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- 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