furthermore, Vg protein and expression results show species sensitivity along a lunar cycle axis suggesting reproductive state during the New Moon may result in heightened sensitivity to stress. These results highlight the importance of species interactions and environmental cues under changing environmental conditions and further our understanding of how thermally transduced stress can impact animal populations through physiological stress.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Weinnig, Alexis Marie
- Description:
- Octocorals are among the most abundant and diverse organisms in the ocean. These animals are present in every ocean and can be found from the intertidal zone (0 m) to abyssal depths (over 6000 m). Gorgonians are octocorals with a solid, internal axis. There are three axial types that differentiate gorgonians: scleraxonians, holaxonians, and calcaxonians. This study analyzed the variation in axial chemical composition within these three gorgonian axis types with x-ray microanalysis, by using quantitative energy dispersive x-ray spectrometry (EDS). EDS successfully quantified the elemental composition of eleven gorgonian octocoral axes. Scleraxonian elemental composition showed significant similarity and suggests that, based specially on axial elemental composition, scleraxonians comprise a unified group. However, holaxonian and clacaxonian elemental compositions were significantly different within each group and thus do not represent concise grouping by axis type.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Melroy, Laura Michelle
- Description:
- Temporal genetic studies of direct developing organisms are rare. Marine invertebrates lacking a planktonic larval stage are expected to have lower dispersal, low gene flow, and a higher potential for local adaptation than organisms with planktonic dispersal. Leptasterias is a genus of brooding sea stars that contains several cryptic species complexes. Population genetic methods were used to resolve patterns of fine-scale population structure in central California Leptasterias using three loci from nuclear and mitochondrial genomes. Historic samples were compared to contemporary samples to delineate changes in species distributions in space and time. Contemporary sampling confirmed a pattern of shared haplotypes at both mitochondrial and nuclear loci around the mouth of San Francisco Bay with distinct, shared haplotypes bracketing populations north and south of the bay. Phylogenetic analysis confirmed the presence of a baylocalized clade and revealed the presence of an additional bay-localized and previously undescribed clade of Leptasterias. Analysis of contemporary and historic samples indicated these two clades may be experiencing a constriction in their southern range limit and suggest a decrease in abundance at sites at which they were once prevalent. Historic sampling revealed a different distribution of diversity along the California coastline compared to contemporary sampling and illustrates the importance of temporal genetic sampling in phylogeographic studies.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Sebilian, Serina Sue
- Description:
- This research examined the effects of temperature (20, 25, and 30°C) and salinity (0, 6, and 12) on the plant traits of the aquatic macrophyte, Stuckenia pectinata, and how changes in these traits influence herbivory by invertebrate grazers. The highest temperatures showed positive effects (e.g., leaf area and sexual reproduction), counter to my predictions, while the highest salinity tended to have negative effects, as expected. Thus, the coolest temperature (20°C) and highest salinity (12), presumably the most stressful treatment for the plants, tended to lower %C, %N, protein content, and phenolic concentrations, while salinities of 0 at this same temperature tended toward higher phenolics, C:N, and %C. Salinities of 12 at 30°C had the highest %N and %P content; however, this treatment also suffered the highest herbivory from the amphipod, Ampithoe valida. Herbivory in salinity treatments of 12 with increasing temperature was negatively correlated with C:N, and positively correlated with %N, %P, and protein content. These results can inform future management, conservation and restoration efforts.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Johnson, KeChaunte Amrie
- Description:
- Delineation of Acartia spp. is essential to assess the biodiversity of copepods in marine ecosystems. Previous phylogenetic analyses show lack of monophyly for A.tonsa and A.hudsonica. Reported average DNA sequence divergence among some Acartia spp. includes >16% for mitochondrial cytochrome oxidase c (COI) and 13%-25% for 18S rRNA. We investigated the genetic diversity of SFE Acartia in comparison to other Acartia spp. sequences from Genbank. Copepods were collected from the SFE across a range of temperatures and salinities and sequenced at COI and nuclear 18S loci for Bayesian phylogenetic comparison. We found £23% COI divergence and >35% 18S divergence among paired comparisons of A. tonsa, A. hudsonica and A. californiensis. Acartia hudsonica SFE haplotypes clustered more closely with northeast Pacific coast (-25% COI divergence) than with northeast Atlantic (-30% divergence) samples. Acartia californiensis from SFE showed <13% divergence in comparison with Genbank haplotypes. SFE and Atlantic coast A. tonsa were -15% 18S and 31-33% COI divergent. These results support high sequence divergence among Acartia species. Further analysis of additional loci is needed to understand the phylogenetic and population structure of SFE Acartia species relative to other populations.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Yates, Devona C.
- Description:
- Field surveys and empirical predation assays (i.e., tethering experiments) were conducted inside and outside of three no-take marine reserves, one established in 2007, and two 30+ years old in central California kelp forests. Densities of micro-invertivours fishes were 1.5x higher and biomass of pooled invertivorous fishes was 2.8x greater inside reserves compared to fished areas. The increased abundance of predators inside reserves translated to a significant reduction in survivorship of two species of decapod crustaceans, the dock shrimp, Pandalus danae, and the cryptic kelp crab, Pugettia richii. Shrimp mortality rates were 4.6x greater, while crab mortality rates were 7x greater inside reserves. Video analyses indicated that micro-invertivorous fishes arrived 2x faster (W) to tethering assays at reserve sites. Major shrimp predators inside reserves were Hexagrammos decagrammus (31%), Embiotoca lateralis (16%), Scorpaenichthys marmoratus (10%), and small sculpins in the family Cottidae (9%). Strike rates per hour were similar across sites, except strike rates by small sculpins, which were 14x greater inside reserves than outside. Based on the condition of the remaining crab carcass after predation events, the majority (72%) of predation events on crabs were attributed to Octopus rubescens.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Turner, Carley Rae
- Description:
- Sea surface pH is projected to decline 0.3 - 0.4 units by the year 2100. In the same time span, global surface temperature is expected to increase up to 4°C. Many studies have recently focused on the interactive effects of multiple stressors on the physiology of intertidal organisms, although, the interaction of pH and temperature incorporating the natural variability of those parameters has hardly been addressed, especially in juvenile organisms. The effects of variable pH decrease and temperature increase on rocky intertidal zone adult porcelain crabs, Petrolisthes cinctipes, have been shown to increase thermal tolerance and depress metabolic rate. One interpretation is that energy demand for homeostasis increases while overall energy supply decreases, which may cause energy to be diverted from activity, growth, and/or reproduction. To determine if energy is re-allocated from growth, juvenile P. cinctipes were exposed to pH 8.0 and pH 7.5 seawater during a high tide period and aerial temperatures of 12°C and 24°C during a low tide period. Survival, growth, and metabolic rates were examined after 26 days of exposure. There were no effects of pH and temperature on survival or growth. However, temperature had an effect on metabolic rate, as metabolic rate increased with elevated temperature. These results suggest that juvenile P. cinctipes may be tolerant of future climate change conditions in the rocky intertidal under medium-term pH and temperature exposure.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Chow, Benson
- Description:
- The earliest, newly settled juvenile stages are a critical phase in the life cycles of sessile marine invertebrates. Individuals must grow quickly to avoid lethal predation, yet they may be stuck in low flow boundary layers where obtaining food for rapid growth is challenging. Newly settled zooids growing with little to no competition on PVC plates were measured. I tested for rate variation from earliest juvenile stages with fine scale measures of surface area and zooidal numbers in two non-native taxa with contrasting internal and external feeding structures. Growth rate variation was observed for specific growth rates at the varied environmental conditions in field environments (marinas). Overall, this data may be used to consider if the most successful invaders show a growth rate advantage particularly at the earliest and most vulnerable stages in the life cycle.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
761. Comparison of anthropometric and psychological characteristics of marathon and ultramarathon runners
- Creator:
- Enriquez, Kathryn Ann
- Description:
- The purpose of this study was to investigate the psychological and physiological characteristics of marathon and ultramarathon runners. Fourteen marathon and 14 ultramarathon recreational runners were assessed for, body height, body mass, BMI, body fat percentage, circumference and skinfold measurements, and completed a semi-structured interview. IBM SPSS Statistics version 24 was used to conduct a MANOVA for all physical measurements to look for main and interaction effects of run group, sex and age. Univariate testing was done for interaction effects to find a simple effect. Statistical significance was set at p < 0.05. A main effect of age (p < 0.05) was found for runners ≤ 45 years having greater thigh circumference than runners ≥ 46 years. A main effect of sex (p < 0.05) was found on body fat percentage with female runners having a higher body fat percentage than male runners. A main effect of sex (p < 0.05) on upper arm circumference was found with male runners having larger upper arm circumferences than female runners. A main effect of sex (p < 0.05) on BMI was found with males having higher BMIs than females. A simple effect was found for calf circumference with female runners ≤ 45 years old having larger calf circumferences than female runners ≥ 45 years old. Interviews found marathoners to be described as lean individuals who participate for the physical health benefits and have set time goals for the future. Ultramarathoners described themselves as individuals who are focused on the total experience and are willing to push themselves to extreme limits.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Hossfeld, Daniel John
- Description:
- Controlled experiments testing effects of temperature, salinity, and aerial exposure were paired with field observations to investigate symbiont expulsion in the abundant intertidal anemone, Anthopleura elegantissima. In the study region, A. elegantissima hosts a single symbiont, the dinoflagellate Symbiodinium muscatinei. The San Francisco Bay outflow creates a tidally influenced low-salinity plume that impacts adjacent coastal sites. Salinity, temperature, and aerial stress induce a bleaching response similar to corals where symbionts are expelled, causing further energetic stress. Using field observations of environmental conditions and symbiont abundance at sites on a gradient of exposure to estuarine outflow, along with fully crossed multifactorial lab experiments, we tested for changes in symbiont abundance in response to various combinations of three stressors. Lab experiments were designed to mimic short term outflow events with low salinity, high temperature, and aerial exposure treatments. The aerial exposure treatment was a statistically significant factor in suppressing symbiont repopulation (ANOVA, p=0.017). Symbiont density decreased with increasing tidal height (ANOVA, p=0.036), suggesting that aerial exposure may affect symbiont density more than sea surface temperature and salinity. Unanticipated documentation of survival in 9 months of sand burial and subsequent repopulation of symbionts is reported in comparison to results from past observations. The study of this symbiosis is useful in examining predicted changes in ocean conditions in tidepool communities.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Rutherford, Erica Marie
- Description:
- Despite the amount of attention it has received, attempts to explain the distribution of genetic diversity have not been fully successful. Competing theories claim that neutral or selective processes have a greater influence on the genetic variation within a population. My study was designed to test this empirically in naturally occurring sympatric lizard populations. Two species of herbivorous lizards and two species of carnivorous lizards were sampled, using trophic level as proxy for long term population size. Results were inconsistent with the neutral theory, and extremely high levels of diversity were found in some loci of the carnivorous lizards. It appears that selective processes may be having an important impact on intraspecific diversity in this reptile community.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Weaver, Crystal Lynn
- Description:
- Restoration of eelgrass (Zostera marina) is underway in a number of regions, yet transplant success remains inconsistent. Eelgrass bed sediments and the microbial communities therein are not well understood, though they may hold the key to improving restoration practices. This research investigated the sediment geochemistry and associated microbial communities of eelgrass in the San Francisco Bay Estuary, aiming to determine the connection between sediment characteristics and eelgrass transplant survival. Using 16S rRNA amplicon sequencing, microbiome analysis showed significant dissimilarities between natural and restored eelgrass beds, though minimal differences between successful and failed restoration sites. Sediment analyses also showed higher levels of organic matter and clay content at restored sites, particularly at those restored sites at which eelgrass has failed to thrive. Overall, I found microbial and biogeochemical evidence for microbial sulfate reduction and the production of sulfide, a phytotoxic metabolite, that was present most acutely at the failed restoration sites. Additionally, a separate mesocosm experiment examined the feasibility of sediment inoculation as a means of preparing a potential restoration site for eelgrass transplanting, though I found no inoculation effects.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Scheinberg, Lauren Ashley
- Description:
- Eelgrass (Zostera marina) beds are highly valued in temperate estuaries worldwide, and decades of declines have led to conservations and restoration programs in many regions. Understanding variation in factors that determine eelgrass success is an important part of these programs. Small invertebrate grazers on eelgrass are generally thought to benefit plants by removing competing algae; however, an amphipod, Ampithoe valida, putatively introduced to San Francisco (SF) Bay, also directly consumes eelgrass and threatens restoration efforts. This feeding behavior differs from that observed in the range of A. valida where it primarily grazes on micro- and macroalgae. The mechanisms as to why feeding preference for eelgrass differs between regionally distinct populations of A. valida are not well understood. The results of a series of feeding tests demonstrate that A. valida in SF Bay is adapted to preferentially consume local eelgrass when offered a choice, and also to more readily consume eelgrass from regionally local estuaries (SF Bay, Bodega Bay and Tomales Bay) over Virginia eelgrass, while Chesapeake Bay A. valida did not exhibit preferences among the same foods. Morphological and chemical differences between eelgrass populations did not clearly drive SF Bay A. valida feeding preferences. This study suggests evolution of feeding behavior in the SF Bay amphipods. Alternatively, Chesapeake A. valida may simply have not acclimated to local eelgrass, perhaps due to greater availability of non-eelgrass foods including macroalgae and epiphytes. Increased amphipod density did not induce a feeding shift from Gracilaria to eelgrass in an experiment with SF Bay amphipods and SF Bay foods; in fact, A. valida consumed eelgrass equally to Gracilaria at all densities. Phylogenetic analysis of COI sequence data from Atlantic and Pacific A. valida showed cryptic diversity; however, analysis of two nuclear genes did not corroborate these findings, suggesting that these are cryptic subspecies that have only recently diverged. The genetic data also suggest a Pacific origin, rather than Atlantic, of A. valida.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Wehrenberg, Megan Liane
- Description:
- The purpose of this project was to examine and compare the mechanisms for growth and reproduction of Gracilariopsis andersonii found along an exposed rocky coast and within an estuarine sand flat. Biomass and reproductive capacity were measured within permanent plots at Pigeon Point (Pescadero, CA) and in the Elkhom Slough (Moss Landing, CA) for one year and while cultivated in the laboratory for 40 days. The rocky coast population relied heavily upon sexual fertilization while the estuarine population relied almost solely upon vegetative fragmentation for propagation, clearly indicating life history plasticity within this species. Additionally, I investigated the sediment size frequency in areas with and devoid of algae and found evidence indicating the alga as a sediment stabilizer. The results of this study indicate that variations in environmental conditions may control the life cycles and therefore demographics of these organisms.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Cox, Daniel McGovern
- Description:
- Massive precipitation experienced in California during the 2016-17 winter brought the salinity of surface waters in San Francisco Bay Estuary (SFBE) down to values not seen in years. Bay-dwelling organisms such as intertidal invertebrates are at risk of mortality in salinity conditions that exceed their tolerance limits. While some fluctuation in salinity and other environmental conditions is a staple feature of estuarine life, extreme salinity conditions during a wet winter may present an exceptional stress. Observations from field and laboratory investigations provide insight in the role of salinity on the composition of mudflat infauna. A field study conducted at six sites along the estuarine gradient of northern SFBE revealed a trend of decreasing species richness and abundance with increasing distance upstream during the wet winter. Low diversity during the wet winter and differential succession of communities at upstream sites relative to downstream sites suggests that massive freshwater years substantially change intertidal mudflat communities depending on their location in the estuarine gradient. Notably, non-native species dominated the intertidal mudflat communities during and after the wet winter across all sites in this study. The lack of a numerically dominant non-native clam, Gemma gemma, in the least saline region was reflected by the higher mortality observed laboratory treatments where salinity was less than ten. Reductions in freshwater availability to SFBE due to drought and diversions may increase likelihood of G. gemma to spread upstream. Yet this spread may be counteracted by occasional extremely wet winters like that of 2016-2017.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Pollak, Tania Nurith
- Description:
- Ischnura gemina, the San Francisco forktail damselfly (Family Coenagriortidae) is endemic to the San Francisco Bay area, and is identified by the International Union for Conservation of Nature as a vulnerable species. Research from the late 1970s through the 1990s indicates a decline in the species’ populations. This study completes a comprehensive survey for I. gemina, and the closely related species I. denticollis, to determine the status of both species in areas previously surveyed. The study also seeks to determine the extent that various habitat variables, such as water chemistry and vegetation structure, predict the presence of I. gemina. Data from this study show a dramatic decline in populations of I. gemina since the 1980s and 1990s. In addition, results from this study indicate that I. gemina persists in sites with cooler temperatures and lower salinity than do other ischnuran or coenagrionid species. Finally, this study considers past research related to species conservation in light of climate change, and assesses the long-term viability of I. gemina under climate change. Of key interest is the tolerance for I. gemina under increasing temperatures and sea level rise. The goal for this research is to provide information on the current status of I. gemina and recommendations for its long-term conservation.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Travis, Nicole Mayu
- Description:
- As a highly urbanized ecosystem, the San Francisco Estuary (SFE) has many wastewater treatment facilities discharging large volumes of high nutrient effluent into the estuary. Phytoplankton primary production can be depressed in the presence of ammonium-rich effluent, and ammonium tolerant phytoplankton species can become successful. The direct response of phytoplankton metabolic processes to anthropogenic nitrogen may play a key role in bottom-up structuring phytoplankton species composition and abundance in the lower Sacramento River, CA.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
770. Climate change effects on photosynthetic symbionts in the sea anemone Anthopleura xanthogrammica
- Creator:
- Fisher, Alison Christine
- Description:
- The giant green sea anemone (Anthopleura xanthogrammica) inhabits the rocky intertidal zone in California and Oregon. Two photosynthetic algal symbionts, zooxanthellae and zoochlorellae, make these anemones important primary producers in the intertidal zone. This study investigated the effects of changes in temperature and pH on anemones and their symbionts over a natural environmental gradient along the coast of California and Oregon. Zoochlorellae responded negatively to warmer temperatures and positively to more acidic conditions, while zooxanthellae responded positively to warmer temperatures and lower pH. Temperature and pH did not significantly affect chlorophyll a concentrations or anemone protein biomass. Depending on the magnitude of future changes in ocean temperatures and acidity, changes in the ranges of the two types of symbionts and increased densities of sea anemones in the rocky intertidal could be expected to occur.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Green, Kristen Marie
- Description:
- Movements of 23 sub-adult and 10 juvenile black rockfish (Sebastes melanops) implanted with acoustic transmitters were monitored during 16 months in Carmel Bay, California. Most tagged sub-adult black rockfish (14 fish) were resident to the study area (>75% time). The remaining 9 sub-adult black rockfish had low residency (<35% time). All tagged juvenile black rockfish vacated the study area within 3 months of release. When tagged fish were in the study area, mean activity space was < 0.4 km2. From October to May, sub-adult black rockfish during daytime moved to deeper waters offshore, returning at night. In the summer, diurnal movements of sub-adult black rockfish decreased, perhaps due to locally abundant food resources associated with seasonal upwelling. The black rockfish is currently managed with other nearshore, residential rockfishes, yet the complex movement patterns of black rockfish described in this study should be considered in a species-specific management plan.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
772. Ocean acidification effects on the nutritional quality of phytoplankton for copepod reproduction
- Creator:
- Meyers, Morgan Teal
- Description:
- Four species of phytoplankton (Rhodomonas salina, Skeletonema marinoi, Prorocentrum micans, Isochrysis galbana) were grown under present-day low (400ppm pCOi, pH~8.1) and predicted-future high (lOOOppm pCOi, pH~7.8) ocean acidification conditions using nitrate-limited semi-continuous batch cultures. For four days, female Acartia tonsa copepods were fed a phytoplankton mixture from either the low or high pCC>2 treatment cultures. Phytoplankton fatty acid profiles were analyzed to assess changes in cellular essential fatty acid (EFA) content. Copepod egg production (EP), hatching success (HS), and egg viability (EV) were analyzed to assess differences in copepod reproductive success. Phytoplankton cultured under high pCC>2 contained less EFAs compared to phytoplankton cultured under low pCC>2. Female copepods fed high pCC>2 phytoplankton had lower EP, HS, and EV compared to females fed low pCC>2 phytoplankton. This laboratory study demonstrates that ocean acidification changes the nutritional quality of primary producers, which affects the potential reproductive success of fundamental primary consumers.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Ingman, Kaytlin Brooke
- Description:
- In the California Current System, baleen whales are used as a proxy for ecosystem health because they have been widely studied as a top predator. Oceanographic variability in the California Current System is dominated by three basin scale climate patterns, the Pacific Decadal Oscillation, the North Pacific Gyre Oscillation, and the Southern Oscillation which influence sea surface temperature, productivity, and upwelling. Humpback (Megaptera novaeangliae), blue (Balaenoptera musculus), and gray (Eschrichtius robustus) whales have been documented altering both timing of migration and switching prey when there are shifts in climate patterns. I hypothesized that both basin-scale climate and local oceanographic conditions would influence annual whale sightings and timing of arrival, peak, departure, and residency in central California. Using twenty-five years of weekly whale counts collected from Southeast Farallon Island, I developed two sets of regression models to test which environmental variables drive whale sightings and timings. I then developed a set of predictive models to determine if differences in sightings and timings could be predicted. I also compared sightings and timing to annual entanglement rates. There have been increased sightings in all species through time and variations are most commonly driven by sea surface temperature. Differences in timings are most influenced by El Nino events. Humpback entanglements are driven by whale arrival to central California, while, number of sightings drive gray whale entanglement rates. These models, and the continuation of long term monitoring, can be used to hopefully reduce the number of entanglements in central California.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Ceja, Alma Yesenia
- Description:
- Climate induced shifts in population distributions are widely documented around the globe as a means of animals behaviorally responding to their physiological tolerance limits. The rocky intertidal shore is known for its highly thermally variable environment within small elevational gradients, driving its exploitation in global warming research. I created an individual-based simulation to test a rule-based size-dependent species distribution model of a well understood population of Petrolisthes cinctipes crabs inhabiting the rocky intertidal shore of Fort Ross State Historic Park, California, which was then implemented to forecast the future distribution under the effects of warming. The model predicts the population will respond by shifting their distribution lower in the intertidal zone. This local distribution shift could result in significant ecosystem-wide community alterations. The generated simulation could be applied to similar systems of less tractable organisms responding to biotic and abiotic variables.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Barry, Shannon Noelle
- Description:
- Batoids exhibit unique body plans, with derived fin morphologies such as the anteriorly expanded pectoral fins that fuse to the head, or distally extended anterior pelvic fin lobes used for a modified swimming technique utilized by skates (Rajidea). The little skate (Leucoraja erinacea), exhibits both of these unique fin morphologies. These fin modifications are not present in a typical shark body plan, and little is known regarding the mechanisms underlying their development. A recent study identified a novel apical ectodermal ridge (AER) associated with the development of the anterior pectoral fin in the little skate, but the role of the posterior FIoxA genes was not featured during skate fin development. We present the first evidence for FIoxA expression (HoxA 11 and HoxA 13) in novel AER domains associated with the development of these novel fin morphologies in a representative batoid, L. erinacea. We found HoxA 13 expression associated with the recently described novel AER in the anterior pectoral fin, and HoxA 11 expression in a novel AER domain in the anterior pelvic fin that we describe here. Further, we found that HoxA 11 expression is associated with the developing fin rays in paired fins. Finally, we found evidence for the “distal phase” FIoxA expression in the developing claspers, suggesting a more complex Hox code than previously described during specification of these modified fin domains.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Lam, Emily Kathryn
- Description:
- Small-scale shifts in species distributions are expected to occur under future climate for many species. These shifts can have consequences as they alter population dynamics, and it is important to understand when and why they occur. The intertidal porcelain crab Petrolisthes cinctipes currently experiences temperatures that can reach near-lethal levels at low tide. However, the thermal thresholds that trigger migration to cooler microhabitats and the extent to which crabs move in response to temperature remain unknown. We tested for effects of body size and reproductive state on escape temperature (T e s c ) . In addition, we tested for the relationship between T eSc and the temperature of peak action potential firing frequency in nerve fibers. We found that both size and reproductive state influence behavioral sensitivity to temperature. Small crabs tolerate significantly higher temperatures before they move to cool refuges (a higher T eSc ) compared to large crabs. In addition, non-gravid crabs have significantly higher T eSc than gravid females. Tesc is positively correlated with peak neural performance of spontaneous action potentials. The vulnerability of marine organisms to global change is predicated by their ability to utilize and integrate physiological and behavioral strategies as a response to temperature, in order to maximize survival and reproductive fitness; understanding these strategies will allow predictions of species distributions under warming.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Kalmbach, Andrew James
- Description:
- The Amazon River Plume (ARP) is a productive region of the Atlantic Ocean where riverine nutrients drive particulate productivity. A portion of the carbon produced by phytoplankton is released as dissolved organic carbon (DOC); this research investigated the effects of the ARP on the extracellular release (ER) of DOC. Particulate production (PP) and ER were measured during two cruises to the region, and were contrasted with salinity, dissolved nitrogen, and phytoplankton taxa and size. Chlorophyll normalized PP and ER were unaffected by size, and assemblages dominated by Trichodesmium sp. released a greater percentage of fixed carbon as DOC than sites mainly composed of diatoms. Salinity and total dissolved nitrogen (TDN) did not affect ER, but phytoplankton released a larger fraction of their total productivity at low TDN and high salinity. Particulate production correlated with total dissolved nitrogen, there was no effect of dissolved inorganic nitrogen on PP or ER, suggesting that the phytoplankton utilize the organic nitrogen pool in lieu of ammonium and nitrate.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Nadel, Miko Rain Abraham
- Description:
- A systematic monograph of the lichen genus Usnea from the remote, under-explored islands of Sao Tome and Principe (ST&P) in tropical West Africa is presented, treating 11 species representing 2 subgenera, Usnea and Eumitria. Ten of the 11 species are reported as new for ST&P, including U. firmula, U. baileyi, U. pectinata, U. aff. flammea, U. sanguinea, U. picta, U. krogiana and three undetermined, potentially new species, Usnea species A, B and C. Usnea articulata is confirmed for the main island of Sao Tome. Determinations were made using morphological data, chemistry via thin layer chromatography, and a molecular phylogeny based on nDNA Internal Transcribed Spacer (ITS) sequences. Usnea baileyi, U. pectinata, U. articulata and Usnea species C represent species complexes consisting of two or more morphotypes each. Comprehensive descriptions, photographs, and a dichotomous key to the species are provided.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
779. Relating benthic microorganism communities and processes to nutrient variability in tidal wetlands
- Creator:
- Lee, Tricia Louise
- Description:
- This study examined the benthic zone of tidal habitats in the San Francisco Estuary (SFE) in order to characterize this understudied part of the ecosystem. Microbial community composition was evaluated in relation to nutrient flux rates from the sediment across the SFE in June 2014. These values are some of the first of their kind and yield insight into the basic biology of the shallow water ecosystems in the SFE and how the benthos relates to overall biogeochemical functioning. Additionally, the benthic microalgae are key players in the carbon cycling of shallow systems of the SFE. Therefore an evaluation of the relative contribution of carbon fixation by these populations in comparison to water column microalgae was also conducted from February to October, 2015 in two historic marshes at China Camp, San Rafael, CA and Rush Ranch, Suisun City, CA, to better understand the overall role that single celled algae play in shallow tidal habitats of the SFE.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Patten, Melissa Virginia
- Description:
- Morphological variations in widely distributed plants may be driven by phenotypic plasticity or by underlying genetic differences. In the brackish open water region of the San Francisco Estuary (SFE), a population of sago pondweed, (Stuckenia pectinata) shows at least two distinct growth forms, which are so different that they were previously thought to be two species. This study confirmed the S. pectinata species identity for all morphologies through sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region. I investigated phenotypic plasticity in response to flow variations in a common garden, and found that morphological traits are plastic but distinct morphotypes did not converge. I then used four microsatellite loci to investigate differentiation between the two morphotypes at three sites within Suisun Bay and the western Sacramento-San Joaquin Delta, and two populations from other central California sites for comparison. I found very few multilocus genotypes (unique combinations of alleles across two or more loci), which could be a reflection of low levels of clonal diversity, or a byproduct of low resolution in my methods. Lastly, I investigated the influence of plant morphology on the ecologically important invertebrate epibiont community. I found a positive relationship of plant surface area, leaf count, and leaf density with invertebrate abundance only at the more saline of the two sites sampled, which had a different invertebrate assemblage than the fresher site. Results of this study suggest that the two growth forms may provide different ecosystem functions and services, which could influence management and restoration decisions in the region.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Richard, Heather
- Description:
- Plastic debris in aquatic environments can accumulate ions from the surrounding water, potentially altering the fate of trace metals in these ecosystems. Mechanisms driving this process are poorly understood, and may be attributed to organic matter fouling the plastic’s surface. In this study, two types of pristine plastic pellets as well as glass pellets were suspended in the San Francisco Bay and biomass and metal accumulation were measured at various time intervals up to 28 days. At each time point, increasing biomass was positively correlated with metal accumulation on plastic pellets. Glass accumulated significantly higher levels of Zn compared with plastic materials regardless of biofilm growth. For other metals that showed an affinity for glass, the importance of biomass as a predictor of metal concentration increased and the differences between glass and plastic decreased over time and as biofilm increased. Future studies should account for the effect of biofilms when estimating contaminant sorption and desorption potential on plastic debris relative to other types of debris materials.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
782. Groundwater recharge sensitivity to low impact development design and future climate variability
- Creator:
- Rodriguez, Jessica
- Description:
- Groundwater sustainability is at the forefront of resource management. In light of climate change and growing populations, meeting future water needs must be met with planning and innovation. This is particularly challenging in cities where recharge is often limited by impervious surfaces and runoff is contaminated by urban pollutants. Low impact development (LID) is a design strategy that mimics the natural hydrologic cycle and is usually implemented as an alternative to the traditional stormwater system. Examples of LID best management practices (BMPs) include rain gardens, bioswales, infiltration trenches, rooftop gardens, and permeable pavement. LID BMPs delay and decrease peak runoff flows and improve water quality, and there is a growing number of studies investigating LID’s effect on groundwater. Understanding potential recharge under LID BMPs and identifying the design features influencing recharge can serve an important role in the move toward groundwater sustainability and management. In this study, I used HYDRUS-1D to model five LID BMPs (two rain gardens, two bioswales, one infiltration trench) from 1948-2099 with observed historic climate data and 9 global climate models (GCMs) at representative concentration pathways (RCP) of 4.5 and 8.5. Mean recharge ranged from 1725-3458 mm/yr under the LID BMPs, with the highest recharge rates occurring under the infiltration trench. Though simulated recharge from historic, 4.5 and 8.5 RCP showed no statistically significant changes in recharge over time, runoff is predicted to increase significantly, indicating that current LID BMPs should be redesigned to store increased inflow expected from climate change. Recharge efficiency during heavy rainfall events such as El Nino can be improved by increasing the loading ratio of a BMP. Results of a one-at a time (OAT) method sensitivity analysis showed that the hydraulic conductivity of the soil underlying a LID BMP has the most influence on recharge and suggested that location is critical for optimizing or minimizing recharge.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Gallagher, Cara Alyse
- Description:
- The occupation of an ecosystem by a new top predator could affect the stability of a food web. In San Francisco Bay (SF Bay), there is evidence for a multi-decadal disappearance of harbor porpoises {Phocoena phocoena) that spanned from the 1940’s to the early 2000’s. Understanding the energetic role of this predator in the food web, in addition to the conditions that allowed for occupation of the Bay, is crucial to shedding light on the possible impacts of this species and on the state of the ecosystem. Here two modelling approaches were used in order to assess the energetics of harbor porpoises in SF Bay. The first model presented was an equation-based, velocity-dependent energy budget of harbor porpoises. As harbor porpoises have been shown to reproduce on an annual calving cycle in some regions, the minimum cost of transport was found for each possible reproductive state (non-pregnant, non-lactating (NPL)=1.6 J k g 'W ; pregnant (P)=1.8 J k g 'W ; lactating (L)=3.1 J k g 'W 1; and pregnant and lactating (PL)=3.2 J k g 'W 1). The total daily costs, in terms of carbon uptake, were then estimated for a NPL porpoise and a PL porpoise (NPL=341.3 g; PL=756.4 g) and when compared using a one-way ANOVA test, the difference was significant (F=15,797, d /= l, p<0.001). The second model presented was an agent-based, ecophysiological model of porpoise foraging in central SF Bay. Energy expenditure was estimated using the swimming speed and the reproductive status of the porpoise agent and energy intake was dependent on foraging success, measured by the capture of anchovy agents in SF Bay. The total daily energetic costs of each reproductive state were found (NPL=8060.4 kJ; P=8776.3 kJ; L= 19269.6 kJ; and PL=19985.6 kJ). The marginal value theorem was used as a test of habitat optimum for harbor porpoises in SF Bay and using the model, it was found that foraging success was more dependent on the number of anchovy schools than the number of anchovies per school. The number of schools that allowed for foraging levels higher than found for wild porpoises for a population of 50 animals foraging inside SF Bay was 41 schools of anchovies. When estimating total energy sequestration by differing numbers of harbor porpoises foraging in SF Bay, competition emerged as a factor influencing foraging success. For 33 and 165 porpoises foraging in SF Bay, total carbon consumed during a 6-hour foraging bout was estimated at 17,111.5 ±1 096.0 and 74,273.5 ± 8171.4 grams of carbon, respectively. As an upper-tropic level species that has recently increased its spatial habitat, it is crucial to investigate the possible impacts of harbor porpoises in San Francisco Bay and these two modelling platforms have allowed for the thorough investigation of the questions proposed.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Manugian, Suzanne Camille
- Description:
- Pacific harbor seals (Phoca vitulina) within San Francisco Bay (SFB) have been described as stable compared with those in coastal northern California, like Tomales Bay (TB). Historical data (1970s - early 2000s) indicated an overall increase in adults and pup production. Recent data, however, revealed SFB and TB adult counts decreased while pup production increased. There is a paucity of life history data, such as survival rates, for northern California harbor seals. For 32 radio-tagged adult females, survival was 98.2% over 20 months 2011 through 2013, constant between bays and influenced by an individual’s axillary girth. Movement between bays supported this survival estimate. Lower resight probability in SFB compared with TB was likely due to multiple factors including sampling bias and haulout quality and area. These are the first adult/subadult survival and resight estimates for harbor seals in California, and suggest the stable SFB population is due to some reason other than poor adult female survival (e.g. emigration, poor pup survival).
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Chen, Jei-Ying
- Description:
- Postulated by Bayer (1955), the calcaxonian gorgonians may have close affinity to the pennatulaceans based on the resemblance of axial structure observed under polarized light microscopy. To further confirm the phylogenetic relationship between the two groups of octocorals, this study applied both polarized light microscopy and scanning electron microscopy to examine the extinction patterns of sclerites and axial skeletons in macro- to ultrastructural scale from the total of thirteen genera of calcaxonian octocorals and nineteen genera of sea pens. The results show significant similarities between calcaxonian gorgonians and sea pens on scleritic crystal orientations and organization of axial structures, together with the inferred phylogeny of forty-six taxa (seventeen gorgonians and twenty-nine pennatulaceans) using ND2 mtDNA sequence data, all strongly support Bayer’s postulation and reveal the sister group relationship between the Ellisellid calcaxonian gorgonians and the pennatulaceans. The X-ray microanalysis was also carried out for inter-family comparison of the axial chemical composition between calcaxonian gorgonians and sea pens for the implication of phylogeny, however the results shown that the axial chemical composition is largely determined by ambient seawater instead of biologically intrinsic differences, therefore it did not provide much resolution to gain plausible phylogenetic implication in consequence.
- Resource Type:
- Thesis
- Campus Tesim:
- San Francisco
- Department:
- Biology
- Creator:
- Scheidt, Thomas W
- Description:
- This environment could explain the rapid proliferation of the bacteria. It wi also considered probable that the destruction, per se, of bronchiolar epithelium by the virus did not contribute significantly to the synergism.
- Resource Type:
- Thesis
- Identifier:
- ocm62263154
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Varoujean, Daniel H.
- Description:
- The genus Echlnorhlnus Blainville contains two species, the brambleshark E, brucus. first described by Bonnatere (1788), and the prickly shark E, cookel. first described by Pietschmann (1928), Due to the considered a variant of E. brucus (Fowler, 1941), Garrick (1960), however, redescribed E, cookei and showed that it deserved recognition as a separate species. He found that, the distinction of E. cookel from E, brucus is definite and striking, at least between sub-adult specimens, but so far can be based only on the buckler-like dermal denticles. There appear to be no significant differences in proportional dimensions, in external morphology, or in details of the teeth. However, the differences in the denticles lie not only in their relative size as mentioned above, though this alone is sufficient, but also in the shape and sculpture of the denticle bases (entire-margined or nearly so, and with rather fine radial ridging in E. brucus. but with strongly indented margins and coarse ridges in E. cookel); the presence in E. brucus of compound denticles up to 35 mm long as a result of fusion of adjacent denticle bases, while such fused denticles are not a feature of E. cookei; and there is the tendency in E. brucus to retain noticeable-sized denticles on the underside of the snout and around the mouth even on large specimens, while in the type of E. cookei and in my specimen this area is virtually smooth, only a few minute denticles being present. Garrick also noted that many past records of E. brucus could have been records of E. cookel. for example, the account of an E. "brucus" given by Hubbs and Clark (1945). This specimen was subsequently found to be E. cookei.
- Resource Type:
- Thesis
- Identifier:
- ocm63681431
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Tinkle, David Paul
- Description:
- In the present study, laboratory demonstrations of susceptibility to infection of potential intermediate hosts are considered to provide only circumstantial evidence that these experimental hosts may also be natural intermediate hosts for tapeworms. Therefore, an important part of this work is devoted to comparing the susceptibility of various beetle species to laboratory infection and the occurrence of natural infections of H. microstomoides and H. citelli in these same beetles.
- Resource Type:
- Thesis
- Identifier:
- ocm62862389
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Wynn, Franklin E.
- Description:
- Models of muscle contraction were proposed as early as the third century B.C. by an Alexandrian physician, Erasistratus, who believed contraction was evoked by the passage of air into the muscle from surrounding blood vessels. Other historical investigators proposed equally supernatural explanations which involved the passage of "animal spirits" into the muscle. It was not until the mid-1800's that Kuhne successfully extracted a contractile protein which he called myosin. From these modest beginnings have evolved models for muscle contraction.
- Resource Type:
- Thesis
- Identifier:
- ocm64201257
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Field, Eugene Allen
- Resource Type:
- Thesis
- Identifier:
- ocm58524504
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Rosay, Bettina
- Description:
- Cyclic changes in the size of female accessory glands are described. The gland enlarges during ovarian development and gradually becomes smaller after oviposition. The results after surgical removal of the gland indicated that its function is not pertinent to development and fertilization of eggs, oviposition, or raft formation.
- Resource Type:
- Thesis
- Identifier:
- ocm62125653
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Nilmeier, Sara E.
- Description:
- The peptide hormone ghrelin has been shown to stimulate growth hormone (GH) release, appetite, and fat deposition in vertebrates. More recently, ghrelin has been shown to play a role in glucose metabolism in mammals. Ghrelin acts through the growth hormone secretagogue receptor (GHS-R). The GHS-R codes for two gene transcripts, GHS-R1a and GHS-R1b. In tilapia, two forms of ghrelin have been identified, ghrelin-C8 and ghrelin-C10. This study measured the effect of ghrelin on the hormonal regulators involved in glucose metabolism, appetite, and growth (GH/IGF-I axis) in the tilapia, Oreochromis mossambicus. Fish were injected with two doses of ghrelin-C8 and ghrelin-C10. Blood and tissue samples were collected at 2, 4, and 8 h post-injection. The low dose of ghrelin-C8 elevated blood glucose levels at 4 h post-injection. Both ghrelin-C8 and -C10 reduced plasma IGF-I levels and ghrelin-C10 elevated IGF-I mRNA levels in the liver. Ghrelin-C8 and -C10 elevated liver GHR2 mRNA levels, however GHR1 mRNA levels remained unaffected. In the brain, ghrelin-C8 and -C10 treatment elevated both GHS-R1a and GHS-R1b mRNA levels. NPY mRNA levels in the brain, a regulator of appetite, were elevated by ghrelin-C10. These data confirm ghrelin�s role in appetite and glucose metabolism and show that ghrelin up-regulates certain components of the GH/IGF-I axis in tilapia.
- Resource Type:
- Thesis
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Ryan, Lloyd C
- Description:
- The purpose of the study was two-fold: first, to identify and describe the air-borne Moniliales encountered in the Fresno area; and second, to determine their relative abundance. Several methods of collecting culturing and identification are described. Since the study extended only from September to April, all references to abundance are restricted to this period. The system of classification followed was patterned after Bessey (1950). All drawings were made with the aid of a camera lucida.
- Resource Type:
- Thesis
- Identifier:
- ocm62050238
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Seto, Chuck Foo
- Description:
- Ever since the discovery of 2,4-Dichlorophenoxyacetic acid (2,4-D) as an effective herbicide during World War II, extensive research effort has been directed to all aspects of this synthesized subs tame that behaves in some respects similar to plant auxin. First, attention was focused on the selective effect; and it became known that 2,4-D was a very effective killer of the broad-leaved plants while it did not affect the grasses and many other monocots in any way at certain concentrations. It also came to be known that three processes were involved in the herbicidal action of the suxi1u, the material entered the plant; it then was translocated throughout the plant; and toxic actions took place at the level of cellular metabolism (Machlis and Torrey, 1936). Many reports on the effects of 2,4—D on physiological and biochemical processes of plants can be found in the literature. Among them are those that Indicate the inhibitory effect on photosynthesis of plants (Wedding et al., 1954, Erickson et al., 1955), and those that show 2,4-D to be stimulatory to plant respiration (Overbeek et al., 1951; Wedding et al., 1954; Humphreys and Dagger, 1957). Mitochondria from soybeans sprayed with 2,4-D have been observed to swell accompanied by increases in rates of phosphorylation and oxidation (Key et al., 1961), Other reports indicate that 2,4-D stimulates cell proliferation (Steward, 1963), promotes carbohydrate depletion (Rasmuseen, 1947), Inhibits lipase activity (Bagen et al. 1949), Inhibits ascorbic acid oxidase (West and Henderson, 1950), and stimulates phosphatase activity (Overbeek et al., 1951). All these experimental reports represent an effort toward the elucidation of the mechanism with which 2,4-13 operates as a herbicide. How we may ask; How is the concentration of 2,4-D related to its herbicidal action? Is it the undis-sociated molecules, or the charged anions, that penetrate the cell membrane? Adequate answers to these questions will provide clues as to how 2,4-D in particular and auxin in general affect the physiological processes of plants.
- Resource Type:
- Thesis
- Identifier:
- ocm62589744
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Boolootian, Richard A
- Description:
- This study is necessary because it represents perhaps the last opportunity to examine Grinnell’s findings. Specimens were trapped and their localities mapped (see map, Fig. 1): then statistical methods were applied to various measurements such as tail length, hind foot length, red pelage color, bullae width, and skull length, in order to understand the systematic relationship among these subspecies.
- Resource Type:
- Thesis
- Identifier:
- ocm57029345
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Holeman, Jodi Jazell
- Description:
- During July _ September 2009, ground ultra low volume (ULV) applications of various registered mosquito adulticide formulations were evaluated in a field assay against both wild populations and an insecticide-susceptible laboratory colony of Culex pipiens sensu lato. Initial applications with piperonyl butoxide (PBO) synergized formulations of natural pyrethrins and selected synthetic pyrethroids indicated that the wild populations in question had varying degrees of resistance to these products. Laboratory bottle-bioassay testing confirmed these observations. Adult female surveillance using carbon dioxide baited CDC traps and Bermuda grass infusion gravid traps were also utilized to quantify population impacts of ground ULV applications. There was no significant difference in pre and post treatment collections made at sites throughout the treatment area. Surveillance collections further supported the assumption of resistance and a lack of measurable control. A combination of malathion (Fyfanon�) and natural pyrethrins, synergized at 10:1 with PBO (Evergreen�), had significant resistance-breaking properties. This study demonstrates the existence of significant pesticide resistance in wild Cx. pipiens s. l. populations in Fresno County, as well as the impact of barriers in urban and rural environments on drift, effective swath and reduced efficacy of ground ULV applications.
- Resource Type:
- Thesis
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Herrgesell, Perry L
- Description:
- Eleven years ago, the California State Legislature authorized the construction of a peripheral drainage canal for the San Joaquin Valley. Observations suggest that drainage water, which ultimately will come from the entire valley, may have adverse effects on water quality in San Francisco Bay and the surrounding delta, into which it will drain. The valley is a vast agricultural area, so the proposed "master drain" would discharge predominantly agricultural waste water into the bay. This has stimulated agricultural waste water studies, but comprehensive data on conditions in agricultural drainage canals are lacking. Most of the published and unpublished information on agricultural runoff that is available was produced by state and federal agencies. There are marked differences in the quality of irrigation water applied to the land and the quality of the residual water draining from the land (Sylvester and Seabloom, 1963). Studies describing changes in physical and chemical factors during irrigation are numerous (Knight, 1969; U. S. Department of Agriculture, 1969; Williams and Wadleigh, 1968; Bullard, 1966; Sylvester and Seabloom, 1963; Reid, 1961; Flippin, 1945). Factors mentioned most frequently in runoff situations are sediment, temperature, oxygen content, inorganic plant nutrients (such as nitrogen and phosphorus), and pesticides (California Department of Water Resources, 1968; Mackenthun and Ingram, 1967). Other sources concerning physical and biotic runoff relationships will be listed in the pertinent sections of the following text. Biotic studies concerning agricultural drainage canals are less numerous. The U. S. Public Health Service (1960) and Vinyard (unpublished) have studied the biota of drainage water, but their work dealt mostly with phytoplankton ecology. Aside from general references on pollution and its effect on organisms, data concerning the total biota, and its possible regulation by waste water conditions, are lacking. Recognizing the need for more information on agricultural runoff, I undertook a study of Main Drain Canal, which carries agricultural drainage. The purpose of the study was twofold: 1) to document the spatial and temporal biotic changes in a drainage canal, and 2) to demonstrate, when possible, whether or not these changes were due to irrigation effluents. The remainder of this paper deals with this analysis of Main Drain Canal and its implications for future drainage projects.
- Resource Type:
- Thesis
- Identifier:
- ocm58724554
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Kannan, Shravan Kumar
- Description:
- Mammalian cells produce different types of cell protrusions (CPs)—like filopodia, lamellipodia, invadopdia, and tunneling nanotubes—that have been implicated in numerous important biological functions, such as cell migration, cell-cell communication, cancer-cell invasion, and the intercellular spread of pathogens. Yet, the proteomes of such structures are not well characterized due to the inability to specifically isolate individual types of protrusions for downstream proteomic analysis. In this study we present a novel method using laser capture microdissection (LCM) in conjunction with microproteomics to specifically isolate such structures and define their proteomes. We successfully isolated TNTs and other cellular projections by LCM using glutaraldehyde (GLU) and dithiobispropionimidate (DTBP) fixation. Although we found the TNTs to be more stable with GLU fixation than the DTBP fixation, the number of protein hits from the lysates of cells fixed with DTBP fixation was found to be significantly higher than GLU fixation. Mass spectrometry (MS) analysis of cells fixed with GLU showed that, using LCM, we were able to isolate 113 proteins specific to TNTs. We found several proteins from cytoskeleton, filopodia, vesicles and mitochondria that have implications in TNT functionality. Thus we demonstrate that LCM/MS system is an innovative combination to isolate proteins specific to such small structures.
- Resource Type:
- Thesis
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Hale, Julie Anne
- Description:
- There is considerable evidence linking cumulative and sustained exposure to estrogens as a key promoter of breast tumor proliferation. Chemicals with estrogenic activity can bind to the estrogen receptor (ER) to affect downstream signaling of estrogen-responsive genes. Organochlorines are a class of chemical pesticides that can act as xenoestrogens to disrupt normal endocrine function. Methoxychlor and Toxaphene are two organochlorine pesticides that have been widely used in California. Statistical data suggest that past use of these pesticides shows a positive association with age-adjusted incidence of breast cancer in Hispanic women in Central California counties. This study investigates the link between these pesticides and molecular mechanisms of breast cancer by examining the hypothesis that Methoxychlor and Toxaphene exposure influence differential protein expression in a cell culture model utilizing cell lines that are either ER positive (ER+) or ER negative (ER-).
- Resource Type:
- Thesis
- Campus Tesim:
- Fresno
- Department:
- Biology
- Creator:
- Avery, Nolan
- Description:
- Suction feeding is one of the primary methods aquatic organisms use to capture prey. Suction feeding in aquatic organisms is well understood in adult fish, but poorly understood in fry. Hydrodynamic theory predicts that suction feeding is not effective in smaller organisms, where a minimum gape diameter is required for a successful suction event. This minimum gape diameter is the lower limit where suction feeding is still viable. Studies have shown that fish larvae have low capture success, but there are few data on similar sized plant suction feeders. Aquatic bladderwort species (Utricularia gibba, U. vulgaris) capture microscopic prey using suction feeding in underwater bladder-shaped traps at dimensions typically less than 1 mm. This project examines how bladderworts suction feed by quantifying the capture success, trap morphology and prey morphology to address the following questions: (1) do smaller traps catch smaller and fewer prey; (2) do smaller traps have a relatively larger gape (characterized as gape diameter relative to total trap size) than larger traps to limit the negative effects of being small on capture success. Bladderwort traps capture prey relative to gape diameter, with smaller bladders catching smaller-sized and fewer prey overall compared to larger bladders. Smaller bladderwort traps display isometric allometry, with smaller traps having relatively same gape length as larger traps.
- Resource Type:
- Thesis
- Campus Tesim:
- Fresno
- Department:
- Biology