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- Creator:
- Melendez, Christopher
- Description:
- Environmental temperature is a crucial environmental factor that influences many physiological functions in fishes. Rainbow trout (Oncorhynchus mykiss) are a native anadromous species that inhabit a variety of freshwater rivers and lakes and are widely distributed throughout the western portion of the United States. Resident rainbow trout populations occupy interior freshwater environments for the entirety of life. Interior bodies of water are most susceptible to changes in environmental temperatures. Therefore, resident rainbow trout are likely to be impacted by variable and rising temperatures, particularly during embryonic development. Understanding temperature effects during development is likely to provide insight into the overall thermal biology of a species and its persistence in a changing climate. To assess the effect of temperature on development of rainbow trout, we examined phenotypes of hatchery embryos reared in various incubation temperatures (5°C, 10°C, 15°C and 17.5°C). To identify the presence of embryonic developmental plasticity within developmental time points, embryos incubated in 5°C were exposed to either 10°C, 15°C or 17.5°C during gastrulation, organogenesis, system integration or growth windows and a 3-dimensional critical window model was applied. An increase in constant incubation temperature increased oxygen consumption rate (V̇O2), and decreased hatchling survival, mass, yolk size, body length and time to 50% hatch. Thermally shifting embryos into increased temperature during distinct windows of development also reduced survival at hatch, and this was most evident following exposure during organogenesis, which may signify the presence of a critical window for this trait. Likewise, thermally shifting embryos into increased temperature resulted in smaller hatchlings. Although there was an initial increase in V̇ O2 in response to temperature, experiencing thermal shifts during development had no persistent effect on V̇ O2 when measured at hatch at 5°C compared to 5°C constant embryos. Collectively, these results suggest that survival and morphological traits of rainbow trout embryos are most sensitive to increased temperature during organogenesis and system integration, but increased temperature does not appear to have a long-term effect on energy use. Environmental temperature plays a fundamental role in developing aquatic vertebrates. Thus, critical window studies such this performed across species will eventually allow for the identification of commonalities in plasticity between different species in response to variables such as temperature.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Akimi, Desiree
- Description:
- To better understand the neural mechanisms for human physiology, an invertebrate’s control on its cardiovascular system should be investigated. The leech’s heartbeat is controlled by segmental ganglia and has a phase delay in its peristaltic heartbeat pattern. This thesis hypothesized a neuromodulator, dopamine, can disrupt the phase delay by affecting inhibitory post synaptic potentials (IPSP). We dissected the leech, isolated a chain of ganglia onto a petri dish, and placed it onto a rig to record synaptic potentials. We recorded and analyzed the ganglia when submersed in saline, dopamine, and saline rinse. We looked at HN4/HN7 phase delay on HE8/HE12 of segmental ganglia. Our results showed dopamine had no effect on any HN/HE pair, except HN 7 and HE 8, HN 4 and HE 8, and HN 7 and HE 12. For HN 7 and HE 8, there was a significant difference in spike-triggered average, area under the IPSP curve, and resting potential between control and rinse. Moreover, there was a significant difference in area under the IPSP curve between control and saline rinse. HN4/HE8 and HN7/HE12 had a significant difference in IPSP size before dopamine and during saline rinse. Overall, the weak synapse between HN 7 and HE 8 might not be due to dopamine because the dopamine effect was not seen in the stronger synapses before and during dopamine (HN4/HE8 and HN7/HE12). We cannot fully conclude dopamine has a significant effect on the synaptic strength between HNs and HEs without more research done.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Cruz, Michelle S.
- Description:
- Chronic non-healing wounds are a growing clinical burden, impacting 6.5 million patients in the United States alone (Sen et al., 2009). A variety of cells take part in the complex process of wound healing, which includes stages such as inflammation, re-epithelialization and maturation. T cells help mediate this process by secreting cytokines, growth factors and activating other cells to infiltrate the region. Two major subtypes of T cells reside in the skin: those expressing an αβ T cell receptor (TCR) chain and those expressing a γδ TCR chain on their cell surface. αβ and γδ T cell receptors recognize unique ligands and thus cells that express these receptors are likely to have different roles in immunity and homeostasis, yet those specific functions are not well known especially in humans. The goal of this study is to develop a method of cellular isolation and characterization for future studies to analyze T cell populations present in the skin. This will allow better understanding of the common and distinct roles played by αβ and γδ T cells in skin immunity and tissue repair. Currently there is intense research in elucidating the specific function of αβ and γδ T cells in human skin (Cruz, Diamond, Russell, & Jameson, 2018). Developing methods of isolation and characterization will allow new avenues for research and will further elucidate the specific roles of αβ and γδ T cells in human skin surveillance and wound repair.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Sheldon, Sarah
- Description:
- San Clemente Loggerhead Shrikes (Lanius ludovicianus mearnsi) have been bred in captivity since 1991 following their listing as an endangered subspecies in 1977. For 25 years, breeding of this captive population has been managed to avoid inbreeding using protocols based on behavior, demographics, genetics, and ecology. Yet despite the broad application of these comprehensive protocols, inbreeding within this subspecies has never been quantified outside this framework. To evaluate the effects of the population bottleneck and captive management techniques on the population, analysis of overall levels of inbreeding, founder representation, and the division of inbreeding into partial coefficients attributable to founder lines was conducted using the pedigree of the population. Inbreeding depression was then measured by comparing inbreeding levels to measures of survival (egg fate and overwintering survival) and to measures of reproductive success (the numbers of offspring produced). Gene diversity was 93%, and the largest average contribution from a single founder to the inbreeding level was 18% in 2015 (founder SB 235). Moderate inbreeding depression (2B=5.38 and 3.06) was identified in juvenile survival and egg fate, but later life history traits that affect fecundity were not affected by inbreeding. This study supports the continuation of releases and parent-rearing as part of the population’s management. It also provides specific recommendations for breeding that avoid descendants of SB 235, while seeking out descendants of SB 230, who has made negligible contribution to the measured levels of inbreeding. These findings should help this longstanding project maintain a viable and sustainable population of Loggerhead Shrikes on San Clemente Island.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Maziarz, Jacob
- Description:
- Wetland ecosystems are among the most biologically productive ecosystems on Earth, yet they are being lost and degraded at an alarming rate. A growing trend to offset this loss is to construct artificial wetlands to replace the destroyed natural wetlands, yet our understanding of how to construct artificial wetlands, and make them functional, is vastly underdeveloped. This study sampled stocks of nitrogen (N) and carbon (C) in an artificial wetland on the California State University San Marcos (CSUSM) campus and compared them to stocks from local wetlands. Samples were taken from both plant biomass and soil to assess the stocks of C and N throughout the wetlands. Plant cover was also measured at each site via a line-intercept method. We hypothesized that C and N stocks would be significantly lower in the artificial wetland than the natural wetlands due to the young age of the artificial wetland while plant cover and biodiversity (species richness) would be similar across all wetlands. The study revealed a large degree of variation among the three wetlands and that soil and vegetation C and N stocks of the CSUSM wetland appeared to plateau after 11 years. However, the CSUSM wetland C and N stocks and plant cover were higher than, or comparable to, the two local wetlands. Plant species composition was unique for each wetland, with only five species shared among two or more sites. The local wetlands showed a great deal of variation between themselves. Batiquitos showed very low soil and plant C and N stocks, while the site at Cannon Road had much higher stocks, especially in its plant biomass. While this study demonstrated that CSUSM was functioning at least on par with local wetlands, it also raises a number of implications regarding the functional status of wetlands in California. The two local wetlands have a history of anthropogenic disturbance and alteration. California wetlands, both those sampled in this study and those from other studies, showed high variability amongst themselves. In some comparisons, artificial wetlands seem to sequester nutrients even better than a natural wetland, but in other comparisons, failed to match nutrient stocks. This high variability can originate from differences in wetland hydrology, plant abundance and species composition, differences in surrounding terrain, and anthropogenic alterations. California wetlands had much lower nutrient stocks compared to wetlands in other parts of the U.S., which is presumably caused by regional differences in hydrology.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Naumann, Kenneth
- Description:
- DNA storage in the nuclei of cells is important for both compaction and the regulation of gene expression. DNA packaging is altered by chemical modifications to the tails of the histone octamer around which the DNA is wrapped, specifically histones H3 and H4. Collectively these various histone marks make up a pattern which has been termed the “histone code”. The multiple interactions between histone modifications and gene expression is not well known in diseased cells. The objective of this study is to better understand the histone modification differences between normal and cancerous cells, and the potential for manipulating this code, due to the reversible state of modifications. By comparing malignant and non-malignant cells before and after treatment with inhibitors targeting histone modification pathways, we are able to observe changes in histone post-translational modification (PTM) levels. These changes indicate it is possible to change the histone pathways to effect gene expression.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Zinda, Joel
- Description:
- The ability to understand the neurophysiological mechanisms that influence any behavior to occur in an organism is the ultimate goal of neurobiology. Neuroscience researchers want to create a neuronal model of the human brain to know how we can produce physiological functions such as walking, throwing, and jumping. Vertebrates have neural structures that are too complex to map neuronal models, so we must start at the invertebrate level. Leeches are simple invertebrates who possess the necessary characteristics to study neuronal regulation. Easily identifiable neurons in the leech allow researchers to record action potential burst activity and evaluate the mechanisms behind physiological functions. Central pattern generators (CPGs) are the “brain” of the leech and are known to control the rhythmic action potential bursting activity that cause certain behaviors to occur. The focus of this investigation was the CPGs that regulate the heart contractions in leeches. Inhibitory heart interneurons 4 (HN(4)) and 7 (HN(7)) within this system of CPGs influence burst activity on heart motor neurons. These heart motor neurons regulate contractions of the heart vessels. Dopamine is a known neuromodulator that either excite or inhibit the bursting of action potentials to produce a variety of behaviors in organisms. The overall goal in this experiment was to assess the effects of dopamine on HN(4) and HN(7) to further establish a model for neuronal regulation in leeches. Response variables of timing and strength of the action potential bursts were calculated before and after different concentrations of dopamine treatment were applied on HN(4) and HN(7). The treatment of dopamine significantly increased the number of spikes in an action potential burst in HN(4) and HN(7), and altered the rhythmic pattern timing of bursting in HN(7). Future experiments will enable researchers to distinguish if these specific inhibitory interneurons regulate the heart contraction by themselves or if the heart motor neurons play the dominate role with a concentration of 1x10-6M dopamine.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Ainslie, Nicholas
- Description:
- Paralemanea is a freshwater red alga genus in the family Lemaneaceae, of which Paralemanea catenata is a member. The cues by which it regulates its triphasic sexual life history are not well known, either in terms of environmental stimuli or mechanisms. The P. catenata genome has not been sequenced, and RNA sequencing was used to perform the initial investigation. Comparing morphological and ecological measurements (total length, internodal length, spermatangial ring height, number of nodes, and node width; temperature, pH, total dissolved solids, photoperiod, salinity, and conductivity) taken over its growing season, in concert with the RNA sequencing data, suggests photoperiod is the environmental stimulus by which P. catenata regulates its life cycle. Involved in this regulation are phototropins and cryptochromes, which are light-sensitive proteins that allow the alga to continuously monitor light levels and respond to this stimulus.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Fleming, Timothy
- Description:
- In 2011 Mars et. al. proposed a novel approach to identifying three different subspecies within European waters of Ulva flexuosa, (subsp. pilifera, paradoxa, and flexuosa). Their use of morphological and molecular techniques to separate each subspecies was used as a guide for this study to determine if these techniques would work for U. flexuosa within California waters. Eleven freshwater, five brackish water, and two saltwater samples of Ulva were collected and were assessed using classic morphological methods and molecular techniques. The molecular methods examined the DNA region ITS1-5.8S-ITS2 (ITS) and the chloroplast RUBISCO LSU (rbcL) genes. The morphological methods followed Mares et al. guide to differentiate between subspecies. All the samples collected, except one, were determined, morphologically to be the within the species criteria for Ulva flexuosa, however, this guide was not able to separate any specimen down to the subspecies level. The molecular analysis suggested that all of the freshwater samples were indeed U. flexuosa and only half of those could be aligned with the subspecies paradoxa. The other freshwater samples did not align themselves with any subspecies and none were aligned with the subspecies pilifera. The samples that were collected in the brackish or saltwater were not shown to be U. flexuosa by molecular analysis but instead two different species either Ulva torta or Ulva linza. The finding of this study suggest that Mares et al. (2011) is not an acceptableguide to assess the identity of U. flexuosa down to the subspecies level with in Southern California, especially in water with higher salinity. The morphological plasticity within the genus Ulva demonstrates the need for more molecular techniques in the identification of U. flexuosa and its subspecies.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Flanders, Elayna
- Description:
- Often the first step in petitioning for a species to be listed under the Endangered Species Act (ESA), or for evaluating management alternatives, is to conduct a population viability analysis (PVA). A PVA is a case-by-case risk analysis used to assess the probability of extinction in the future (Schaffer 1990). PVAs use data on demographic rates, and assumptions about population processes, as well as assumptions about threat conditions and their effects on demography (Doak, et al., 2015). A PVA can indicate the urgency of instituting recovery efforts, identify which demographic rates are particularly important for persistence, and provide information needed to determine eligibility for listing of a species under the ESA. This project assesses whether information needed to run a PVA for species of conservation concern can be found in the Birds of North America (BNA), which is a comprehensive set of species accounts written by recognized experts, for all breeding birds in North America. The BNA was used to document whether data on demographic characteristics, ecological characteristics, and anthropogenic threats were available for each 721 bird species. Because consistent patterns of missing information can help direct research efforts, possible explanations for knowledge gaps of information needed to run a PVA were researched; body mass, ecoregion occupancy, conservation status listing, and taxonomic order were explored as the potential drivers of knowledge gaps. Species mass did not prove to be a significant driving factor; however, limited data were available for analysis. Conservation status listing was not a significant driving factor, data indicated no consistent tendency for listed species to have more or less information known about them. Overall results show that the ecoregions a species occupies (p=0.005) and the taxonomic Order it belongs to (p=0.005) are the best predictors of knowledge gaps for species of breeding birds of North America. Taxonomic Order indicated that anthropogenic threats are either all well known together or all unknown together for bird Orders observed. Additional research is needed to identify why these patterns exist and how to fill the gaps in knowledge. Surprisingly, across all species there was no information about the anthropogenic threats evaluated 42% of the time. Anthropogenic threat studies will become increasingly important as bird populations fluctuate and human impacts on the environment continue to increase.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Holt, Kali
- Description:
- A large portion of nitrogen deposition on southern California’s chaparral and coastal sage scrub (CSS) is due to anthropogenic sources. The implications of increasing soil nitrogen, and the relationship between soil nitrogen and carbon on soil microorganism growth and activity, are not well understood. Possible interactions between N inputs and soil C availability on soil respiration and microbial biomass were assessed in chaparral and CSS plots that have been experimentally treated with N for about 12 years. Soil (microbial + autotrophic) respiration and microbial biomass were measured in four conditions: in plots exposed to added and ambient N, and within these plots, under shrubs and in open spaces, which represent microsites with differing N and C availability. We measured soil respiration and microbial biomass in these conditions every 3 months for a period of 1 year to test the hypothesis that respiration and microbial biomass would (1) increase in plots with higher C and N availability and (2) be higher during the winter and spring because of higher soil water availability. Our results indicate that soil respiration was significantly higher under shrubs but not in plots exposed to added N while microbial biomass was significantly higher in plots exposed to added N but not under shrubs. Soil respiration and microbial biomass were higher in the summer months than during the winter and spring months. These results were observed for both CSS and chaparral, indicating that the effects of long-term N exposure on soil microbial activity and biomass may be general for semiarid shrublands. While speculative, the N-induced increase in microbial biomass, without an increase in activity (respiration), suggests that N exposure has altered the soil microbial community. A change in the soil microbial community has important implications for soil N and C cycling and storage, especially in semi-arid chaparral ecosystems subject to large inputs of atmospheric N.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Zappia, Anthony
- Description:
- The Brazilian savanna, locally known as the Cerrado, is a major ecosystem that covers a vast majority of central Brazil. Little is known about how woody growth within the Cerrado is affected by soil physical and chemical properties. In this study, the relationship between woody growth and soil physical and chemical properties was assessed in upland and seasonally flooded (hyperseasonal) cerrado located in the Cuiaba Basin and Pantanal of Mato Grosso, Brazil, respectively. We sampled from nine vegetation stands representative of the Cerrado. Diameter at breast height, wood cores, and soil nutrient concentration were measured every 5-10 m along a 100 m transect randomly installed in each stand. Correlation coefficients were used to assess the relationships between selected ecosystem and surface soil variables. Wood Carbon (C) storage was positively correlated with nitrogen (N), potassium (K), cation exchange capacity (CEC), and clay/silt soil content but was negatively correlated with sand soil content and bulk density. ANCOVA tests were used to analyze the relationships between C storage and surface soil variables based on site hydrology. There were no differences in the relationships between C storage and soil properties despite different hydrological regimes for upland and hyperseasonal sites. Ultimately, this study suggests that cerrado C storage is nutrient limited. Anthropogenic activities, such as deforestation, cattle ranching, and climate change, within the area could threaten and alter the relationships between cerrado vegetation growth and soil nutrient availability. This study aids in profiling cerrado ecosystem C storage and examines its role as a C sink in the global C cycle
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Teshera, Mark
- Description:
- Most extant bear species are threatened or endangered. One of the species not endangered, the American black bear (Ursus americanus), provides a practical reproductive model that can be applied to the conservation of other ursid species, due to their high abundance and similar reproductive biology. This thesis contains detailed information regarding precopulatory and postcopulatory sexual selection in this species. Specifically, female mate choice, sperm competition, and the possibility of cryptic female choice are examined. This is the first study able to thoroughly examine these reproductive strategies in bears, through the use of an experimental setup. Chapter 1 is comprised of an introduction, experimental aims, and hypotheses. In chapter 2, we demonstrate that females do not select mates based upon morphological traits or social status, and provide evidence indicating that females may use cryptic female choice. Chapter 3 discusses the implications of the results for management of captive and wild bears. We quantified successful mounts (those that resulted in ejaculation), unsuccessful mounts, quivering durations (a proxy for ejaculation quantity), paternity assessment of embryos, and breeding order of males. Our results indicate that large, prime-age, dominant males were not as strongly selected for as mates as would be expected in the wild. Additionally, males that sired embryos did not ejaculate more than non-sires, which is the opposite trend that would be expected in the presence of sperm competition. In fact, the prenatal reproductive success of large, prime, dominant males was significantly less than the postnatal reproductive success of these same types of males in the wild, further calling into question the hypothesis that black bears solely use sperm competition. Our results suggest the need for reevaluation of pre- and postcopulatory sexual selection in black bears.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Stewart, Lauren
- Description:
- Literature focusing on the reproductive mechanisms in bears is often limited and only has a narrow scope. However, with six out of eight bear species being considered threatened or endangered, it seems critical that more information about reproduction be obtained through empirical studies. One of the reasons that little is known about reproduction in bears is due to a variety of reproductive mechanisms that bears have evolved that make studying reproduction difficult. This in addition to their solitary nature, makes long-term studies of wild bears challenging. These reproductive mechanisms include: induced ovulation, pseudopregnancy, delayed implantation (embryonic diapause), seasonal breeding, multiple paternity, and polyestrus (with subsequent ovulation events). The current thesis focuses on two separate, but related, projects that I was involved in, focusing on reproduction in American black bears (Ursus americanus) and the polar bear (Ursus maritimus). In the first portion of my thesis, I re-examine the ovulation mechanism in American black bears, and in the second portion of my thesis, I work to determine whether a captive female polar bear had ovarian activity. In bear biology, it has been accepted that American black bears are coitus-induced ovulators, although there is little empirical evidence that supports this. Induced ovulation is a process in which ovulation is caused by an external stimulus. In Chapter 2, we work to determine whether coitus is the only stimulus that induces ovulation in American black bears. We did this using physiological measures of estrus (vulva score), steroid analyses on urine and serum samples during embryonic diapause, and histology of ovarian structures. All of these measures serve as proxies for or direct evidence of ovulation. Females were categorized into three groups: mated, not observed mating, and isolated. These groups were compared to detect differences in estrus length, length of time it takes to exit estrus after mating, progesterone (P4) concentrations during embryonic diapause and estrogen (E2) patterns during estrus. In the current study, we found that the length of estrus and the time it takes to exit estrus were not statistically different between the female groups. Likewise, we found that the concentrations of P4 during both early and late embryonic diapause were equally elevated. We also found that isolated females exhibited E2 patterns indicative of ovulation. Finally, we confirmed that two of our females that were not observed mating had CL present on their ovaries via histological analysis. From this, we were able to conclude that American black bears are ovulating due to a stimulus other than coitus. We were unable to determine what stimulus, if any, induces ovulation in or if American black bears are spontaneous ovulators due to limitations in study design and the field site. Similar to American black bears, polar bears are also considered coitus-induced ovulators although there is little empirical evidence supporting this. Because polar bears are considered coitus-induced ovulators, it would be expected that a mature female, housed singly, without any male stimuli would exhibit no signs of pseudopregnancy or ovulation due to no possibility for coital or other stimulation. Although this prediction agrees with the current literature, zoo keepers at the Milwaukee County (MKE) Zoo reported that their 30 year old female was exhibiting the behavioral signs of pregnancy. As result, the MKE Zoo asked Dr. Spady to look into ways to determine whether their female was still cycling. Because P4 is associated with pregnancy and pseudopregnancy, and is known to increase after fertilization and again at implantation, we decided to use this as our measure for ovarian activity. Keepers at the MKE Zoo collected fecal samples whenever possible for four years and then shipped them to CSUSM. In the lab at CSUSM, we used liquid phase extraction to separate the steroid metabolites from the fecal samples. We then measured the concentrations of progestins (P) in the samples via an EIA. We found that in 2010 and 2014, the female from the MKE Zoo exhibited P patterns that match what would be expected in a pregnant/pseudopregnant bear. In 2011, we determined that the female was not cycling and likely exhibited a luteal cyst which would have caused elevated P concentrations at times that would otherwise not be expected. In 2015, we also suspected that this female exhibited a luteal cyst due to elevated P concentrations early in the year, but because we do not have samples from later in the year, we were unable to determine if this female exhibited an active luteal phase and was therefore cycling. Because we were able to observe an active luteal phase in this female, we can infer that this female also likely ovulated. Because this female was isolated throughout the study, then it is likely that, like in American black bears, polar bears are not only coitus-induced ovulators. Knowledge obtained through the work of this thesis can be used to better inform both captive and wild management. The fact that ovulation may not require coitus to occur in both American black bears and polar bears means that ovulation and pseudopregnancy are occurring at higher rates than currently expected. If this is true, this knowledge can be used to better inform methods for pregnancy determination. Furthermore, this knowledge can better inform management of captive populations, for example, the reduction of invasive ovulation induction techniques during artificial insemination procedures. There is still much to learn in regards to reproduction in bears, but this thesis reopens issues that may have been misleading researchers in previous years.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Allen, Nickolas
- Description:
- The mitochondrial electron transport chain (mETC) plays a central role in the bioenergetics of all eukaryotic cells. However, the structure of the mETC varies somewhat between plants and higher animals. Plants have a more branched mETC, providing alternative pathways for electron flow, including type II NAD(P)H dehydrogenases (ND) and alternative oxidases (AOX). Recent studies suggest that these “alternative respiratory pathways” may help to minimize the production of reactive oxygen species (ROS) by the mETC. To better understand the connections between mETC structure and ROS production in plants, we transformed Arabidopsis thaliana with several RNAi vectors designed to silence all AOX genes (5 total) or all external ND genes (NDout) (4 total) in the Arabidopsis genome. Real time RT-PCR analyses demonstrated significantly reduced levels of target AOX and NDout transcripts in several transgenic lines. In vivo respiratory assays of AOX-silenced lines showed significantly reduced AOX capacity (~40% reduction) compared to wild-type. Likewise, we saw a decrease in external calcium-dependent NADH oxidation in mitochondria isolated from NDout-silenced lines. Hydrogen peroxide production and lipid peroxidation levels were also measured in AOX- and NDout-silenced lines. The strongest effects were seen in an AOX-silenced line, which showed a 72% increase in leaf H2O2 content in leaf tissue, a 54% increases in H2O2 production in isolated mitochondria, and a 45% increase in total lipid peroxidation. These results suggest that the AOX gene family may play an important role in controlling in vivo mitochondrial ROS production in plants.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Walters, Laura
- Description:
- Although the enzyme polyphenol oxidase (PPO) is well studied for its role in postharvest browning of commercial crops, its specific physiological function in plants is poorly understood. Previous research on the physiological role of PPO in walnut (Juglans regia) suggested that PPO is involved in secondary metabolism, namely in dopamine and esculetin biosynthesis. Dopamine is a precursor to plant-synthesized benzylisoquinoline alkaloids (BIAs) such as codeine and morphine, and esculetin is an antioxidant with promising anticancer properties. This study was performed to further define the role of PPO in the synthesis of esculetin and dopamine-derived metabolites in plants, using walnut, California poppy (Eschscholzia californica), and red clover (Trifolium pratense) as experimental systems. PPO enzyme kinetics and substrate specificity were characterized in each plant system, and PPO function was studied in plants displaying suppressed PPO gene expression (walnut, red clover) or inhibited PPO enzyme activity (poppy). Substrate specificity assays with red clover PPO revealed a lack of activity with substrates relevant to dopamine and esculetin biosynthesis. GC-MS analysis revealed the absence of both dopamine and esculetin in wild-type lines. Collectively, these results suggest that PPO is not involved in dopamine or esculetin biosynthesis in red clover. In walnut, in vitro enzyme kinetic assays suggest that tyramine and caffeic acid are the preferred substrates in PPO-mediated dopamine and esculetin synthesis, respectively. Poppy cell cultures in which PPO enzyme activity was chemically inhibited using the inhibitor kojic acid had significantly reduced BIA content in the culture supernatant compared to control samples. Overall, these results suggest that the previously characterized role of walnut PPO in dopamine and esculetin biosynthesis is not shared in all plant species. Instead, this PPO function may be taxonomically limited, much like previously characterized roles for specific PPO enzymes in betalain synthesis in beets (order Caryophyllales) and aurone synthesis in snapdragons (Antirrhinum majus).
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Lopez, Sarah
- Description:
- In the push to determine a means to decrease the rate of biological aging in humans, conclusions about over-the-counter use of some anti-aging drugs may be premature. Rapamycin is one drug that, while currently prescribed as an immunosuppressant for various organ transplant recipients, is also being investigated by the National Institutes of Health for over-the-counter use. The presence of intestinal parasites (such as helminths) in the United States is rarely noticed, but intestinal parasitic infections do occur in the United States and citizens of the United States have wide access to over-the-counter drugs. Using rapamycin as an over-the-counter option to combat biological aging, without understanding the effects of rapamycin on susceptibility to parasites, may be deleterious. For my thesis, I examined the effects of rapamycin ingestion by hosts on (1) host susceptibility to two parasite species and (2) on growth and reproduction of the parasites. I found that parasitized hosts food intake, or body mass did not differ between diets, but there was a significant initial increase in body mass and food intake decreased after infection regardless of diet. The rapamycin-fed hosts that were infected with nematodes had a significant decrease in parasite specific immunoglobulin (Ig) G1 when compared to the parasitized hosts on control chow, but for mice infected with the cestode there was no difference in parasite-specific IgG1. Despite changes in IgG1 production, the thymus wet mass, total number of thymus cells, and differential white blood cell counts did not differ for parasitized hosts on rapamycin diet compared to parasitized hosts on control diet. Increase in eosinophil production occurred as expected during nematode infection regardless of diet, but was lessened during cestode infection for rapamycin-fed mice. The infection intensity in the host from either parasite did not differ between diets. The worm length for nematodes did not differ between the host diets, but worms taken from hosts on the rapamycin diet had a significant increase in egg output when compared to worms taken from mice on control chow. Cestodes from hosts on the rapamycin diet had a significant increase in worm mass and egg output when compared to worms taken from mice on the control diet. My pursuit to gain knowledge of the effects of rapamycin on hosts with intestinal parasites has left several questions unanswered, but we have determined that rapamycin ingestion by the host may benefit growth and reproduction of some helminth parasites.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Dunning, Andrea
- Description:
- Roads are recognized as a source of increased mortality and restricted movement among populations, and are expected to impact population connectivity. However, roads that are permeable barriers would still allow some degree of gene flow, and reduced abundance near roads might partially offset the smaller number of migrants across the road by increasing the genetic dissimilarity of individuals on either side of the road. Matings that do occur across the road may therefore be negatively assortative with respect to genotype, increasing levels of gene flow. I examined dispersal and gene flow in simulated populations of terrestrial territorial vertebrate organisms with juvenile dispersal, roughly based on Agassiz's Desert Tortoise (Gopherus agassizii), a species known to show population-level changes in abundance near roads. I looked at population abundance and gene flow in the absence roads, compared with populations with roads that are impermeable barriers, roads that are permeable with different levels of mortality, and roads that are impermeable barriers with crossing areas. Increased levels of road mortality significantly decreased population abundance immediately surrounding the road, with the width of the population depletion zone increasing with increasing road mortality. Allele frequency in the immediate vicinity of the road was not affected by the decreased population, and gene flow was maintained across the roads, with only the most deadly road showing some long-term attenuation of gene flow. Decreased population abundance around the road was not accompanied by a corresponding decrease in gene flow. Although roads have well documented negative effects on population abundance, managers should not assume that reduced abundance means reduced gene flow in all cases, and fencing to avoid road mortality is expected to reduce gene flow more than road mortality does in many cases. Conservation actions to prevent road mortality need to also address potential loss of gene flow, and follow up to make sure mitigation measures are effective.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Hentz, Cloe
- Description:
- The tropical savanna of Brazil (cerrado) is extremely species diverse and it encompasses many different physiological features. These physiological differences are influenced by rainfall and nutrient availability in the soil. Plant litter decomposition recycles nutrients from plants to soil and in turn, affects nutrient availability and plant growth. However, the rate at which these nutrients become available to the soil, and how mineralization is affected by litter inputs, are poorly understood. Thus, a field experiment was conducted to assess how litter inputs and reductions affect nitrogen (N) and phosphorus (P) availability. It was hypothesized that N and P mineralization would be significantly influenced by manipulation of the surface litter and that there would be a positive correlation between soil moisture and nutrient mineralization. Results showed that litter inputs or reductions did not significantly affect net mineralization, extractable soil organic carbon (SOC), P, and N, and total mineralization. There were significant differences between sites and over time for net N and SOC mineralization, extractable SOC, N, and P, and total mineralization. There were also site versus time interactions found for net N and SOC mineralization and extractable N and SOC due to the transition between wet to dry seasons within the duration of the experiment. Four variable step-wise regressions (air temperature, relative humidity, soil moisture, and precipitation) helped explain the abiotic factors that contribute to the variance in P, N, and SOC mineralization and extractable P, N, SOC at each site. Our results indicate that a short term manipulative experiment (six months) was not an adequate amount of time to alter nutrient availability in response to litter manipulation. Extending this study could produce significant results and help explain the effects of land use changes on nutrient output in these highly manipulated tropical forests.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Dutt, Shelley
- Description:
- The major objective of immunosuppressive therapy is to mitigate graft rejection while retaining the ability of the immune system to fight pathogens and repair tissue. Immunosuppressant drugs that inhibit mammalian target of rapamycin (mTOR) signaling represent an important class of drugs, but they have been associated with adverse effects, including problems with wound healing, that detract from more extensive use. Derivatives of these drugs, such as everolimus, have been developed, however there have been no prospective studies to monitor wound closure in patients receiving this drug. The objective of this study was to determine whether everolimus impairs wound closure in kidney transplant recipients by monitoring the closure of 3-mm biopsy wounds over a period of 7-9 days and monitoring gene expression in the non-wounded skin. We did not observe a delay in wound closure in patients receiving everolimus and a standard immunosuppressant drug regimen as compared to the control group- patients only on standard immunosuppressant therapy. In addition, no significant changes in autophagy related 13, epidermal growth factor, insulin-like growth factor binding protein 3, interleukin 2, Kruppel-like factor 4, transforming growth factor, beta 1 expression were found. T cell activation and cytokine production were examined within the peripheral blood of the same patients. Interestingly cells isolated from patients receiving everolimus were more sensitive to cell death as compared to the control group. Upon mitogen stimulation, T cells isolated from the control and everolimus administered patients were able to become activated and upregulate CD 69, CD27, and IFN-γ. Together these data suggest that mTOR immunosuppression by everolimus does not independently delay wound closure.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Guerrero, Zarela
- Description:
- This study focused on the in situ leaf decomposition of Artemisia californica Less. using the litterbag method. Litterbags (10 x 10 cm) were constructed using 2 mm mesh screening material for the top cover to allow microarthropods to pass freely and a 0.04 mm mesh bottom to prevent material loss. Litter was collected from two types of A. californica shrubs; ones exposed to elevated N levels (N+) for 8 years and others exposed to ambient N levels (control). Two grams of fresh litter were used to fill each bag, and 96 control litter and 96 N+ litter bags were deployed at the site for a total of 182 bags. Twenty-four bags (12 containing control litter and 12 containing N+ litter) were placed randomly within each of the eight (4 control and 4 N enriched) 10 m x 10 m plots. The bags were periodically brought back to the lab to assess mass loss and litter C and N concentration. Mass loss was determined by drying and weighing the litter remaining in the litter bag and litter N and C concentration was determined by elemental analysis. The hypotheses tested during this experiment were that nitrogen addition was going to cause an increase in litter decomposition rates because of an increase in litter quality; that nitrogen addition was going to cause an increase in mineralization because nitrogen enriched litter will provided more nitrogen for bacterial activity. Finally, that nitrogen addition was going to cause an increase in mineralization because there would be an extra amount of nitrogen in the soil which would decrease the potential for microbial nitrogen limitation. Experimental nitrogen addition altered the chemical composition of the litter by reducing the total carbon (C) and soluble C content of the litter. Litter collected from plots that had been previously enriched with nitrogen (N+) had higher decomposition rates (k-values) than the litter collected from control plots, which means that they lost mass quicker over time. The type of soil that the bags were incubating in did not have any effect on the litter decomposition rate regardless of | 2 the litter’s origin. N+ litter had higher levels of nitrogen concentration over time and litter decomposing in nitrogen enriched soils also had a higher concentration of nitrogen throughout the experiment. Because of the patterns observed throughout this experiment, we can conclude that experimental nitrogen deposition increased litter decomposition rates by improving litter quality (C:N ratio). Understanding how nitrogen deposition affects these communities will help understand how N and C cycling and soil C storage are altered by human-induced N inputs.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Fenner, Andrea
- Description:
- Anthropogenic nitrogen (N) deposition represents a significant input of N into coastal sage scrub (CSS) and chaparral ecosystems of Southern California. Increased N deposition has the potential to alter the decomposition rate of soil organic matter (SOM) in N limited terrestrial ecosystems through altering the enzymatic activity of soil microorganisms that play a key role in the decomposition process. Since few reports have examined the effects of N deposition on the enzymatic activity of soil microorganisms in semi-arid shrublands, this study aimed to determine how N deposition affects the enzymatic activity of microorganisms that drive the decomposition process. Based on results from other ecosystems, we hypothesized that added N would suppress the enzymatic activity of ligninolytic enzymes (phenol oxidase and peroxidase) and would increase the enzymatic activity of the cellulolytic enzyme, p-Nitrophenyl-ß-D-glucosidase. Enzyme assays were conducted on soil samples collected from eight plots located at two field sites where N addition experiments had been conducted over the last 10 years. Field sites were composed of four unmanipulated control plots and four experimental plots, which received 50 kg N/ha annually. Data collected from the chaparral site indicated that there was a significant difference in peroxidase activity between control and N treatment plots (p-value= 0.016) and a significant difference over time for control and treatment plots in p-Nitrophenyl-ß-D-glucosidase activity (p-value= 0.032) and phenol oxidase activity (p-value= 0.003). Data collected from the CSS site indicated that there was a significant difference in peroxidase activity between control and N treatment plots (p-value= 0.010) and a significant difference over time in peroxidase activity (p-value= 0.001). In addition, there was a significant difference over time for control and treatment plots in p-Nitrophenyl-ß-D-glucosidase activity (p-value= 0.0003) and phenol oxidase activity (p-value= 0.001). The decrease in p-Nitrophenyl-ß-D-glucosidase activity and the lack of suppression of phenol oxidase in some added N plots when compared to control plots differed from our initial hypothesis and was inconsistent with other findings from previous literature. However, much of the findings from previous literature focus on how N deposition affects the activity of enzymes involved in the decomposition of litter not SOM, and because peroxidase may be important in the degradation of older structural C, which is typical of soils, it may not be too surprising that our results indicate that only peroxidase was significantly affected by N addition. Little is known about how N deposition affects the enzymatic activity of enzymes involved in the decomposition of SOM, and whether the activity of these enzymes follow the same patterns of those involved in the decomposition of litter. Findings from this study may provide the insight needed to determine how N deposition affects the activity of enzymes involved in the decomposition of SOM thus, giving us a better understanding of how N deposition affects decomposition rates of SOM in semi-arid shrublands.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Bagood, Michelle D.
- Description:
- Hookworm infection in humans causes substantial morbidity; however, the relationship between infection and host exercise has not been quantified experimentally for these types of parasites. Human immune response to hookworms is often modeled using laboratory mice (Mus musculus) infected with the intestinal nematode Heligmosomoides bakeri. I used this model to test (1) if voluntary exercise prior to infection would affect susceptibility of mice to H. bakeri, (2) if H. bakeri infection would change voluntary exercise of mice during the early (acute) and late (chronic) stages of infection, (3) if H. bakeri infection or voluntary exercise would alter energy acquisition/allocation of mice, and (4) if blood physiology had a relationship to either voluntary exercise or H. bakeri infection. I found no effects of voluntary exercise on infection susceptibility, as measured by systemic levels of H. bakeri specific immunoglobulin G1 (IgG1), infection intensity, parasite sex ratio, and parasite reproduction. I found no effects of H. bakeri infection on voluntary exercise, as measured by wheel running parameters and home cage activity. Voluntary exercise decreased apparent dry matter digestibility (DMD), but increased food intake, resulting in increased total body mass. H. bakeri infection increased DMD, but had no effect on food intake, and increased total body mass by the end of the experiment. Actual energy assimilated (after accounting for food intake and digestibility) increased with voluntary exercise, but did not change with H. bakeri infection. H. bakeri infection caused an increase in the small intestine mass per length, small intestine length and spleen mass, but a decrease in stomach, liver, and heart masses, while exercise increased cecum and liver masses. Overall, the data suggest that infection and exercise placed different demands, and in response the mice adjusted their energy acquisition and body composition accordingly. Additionally, I found blood physiology changed for both voluntary exercise and H. bakeri infection, again in very different ways. Non-exercised mice had decreased hematocrit on Day 14 post-infection (PI), while exercised mice had increased hematocrit on Day 6 PI and then levels returned to baseline on Day 14 PI. Hematocrit levels for infected mice increased on Day 6 PI and then decreased below baseline on Day 14 PI. Also, infected mice had 8% lower hemoglobin levels than uninfected mice on Day 14 PI. Blood physiology varied among exercised and infected mice, but because these changes were only tested on certain days of the experiment they did not show a clear effect of either treatment. Taken together, my data showed that voluntary exercise and H. bakeri infection separately and distinctly affected how the mouse acquired energy, where the mouse invested that energy (in terms of organ masses and fat/lean tissues), and how blood components changed.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Croyle, Kaitlin
- Description:
- Endangered species propagation is an important component of wildlife conservation. Perivitelline membrane (PVM)-bound sperm detection has recently been incorporated into avian breeding programs to assess egg fertility, verify breeding or artificial insemination, and to evaluate male reproductive status. Due to similarities between avian and chelonian egg structure and development, 191 eggs representing 17 turtle and tortoise species were used to determine PVM-bound sperm presence and the potential for use in breeding management and research. Presumed fertile Centrochelys sulcata, Manouria emys, and Stigmochelys pardalis eggs were acquired to evaluate the effect of incubation and storage on the ability to detect sperm. Recovered membranes were stained with Hoechst 33342 and examined for sperm presence using fluorescence microscopy. Mitochondrial DNA was isolated, amplified, and sequenced from freshly laid Astrochelys radiate, C. sulcata, and S. pardalis eggs exhibiting PVM-bound sperm. Sperm were positively identified for up to 206 days post-oviposition following storage, cooling, and/or incubation. Microbial infection frequently hindered the ability to detect sperm. Storage at -20 degrees Celsius was found to be the best method for preserving eggs prior to analysis. PVM-bound sperm detection is a promising tool for the reproductive management of both captive and wild populations of turtles and tortoises. Sperm-derived mtDNA has applications for species identification, parentage analysis, and the study of sperm competition. This project is the first to successfully demonstrate the presence and use of PVM-bound sperm detection in chelonian eggs.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Rupert, Shannon Marie
- Description:
- According to sex allocation theory and evolutionarily stable strategy models, several characteristics, including a greater than twofold increase in male fitness, are required for functional androdioecy. Lloydia serotina (Liliaceae ), a morphologically androdioecious alpine lily, exhibits most of these characteristics: populations contain many more hermaphrodites than males and both sexes produce viable pollen. Pollen production is roughly equal between sexes, however, so the increase in fitness in males is not due to pollen production. To determine whether alternative variables could account for enhanced fitness in males, populations of L. serotina were studied in Olympic National Park and Niwot Ridge Biosphere Reserve using both observational and manipulative experiments. Bulb size was significantly larger in males than in both hermaphrodite and non-flowering plants, suggesting the possibility that males flower more frequently. Manipulative experiments comparing resource allocation patterns suggested that males allocate more of their post-maintenance energy to clonal reproduction early in the growing season. Thus, trade-offs in vegetative versus sexual reproduction may increase fitness in males when pollen production cannot. Males may be maintained in populations of L. serotina because they devote resources not used for female function to vegetative reproduction while retaining full male function, thus increasing the males' fitness component. These factors may create the necessary twofold increase in fitness in males required to maintain them over evolutionary time.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Miller, Julie
- Description:
- This research investigates the reproductive biology of the California state threatened plant, Hazardia orcuttii (Asteraceae). The only documented U.S. location of this perennial shrub. is in Encinitas, San Diego County, California. Very little ecological or life history data existed for this plant, since its first local record in 1981. Shrub and inflorescence reproductive phenology studies reveal long flowering and seed-producing seasons (6 months and 5.5 months respectively). Shrubs of different sizes show little difference in their flowering phenology (budding and seeding at the same times). Smallest shrubs bloom longer and start producing seeds later. Germination was tested under varying conditions of temperature, light, soil type and soil moisture. Hazardia orcuttii germinates better in alternating photoperiods than in dark, indicating soil or leaf cover may not be a favored environment for recruitment. Four temperature regimes were tested (temperatures oscillated with light and dark, high temperatures correlating with light). These regimes were alternating 20°CI12°C, 25°C/18°C, 15°C/8°C and steady15°C. H orcuttii germinated best in steady 15°C (average temperature of a Southern California fall day) (83 percent). The most achenes germinated in loamy sand (7 5 percent )percent) compared to sandy loam or sandy clay and in higher soil moisture (20 percent) compared to 15 or 10 percent. Of significance is zero (0) seeds germinated in 10 percent moisture/sandy clay, which is the soil ~exture in native areas surrounding existing shrubs. There is a strong interaction between soil texture and soil moisture variables. In soil types sandy loam and sandy clay, 5 to 50 percent of achenes did not germinate but were viable. Viable achene production was estimated over monthly intervals. Achenes produced by shrubs greater than 55 em, averaged 6.5 percent viability, while shrubs 55 em or less produced zero (0) percent viable seeds. The most and least viable achenes were produced in November and March respectively. There was a high amount of insect damage to achenes, affecting number of viable achenes. The percentage of insect damaged achenes was between 24 and 63 percent. This research substantially increases the understanding of the reproductive ecology of this rare plant and can serve to aid in developing better conservation and restoration efforts, because the soil germination data obtained will assist with future re-introduction projects. Keywords: reproduction, seed, germination, phenology, Asteraceae, Hazardia orcuttii.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Porter, William R
- Description:
- Many biologists use passive-infrared motion detectors (PIDs) to monitor the motion or presence of warm-blooded animals in their research. This study determined some of the capabilities of a commercially available PID. Three small-mammal proxies (4.45 em, 14.7 em, and 21.5 em containers of warm water) were passed in front of eight identical PIDs. The PID responses (at conditions of 0.5 to 10 oc above background, 0.5 m to 16m distance, and 1 to 120 crn/s velocity) confirmed that target size, distance, subject -background temperature difference (L\ T), and velocity are primary variables and helped define the detection limits of the PID. Tests using a fixed L\ T and constant angular velocity showed that PID detection of the three different proxy sizes was equal for equal angular size. The repeatability of PID detections was highly consistent, but with a small directional dependency. There was some variation in overall sensitivity between PIDs, also with a directional bias. Tests on a large dog were used to calculate a proxy size (0.476 m2 ) that could have been substituted for the dog. Best use of PIDs by biologists depends on knowledge of PID capabilities and on use of motion-trap designs that maximize reliable capture rates by the PID. The test results here, while partially specific to this PID configuration, will provide biologists with a basic understanding of PID capabilities potentially useful in their own research. Keywords infrared, monitoring, motion detector, passive infrared detector, PID, PIR, sensor, trap, wildlife
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Snow, Robin M
- Description:
- The importance of perennial access to water for invasive plants in arid environments was examined at eighteen sites containing Eucalyptus groves in proximity to a water source within San Diego County between June I stand September 30111, 2009. Diameter at breast height (d.b.h.) measurements, a useful indicator of tree size, were measured along transect lines at each site prior to September. D.b.h. distribution curves were examined for significant gaps which should indicate missing cohorts, which were expected where water is intermittent due to variation in germination rates and seedling mortality during drought conditions. In September, the peak of the dry season, each site was evaluated for water presence in the stream bed, evidence of seedling mortality and surface soil moisture. Arc View 9.2 software was used to gather data on elevation, slope (mean, s), proportion of sandy loam type soil present, and to digitize polygons around the canopy area of study sites. Soil type, surface soil moisture, seedling prevalence, slope, and September presence of water were evaluated as predictors of total canopy area, proportion of seedlings present, and proportion of significant gaps in the size class distribution. The total canopy area and proportion of seedlings could not be predicted using the measured variables, however, the proportion of significant gaps was explained by slope (s), seedling proportion, gap cutoff size, soil moisture at Om from the stream bed and September water presence (an indicator of perennial access to water). The low number of gaps seen at sites with access to perennial water sources suggests that continuous access to water is a risk factor for river red gum establishment and recruitment. Alteration of the natural flow regime, from seasonal to perennial, by supplemental water inputs may represent an emerging threat to riparian ecosystems in semi-arid environments. KEYWORDS California, Eucalyptus, impacts, invasive, riparian, water Item only available to the CSUSM community. Authentication with campus user name and password required.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Kroon, Joanna L
- Description:
- Cortaderia selloana, or pampas grass, is a serious invader of disturbed, coastal and riparian ecosystems in Southern California. The purpose of this study was to determine how the growth and physiology of C. selloana respond to various combinations of soil nitrogen and water table depth. Growth factors examined included plant biomass, plant height and width, number of tillers per plant and specific leaf area (SLA). Physiological factors examined included water use, photosynthesis and tissue nitrogen and phosphorous contents. These response variables were examined in a manipulative study using a 2 x 3 random factoral design with two water table and three nitrogen levels. Water, nitrogen and the interaction between the two were found to have a significant influence on many of the growth and physiological factors of Cortaderia selloana. Added nitrogen caused increases in plant biomass that were 5 to 9 times higher than plants exposed to ambient nitrogen. Both water and nitrogen influenced the number of tillers per plant, where a lower water table and higher nitrogen availability caused an increase in the number of tillers. C. selloana also responded to increased water and nitrogen with greater average plant height and reduced plant width. By examining which plant response factors are enhanced by the various combinations of water and nitrogen treatments, we hope to gain insight into the invasive nature and success of C. selloana in order to ultimately find less destructive methods to control and prevent the invasion of this invasive grass in the future. Keywords: Biomass, Cortaderia selloana, Disturbed ecosystems, Invasive species, Pampas grass, Riparian ecosystems, Specific leaf area
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Zorba-Denison, Gypsiana
- Description:
- Southern California's geography and expanding population have caused an increasing amount of atmospheric nitrogen (N) deposition into semi-arid shrubland ecosystems. However, the effects of N deposition on semi-arid shrublands of Southern California are still poorly known and must be addressed. This research investigated soil nitrogen storage in several areas of Southern California, which received different levels of exposure to atmospheric nitrogen pollution. Soil samples from five sites of varying atmospheric deposition were analyzed for available and total N, and C, pH and soil organic matter content. The results indicate that soil derived from sites with high pollution exposure had correspondingly higher total N and extractable N, lower pH, and lower C:N ratios than sites with lower pollution exposure. Analysis of resin bags buried below the soil surface (0-1 0 em) showed that accumulation rates of both NH4 and N03 were 1-2 orders of magnitude higher at polluted air sites than at clean air sites, and that soil pH was 0.5 pH point lower in high N pollution sites. These data suggest that atmospheric N deposition can significantly increase soil N storage and rates of N cycling in southern California shrublands. Key words: Nitrogen, carbon, storage, cycling, deposition, C:N, chaparral, coastal sage scrub.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Stricker, Kelcey
- Description:
- Human induced fragmentation of habitat through urbanization and road construction blocks routes of immigration and emigration for wildlife and can interrupt metapopulation dynamics, leading to localized extinction events. To determine the effect of the I-15 highway on the mammalian mesopredator community composition in a protected wildlife corridor, the Santa Ana Palomar Mountains Linkage (SAPML), 32 camera stations (e.g. camera traps) were placed at varying distances from the road from 2012-2013. Cameras were also placed at the entrances to culverts that run under the I-15 in an attempt to capture mammals that may pass under the road. Out of 1043 sampling days, 765 video clips were captured of which 232 recorded positive detections of the focal species. While distance from road and noise pollution from traffic were predicted to have the greatest effects on mammalian community composition, habitat type was found to be the strongest predictor of detection of bobcat (Lynx rufus), coyote (Canis latrans), and gray fox (Urocyon cinereoargenteus). There were an insufficient number of video clips recorded of mammalian wildlife using the culverts, limiting the ability to conduct a rigorous statistical analysis on the effectiveness of culverts as wildlife passages in the SAPML. However, anecdotal evidence suggests that at least some individuals of coyote, bobcat, gray fox, and raccoon (Procyon lotor) are successfully moving through these culverts.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Williams, David Earl
- Description:
- While performing, racehorses use the transverse gallop gait. When a racehorse begins to gallop, it must use either the right lead stride pattern (RLSP) or the left lead stride pattern (LLSP). When racehorses make a trot-to-gallop transition, 91% start with their RLSP and 9% start with their LLSP (n=209). When breaking from the gate, 90% of all racehorses use their RLSP and 10% use their LLSP (n=9,116). When individual horses were observed breaking from the gate in five to seven races, they used the same lead 94% of the time (n=32). When a mirror image of the hoofprints from a RLSP was superimposed on the hoofprints of a LLSP for the same racehorse, the placement of the hoofprints was not identical. This suggests that running efficiency might be different in the RLSP and the LLSP. The preference of stride patterns, along with a potential differences in efficiency, could have important consequences for racehorse performance.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Whalen, William E
- Description:
- The ubiquitous coccolithophore Emiliania huxleyi (E. huxley1) plays a significant role in global short-and long tenn oceanic carbon flux, warranting the recent sequencing of this organism by the United States Department of Energy Joint Genome Institute. Further progress in the study of the genomics, especially gene regulation of responses to the environment, for this keystone calcifying marine alga requires the development of a reliable method for genetic transfonnation. This report details efforts to develop a genetic transformation system for E. huxleyi. This includes the identification and characterization of a selective marker/agent system, the bialaphos resistance (BAR) gene and glufosinate ammonium; the development of DNA constructs containing the BAR gene driven by an endogenous promoter; testing of DNA delivery tools (primarily microparticle bombardment); post treatment selective culture for enrichment of potential transformants; and verification of transformation using real-time PCR and Western blots. Although the evidence of transient expression of foreign genes in the treated Emiliania huxleyi strain 1516 cells. cells was promising, and our efforts help pave the way for further development, more work is needed to secure a reliable genetic transfonnation system for E. huxleyi. Keywords: Haptophyte algae, coccolithophore, Emiliania huxleyi, genetic transformation, electroporation, microparticle bombardment, bialaphos resistance, BAR gene, glufosinate ammonium.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Veazey, Gregory Darryl
- Description:
- White Spot Syndrome Virus (WSSV), a dsDNA virus, is the most important viral pathogen in cultured penaeid shrimp worldwide. In cultured shrimp, WSSV infection can reach a cumulative mortality of up to 100% within 3-10 days upon infection. Intensive shrimp cultivation, inadequate sanitation, and worldwide trade have aggravated the disease dissemination. As such, WSSV has become an epizootic disease and is not only a major threat to shrimp culture but also to marine ecology. In recent years, considerable progress has been made in characterizing the WSSV at the molecular level and developing highly sensitive methods for WSSV detection. However, information pertaining to shrimp cellular genes that are involved in WSSVhost interaction is very limited. To address this issue, this research project took an expressed sequence tags (ESTs) approach to isolate and characterize randomly selected eDNA clones from a hepatopancreas eDNA library ofWSSV-infected shrimp, in order to isolate genes that might play a role in WSSV pathogenesis. The expression of immune/receptor genes, lectin (PsEST 640) and a low-density lipoprotein receptor (PsEST 160) were identified by EST analysis, were measured by RT-PCR. Real-time quantitative (RT-PCR) using SYBR Green chemistry has been shown to be a rapid and highly sensitive detection method for shrimp viruses as well as to measure cellular gene expression in shrimp. A statistically significant difference was observed in the expression of lectin at 32 h p.i. with upregulation in healthy compared to that ofWSSV-infected. LDLr, a receptor known to interact with viruses, had increased expression in the WSSV-infected individuals at 4 h p.i. compared to the healthy. Our data suggests that lectin is a highly diverse, inducible protein that may play a direct/indirect role in either binding WSSV and/or initiating some humoral defense mechanism (i.e. prophenoloxidase cascade). In addition, LDLr gene was found to play a role in shrimp-WSSV interaction, and possibly be a receptor to which the virus binds.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Urbach, Michael Jay
- Description:
- In aquaculture facilities worldwide, T enacibaculum maritimum is a common marine pathogen that infects important marine fish species causing flexibacteriosis. Monitoring T. maritimum levels is important for effective treatment to mediate possible outbreaks and to avoid the spread of disease and associated mortalities. In an effort to improve surveillance for the presence of T. maritimum, a rapid, real time PCR assay was developed. By amplification and detection of the 16s ribosomal gene using TaqMan chemistry, relative quantitation of the pathogen is possible from mixed environmental water samples. This protocol allows T. maritimum levels to be assayed quickly from seawater samples without obtaining invasive tissue samples and prior to presentation of gross signs of infection. Keywords: Real-time PCR, Tenacibaculum maritimus, Pathogen assay, TaqMan
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Tamulis, Walter Gregory
- Description:
- Retrotransposons encompass a specific class of mobile genetic elements that are widespread across eukaryotic genomes, the impact of which are just beginning to be deciphered. In a step towards understanding their role in litopenaied shrimp, we have herein identified ten non-LTR retrotransposons and their putative phylogenetic placement. Two Litopenaeus stylirostris elements were discovered through standard and degenerate PCR amplification using previously defined non-L TR primers. A third genomic L. stylirostris element was identified using specific priming from an amplification protocol. These three PCR-derived sequences showed conserved domains of the non-LTR reverse transcriptase gene. A degenerate, 3' located non-L TR retrotransposon showing homology to ZEPP elements was isolated through screening of an L. stylirostris genomic library. In silica searching of genome databases and subsequent contig construction yielded six non-LTR retrotransposons (both genomic and expressed) in the Litopenaeus vannamei genome that also exhibited the highly conserved domains. Phylogenetic placement among representatives from all non-LTR clades showed a possibly novel monophyletic group. This group included elements from both L. stylirostris and L. vannamei and appeared most closely related to the highly active R TE clade. Our remaining four sequences placed in the CRl and I clades of retrotransposons, with one showing high similarity to ancient Penelope elements. This research identifies active retrotransposons in litopenaied genomes. Keywords: retrotransposon, litopenaied, penaied, non-LTR, IHHNV
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Stutzer, Gregory Martin
- Description:
- Biotelemetry studies assume that vital biological processes are unaffected by the attachment method and presence of the transmitter. I examined the effects surgically implanted transmitters (representing 0.2-0.9 % of body weight) had on feeding activity, growth, tissue reaction, and survival of 70 adult white seabass, Atractoscion nobilis, (72.5-120.4 em total length) over a 451-day period. On day 97 (expected transmitter life), analysis of growth in standard length revealed no significant difference among fish exposed only to handling and anesthesia (controls), surgery but no implanted transmitter (sham-surgery), dummy transmitters surgically implanted (dummy-surgery), and functional transmitters surgically implanted (active-surgery). However, during this period active-surgery fish gained significantly less weight than sham-surgery fish. No significant difference in growth occurred among control, sham-surgery, and dummy-tagged fish over the remaining 354 days of the study. Differences in feeding activity of fish among the four treatment groups were significant during 12 recorded feeding trials over the first 32 days, but were likely influenced by the behavior of a few dominant individuals .. Incision healing was complete after 97 days, with light necrosis at the insertion points of sutures. All transmitters were completely encapsulated by fibrous connective tissue within 97 days. No gross morphological differences were observed in the tissue encapsulating dummy or active transmitters, and no fish expelled transmitters through the body wall, via the intestinal tract, or incision site over the 451 day study period. Two mortalities occurred during the study when sham-surgery fish died on day 17 and 41. My results show that with the described surgical procedures, intraperitoneal implantation provides a suitable technique for future biotelemetry studies on adult white seabass.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Steinberg, Judith Skye
- Description:
- Serial analysis of gene expression (SAGE) was used to examine gene expression profiles of healthy (pathogen-free) Litopenaeus stylirostris. Of the one thousand eight hundred forty-two SAGE clones sequenced, we found seven thousand six hundred and sixtysix SAGE tags. Transcript identification of the healthy L. stylirostris SAGE tags was completed using the reference databases, from SAGEmap. A total of six thousand five hundred forty SAGE tags to gene assignments were matched to a UniGene ID. The set of reliable SAGE tags were used to biologically characterize their function using the Gene Ontology database. SAGE tags that represented transcripts that encode genes found in the Gene Ontology database were divided into seventeen categories according to the major functions of their encoded proteins. From these characterized genes, one hundred four genes were found to be immunity related genes, some which have been seen for the first time in penaeid shrimp, such as neutrophil cytosolic factor 1, and eosonophil peroxidase. The genes identified in this healthy L. stylirostris SAGE library are just the beginning to understanding global gene expression in shrimp. Future research includes sequencing an infectious hypodermal and hematopoietic necrosis virus (lliHNV) infected L. stylirostris SAGE library to compare to the healthy L. stylirostris SAGE library and analyze gene expression of immune related genes including what has been found in this research. Key Words: Litopenaeus. stylirostris, Serial Analysis of Gene Expression; penaeid, innate immunity, ditag, SAGEmap
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Solomon, Christopher R
- Description:
- Of the two rhesus macaque subspecies used for AIDS studies, the Simian immunodeficiency virus-infected Indian rhesus macaque (Macaca mulatta) is the most established model of HIV infection, providing both insight into pathogenesis and a system for testing novel vaccines. Despite the Chinese rhesus macaque potentially being a more relevant model for AIDS outcomes than the Indian rhesus macaque, the Chinese-origin rhesus macaques have not been as well-characterized for their major histocompatibility complex (MHC) composition and function, reducing their greater utilization. In this study, we characterized a total of 50 unique Chinese rhesus macaques from several varying origins for their entire MHC class I allele composition and identified a total of 58 unique complete MHC class I sequences. Only nine of the sequences had been associated with Indian rhesus macaques, and 28/58 (48.3%) ofthe sequences identified were noveL From all MHC alleles detected, we prioritized Mamu-AJ *02201 for functional characterization based on its higher frequency of expression. Upon the development of MHC/peptide binding assays and definition of its associated motif, we revealed that this allele shares peptide binding characteristics with the HLA-B7 supertype, the most frequent supertype in human populations. These studies provide the first functional characterization of an MHC class I molecule in the context of Chinese rhesus macaques and the first instance of HLA-B7 analogy for rhesus macaques. Keywords: MHC, liLA, SIV, CTL, Rhesus macaque
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Sendall, Kerrie
- Description:
- Measurements of the leaf photosynthetic light response, water potential, and specific leaf area of two tropical transitional forest tree species, Tovomita schomburgkii and Brosimum lactescens, were quantified to establish how these properties are affected by seasonal variations in rainfall and leaf canopy position. The study was conducted at a site near Sinop Mato Grosso, Brazil, which is located within the ecotone of savanna and tropical rain forest. Understory T. schomburgkii leaves showed no significant difference in water potential ('I'L) between the dry season (June-Sept.) and the wet season (Dec.-Feb.); however mid-and upper-canopy leaves of both species exhibited significantly lower water potential during the dry season. Both species exhibited seasonal variations in light saturated photosynthesis (P m), dark respiration (Rd), and maximum stomatal conductance (gmax) which were positively correlated with precipitation. Internal leaf C02 concentrations (Ci) were consistently lower during the dry season suggesting that declines in stomatal conductance of C02 caused decreased levels of maximum photosynthesis. During the wet season P m and RI of both species were significantly negatively correlated with specific leaf area (SLA) but during the dry season this correlation was only observed in T. schomburgkii. These results suggest that seasonal drought has important implications for the physiology of semi-deciduous Amazonian forest trees and that the seasonal trends ofPm, RJ, and gmax are more comparable to savanna than to tropical rain forest. Keywords: photosynthesis, seasonality, tropical transitional forest, Tovomita schomburgkii, Brosimum lactescens
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Rosaler, Jeffrey R
- Description:
- The annealing algorithm in MARXAN was used to build possible marine reserves by selecting the best of 26 heterogeneous rocky intertidal sites using various modeling parameters. Because comprehensive data on biological diversity is impractical to gather for large areas, four surrogate data sets were used to design marine reserves; habitat, substrate, mobile species abundance and sessile species percent coverage. Habitat data was quantitatively assessed for the entire 7.12 miles of Laguna Beach coastline. Habitat characteristics observed were; substrate type; formation type; slope; habitat heterogeneity; presence of microhabitats and wave exposure. The habitat data was used to develop a map and database of these heterogeneous intertidal areas in ArcGIS. Using the ArcGIS, substrate coverage in square feet was determined for each site. Species assemblage data was collected for 26 of the rocky intertidal sites. Macro-algae and macro-invertebrate abundance and coverage were quantified for a 30 m2 area of each site. Three transeets and nine quadrats were placed at random within the 30 rn2 area to determine mobile species abundance and sessile species percent coverage. Variable by site Multi Dimensional Scaling showed similarities between surrogates and Canonical Correspondence Analysis ordination displayed a significant correlation between substrate and species distribution. MARXAN was used to develop a network of sites for each biodiversity surrogate, conserving 10%, 30% and 50% of the surrogate input variables and minimizing the sites chosen. Mean species richness and diversity were higher in the sites chosen to be included in a reserve than outside a reserve, for the mobile and sessile surrogates. Mean species richness and diversity were higher for reserves designed based on species assemblages than reserves designed based on habitat or substrate, but not significantly so. These findings suggest that habitat level surrogates would be an effective method to identify valuable intertidal areas as high priority sites for inclusion in a larger MP A network. Site irreplaceability analysis determined that several sites were chosen > 65% of the time for all annealing runs. The habitat at these sites suggests that two different types of intertidal produce unique species assemblages: low sloping boulder fields and large areas of bedrock bench. Given that different habitats produce diverse species assemblages, it would therefore be important to include representatives of multiple intertidal habitat variations in a reserve network. Keywords Marine reserves, habitat diversity, species richness, species diversity, rocky intertidal habitat, marine protected areas, MARXAN, coastal resource management.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Robles-Sikisaka, Refugio
- Description:
- Taura syndrome disease, caused by Taura syndrome virus (TSV), is one of the most important viral diseases of penaeid shrimp in the Western Hemisphere. A 3278 bp eDNA representing the 3' end of the TSV genome was cloned and sequenced. Sequence analyses revealed a 5'-terminal 19 non -coding bases followed by a long open reading frame encoding 10 11 amino acids (aa), and a 3' untranslated region of 225 nts. The deduced aa sequence of TSV showed significant similarities with those of the coat proteins of several insect picomaviruses. A single transcript of approximately 10 kb was detected by Northern blot hybridization suggesting that the TSV coat protein gene is not expressed as a subgenomic RNA. The genome organization ofTSV is similar to insect picornaviruses. Therefore, this is the first molecular evidence of occurrence of a picomavirus in the class Decapoda. The putative VP2 and VP3 capsid protein genes ofTSV from 17 geographical isolates collected from US, Mexico and Taiwan were amplified by RT-PCR to assess the genetic diversity and phylogenetic relationships among isolates. Alignment of the capsid proteins showed nonconservative changes that may be involved in antigenicity and/ or virulence of the isolates. Phylogenetic analyses revealed that the TSV isolates clustered in two main groups, one Mexican group and one mixed group of Mexican, Taiwan and Texas isolates indicating a shared phylogenetic relationship and a possible common origin.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Robertson, Lyndsey
- Description:
- The overall objective of this research was to identify and characterize the myostatin or myostatin-like gene sequence in the commercially important aquaculture species Litopenaeus stylirostris. Myostatin is a negative regulator of muscle growth and when disrupted can cause a "double muscled" phenotype (McPherron et al., 1997). Two main approaches were taken: the first was to isolate an mRNA (eDNA) copy and the second was to identify a genomic copy of the gene. The methodologies used were a eDNA PCR screen, screening a genomic library and a genomic PCR screen. Our results indicate there is at least one form of the TGF-B superfamily of genes present in the L. stylirostris genome. The isolated gene fragment is an exact match to the L. vannamei TGF-B sequence. Additional characterization of our sequence indicates that it most closely resembles a BMP6 type TGF-B gene. Our fragment is located in the 3' highly conserved C terminus region, common to all TGF-B gene members, and just downstream of the proteolytic processing site. This research lays the groundwork and provides promising progress towards the isolation and characterization of important TGF-B genes in L. stylirostris that potentially control or regulate growth in this important aquaculture shrimp. The characterization of growth related genes from an animal of commercial importance such as L. stylirostris can lead to important contributions that will positively impact the shrimp aquaculture industry. Key words: Litopenaeus stylirostris, shrimp, myostatin, transforming growth factor beta superfamily (TGF-B).
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Lawrence, Shelley
- Description:
- Coastal sage scrub and chaparral vegetation of Southern California have become fragmented due to a loss of habitat over the past several decades, which has been caused by several contributing factors such as agriculture, urbanization, increased fire frequency and intensity. Although nitrogen deposition has also been found to be a contributing factor to the loss of coastal sage scrub (CSS) and chaparral habitats in previous studies, the mechanism for these effects not been examined. Leaf tissue from existing field plots, fertilized with nitrogen since 2003, was analyzed for carbon allocation patterns and nutrient retention on a seasonal and annual basis from 2006, 2008 and 2010. Nitrogen fertilization did not have an effect on carbon allocation to cellulose, holocellulose or lignin fractions of leaf tissue in CSS California sagebrush (Artemisia californica) or chaparral chamise (Adenostoma fasciculatum) shrubs. However, it was found that seasonal and interannual variation in soluble carbon were highest in both species, but without any N treatment interaction. It was also found that year and season did have a significant effect on carbon allocation, and these temporal variations were correlated with precipitation rates and nutrient availability. The lack of nitrogen effect in the soluble carbon, holocellulose and lignin fractions suggests these avenues of carbon allocation are linked to life history traits that are specific to each species such as drought tolerance, woodiness, and maturation.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Sette, Alex, Greenbaum, Jason, Lopez, Colleen, Fu, Alex, Peters, Bjoern, Mothe, Bianca, and Lopez, Matias
- Description:
- Next generation sequencing (NGS) technology has revolutionized the ability to identify important gene sets, including Major Histocompatibility Complex (MHC) alleles, the most polymorphic set of genes in the human and non-human primate genomes. The characterization of MHC class I and II alleles serves various roles in the development of resources and tools needed for vaccine development. In this study, we explored the use of the Illumina MiSeq sequencing system along with the development of software tools to identify MHC class I A and B loci in rhesus macaques. The MiSeq platform combines shotgun sequencing and bridge PCR to provide a high degree of sequence coverage through millions of short reads. The large quantity of reads allows for the statistical exclusion of sequencing errors present in the sequence data. As an alternative to commercially available packages, this study presents the software code for an easily adaptable, user-friendly analysis tool that can be used to genotype rhesus macaques MHC alleles with next generation sequencing data. This tool, referred to as the “Allele Identification Program” (AIP), can be employed by anyone possessing basic computer programming skills. Using the AIP to analyze the MiSeq data proved effective, efficient and inexpensive, potentially making full-length MHC sequencing more accessible for nonhuman primate research.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Nassirpour, Rounak
- Description:
- Arginine-vasopressin (AVP) is a member of the oxytocin/vasopressin family, which are structurally related nonapeptides. A VP-immunoreactivity (A VPD was localized to a set of neurons in the central nervous system (CNS) of the medicinal leech using hnrnunocytochemistry. Although the general staining pattern in the midbody ganglia is confined to 5 bilateral pairs of neurons, there are variations to this immunoreactivity. Of particular interest is a pair of immunoreactive neurons in the head brain area that based on anatomy could be classified as projection neurons. The A VPI seems to be confined to the CNS. Attempts at isolating the immunoreactive substance from the nerve cord extract through SDS-PAGE and western immunoblot analysis were unsuccessful probably due to the small molecular size of the peptide. Bath-application of 104 - 1 o-s M concentrations of synthetic A VP caused a highly pronounced hyperpolarization effect in the heart excitatory (HE) motor neurons in 100% of the experiments performed. Further analysis revealed that A VP is not affecting the heart central pattern generators and is modifying the HE neurons directly. In 60% of the current injection studies we observed a change in the membrane properties ofthe HE cells indicative of ion channels opening. Since this second effect far outlasted the hyperpolarization effect, it seems that A VP might have two independent effects on the HE motor neurons. In addition, due to the long period of time required for the onset of the effect to occur, we believe that A VP is acting through a modulatory synapse. These findings extend the oxytocin/vasopressin-like peptides in the annelid phylum to include Hirudo medicinalis. Item only available to the CSUSM community. Authentication with campus user name and password required.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Mustard, Robert R
- Description:
- Southern California native plant communities, such as coastal sage scrub (CSS) and chaparral, are subject to a wide range of atmospheric nitrogen deposition produced from anthropogenic sources. The effect ofN deposition on the soils of two such plant communities-Santa Margarita Ecological Reserve (CSS) and Sky Oaks Field Station (chaparral) -was recently studied (90, 92). An in situ N-addition experiment has been conducted at these two sites to simulate deposition of atmospheric nitrogen compounds. Permanent plots (1 0 x 1Om) were exposed either to ambient N deposition alone (the control plots), or received an additional 50 kg N ha"1 yr-1 ofNIW03 fertilizer (experimental plots) during the fall. Microbial biomass and extractable inorganic nitrogen (N03-+ NJ4) concentrations were measured every three months over a one-year period. Extracts of soil samples from theN-added plots at both Santa Margarita and Sky Oaks had significantly higher levels of N03-than the control plots. There were no significant differences in microbial biomass between treatments (control v. manipulated (N-added)) at the two sites; there were significant effects of time on microbial biomass at both sites, however. The rates of microbial transformation of nitrogenous compounds were also examined over a ten-day period of soil incubation under controlled conditions. There were no differences in the potential for net ammonification between the control and VI N-added plots at either site. There was, however, a significant increase in potential nitrification in the N-added plots in chaparral, and both sites showed a significant seasonal effect on net nitrification rates. These results indicate that nitrification rates may increase in response to deposition of anthropogenic N in both coastal sage scrub and chaparral habitats. These fmdings have implications for the potential loss ofN as N03-in runoff into the groundwater or as greenhouse gas products (NO and N20) from microbial nitrification processes. Keywords: Microbial biomass; ninhydrin-reactive N· Nitrogen cycle; ' ammonification; nitrification; mineralization; global climate change.
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Moore, Brenda Juanita
- Description:
- To understand the complex network of the biological processes of an organism, transcription factors (TFs) and their direct target genes must be identified. In Arabidopsis, the TF GLABRA3 (GL3) is involved in trichome initiation and development. To identify the direct target genes of GL3, an inducible activation system coupled with microarray analysis was performed. To this end, two week old Arabidopsis seedling plants expressing the GL3-GR (glucocorticoid receptor) fusion protein with a native promoter (pGL3) were treated for two hours with dexamethasone alone (DEX), dexamethasone + cycloheximide (DEX +CHX), cycloheximide (CHX) and mock solution (M). Ten genes were selected as candidate genes in DEX and DEX +CHX (in relation to Mock and CHX) respectively and validated by real-time RT-PCR. The results showed that the ten genes were not up-regulated greater than two-fold and the induction of these genes did not occur rapidly after the two hour treatment in the pGL3::GL3-GR plants, indicating these candidate genes may in fact be indirect targets. Gene Ontology analysis of the candidate genes revealed that the GL3 pathway have involvement in biological processes related to abiotic or biotic stress, signal transduction, transcription, and transport. These target genes suggest that GL3 is associated with other TFs and proteins in combinatorial manner. Keywords Arabidopsis, GL3, trichomes, transcription factor, microarray, real-time RT-PCR
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- Mikse, Oliver Roland
- Description:
- The global aim ofthis research is to elucidate the role of retrotransposons in stress and immune response. As cloning and sequencing of genes has become commonplace, researchers are finding that the insertion and activity of transposable elements including retrotransposons may directly influence phenotype. There is now evidence that external as well as internal stress, such as that caused by pathogens, will activate the movement of retrotransposons within the genome and this movement may play a role in the organism's immune response (Wessler 1996; Grandbastien 1998). An understanding of the mechanisms behind this movement and determining the identity of the genes that are disrupted due to retrotransposon insertion will lead us to an understanding of the genes involved in the immune pathway. Preliminary data indicates that stress may also induce retrotransposon expression in shrimp (Penaeus stylirostris) making this an informative system for further investigation. In a previous study, genetic markers were identified for infectious hypodermal and hematopoietic virus (IHHNV) resistant and susceptible shrimp populations (Hizer et al. 2002). Sequence characterization of two of the markers revealed partial coding regions of the reverse transcriptase gene for retrotransposable elements. In addition, increased expression activity and movement of the retrotransposon in the virally infected shrimp was observed using real-time PCR. Therefore, the overall goal of this project is to isolate the full-length retrotransposable element and to determine its genomic and expression activity in response to viral stress. The specific objectives of this study are: to identify the full non-long terminal repeat (L TR) element; to identify differences in number of elements present between healthy and virally challenged shrimp; to determine if these elements lie within important genes; and to determine if activation of these elements is important in viral pathogenesis. These studies will increase the limited body ofknowledge ofnon-LTR retrotransposons role in response to stress. Specifically, it will begin to address whether transposition events are consequential in stress immune response to viral pathogenesis. Key Words: Representational Difference Analysis, Penaeus stylirostris, IHHNV, Retrotransposon
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science
- Creator:
- McCague, Jennifer
- Description:
- Quinones are a class of molecules whose effect on cell growth and apoptosis pathways are poorly understood, yet several quinones are widely used as food preservatives and in cosmetics. This study takes advantage of protein microarray technology to identify specific protein-quinone interactions and to establish which class of proteins that quinones commonly interact with. This will enable us to gain a greater understanding of the biological pathways quinones may influence. Protein microarrays are sophisticated biological tools that allow the simultaneous examination of vast numbers of protein interactions. In this study protein microarray technology was used to examine the interaction oftertbutylhydroquinone (tBHQ) with ~5000 yeast and ~3000 human proteins. Strong interactions identified using the protein arrays were subsequently validated using traditional biochemical assays. The results indicated that tBHQ has a tendency to interact with DNA binding proteins, especially kinases, and exhibits a non-specific, weak kinase inhibitory effect. The results of this study indicated that tBHQ (1) reduced the growth rate of yeast in culture, (2) positively interacted with the yeast, Sir2 protein, and (3) it specifically inhibited the deacetylase activity of human Sir2. Keywords: Microarray, tert-butylhydroquinone, quinones, SIR2, Antioxidant Response Element
- Resource Type:
- Thesis
- Campus Tesim:
- San Marcos
- Department:
- Biological Science