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- Creator:
- Lona, Irene
- Description:
- Walnut (Juglans) and wingnut (Pterocarya) trees have been declining in response to Thousand Cankers Disease (TCD). The TCD pathogen, Geosmithia morbida, is vectored by a phloeophagous bark beetle, the walnut twig beetle (Pityophthorus juglandis Blackman). To understand P. juglandis host selection, the following were investigated at two orchards in Northern California: 1) The susceptibility of two walnut species (Juglans californica and J . major) native to the western USA by comparing P. juglandis flight and landing responses to unbaited branch sections and 2) The relationship between English walnut (Juglans regia) tree health, represented by several levels of plant water stress, and P. juglandis colonization success. P. juglandis preferred to land on J. californica over J. major. With J. regia, there was no significant difference in P. juglandis activity between branches from trees in high water stress and low water stress groups (both baited with P. juglandis aggregation pheromone). No P. juglandis colonization activity was observed in unbaited branches from the negative control group (unbaited). Activity by P. juglandis was found primarily on 4 cm diameter branches. Other invasive bark and ambrosia beetles such as Hypothenemus eruditus and Xyleborinus saxeseni; and an invasive longhorned beetle, Nathrius brevipennis preferred to land on J. major over J. californica. Collections of H. eruditus and an invasive ambrosia beetle, Xyleborus affinis, in Butte County reflect the northernmost records of these species in California. No significant relationships were found in J. regia between water stress and activity by N. brevipennis and a parasitoid Gildoria sp; however, activity by N. brevipennis and Gildoria sp. was found primarily on secondary 1 cm diameter branches (twigs). In conjunction with this study, significant flight responses of N. brevipennis and X. saxeseni to ethanol were recorded in a J. regia orchard. Overall, this study demonstrated that volatile cues from Juglans may influence host selection by P. juglandis and associated insects.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Cochran, Holly Jean
- Description:
- My study aimed to quantify nesting habitat availability for cavity-nesting birds in restored and remnant patches of riparian forest on the Sacramento River. I explored three hypotheses: 1) that older restored forests will attract more cavity-nesting birds in comparison to younger restored forests because more mature habitat features are available; 2) that the vegetation structure between remnant forests, younger restored forests, and older restored forests are distinct, owing to temporal developmental processes that differ in each subset of forest; and, 3) that the vegetation structure within each forest type affects the presence of secondary cavity- nesting birds and primary cavity-nesting birds differently because of their distinct nesting requirements. I performed vegetation surveys, cavity surveys, and bird point-count surveys to describe habitat structure and estimate bird density, cavity availability, and suitable cavity- building substrate (potential nesting substrate) in the form of snags and broken tree limbs. Surveys were conducted in each of six different aged riparian forests (remnant and 13- to 21- year old restored) in Glenn and Tehama Counties in Northern California. In restored forests, I determined that restoration sites between the ages of 13- and 21- years old (time since initial planting) do not have significantly different habitat availability for cavity-nesting birds. Features included in this analysis were potential nesting substrate and cavity density (p=0.176 and p=0.121 respectively). When comparing remnant forests with restored forests, the potential nesting substrate and cavity density were significantly different (p=0.005 and 0.003, respectively). A multivariate analysis of the vegetation structure comparing restoration forests and remnant forests showed there are trends in vegetation features that can differentiate remnant forests and 13-year old restored forests. Through a mixed model linear regression, I determined that primary cavity nesters were more sensitive to specific habitat features than secondary cavity nesters. Tree density, snag density, and forest age were important for both groups, but secondary cavity nesters were also sensitive to the number of different tree species present and the amount of potential nesting substrate available. It may be inferred that secondary cavity nesters are more likely to be observed in remnant forests, since these forests have a wider variety of tree species and far more potential nesting substrate available than restored forests.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Bianchini, Elizabeth A.
- Description:
- Recent human infections with avian influenza viruses (AIV) highlight the need for continued surveillance of AIV in waterfowl. California’s Sacramento Valley is an important wintering site for waterfowl from which avian influenza viruses may be isolated. To determine host correlates of AIV infection and better understand the risk posed by AIV circulating in California, we collected cloacal swabs from 2,066 hunter-killed ducks across four hunting seasons at different locations in the Sacramento Valley. We determined that Northern shovelers have a higher AIV infection rate than other waterfowl species from which we commonly sampled and that the relationship between sex and AIV infection is a poorly understood factor that needs to be investigated on a species level. Additionally, we detected three viruses of the subtype H7N3. Whole genome sequencing of these viruses revealed genetic markers that have been correlated with increased pathogenesis in mammals. All three H7N3 viruses were capable of replication in mammalian cells at levels similar to a human seasonal H1N1 virus. Additionally, at least one of these H7N3 viruses is able to cause disease in mice similarly to a human seasonal H1N1 virus. These results provide insights into host factors of AIV susceptibility that can help guide future surveillance efforts as well as evidence of novel subtype H7N3 with mammalian adaptations that could pose a risk to public health and therefore should be monitored closely.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Stompe, Dylan K.
- Description:
- This study examined the diets of two predatory fish species, the native Sacramento Pikeminnow (Ptychocheilus grandis) and the introduced Striped Bass (Morone saxitilis), within the Sacramento River, CA, USA. Sampling occurred between March and December 2017 and was comprised of two primary components. The northern survey component was done via hook and line sampling, on a 35 kilometer reach near Chico, CA, and the southern survey component was done via seven fyke traps located near Sacramento, CA. Stomach contents were collected via non-lethal gastric lavage and were later processed using visual, gravimetric, and genetic techniques. Relative abundance of Sacramento Pikeminnow was significantly higher at man-made structure sites and Striped Bass relative abundance was positively correlated with water temperature. Diets of Sacramento Pikeminnow and Striped Bass captured near Chico, CA were not different, and Striped Bass captured near Chico, CA had significantly different diets to those captured near Sacramento, CA as determined by PERMANOVA analysis.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Rich, Shannon
- Description:
- Flammulated owls (Psiloscops flammeolus) are small nocturnal owls that are thought to migrate long distances every year from summer breeding grounds in the western United States and southern Canada to winter habitat in Mexico. They are cryptic and elusive cavity nesters and little is known about their migratory patterns or winter habitat. They have been named a Species of Concern by the U.S Fish and Wildlife Service be cause of potential habitat destruction. The goal of this research was to track the movements of these owls during their migratory season and over the winter using light-level geolocators, which records ambient light levels that correspond to sunrise and sunset times to determine specific bird locations. During 2012-2013, 60 geolocators were attached to male and female flammulated owls in breeding sites in Washington, Colorado, Utah, and California. In 2013-2014, 16 of these geolocators were recovered from birds in California, Utah, and Colorado. The migratory routes of these birds were analyzed using GIS and further analysis was performed to determine habitat characteristics of their winter home ranges in Mexico. Consistencies in migratory routes and wintering areas between owls from different breeding locations contributed to greater knowledge about the migratory ecology of this owl. Novel results for the migratory behavior of a mated pair from California who used comparable routes and wintering areas before returning to breed together the following year, as well as a female owl from Utah with multiple years of data that showed her using a very similar route and wintering area between years also provided new information that was not yet confirmed about female flammulated owls. This geolocator analysis along with additional research on habitat preferences of flammulated owls in California is the first step in assessing the current status of this species with the goal of a broader western U.S. effort in the future.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Pukini, W. Cory
- Description:
- Kelp forest ecosystems are sensitive to changing global environmental conditions and unsustainable fishing practices (Tegner and Dayton 2000). Natural resource managers have implemented marine protected areas (MPAs) to mitigate ecosystem collapse and conserve fisheries stocks around the globe (Castilla and Moreno 1982). In California, MPAs have been primarily established as a way to mitigate unsustainable fishing practices of the past, while insuring a future for marine resources (Airamé et al. 2003). The establishment and implementation of MPAs has proven an effective conservation tool, but further research is needed to better understand the habitat selection process (Young et al. 2010). This study examined nearshore benthic habitat associations between select species in kelp forest ecosystems of the northern Channel Islands within the Channel Islands National Park, with the intended purpose of identifying specific habitat characteristics for a suite of selected species. Important habitat associations help inform continued and adaptive management efforts and guide the establishment of new MPAs in kelp forest ecosystems. Mapping efforts to help characterize habitat were focused on long-term biological monitoring sites that are part of the Channel Islands National Park Kelp Forest Management (KFM) program (Kushner et al. 2018). Side scan and multibeam sonar technologies were used to map previously uncharted areas of the rocky reef and seafloor of nearshore environments of Anacapa and Santa Cruz Islands at a fine scale resolution of 10-15 cm and data was summarized to characterize habitat at the two-meter^2 and 10m^2 (two and ten-meter) scales. Physical habitat parameters of interest included bathymetry (average depth from sea surface), rugosity (a ratio that measures the topographic complexity of the seafloor), and slope (gradient or steepness of elevation change within a defined area). Eleven sites were sampled for physical variables and species encounters recorded between 2005 and 2013 provided the data to analyze associations between the physical setting and habitat use. Five of the eleven sampled areas in my study were found within MPAs including State Marine Reserves (SMRs) and State Marine Conservation Areas (SMCAs). Six of the eleven sites were located on Santa Cruz Island and five were on Anacapa Island. Selection of target species was derived from a preexisting list of monitored kelp forest inhabitants. Target species were selected with the help of Channel Islands National Park KFM biologists to represent the broadest spectrum of benthic microhabitat users in the kelp forest community. The eight species selected for my study at the two-meter scale have well documented ecological roles within the Channel Island National Park. Two of these species, giant kelp and giant spined sea star, were also observed and analyzed at a larger ten-meter scale. A backwards eliminating stepwise regression (BESR) model for habitat characterization between seafloor statistics (bathymetry, rugosity, and slope) and select kelp forest species was implemented to identify habitat associ ations. In addition, protection status and island were included in the analysis. Results showed that species indicative of healthy kelp forest ecosystems were found in greater numbers inside the MPA boundaries, while the inverse was true for species that represent disturbed systems. In addition, the ten-meter sampling scale was found to be a more accurate predictor of species encounters for the two target species. My study also identified fine scale habitat preference varied among several target species (i.e., purple sea urchin encounters were highly dependent on bathymetry). The results of this research are important to natural resource managers and are intended to help inform decision makers responsible for kelp forest ecosystems and the establishment and implementation of MPAs.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Hanson, Tina
- Description:
- 95% of the cases of chronic myeloid leukemia (CML) are caused by a chromosomal translocation linking the breakpoint cluster region (BCR) gene to the Abelson murine leukemia viral oncogene-1 (ABL1). Downstream of BCR-ABL is growth receptor bound protein-2 (GRB2), which binds to BCR-ABL via its src-homology-2 (SH2) domain. This binding constitutively activates growth pathways while down regulating apoptosis leading to an over proliferation of immature and dysfunctional myeloid cells. Four novel SH2 antagonists were developed with three of the four showing a significant reduction in proliferation of a BCR-ABL+ leukemia cell line. To elucidate the mechanism of action, an enzyme-linked immunosorbent assay (ELISA), a surface plasmon resonance (SPR) assay, and a cellulose nitrate (CN) filter assay were performed. These assays indicated that one of the three effective molecules, NHD2-15, antagonized the SH2 domain of GRB2 with a Kd value of 119 ± 2 μM, bringing us closer to developing a new treatment for CML.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Belmonte, Rebecca
- Description:
- Zebrafish (Danio rerio) is an excellent model organism for studying embryonic vertebrate development due to their conserved genome with humans, external development, and ease of observation under the microscope. The gene SON is found on the twenty-first chromosome of humans and is often overexpressed in patients with leukemias, particularly acute megakaryoblastic leukemia. Previously, we showed that mutations in the mRNA splicing co-factor gene SON cause malformations in human and zebrafish spines and brains. We performed these studies by knocking down the expression of the zebrafish homolog of SON in zebrafish at the single-cell developmental stage with specific morpholinos (MOs). In addition to the brain and spinal malformations we also observed abnormal blood cell levels with son knockdown. We then investigated how blood production was altered when levels of son were lowered. Decreased levels of SON resulted in impaired blood flow and lower amounts of red blood cells when visualized with hbaa:GFP transgenic fish. There was also a reduction in thrombocytes seen with cd41:GFP fish and verified with flow cytometry, and myeloid cells, as seen with mpx:GFP fish. We also saw a significant decrease in the quantity of T cells, visualized with lck:GFP fish. However, when we plated the hematopoietic stem and progenitor cells (HSPCs) from zebrafish with reduced levels of son, we saw no difference in colony forming capability. Further investigation of son and its effect on blood development should establish how misexpression of this gene negatively impacts human health.
- Resource Type:
- Graduate project
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Schleiger, Rachel
- Description:
- Meadows in the Sierra Nevada are characterized as wet, heterogeneous habitats with diverse plant communities, often being biodiversity hot spots. These meadows not only provide resources for wildlife but also filter and store snowmelt, providing sustained water sources for both wildlife and Californians. Recognition of meadow significance combined with persistent human disturbance motivates restoration efforts to improve hydrologic connections and biotic health within these meadows. This research is evaluating the trajectory of a restored montane meadow in Sierra Nevada, California. Comparing soil moisture, plant community composition, and exotic species extent of this restored meadow to disturbed and less disturbed meadows provided context for this assessment. Results indicated soil moisture was highest in the restored meadow followed by the disturbed then less-disturbed sites. After further investigation, the less-disturbed sites were found to have significantly less total annual precipitation which greatly impacted overall plant composition. As such, the less-disturbed sites were deemed inappropriate for comparison and the restored sites trajectory assessment was thus more focused on comparisons to the disturbed sites. The restored site was found to have lower moisture heterogeneity but higher hydrologic connectivity compared to the disturbed sites, traits more definitive of wet montane meadows. Species richness, status, plant type, and wetland classifications at the restored site were also more definitive of wet montane meadows compared to the disturbed sites. However, the restored site did have concerning areas of exotic species, especially in drier soils. Currently, rewetting techniques applied appear to be successful. Although, it is clear that adaptive management is needed to address issues of concern and help keep a continued positive ecological trajectory at this restored site, especially when heading into an uncertain future.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Buchholtz, Clara
- Description:
- Tamalia coweni is unusual among gall-forming aphids in that it will often share its gall space with other members of its species, even as this has been shown to lower its fitness. Previous research utilizing manipulated densities of T. coweni on inflorescences of its host plant has indicated that population density is a strong predictor of gall-sharing rates, while kinship appears to be less predictive. The current study expands on this finding by investigating gall-sharing rates under natural population density conditions in leaf galls. In addition, it does an initial examination of whether gall-sharing correlates with preferential or optimal galling sites, and in line with the preference-performance aspect of the Plant Vigor Hypothesis (PVH). Cofounding rates were found to strongly align with those from studies using artificial aphid densities, and population density was shown to be a strong predictor of cofounding rates in a natural setting. Although strong patterns showing basal leaf positions were more frequently chosen as galling sites than distal ones, there was no evidence these sites were more likely to be cofounded. Over all, gall and cofounding distributions did not show a strong alignment with the PVH. Instead, other factors, notably timing, may offer more promising explanations, and offer a rich set of questions for further examination.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Ocken, Michelle A.
- Description:
- The western burrowing owl (Athene cunicularia hypugaea) is a small fossorial owl found in the western United States, Canada and northern Mexico (Shuford and Gardali 2008). Populations in northern California have suffered recent declines, and a better understanding of their habitat requirements is needed in order to make better management decisions (Wellicome and Holroyd 2001). For this study I described internal and external characteristics found in owl burrow sites in the northern Sacramento Valley, California in the fall and winter months. I measured and recorded a variety of characteristics at 17 locations confirmed to be utilized by burrowing owls. I used iButton® data loggers to record internal humidity and temperature throughout the day for multiple years. I calculated means by season and semidiurnal period and compared them to ambient means. The physical attributes I recorded included burrow entrance direction, burrow type, distance to water, type of water source, whether the area was grazed, and whether burrowing mammals were present. Using a 1-m2 quadrat, I recorded vegetation height and density three meters in front of, behind and to each side of each burrow entrance and calculated the means for each site. I also utilized student research assistants to conduct visual occupancy surveys to determine the season(s) of usage for each burrow. Observations were summarized for burrow types. All sites were on or near land grazed by cattle in the winter. Natural burrows were all located in cut-banks of seasonal drainages. Seventy-one percent of all burrows were located within 6.55 m of water in the winter. Natural burrow internal temperature means were consistently higher in the mornings and lower in the evenings than ambient conditions for every season, except for winter, which was slightly higher. Artificial burrows and rock piles displayed a similar pattern but were consistent across seasons. Culvert temperature means were higher than ambient means in all seasons and semidiurnal periods except for spring which showed lower internal means than the ambient means. The greatest difference between internal and ambient temperature means was 10.35° C (SD=2.83) for artificial burrows (n=676). Internal relative humidity [rH] means tended to be higher than ambient means for all natural and culvert sites. For artificial burrows, internal rH means were lower in the A.M. and higher in the P.M. than ambient means for every season. Internal humidity means for rock pile burrows were higher than ambient means in the P.M. The greatest difference between internal and ambient relative humidity means was 55.17% (SD=26.15) for natural burrows (n=763).
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Silver, Courtney S.
- Description:
- Vocalizations are the main form of communication between anurans, and each species can have an array of calls that can range from simple to complex. Local dialects from different populations of the same species can inhibit intraspecific communication, especially when females prefer a specific range of spectral and temporal properties in their mates’ calls. Vocal sacs are anatomical features used for communication in anurans and their structure and size are variable among anuran species. Rana boylii, a candidate species under the California Endangered Species Act and the focus of this study, primarily call underwater using small, paired subgular vocal sacs. Most studies of frog vocalizations have focused on aerial calls, partly due to the ease of recording vocalizations above water. Consequently, characterization of R. boylii’s call spectrum, as with other taxa that vocalize under water, has proven challenging. One previous study distinguished five R. boylii calls, but did not characterize variation among populations. This study examined variation in spectral (dominant frequency and high frequency) and temporal properties (call duration, pulse number, pulse rate, pulse duration, note number, and note duration) of call types among three disjunct populations of R. boylii. Rana boylii had a substantial amount of variation among populations not only in the spectral and temporal properties of calls, but also in the call types they emit. Two novel call types were described: the chuckle and the warble. Two locations had call types with frequency ranges that peaked above 20 kHz (ultrasonic), which could be a direct effect of the distinct environmental conditions at these sites. Rana boylii’s diverse array of calls showed previously undocumented significant differences between populations. The results of this study highlight that different populations of the same species might not possess the same communication strategies.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Lawson, Gin
- Description:
- Early detection of invasive species and evaluation of their impact on native ecosystems is key to conservation efforts. The use of environmental DNA (eDNA) has emerged as a useful tool to complement traditional field surveys in studying both the range and the effect of invasive species. eDNA is genetic material released by an organism into the environment; eDNA extracted from environmental samples can be used to determine the location of a species and its distribution, or to identify prey items contained within fecal samples. In this study, I developed eDNA techniques to detect an invasive turtle species, the red-eared slider (Trachemys scripta) in water samples collected under both laboratory and field conditions and to detect specific prey items in fecal samples collected from Trachemys scripta in the laboratory. Turtle detection used qPCR primers designed to target the D-loop region of mitochondria. eDNA in water samples was concentrated onto a cellulose nitrate filter, and extracted DNA was amplified using qPCR. Water samples taken from laboratory aquaria and from a wastewater treatment facility in Chico produced two positive detections. Water samples from another site not known to house turtles, the Sacramento Zoo, produced a weak positive detection. I also detected Danio rerio in fecal samples collected from Trachemys scripta. Zebrafish detection used qPCR primers designed to target the D-loop region of mitochondria. After adding Danio rerio to food pellets in Trachemys scripta‘s diet, I used a PCI precipitation method to extract eDNA from feces and was able to positively identify Danio rerio in fecal samples. For dietary analysis, eDNA provides ecologists with a powerful tool for identifying food items in feces. Of 328 extant species of turtle, approximately 50% are listed as endangered, and many are threatened by invasive species. These techniques for the detection of invasive species and evaluation of their impact can contribute to global turtle conservation efforts.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
14. Characterization of isthmin-1 (ISM-1) in vertebrate hematopoietic proliferation and differentiation
- Creator:
- Berrun, Arturo C.
- Description:
- Hematopoiesis is a highly regulated biological process that begins with a singular adult stem cell called the hematopoietic stem cell (HSC). HSCs are responsible for generation of trillions of cells a day, yet the pathways that instruct an HSC to self-renew and differentiate into mature blood cells are not fully known. To understand these molecular pathways, we investigated novel genes expressed in hematopoietic-supportive cell lines. We sequenced the transcriptome of three stromal cell lines derived from developing and mature zebrafish and identified 100 highly expressed transcripts. For our studies, we focused on ism-1 due to its shared synteny with humans. To characterize ism-1, we performed loss-of-function experiments to identify if mature blood cell production was disrupted. Myeloid, erythroid and lymphoid lineages were visualized and scored with transgenic zebrafish expressing lineage-specific markers. ism-1 knockdown led to reduced proliferation of neutrophils, macrophages, erythrocytes, and T cells. Analysis of methylcellulose plating with ism-1 morphants also showed a reduction in total hematopoietic stem and progenitor cell (HSPC) proliferation. Overall, we identified that ism-1 is required for normal proliferation and differentiation of HSPCs and their downstream progeny in zebrafish hematopoiesis. Further investigation into ism-1 and its associated signaling pathways may lead to the discovery of novel drug therapies for blood-based diseases and help expand HSPCs in vitro.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Moran, Amy J.
- Description:
- Phosphite (Pt), a traditional fungicide and novel fertilizer alternative used for P sourcing in agricultural soils, offers a potential for the conservation of phosphate (Pi), an essential and non-renewable limited resource. This potential has relied on the ability of some soil bacterial species to oxidize Pt to Pi, as a P source. However, bacterial species lacking this ability may suffer detrimental effects by increased use of Pt in the environment. We set out to explore the physiological impact of P fertilizers on bacteria in rhizosphere soil and to elucidate possible broad outcomes of Pt application to agricultural soils. Bacterial populations from destructive greenhouse samples of rhizosphere soil under various P treatments were examined over 113 days. Pt-oxidizing bacteria were enriched in Pt-treated soil (changing from 18 to 39% of culturable bacteria) but were disadvantaged in Pi-treated soil, decreasing 73.6% (changing from 30 to 7% of culturable bacteria). In contrast, non-oxidizers increased 3.1-fold in Pt-treated soil, exhibiting survival in soil samples with low Pi but high levels of Pt. Pt-oxidizers were determined to grow differently in Pi relative to Pt, in pure culture. Three Pt-oxidizers (A. wautersii, P. stutzeri, and P. putida) exhibited 4.6, 1.47, 1.56-fold shorter generation times in 2.0 mM Pi compared to 2.0 mM Pt indicating that although these bacteria can oxidize Pt, Pi as a P source results in faster growth. In Pt, A. wautersii and P. putida final cell mass decreased 43.9% and 22.1% (respectively), compared to growth in Pi, further supporting the benefit of Pi over Pt as a P source in these bacteria. In contrast, P. stutzeri showed a 15.3% increase in final cell mass in Pt compared to Pi, suggesting that Pt may be more useful as a P source for this organism. To check for detrimental effects of high levels of Pi on Pt-oxidizers which did poorly in the Pi-treated soil compared to non-oxidizers, we compared generation times and net final cell mass of three Pt-oxidizers (P. putida, S. melitoti, and Methylobacterium), to those of three non-oxidizers (P 6B, Flavobacterium, P. oleovorans subsp. lubricantis), while growing in high Pi (1.6 mM). The (g) for the Pt-oxidizers ranged from 7.74 – 13.51 hours, while the (g) for the non-oxidizer group ranged from 5.24 – 6.98 hours. Although the growth rates of the Pt-oxidizers were slower in high Pi compared to non-oxidizers, showing detriment to the oxidizers, the Pt-oxidizers reached a higher overall increase in cell mass based on a greater max increase in A values (0.60 – 0.74 A) in high Pi compared to that observed for the non-oxidizers (0.51 – 0.54 A). Both (g) and cell mass show unique growth differences linked to the bacteria’s Pt-oxidation status. Growing the same non-oxidizers in low Pi (0.2 mM), we explored an ability to tolerate Pi-scarcity as a means for non-oxidizer increases in the Pt-treated soil where only low Pi levels were present. In low Pi, non-oxidizers grew slower ((g)= 6.68 - 11.60 hrs) compared to in high Pi ((g)= 5.24 - 6.98 hrs). Net increase of cell mass was the same in two of the organisms but was limiting for Flavobacterium (low, 0.40 +/-0.010 A, high, 0.54 +/- 0.015 A). LMB stained Flavobacterium cells showed metachromatic granules after growth on LBA, elucidating storage, a possible means of non-oxidizer survival in Pt-treated soil. Two Pt-oxidizers, Methylobacterium and Acidovorax, showed metachromatic granules after growth on LBA and Pt solid media. Also, we observed at least 100 uM (5.35% of original Pt) released Pi during growth of Pt-oxidizers (Methylobacterium, S. melitoti, and P. putida) in liquid media containing Pt as the sole P source. P. putida showed Pi in media after one day, supporting Pt oxidation followed by Pi secretion by cells instead of cell death as Pi release mechanism. Minimum inhibitory concentrations of Pt were attempted for both non-oxidizers and Pt-oxidizers. pH was shown as the agent of inhibition in all but one organism. While Pt-oxidizer, P. putida, was less sensitive to lethality, P. oleovorans subsp. lubricantis, a non-oxidizer, was inhibited at 50% lower (12.5 mM MIC, 25 mM MBC) Pt concentration compared to all the other studied organisms and pH control confirmed Pt as the probable inhibitory agent. Furthermore, an immediate arrest in growth occurred upon addition of Pt (at the MIC) to mid-exponential phase cultures of P. oleovorans subsp. lubricantis growing on Pi, suggesting competition between Pt and Pi at essential binding sites for transport or metabolism. A. wautersii exhibited a diauxie effect when transferred from a Pi pre-growth to the Pt growth media in the prior growth assay showing no immediate interruption of growth by the introduction of Pt. From these studies, it is clear that both Pi and Pt treatments affect soil bacterial composition and physiology thus their application to the environment merits further investigation.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Diaz, Pablo Emiliano
- Description:
- Diabetes is a disease in which patients exhibit deficiencies in their ability to secrete or respond to insulin and is affecting both national and worldwide populations. There are two types of diabetes, type I and type II. In type II diabetes patients, tissues become insulin resistant, requiring pancreatic β-cells to produce more insulin. MicroRNAs (miRNAs) are small 21-23 nucleotide non-coding RNAs that target the 3’ untranslated region (UTR) of gene transcripts, inhibiting their expression. One miRNA, miR-375, appears in diabetic’s serum more than non-diabetic patients. In diabetic patients with elevated miR-375, β-cell numbers were reduced while pancreatic α-cells increased. In this thesis, I focus on the effects that miR-375 has on β-cell and α-cell proliferation. When inhibiting miR-375 I discovered that α-cells in culture proliferated about 20% less, as one might see in diabetics. Conversely, β-cells in culture proliferated about 20% more, again, as one might see in diabetics. I also focus on target genes of the miR-375: Rasd1 and Pdk1. Rasd1 is a negative regulator of cell proliferation in G coupled protein receptor signaling. Pdk1 is involved in the PI3/Akt pathway for promoting cell proliferation. I predicted that the negative regulator Rasd1 would be less abundant in α-cells compared to β-cells, and in fact this is what I discovered. Though inconclusive, knock down of miR-375 suggests Rasd1 is targeted in α-cells but not in β-cells. The results suggest that miR-375 is important for cell proliferation within α-cells but is inhibitory to β-cell.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Brooke, Charles
- Description:
- Iron-rich coastal wetlands may act as sinks for heavy metal contaminants such as mercury, but may also remobilize this biotoxin, as well as mediate chemical changes that affect bioavailablity and toxicity. Walker Marsh is an iron-rich intertidal salt marsh dominated by the halophyte Salicornia sp. that lies between a remediated mercury mine and the San Francisco Bay Delta. Salicornia sp. rhizospheres are an ideal in situ model for studying mercury cycling because radial oxygen loss at their roots causes cycling between oxic and anoxic states, supporting active iron cycling, which in turn can affect mercury mobility. To understand these relationships, Salicornia sp. rhizosphere sediment was compared to adjacent bulk sediment for mercury and iron concentrations, microbial community composition, and mercury resistance biomarker genes. Reactive iron concentrations in rhizosphere sediments were significantly greater than bulk sediments, but average total mercury concentrations were nearly 10% lower. Microbial 16S rRNA gene sequence community analysis showed significant difference between microbial communities of rhizosphere and bulk sediment, and the physiology of highly connected taxa were aerobic in rhizosphere sediment and anaerobic in bulk sediment. Not all rhizosphere samples were iron-rich, however, those that were showed a strong inverse correlation of mercury and iron concentrations (r = -0.80, p ≤ 0.02) suggesting iron cycling supports mercury mobility. To see if biotic iron cycling increased mercury bioavailability in rhizospheres, the mercury resistance gene merA using was quantified by qPCR. This showed a strong presence of mercury-resistant organisms in all samples collected, but showed no difference between iron-rich rhizospheres and bulk sediment. These observations suggest biotic iron cycling promotes mercury mobility but not bioavailability, which may be controlled by abiotic factors.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Smith, Jesse S.
- Description:
- Growth receptor bound protein-2 (GRB2) is an intracellular adapter protein responsible for linking receptor tyrosine kinases to downstream signaling proteins involved in cellular growth and differentiation. GRB2 is overexpressed in certain forms of human cancer, but no research has investigated GRB2 overexpression in chronic myeloid leukemia (CML), a disease involving the over-proliferation of myeloid cells. GRB2 is upstream of several cellular signaling pathways involved in the tyrosine kinase (TK) breakpoint cluster region-Abelson murine leukemia viral oncogene-1 (BCR-ABL). BCRABL is the transforming factor in 95% of CML cases. Here we demonstrate that GRB2 is overexpressed in the human CML cell line K562. Furthermore, we demonstrate that GRB2 overexpression increases proliferation of K562 cells. Additionally, we show that in vivo overexpression of GRB2 in zebrafish (Danio rerio) causes a 2-fold expansion of myeloid cells relative to mock-injected fish at 24 hours post fertilization (hpf). Finally, we demonstrate that targeted antagonism of GRB2’s SH2 binding region blocks proliferation of K562 cells. Our findings demonstrate the role of GRB2 overexpression in the proliferation of both normal and malignant myeloid cells. These findings highlight GRB2 overexpression as a potential biomarker for disease prevention, treatment optimization, and a target for new drug therapies to treat CML.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Cobb, Sean
- Description:
- Marine ciliates are important consumers of marine phytoplankton and represent a vital link in the food web. These unicellular grazers exhibit complex feeding behaviors and can be highly selective in their prey choices. Recently, Echevarria et al. (2016) showed that the marine tintinnid ciliate Favella sp. preferentially ingested natural dinoflagellate prey Heterocapsa triquetra over prey proxies (polystyrene beads), which appeared to be mediated by contact-based cues at the cytostome, the cell’s oral apparatus. In the present study, I investigated the nature of this contact-based recognition. I offered a variety of neoglycoprotein-coated 15 μm polystyrene microspheres alongside natural prey to Favella sp. and observed ingestion over 10-20 min. Although uncoated beads, or those coated with only the chemical linker or protein, were ingested at very low rates, beads coated with mannose and fructose were ingested as much as or more than natural prey. Beads coated with other sugars (fucose, galactose, methyl-mannopyranoside, lactose, mannitol, glucose, and sucrose) were ingested at intermediate rates. Furthermore, pre-incubation with 10-50 μM dissolved sugars could inhibit uptake of live prey in a specific manner. I examined the genome of Tetrahymena, a model ciliate, for potential sugar-binding cell surface proteins and found a number of potential candidates. These results suggest that ciliates may employ sugar-binding proteins as part of their mechanism for prey recognition, similar to many other organisms. Prey selection likely depends on other surface molecules such as proteins, and my results also suggest an explanation for the paradoxical observation that additions of dissolved small side-chain amino acids can inhibit feeding by Favella and other marine grazers.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Sekar, Keerthana
- Description:
- Macrophages are important for protection against infection with influenza viruses, they may also contribute to disease severity during H5N1 influenza virus infection through the virus induced alteration of important antiviral functions. One reason for these changes might be due to the ability of H5N1 viruses to replicate efficiently in the macrophage. Thus, we hypothesized that H5 virus infection alters the macrophage antiviral response and abrogates the IFN-γ response in RAW264.7 macrophages in a replication dependent manner. Infection of macrophage with live H5 virus decreased the phagocytic activity of IFN-γ activated RAW264.7 cells. Similarly, a reduction in nitric oxide (NO) production was also observed in IFN-γ activated macrophages infected with live H5 virus. Interestingly, infection with UV-inactivated H5 virus restored the phagocytic activity and NO production of IFN-γ activated macrophages. This shows that replication of H5 influenza virus is critical and is required to evade the macrophage antiviral response. H5 virus interferes with these macrophage functions by inhibiting IFN-γ signaling. While tyrosine phosphorylation of STAT1 was found to be intact in IFN-γ activated macrophages infected with H5 virus, expression of the IFN-γ stimulated gene IRF-1 was, blocked. Thus H5 influenza virus alters the antiviral response of macrophages and antagonize the IFN-γ response in macrophages in a replication dependent manner.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Patel, Raj
- Description:
- The characterization of bacterial metabolic pathways oxidizing phosphite have been characterized. However, bacterial oxidation of phosphite in the environment and its impact on the biogeochemistry has been largely ignored. In this study I attempted to answer 1) do excessive phosphite concentrations in soil significantly alter bacterial populations in soil; and 2) to what extent do these changes affect the overall bacterial community. To answer these questions we performed a soil competition assay, utilizing isogenic reporter bacteria (1 oxidizer and 1 non-oxidizer of phosphite) that were inoculated into an intact soil environment and recovered them from the same soil environment, and tracked their population decreases and increases over time in relation to different phosphorus treatments, including phosphite. We saw a significant change in our reporter bacteria in the phosphite treatment, and saw potential phosphate recycling occur via phosphite oxidizing bacteria utilizing phosphite as a sole phosphorus source and subsequently recycling the phosphate into the soil environment for phosphite nonoxidizers to use as a sole phosphorus source. Denaturing Gradient Gel Electrophoresis also displayed significant change in bacterial populations over time in the soil sample used for the soil competition assay. My results indicate that excessive dumping of phosphite into soil can lead to major bacterial population change, the exact effects from this change still need to be investigated by future researchers, which directly will contribute to the little known phosphorus cycle.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Woodruff, Glenn
- Description:
- Geographic variation research is an important topic of study, providing insight into trends of organismal origin, dispersal and evolution. By virtue of investigating these trends, this research also exposes areas where conservation efforts are needed to prevent the decline of vulnerable populations. The Sutter Buttes are an isolated patch of mountainous habitat in the middle of the Sacramento Valley. The buttes are separated from the Sierra Nevada by a minimum of nine miles to the east and from the Coast Range by ### miles to the west . The isolation of organisms in the Sutter Buttes has been proposed numerous times, and has also been the subject of research on several other projects looking at the relationship between populations of organisms in the Sutter Buttes and those in neighboring mountain ranges. This project utilizes liquid chromatography and mass spectrometry to separate and identify proteins in the venom of multiple individuals of northern Pacific rattlesnake (Crotalus oreganus oreganus) from two regions: the Sutter Buttes and the nearby Sierra Nevada. I provide a whole venom profile for this subspecies of western rattlesnake, and identify specific proteins found to be significantly different in abundance between populations of C. o. oreganus inhabiting the two regions. Significant differences in the relative abundance of three venom proteins provide evidence of restricted connectivity between the two neighboring regions, indicating geographic isolation for certain organisms inhabiting the Sutter Buttes. This has important implications for local adaptation and conservation of unique geographic variants in rattlesnakes.
- Resource Type:
- Graduate project
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Stanton, Alexander R.
- Description:
- Type 2 Diabetes (T2D) is a disease which affects a large percentage of the United States and the risk of developing T2D is increasing according to recent CDC estimates. T2D can be fatal, and although patients are living longer with it, the costs of caring for this disease are burdensome on both the patients and the health care system. Better understanding of the aberrations in cell signaling during T2D could lead to insights that may restore proper signaling. Investigations of genetic dysregulation in these patients has implicated the overexpression of the small regulatory RNA microRNA(miR)-375. These miRNA are post-transcriptional regulators that function through translational silencing, and two of the genes which miR-375 silences are involved in the pancreatic β-cell viability and insulin exocytosis (phosphoinositide-dependent kinase-1 and myotrophin respectively). The factors which govern the activation and repression of miR-375 are not well known, but it is downregulated by the cyclic adenosine monophosphate (cAMP)/ protein kinase A (PKA) pathway through an unknown mechanism. Since cAMP activates PKA, which then activates histone deacetylase (HDAC) 1 and 2 through phosphorylation, deacetylation is a possible mechanism for repression during this pathway. This study has identified two regions of the miR-375 upstream promoter which are deacetylated at histone H3 lysine 9/14 corresponding with decreased transcriptional initiation by cAMP induction. Observed cAMP-induced deacetylation does not cause overall changes in the chromatin structure of the miR-375 upstream promoter as analyzed by a micrococcal nuclease protection assay. The necessity of HDAC in this process is still unclear due to the broad effects of HDAC inhibition by HDAC inhibitor trichostatin A. While some regions of the promoter are deacetylated during cAMP signaling, the moderate changes it confers suggest that it may only be partially responsible for the repression of miR-375.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Yasuda, Catherine
- Description:
- Panamint alligator lizards (Elgaria panamintina) are a rare lizard species endemic to Inyo County, California. Little is known about the species and it is thought to be of conservation concern. Monitoring efforts for rare species requires conservative marking methods, however most marking methods for herpetofauna are invasive and potentially harmful. I evaluated a non-invasive method of individual identification using photographs of Elgaria head lepidosis in the freeware program Interactive Individual Identification System. Two hundred and thirty nine specimens from four species of alligator lizards were evaluated with a method accuracy of over 99%. In addition to being highly accurate, this marking method was low cost, fast, and efficient. I also reviewed the existing research on E. panamintina and the threats to its survival. Using this information, I developed a Maximum Entropy species distribution model to determine where the species may occur on the landscape. While the model exhibited a high likelihood of statistical overfitting, it successfully predicted the presence of E. panamintina in several previously undocumented locations. Twenty seven hours of field survey efforts yielded only one individual indicating that this species is likely rare and difficult to detect. Further field surveys guided by the species distribution model will likely uncover additional new populations of this species.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Mills, Ayla Joy
- Description:
- Ammophila arenaria was introduced to North America in 1868 for sand stabilization, and since its introduction it has invaded most of the dune ecosystems of the Pacific coast of North America. The 222 ha dune ecosystem at Gold Bluffs Beach within Prairie Creek Redwoods State Park (Humboldt County, California) has become heavily invaded by A. arenaria , and if left unmanaged this habitat was likely to become a dense monoculture of A. arenaria. My hypothesis tests the efficacy of mechanical (excavators and dozers) and manual (hand-pulling) removal methods on plant community composition and regeneration. Vegetation was characterized and monitored before, during, and after A. arenaria removal. Six 25 m² plots running parallel to the shoreline were set up within each of the different removal sites (two mechanical, two manual, two control) for a total of 36 plots. Each plot was marked with GPS and rebar and three equally-spaced transects were established with five 1m² plots along each transect. Species percent cover values within the plots were established and subsequently monitored every 3 months to quantitatively evaluate A. arenaria reestablishment and native plant recovery. Mechanical removal sites had significantly lower A. arenaria regrowth than the hand removal and the control sites when averaged over all time intervals. One year postremoval, however, A. arenaria regrowth in the hand and mechanical removal sites was not significantly different. The hand removal sites had significantly more native plant cover three months post-removal than the mechanical removal sites, but this difference no longer held at one year post-removal. Mechanical removal of A. arenaria has proven to be an effective removal technique that has not impeded native plant recovery at Gold Bluffs Beach, but as with most techniques for removing A. arenaria, properly timed follow up treatment is necessary. Documenting which removal technique is most effective at eliminating A. arenaria is imperative for the conservation management of coastal dunes and the rare species that rely on them. Ultimately, my research provides the basis to establish a conservation management protocol to effectively control one of the worst invasive plants in coastal ecosystems of the Pacific Northwest, while minimizing damage to native plant communities.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Sideli, Gina Maria
- Description:
- Perennial grain crops are presently offered as a solution to current agricultural problems such as soil erosion, excessive water use, and water quality degradation while supporting ecosystem services. A longer growing season allows for a substantial root system to develop for the assimilation of nutrients and water at greater depths, minimizes nitrogen loss and conservation of water. A wild, perennial sunflower, Helianthus cusickii, close relative to the domestic sunflower, Helianthus annuus, has the potential to offer beneficial alleles for crop improvement to H. annuus. In particular, Helianthus cusickii could be a source of genes for drought tolerance, since it is found on dry, rocky sites in low rainfall regions and has a distinctively robust taproot. Here I evaluate the agronomic value of H. cusickii and whether it merits further research in sunflower crop improvement. Specifically, I characterize genetic variation via microsatellites within and among populations of H. cusickii and phenotypically assess important, agronomic traits in field trials. A study of nine populations demonstrated H. cusickii had a considerable amount of diversity and low population structure with He = 0.47 and FST = 0.247. Growth performance studies showed that H. cusickii did not adapt well under field conditions in southern Kansas during two field seasons. These results did indicate that H. cusickii had greater vigor and survival in an unirrigated field with earlier planting, rather than an irrigated field with later planting, however this also resulted in smaller sized plants. Comparison of annual and perennial root traits showed an average root:shoot ratio of 0.735 in H. cusickii, and an average root:shoot ratio of 0.442 in H. annuus. Interspecific crosses (H. cusickii x H. annuus) between 23 plants resulted in the formation of 20 seeds, however plants grown from the hybrid seed did not reach anthesis. I conclude, based on these experiments that H. cusickii holds potential for use of donor genes in domestic sunflower cropping systems. As this research served as a preliminary analysis of this wild perennial sunflower, further studies would be needed in order to assess plant water relations and the most beneficial quantitative trait loci. Keywords: Helianthus annuus, Helianthus cusickii, phenotyping, genetic diversity, germplasm-bank accessions, microsatellite markers, perennialization
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- McCall, William
- Description:
- Deviations from symmetrical growth in bilateral characters of an organism are referred to as bilateral asymmetries and can be found in three forms: 1) anti-symmetry (AS), 2) fluctuating asymmetry (FA), and 3) directional asymmetry (DA). In this study turtle shell ventral morphological characters (plastron scutes) were measured to determine if bilateral differences were present. We compared turtles from populations with minor human modifications, Big Chico Creek Ecological Reserve (BCCER) and Butte Creek Ecological Preserve (BCEP) to a site with major human modification, Chico Wastewater Pollution Control Plant (CWPCP). Over the course of three collection seasons (2010-2012) a total of 231 adult E. marmorata were measured and photographed. With modern imaging software asymmetry values were determined from scute pair differences (right-left). Shell and body measurements (SBMs) were also recorded for each turtle. Significant differences in SBMs were found between sites and sexes. Individuals from CWPCP were generally larger in all SBMs than BCCER and BCEP individuals. Male pond turtles were generally larger in all SBMs than females. Significant differences in FA values were found in femoral scutes between sites. FA values were generally larger in individuals from CWPCP. Significant differences in DA values of gular, humeral, pectoral, and femoral scutes were found among sites and between sexes. Males had significantly larger DA values in the pectoral and abdominal scutes and these differences were more extreme in the two populations with male-biased sex ratios. This suggests that DA could be related to male-to-male competition for mates.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Chin-Curtis, Alena
- Description:
- Glutamate (Glu) is an important excitatory neurotransmitter in the brain. It binds to ionotropic Glu receptors located in the postsynaptic membrane and allows calcium into the cell. Abnormally high levels of Glu can induce excitotoxicity (seizure), which results in high intracellular calcium, mitochondrial dysfunction, and cell death. It has been shown in vivo that FVB/N (FVB) mice are susceptible to Glu-induced excitotoxicity, while C57BL/6 (B6) mice are resistant. Previous studies have suggested that this might be due to calcium impermeable GluR2 α-amino-3-hydroxy-5- methylisoxazole-4-propionic acid (GluR2 AMPA) receptors. In order to determine whether GluR2 AMPA receptors play a role in susceptibility differences of FVB and B6 mice, two excitotoxic treatments were used. Glu was used to stimulate GluR2 AMPA receptors, while potassium chloride (KCl) was used to bypass Glu receptors and depolarize the cell via voltage-gated calcium channels. Additionally, Cyclosporine A (CsA) has also been shown to block mitochondrial permeability transition pores (mPTPs), which reduces calcium influx into the mitochondria and prevents dysfunction. Various concentrations of CsA were used to determine its effect on both mice during Glu excitotoxicity. Results showed that FVB mice expired and B6 mice survived Glu excitotoxicity alone, while both strains expired after KCl excitotoxicity alone. CsA was neuroprotective at all doses in susceptible FVB mice during Glu excitotoxicity, but was detrimental towards resistant B6 mice at high concentrations. CsA was also neuroprotective against KCl-induced excitotoxicity in both strains of mice. This suggests that GluR2 AMPA receptors are responsible for susceptibility differences of the two mice, but something downstream of the GluR2 AMPA receptors is responsible for regulating cell death during excitotoxicity. Furthermore, these findings suggest that while CsA appears to have advantageous properties, certain subjects might be sensitive to high doses of the drug.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Williams, Melanie Suzanne
- Description:
- Many rare and threatened California plant species are endemic to ultramafic serpentine soils. Understanding what specifically makes these species rare is of high value to conservation and management efforts statewide. While there is no one definition of what makes a plant rare, there are many characteristics that are thought to contribute to a species’ rarity. My study focuses on environmental and reproductive attributes of a rare serpentine endemic species to evaluate their contribution to the plant’s rarity. Packera layneae, or Layne’s Butterweed, is a federally threatened and state listed rare species occurring in small, fragmented populations on gabbro and serpentine soils in the northern California Sierra Nevada. I evaluated environmental factors that potentially define its restrictive habitat, including elevation, light availability, duff depth, and slope. I found the studied populations to occur between 2140 and 2920 feet in elevation, and to have established in a variety of habitats where the evaluated environmental factors were moderate, including presence beneath intermediate canopy cover (40-60% of available light), widely variable duff depth (0.25 to nearly 6cm), and generally lower slopes (5 to 16%). I also conducted an experiment to evaluate the role of dispersal limitation as a contributing factor to this species’ limited distribution, and found that this species disperses the majority of its seeds very close to the parent plant. I also conducted an experiment to determine the specific germination requirements for P. layneae, and found that its seeds will germinate in a variety of soil types, but only following a period of light exclusion. Using the modeling program Maxent, a species distribution model was constructed using presence locations in conjunction with environmental variables in an attempt to yield a predictive map of potential habitat occupied by this species. Unfortunately, the very small number of known populations available for input into the model, in combination with high environmental variability across presence locations, resulted in a model with reduced predictive function. Determining why this species is so patchily distributed and understanding its unique habitat and physiological requirements will be vital to its conservation and long-term success. This work will also contribute to our understanding of plant rarity and help guide management efforts.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Shaw, Julie
- Description:
- Northern Saw-Whet Owls (NSWO, Aegolius acadicus), one of the smallest owls in North America, migrate in large numbers every fall from higher latitudes and elevation to overwinter at both lower latitude and elevation. While extensive efforts have been devoted to understanding their migration patterns in the eastern US, little is known regarding NSWO migration patterns or winter habitat preferences in the west. The goals of this study were to determine wintering destination of local migrant NSWO, winter habitat, and diet patterns for the first time in California using the Big Chico Creek Ecological Reserve (BCCER) as a study area. NSWO were captured at BCCER during fall migration and fitted with 2.5-gram radio-transmitters. During the fall/winter of 2010-2012, a total of 19 NSWO were tagged and 112 different roost sites were described. Over 80% of diurnal roosts were between two species: toyon (Heteromeles arbutifolia) and canyon live oak (Quercus chrysolepis). Paired random sites were also sampled 50 meters from roost sites to determine roosting preferences. Shrub canopy cover was found to be significantly higher at owl roosts compared to random. A diet analysis of 77 pellets collected between ten owls showed NSWO took few prey species, primarily consuming western harvest mice (Reithrodontomys megalotis), comprising 48% of 103 prey items. Voles (Microtus spp.) and deermice (Peromyscus spp.) made up the remainder of the diet. Though NSWO are a common species, little is known about their general habits in the west; therefore results from this study contribute to our understanding of this species.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Daniele, Ninette R.
- Description:
- Freshwater turtles worldwide are declining due to a variety of human caused impacts. The Western Pond Turtle (Emys marmorata) is native to the pacific coast of the North America and is also in decline. Many Western Pond Turtles live in human-modified habitats. The ecophysiology of this species in impacted habitats is largely unknown and blood profile baselines from healthy populations in natural habitats are lacking. Western Pond Turtles were sampled from a nature reserve (n=61) and wastewater treatment facility (n=37) and blood profiles were performed, which included determination of hematocrit and thirteen serum chemistry analytes. Baseline blood profiles for a subset of clinically healthy E. marmorata from a highly natural habitat were documented, including values for gravid females, with significant differences noted between males and females for 8 chemistries. Blood profiles were also compared between all sampled male turtles from the nature reserve and the wastewater facility populations; with significant differences found in ten blood analytes between populations at these habitats. The blood profile baselines from the nature reserve population will be helpful to wildlife veterinarians in evaluating disease in this species and possibly other Emydid turtles. Furthermore, the differences in blood profiles between populations suggest that turtles from altered habitats may have impacted physiologies and that blood profiles, with further study, may be useful in assessing the suitability of modified habitats. Managers may use this work in assessing the health of Western Pond Turtle populations and planning conservation strategies in altered landscapes.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Ervin, Bryan
- Description:
- In the pursuit of producing cleaner fuels, plant lignocellulose is a source of fermentable sugars that don’t compete with food production. Conversion of plant components, or lignocellulose, into biofuels typically requires hot and acidic pre-treatment conditions not suitable to most commercial fungal enzymes. In this work, I evaluated seven Ascomycota fungi associated with Boiling Springs Lake (BSL) in Lassen Volcanic National Park, a hot and acid environment, for utilization of lignocellulose material. Due to the conditions of BSL, I hypothesized these fungal isolates produce thermal/acidic stable enzymes. To test this, the fungi were screened for: growth on purified or natural components under hot, acid conditions; lignocellulose degradation genes with PCR; and, potential lignin degradation via a (per)oxidase assay. Growth analysis showed Acidomyces and Ochroconis growing >40 °C and pH <4; Aspergillus, Paecilomyces and Penicillium preferred cooler temperatures for acidic media but still grew above 40 °C; Phialophora only grew up to 27 °C under both acidic and neutral conditions; and Cladosporium showed a preference for cool, neutral conditions. The most promising material utilizers, Acidomyces, Ochroconis and Paecilomyces used cellobiose, xylan, pine and incense cedar needles for growth at 40 °C and pH 2. The remaining fungi used fewer materials. PCR results showed Acidomyces, Paecilomyces, and Ochroconis containing orthologs to known fungal lignocellulose degradation genes. Additionally, Acidomyces and Ochroconis showed extracellular (per)oxidase activity at 40 °C and pH 2. From these combined results, I concluded that Acidomyces, Ochroconis and Paecilomyces have potential for use in the pretreatment of lignocellulosic biofuels.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Hoddick, Sarah
- Description:
- Emiliania huxleyi is a marine haptophyte alga known for its ability to generate large volumes of calcite coccoliths. It also synthesizes a unique suite of neutral lipid (PolyUnsaturated Long Chain Alkenes, Alkenones and Alkenoates, or PULCA), whose biosynthetic pathways are currently unknown. Like energy-storage triacylglycerides, which they replace, these lipids are packaged into lipid bodies (LBs), and a prior study used a proteomics screen of isolated LBs and endomembranes from E. huxleyi CCMP 1516 to generate a list of candidate proteins possibly associated with PULCA biosynthesis, mobilization, and catabolism. The goal of this thesis was to study gene expression these proteins under conditions of neutral lipid accumulation and degradation, including batch growth with addition of sodium bicarbonate, and during light-dark manipulations. I designed quantitative PCR (qPCR) primers for almost 120 genes identified by the proteomics screen, and optimized mRNA extraction, reverse transcription to cDNA, and qPCR. I confirmed neutral lipid accumulation during nutrient (phosphate) limitation in the light after sodium bicarbonate dosing, and catabolism during continuous darkness. I was able to quantify gene expression changes of many LB-associated genes, most with low expression values, as well as a number of control genes and other genes used in other studies. I observed several striking patterns of gene expression in the experiments. In the growth curve + bicarbonate experiment, many LB-associated genes likely related to acyl lipid biosynthesis showed 10-100-fold expression increases as neutral lipids accumulated. However, the timing of increases varied: some increased before bicarbonate addition, while others only after. In contrast, several genes for prenyl and sphingolipid pathways did not show such striking increases, and a few genes possibly related to acyl lipid catabolism decreased. Most genes associated with photosynthesis, structural proteins, and trafficking did not show significant changes, but several genes for carbohydrate metabolism also increased sharply, highlighting the likely connection between carbohydrate and lipid metabolism. In contrast, the light-dark experiment showed few large changes in expression, and several genes showed strong down-regulation, although patterns were not consistent. But because of the large numbers of time points and treatments in this experiment, I was only able to survey a few genes by qPCR, and these results are very tentative. In both experiments, I was able to quantify only a fraction of the LB-associated genes, due to the large effort necessary to screen genes by qPCR, and also due to degradation of mRNA stored at -80 oC. Although my study examined far more genes and time points than most qPCR studies, and I confirmed the likely role of acyl lipid biosynthesis pathways in PULCA production, an important outcome of this study is the need in future to use more comprehensive genome-wide techniques, such as RNA-seq, to evaluate the large numbers of genes likely involved in the pathways of neutral lipid biosynthesis.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Gottschalk Fisher, Erin
- Description:
- Vernal pool habitats have been significantly reduced by conversion to incompatible agriculture and urbanization. As a result, a number of vernal pool dependent species have become rare, including Colusa grass (Neostapfia colusana) and Greene’s tuctoria (Tuctoria greenei). This study examined the potential for introductions of the rare grasses into vernal pool habitats. To this end, four study sites were established, two sites for each species – one introduction site with restored or created vernal pools and one reference site with existing populations of the rare grass. The year prior to introductions, pool hydrology and reference populations were monitored and mapped to inform introduction success. Using seed and inflorescence packets, the species were introduced into the restored/created pools and, for comparison, reintroduction into the reference pools. For Greene’s tuctoria, germination and survivorship to reproduction occurred at both introduction and reintroduction pools. The introduction pools had significantly higher average percent germination (60%) than the reintroduction pools (35%), which may be a result of disturbance to the germination and early seedling stage at the reintroduction pools. Plants from seed packets had significantly higher vigor but showed a trend towards lower reproductive output compared to the plants growing from the higher-density inflorescence packets. In the second year, despite relatively low rainfall and only partial pool filling, the introduction pools supported over 2,000 second generation Greene’s tuctoria plants. For Colusa grass, germination occurred at both the introduction pools (13%) and reintroduction pools (23%); however only one plant survived to reproduce at the introduction pools while reintroduction pools had 40% survivorship to reproduction. Soil testing suggested that the low survivorship may be due to elevated salinity at the introduction pools. The differences between species and packet methods illuminated different paths to potential success in introducing new populations. The results of this research are imperative in informing recovery efforts for Colusa grass and Greene’s tuctoria populations as well as for other rare vernal pool plants.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Almasary, Areeje
- Description:
- Microorganisms can live in environments where macroscopic organisms cannot survive, such as in the extremely acidic geothermal Boiling Spring Lake (BSL) in Lassen Volcanic National Park, CA. BSL is an oligotrophic lake with thriving microbial populations whose carbon (C) sources are still poorly understood. In this study, I examined the possibility that allochthonous leaf litter (mostly pine needles) observed falling in the lake can fuel microbial production in BSL. Coniferous needles are known to be particularly difficult to colonize by microbes and have low decay rates, but no studies have examined the combined effects of low pH and high temperature on pine needle leaching and decomposition. In both lab- and field-based experiments, I found coniferous leaves had high decay rates during leaching and decomposition in BSL compared to those reported in the literature for other neutral pH and mesophilic lakes and streams. Thus, the acid and high temperatures appear to help condition the leaves and make their C more biologically available. I also found little difference in decay between fresh and dry leaves, but when needles were cut, I observed faster leaching rates and slower decomposition rates, suggesting the effects of mechanical weathering are important, possibly by degrading the waxy cuticle barrier. I also observed that leaves decayed more slowly in 0.2 μm-filtered BSL water, suggesting both native and introduced microbes contribute to leaf breakdown. Based upon bacterial growth experiments and recovery of an ascomycete fungus, both prokaryotes and eukaryotes seem to contribute to leaf decay. The addition of a nitrogen (N) source (yeast extract) enhanced prokaryote growth more than adding a simple carbon such as glucose, suggesting BSL is both C and nitrogen limited. I also used radioisotopes to assess primary and secondary production rates, and observed autotrophic growth was low, and dominated by chemoautotrophy, while heterotrophic uptake rates varied depending on the organic substrate used, and were highest for acetate. These results suggest that allochthonous carbon is important in fueling microbial production in the lake. I constructed a preliminary C budget for the lake by measuring leaf deposition and estimating other dissolved organic carbon (DOC) sources from BLS’s hydrologic budget.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Bergmann, Jean-Phillippe W.
- Description:
- Reproductive isolation is critical to speciation and therefore biodiversity. The immediate goal of such studies is to identify which barriers contribute most to overall reproductive isolation between species, in order to gain a broader understanding of the process of speciation. Mimulus guttatus and M. glaucescens have postzygotic barriers to hybridization, but their prezygotic barriers remain unstudied. I examined potential premating prezygotic barriers such as phenology, pollinator behavior and floral morphology, as well as possible post-pollination prezygotic barriers such as pollen adhesion, germination and pollen tube growth rates between species. We found no significant barriers to hybridization between species for any traits, although we did identify subtle differences in herkogamy and corolla tube width. We conclude that prezygotic barriers to reproduction between M. guttatus and M. glaucescens are weak, and contrast with evidence for postzygotic barriers such as reduced seed set and delayed flowering in hybrids. Additional research should focus on microhabitat preferences and a population genetic analysis to determine whether introgression can occur between natural populations.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Araujo Sariñana, Juan C.
- Description:
- Diabetes is one of the United States’ worst epidemics; the dangers associated with the disease can be both fatal and varied. The constant presence of high concentrations of glucose and free fatty acids (FFA) becomes a source of stress for cells, which results in programmed cell death (apoptosis). Our lab has identified a microRNA (miRNA), miR- 191, that may be involved in the stress response of pancreatic beta cells. miRNAs have been recognized as key regulators of the translation of messenger RNA (mRNA). miRNAs are involved in virtually all cellular processes, have the ability to target multiple genes, and play important roles in diseases such as cancer and diabetes. Previous research suggested that miR-191 is under the control of the pancreatic and duodenal homeobox 1 transcription factor (PDX-1) and of the neurogenic differentiation 1 transcription factor (NeuroD1), both of which are regulated in the presence of glucose. I have also observed that miR-191 is up-regulated when rat insulinoma cells (INS-1) are treated with glucose. Bioinformatic analysis suggests possible roles for miR-191 in regulating apoptotic genes. Inhibiting miR-191 in a UV-induced stress assay in insulinoma (INS-1) cells results in decreased cell death. Decreased cell death was also observed when miR-191 was knocked down in samples that were treated with 30 mM glucose and 0.5 mM palmitate. It is not yet clear how miR-191 is involved in the beta cell stress response but based on data presented here it appears that miR-191 is promoting apoptosis in response to stressful conditions.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Grewal, Mandeep
- Description:
- Hydrophobic polymer lignin provides water proofing and structural integrity to cell wall which help plants adapt to terrestrial environment. Secretory peroxidases are thought to generate monolignol radicals that polymerize to form lignin. In Arabidopsis thaliana there are 73 secretory peroxidases .Identification of tissue, cellular, and subcellular location for individual peroxidases can help assigning their function. All secretory peroxidases contain signal peptide for entry into endomembrane system. Some peroxidases have hydrophobic carboxy-termini targeting to them to vacuole. Peroxidases lacking hydrophobic carboxy-terminal are targeted to wall. We tagged A. thaliana secretory peroxidase, AT2G34060, with yellow fluorescent protein. Plants transformed with this construct expressed AT2G34060 in the protoxylem cells of the roots of one to eight day old seedlings. AT2G34060 has a hydrophobic Carboxyterminal and aminotransferase domain. This peroxidase is located in vesicles arranged in a helical fluorescent pattern similar to microtubule pattern. Overexpression of AT2G34060 reduced the root length. A vesicular location and reduction in growth by overexpression suggests that AT2G43060 supports lignification by producing monolignol precursors through its putative aminotransferase ability. AT2G34060 may also be involved in deglycosylation of monolignols during their vesicular transport to the wall. The availability of monolignols may be a limiting factor in the lignification process. Therefore, a higher number of available monolignols may lead to shorter roots through higher lignification. Our work identifies a peroxidase that appears in cells undergoing lignifications and its subcellular location in vesicles is consistent with formation of lignin. Also, root shorting through overexpression is consistent with role in lignification.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Wallace, Lindsey Kaylee
- Description:
- Emiliania huxleyi and some related prymnesiophyte algae produce a novel group of polyunsaturated long-chain C37-39 alkenones, alkenoates, and alkenes as their major neutral lipids, however their biosynthesis pathway is unknown. Like triglycerides, these lipids are believed to be utilized as storage lipids and are accumulated in lipid bodies to be used as a fuel source, presumably. Also C31-33 cis-alkenes have been identified in E. huxleyi but are believed to be different in synthesis and function. By studying the synthesis of these lipids I set out to discern how these two types of neutral lipids are formed in E. huxleyi. I used a combination of techniques, including GC-MS analysis, radiolabeling, and inhibitors, to examine lipid pools during growth cycles, bicarbonate dosing, and light-dark manipulations. By using GC-MS analysis I identified the presence of C31-33 cis-alkenes exclusively in E. huxleyi strains CCMP 1516 and 371, and Isochrysis galbania strain CCMP 1323; where E. huxleyi strains CCMP 1742, 3266, and 3268 had both cis-alkenes and C37-38 trans-alkenes. I also found accumulation of both cis-alkenes and C37-38 trans-alkenes in light to dark manipulations was similar to that seen in storage lipids, suggesting that the long chain cis-alkenes are in fact another storage lipid and may share a similar synthesis pathway to the trans-alkenes. Using radiolabeling studies I found external acetate is not acquired under light dependent mechanisms and is utilized primarily in production of polar lipids; while external bicarbonate acquisition and use in lipid synthesis is light-dependent, and as a cellular building block it is distributed more evenly amongst lipid pools. Also, flow of carbon into CCMP 1516 and 3268 cells from external bicarbonate into lipid pools is inhibited by cerulenin (fatty acid synthase inhibitor), flufenacet (elongase inhibitor), and quizaloflop (acetyl-CoA carboxylase inhibitor). Platensimycin (fatty acid synthase II inhibitor) only affects flow of bicarbonate into CCMP 1516 C31-33 cis-alkenes. Finally, flow of carbon into CCMP 1516 cells from external acetate into lipid pools is inhibited by cerulenin. Flufenacet and quizaloflop only affects flow of acetate into C37-39 trans-alkenes. Platensimycin has no effect on the flow of acetate into lipid pools in CCMP 1516. Though these results show precursors of acetate and bicarbonate are used in the synthesis of these neutral lipids, and through inhibitor studies I have identified many mechanisms vital to their synthesis, the biosynthetic pathway is yet unclear.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Obaidi, Freshta
- Description:
- Class III plant peroxidases are found in all land plants and lignification, suberization, and pathogen defense are three of the many functions served by these enzymes. The numerous peroxidase functions and the large multigenic families peroxidases are a part of have made it difficult to study class III peroxidases. The goal of this study was to determine the in vivo localization of Arabidopsis thaliana peroxidases At2g43480 and At3g21770 by using a fluorescent protein tag. Because both peroxidases have an endoplasmic reticulum signal peptide and lack a hydrophobic C-terminus, it was expected that both would be found at the cell wall. At2g43480 was not expressed in the cell wall and it may be involved in plant defense or modifying monolignols for suberization. At3g21770 was expressed in the cell wall of xylem tissue, lateral root cap cells, and columella cells, where it may be involved in lignification. In epidermal guard cells, At3g21770 was expressed intracellularly and may function in deposition of cell wall material in plasmodesmata to cytoplasmically isolate maturing guard cells. The possibility of At2g43480 involved in monolignol modifications and At3g21770 involved in lignification is significant because lignin is an abundant plant cell wall polymer and its regulation is beneficial to the paper pulping industry and to biofuel production
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Ha, Melissa K.
- Description:
- Indirect biotic interactions can change seasonally with changes in the abundance of other community members. In this way, pollinator sharing between plant species may range from competition to facilitation depending on the seasonal pollinator community. I examined this phenomenon with experimental arrays in which flowering time of Clarkia unguiculata plants was crossed factorially with four floral neighborhood treatments including a manipulation of C. unguiculata density, arrays with other Clarkia, and arrays with plants in other genera. I measured pollinator composition, number of pollinator visits, and pollen limitation of seed set. Clarkia unguiculata plants growing with other Clarkia species (congeners) were less pollen-limited, indicated by the difference in seed set between pollen-supplemented (S) and unsupplemented (U) plants, than those growing among conspecifics in only the late season, suggesting late-season facilitation (95% CI for seed set (S-U) conspecifics = (69.9, 88.9); 95% CI for seed set (S-U) congeners= (24.8, 44.6)). The outcome of pollinator-mediated interactions thus varied temporally, and this could be due to differences in pollinator effectiveness among pollinator species rather than pollinator visit frequencies. The identities of pollinators varied between flowering times (Pearson Χ2 = 114.8, d.f. = 4, P < 0.001), and early- and late-season pollinators may have responded differently to floral neighborhoods. Evidence, for temporal variation such as found here in the outcome of an indirect interaction mediated by mutualists, offers a partial mechanism for the success of a species within a community.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Ashe, Jeremey Brandon
- Description:
- I studied fall and winter habitat utilization of Eurasian Wigeon (Anas penelope), and American Wigeon (Anas americana) using time budgets in the Sacramento Valley, California. Habitat utilization by American and Eurasian Wigeon differed only in the proportion of time spent in locomotion and vigilance. Resting, feeding, and locomotion were the top three behaviors exhibited by wigeon (American and Eurasian Wigeon collectively) during each month and in each pond. Increased feeding by wigeon from November through February suggested an increase in their energetic demands. Seasonally flooded wetlands were determined to be an important habitat for wigeon, as feeding and resting were the most common behaviors each month in these habitats. Asymmetric aggressive behavior patterns of Eurasian Wigeon toward American Wigeon suggested these wigeon species may be competing for resources. I studied the migration patterns of Eurasian Wigeon and their associations with Highly Pathogenic Avian Influenza Virus H5N1. One Eurasian Wigeon was equipped with a North Star solar-powered 16g platform transmitter terminal (PTT). I followed this bird’s two-day migration to Central Washington and, subsequently, its daily movements for the final six months of its life. Using a data base of all banded Eurasian Wigeon from 1929 to 2010, a map was constructed showing migration routes, stopovers, and a pattern of winter philopatry. In addition, oral and cloacal swabs of eight Eurasian Wigeon were taken, with negative results for H5N1.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
43. Ecogeographical and intrinsic postzygotic isolation between MIMULUS GLAUCESCENS and MIMULUS GUTTATUS
- Creator:
- Habecker, Nicole M.
- Description:
- The mechanisms by which species are formed is a central question in evolutionary biology. The Biological Species Concept has provided a framework for quantifying, via reproductive isolation, the extent of divergence between populations. The relative strengths and importance of individual reproductive isolation barriers is unclear. This study estimated the strength of ecogeographic (prezygotic) isolation and intrinsic (postzygotic) isolation barriers (genetic incompatibilities between hybrids) between the closely related annual monkeyflowers, Mimulus glaucescens and M. guttatus. Georeferenced herbarium records and environmental data were used to model each species ecological niche and to measure their habitat overlap. Reciprocal crosses between species were performed to measure hybrid seed set, germination success of the resulting seeds, biomass of F1 adult plants, total number of days to first flower (developmental rate), total flower production, ovule numbers, and pollen viability, as intrinsic postzygotic isolation. The species exhibited both ecogeographical isolation and non-reciprocal intrinsic isolation (observed in seed set, developmental rate, and ovule production). These results suggest that isolation was a result of geologic history causing divergent ecological selection, where ecogeographical isolation acted before and limited a minimum of 45% gene flow compared to intrinsic postzygotic isolation factors, which acted later and limited a minimum of 21% of the gene flow on average between M. glaucescens and M. guttatus. The morphological differences between these species may reflect their genetic differences due to local adaptation.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Clark, Elizabeth
- Description:
- MicroRNAs are important regulators of eukaryotic cellular processes and their misregulation is associated with many human diseases. MicroRNA-375, a regulator of insulin secretion in pancreatic beta cells, is misregulated in human type 2 diabetes. The aim of this study is to elucidate the regulation of microRNA-375. My hypothesis is that microRNA-375 is regulated in pancreatic beta cells through protein kinase A. With this hypothesis, I aimed to uncover fundamental mechanisms which lead to type 2 diabetes. Using bioinformatics, I identified putative binding sites in the microRNA-375 promotor for transcription factors in the protein kinase A pathway. With microRNA target prediction algorithms, I found some of these transcription factors may in turn be targeted by microRNA-375. Luciferase reporter assays indicated that cyclic-AMP increases the transcriptional activity of discrete regions of the microRNA-375 promoter. Chromatin immunoprecipitation assays revealed RNA polymerase II associates with the microRNA-375 promoter in response to cyclic-AMP. Cell treatments and real time PCR indicate that microRNA-375 is regulated by glucose and cyclic-AMP in a protein kinase A dependent manner.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Bowen, Heather L.
- Description:
- Body shape of juvenile fall-run Chinook salmon (Oncorhynchus tshawytscha) reared in a perennial stream environment were compared to juveniles reared in an ephemeral stream environment. In the Central Valley of California, habitat characteristics differ substantially between these two stream types and therefore present different challenges with respect to water discharge, water temperature, food availability, and habitat complexity. Using multivariate analyses conducted via geometric morphometrics, this study presents morphological differences observed within and between two stream types. As predicted, juvenile Chinook salmon exhibit rearing habitat-specific body shapes. Differences in juvenile Chinook salmon morphology between stream types were primarily associated with expansion of the mid-body region relative to, differences in body length. Specifically, juvenile Chinook salmon that reared in the ephemeral stream expressed increased body depth dominated by dorsal-ventral elongation of the dorsal fin-body insertion points, increased adipose fin-body dorsa-posterior angle, and increased anal fin-body ventral posterior angle. Additionally, eye position and gill opercula-body insertion points were anteriorly shifted in the juvenile body shape of the ephemeral stream. Differences between ephemeral and perennial stream environments likely influence the body shapes observed in this study, and suggest that juvenile Chinook salmon are morphologically flexible and readily adapt to rearing habitat conditions
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Reeder, William Henry Harrison IV
- Description:
- ABSTRACT DIVERSITY AND ACTIVITIES OF PHAGOTROPHIC MICRO-EUKARYOTES IN BOILING SPRINGS LAKE, LASSEN VOLCANIC NATIONAL PARK by William Henry Harrison Reeder IV Master of Science in Biological Science California State University, Chico Fall 2011 The biology of extreme environments has focused on diversity and adaptations, largely concentrating on the prokaryotic community. Only recently have investigations targeted eukaryotic diversity in extreme environments, and few studies have examined food web interactions. In this thesis, I studied the protist grazing component of the Boiling Springs Lake (BSL) food web. Boiling Springs Lake is a flooded fumarole that contains a 1.8 ha pool of pH 2.2, 52°C water in California’s Lassen Volcanic National Park. It is an NSF-funded Microbial Observatory focused on understanding the diversity and interactions of the entire microbial community. Using a combination of culture and genetic approaches, I found the major predator in BSL to be a unique vahlkampfiid amoeba capable of surviving the physical extremes of BSL. It is closely related via rRNA sequence to Tetramitus thermacidophilus, a heterolobose amoeboflagellate recently isolated from volcanic geothermal acidic sites in Europe and Russia, and an uncultured heterolobosean amoebae from the nearby Iron Mountain Mine acid mine drainage site. Transects studies showed the organism is endemic to the lake, and cysts were present at an average of ~500 viable cells mg-1 on the shoreline. The amoeba form is active up to 52 C, is a strict acidophile, and was observed grazing on native ascomycete Phialophora sp., as well as bacteria such as Micrococcus sp. Other grazing protists were identified in lakeshore environments, but were unable to grow in the extreme conditions of the lake. These include the lobose amoebae Hartmannella sp. and Acanthamoeba sp., and the kinetoplastid flagellate Bodo sp. Acanthamoeba and Bodo were acid tolerant, but could not grow at temperatures above 30C, while Hartmentalla was thermotolerant but could not grow at low pH. Microscopic analysis showed the presence of a variety of other morphotypes that I tentatively identified as ciliates, euglenids, cercozoans, and various flagellates from colder areas around the lake. However, I was not able to culture these, and no genetic identification was obtained. Additionally, I observed apparent large DNA viruses in Acanthamoeba sp. cultures, which resembled Mimivirus. While still tentative, this is possibly the first observation of a eukaryotic virus from an acidothermal environment.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Sall, Bennett R.
- Description:
- Wild-land fires are a dynamic and destructive force in natural ecosystems. In recent decades, fire disturbances have increased concerns and awareness over significant economic loss and landscape change. The focus of this research allowed for the utilization of Landsat 5 imagery, analysis software, and ground based methods to study two northern California wild-land fires: Butte Humboldt Complex (BHC) and Butte Lightning Complex (BLC) of 2008. Multi-temporal and NDVI satellite imagery were used to visually assess levels of landscape change, under two temporal scales. Visual interpretation indicated noticeable levels of landscape change and relevant insight into the magnitude and impact of both wild-land fires. Satellite NDVI, local temperature, and precipitation time-based (1998-2010) data were incorporated to contrast pre- and post-wild-land fire vegetation response and recovery. NDVI trends may have been influenced by low precipitation, substrate flammability, and vegetation accumulation. Statistical analysis using Coefficient of Determination R2 comparison of satellite to ground based NDVI, resulted in weak linear correlations for BHC (R2 = 0.0859) and Richardson Springs (R2 = 0.3555), in contrast to a slightly negative correlation for BLC (R2 = 0.001). Normalized Burn Ratio (NBR) and delta NBR data allowed for quantitative analysis of burn severity levels. Delta NBR results indicated unburned, low severity, and low re-growth for BHC “burned center” subplots. In contrast, delta NBR values for BLC “burned center” subplots indicated low and mid to high burn severity levels. Examination pre- and post-wild-land fire vegetation demonstrated potential for wildland fires and associated influences to be detected by way of remote sensing technology.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Gilbart, Meghan
- Description:
- ABSTRACT THE HEALTH OF BLUE ELDERBERRY (Sambucus mexicana) AND COLONIZATION BY THE VALLEY ELDERBERRY LONGHORN BEETLE (Desmocerus californicus dimorphus) IN RESTORED RIPARIAN HABITAT by Meghan Gilbart Master of Science in Biological Sciences California State University, Chico Summer 2009 Horticultural restoration of floodplains recreates riparian habitat that is critical to a diversity of wildlife, including many endemic, threatened and endangered species. This type of restoration frequently occurs on highly regulated rivers, where the natural processes that shape riparian plant communities have been modified and truncated. The truncation of river processes places importance on restoration planting designs, which must consider the heterogeneous nature of the environment, complex natural vegetation structure as well as the succession of plants adapted to fluvial systems. One of the largest riparian restoration efforts in the country is along the regulated Sacramento River in the Central Valley of California, where restoration targets imperiled xii wildlife such as the federally threatened Valley elderberry longhorn beetle (Desmocerus californicus dimorphus, VELB). The VELB is endemic to the Central Valley and specializes on facultative riparian blue elderberry shrubs. As a target species of the restoration, over 96,000 elderberry shrubs have been planted in the last 16 years in a range of planting designs to create VELB habitat. The planting designs that include elderberry range from open to closed canopy communities, yet there has been no monitoring of elderberry among the different planting designs beyond the initial three-year monitoring period. Using a factorial design, I sampled elderberry shrubs across both open and closed planting designs, and in old and young sites in 23 restoration fields of the Sacramento River National Wildlife Refuge to evaluate the current health of planted elderberry and the corresponding occupation by VELB. My results indicate that open, low cover planting designs can allow elderberry to develop into larger, more robust shrubs that will reach maturity, whereas closed canopy designs likely stress elderberry shrubs and reduce living material over time. Recent VELB occupation was observed in 78% of all fields but only 21% of all shrubs searched. Beetle occupation increased with restoration age but showed a weaker and inconsistent relationship with cover. Closed canopy planting designs may attract beetles initially through chemicals released by stressed elderberry shrubs, but in light of successional changes that will take place in the planted fields over time, open canopy planting designs provide more consistent habitat. A diversity of planting designs is therefore recommended for restoration of VELB habitat, but both elderberry health and VELB occupation should be monitored over time in these sites as plants continue to age.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Layhee, Megan
- Description:
- ABSTRACT EMPLOYING STABLE ISOTOPES TO INVESTIGATE THE IMPACTS OF INVASIVE SPECIES ON HAWAIIAN STREAM FOOD WEBS by Megan Layhee Master of Science in Biological Sciences California State University, Chico Spring 2011 Anthropogenic disturbance around the world is restructuring ecosystems and changing interactions within ecological communities. In the Hawaiian Islands, one of the most significant forces of disturbance is the widespread presence of invasive species. In this study stable isotopes of carbon and nitrogen were used to examine trophic and energy flow changes occurring in Hawaiian stream communities due to biotic disturbances including invasive species. On the island of Kaua’i, we extensively sampled all members of the stream community, including primary producers and consumers, from four streams with varying levels of disturbance. The streams chosen in this study included Limahuli, Kapa’a, Hulē’ia and ‘Opaeka’a. δ13C, δ15N signatures, and trophic positions of stream members were calculated to determine differences in overall food web structure, changes to native consumer isotopic signatures, and differences in food web diversity and trophic redundancy. Comparison of streams with varying levels of disturbance showed that 1) overall food web structure varied dramatically among locations, 2) natives were nearly absent in heavily disturbed and highly invaded streams while at the same time a suite of non-native consumers are replacing the trophic roles left by the natives, 3) isotopic signatures and trophic position of native consumers were not significantly different across streams, and 4) heavily disturbed and highly invaded streams had more trophic diversity and generally lower trophic redundancy. Our study was able to quantitatively depict and compare differences in both the structure and trophic interactions of Hawaiian freshwater ecosystems webs due to varying levels of disturbance and species invasion.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Walther, Rebecca C.
- Description:
- ABSTRACT SPATIAL AND TEMPORAL ECOLOGY OF FISH LARVAE IN SEASONAL AND PERENNIAL TRIBUTARIES OF THE SACRAMENTO RIVER, CALIFORNIA by Rebecca C. Walther Master of Science in Biological Sciences California State University, Chico Spring 2009 Many studies have shown the benefits of off-channel habitats, such as floodplains, for the early life stages of fishes, but little work has examined the differences in the abundance and distribution of fish larvae between seasonal and perennial stream habitats. To examine this, drift nets were used to compare the spatial and temporal distribution of fish larvae among two seasonal and two perennial tributaries of the Sacramento River, California, during the winter and spring of 2004. Additionally, a detailed examination of the distribution of fish larvae in Mud Creek, a seasonal stream, was conducted in 2006 and 2007. Higher temperatures and an earlier date of first occurrence of fish larvae in the seasonal streams were observed. In addition, Mud Creek produced extremely high numbers of fish larvae and had the greatest diversity and species richness xii among the four sample streams. Taken together, the findings suggest that seasonal streams in the Central Valley are used as spawning and rearing habitat, and the associated warmer water temperatures may elicit earlier adult spawning. These same factors may also contribute to increased fitness and survival of fish larvae, which in turn can enhance recruitment success and year class strength for native fishes, many of which are in decline.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences