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- Creator:
- Obaidi, Freshta
- Description:
- Class III plant peroxidases are found in all land plants and lignification, suberization, and pathogen defense are three of the many functions served by these enzymes. The numerous peroxidase functions and the large multigenic families peroxidases are a part of have made it difficult to study class III peroxidases. The goal of this study was to determine the in vivo localization of Arabidopsis thaliana peroxidases At2g43480 and At3g21770 by using a fluorescent protein tag. Because both peroxidases have an endoplasmic reticulum signal peptide and lack a hydrophobic C-terminus, it was expected that both would be found at the cell wall. At2g43480 was not expressed in the cell wall and it may be involved in plant defense or modifying monolignols for suberization. At3g21770 was expressed in the cell wall of xylem tissue, lateral root cap cells, and columella cells, where it may be involved in lignification. In epidermal guard cells, At3g21770 was expressed intracellularly and may function in deposition of cell wall material in plasmodesmata to cytoplasmically isolate maturing guard cells. The possibility of At2g43480 involved in monolignol modifications and At3g21770 involved in lignification is significant because lignin is an abundant plant cell wall polymer and its regulation is beneficial to the paper pulping industry and to biofuel production
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Wallace, Lindsey Kaylee
- Description:
- Emiliania huxleyi and some related prymnesiophyte algae produce a novel group of polyunsaturated long-chain C37-39 alkenones, alkenoates, and alkenes as their major neutral lipids, however their biosynthesis pathway is unknown. Like triglycerides, these lipids are believed to be utilized as storage lipids and are accumulated in lipid bodies to be used as a fuel source, presumably. Also C31-33 cis-alkenes have been identified in E. huxleyi but are believed to be different in synthesis and function. By studying the synthesis of these lipids I set out to discern how these two types of neutral lipids are formed in E. huxleyi. I used a combination of techniques, including GC-MS analysis, radiolabeling, and inhibitors, to examine lipid pools during growth cycles, bicarbonate dosing, and light-dark manipulations. By using GC-MS analysis I identified the presence of C31-33 cis-alkenes exclusively in E. huxleyi strains CCMP 1516 and 371, and Isochrysis galbania strain CCMP 1323; where E. huxleyi strains CCMP 1742, 3266, and 3268 had both cis-alkenes and C37-38 trans-alkenes. I also found accumulation of both cis-alkenes and C37-38 trans-alkenes in light to dark manipulations was similar to that seen in storage lipids, suggesting that the long chain cis-alkenes are in fact another storage lipid and may share a similar synthesis pathway to the trans-alkenes. Using radiolabeling studies I found external acetate is not acquired under light dependent mechanisms and is utilized primarily in production of polar lipids; while external bicarbonate acquisition and use in lipid synthesis is light-dependent, and as a cellular building block it is distributed more evenly amongst lipid pools. Also, flow of carbon into CCMP 1516 and 3268 cells from external bicarbonate into lipid pools is inhibited by cerulenin (fatty acid synthase inhibitor), flufenacet (elongase inhibitor), and quizaloflop (acetyl-CoA carboxylase inhibitor). Platensimycin (fatty acid synthase II inhibitor) only affects flow of bicarbonate into CCMP 1516 C31-33 cis-alkenes. Finally, flow of carbon into CCMP 1516 cells from external acetate into lipid pools is inhibited by cerulenin. Flufenacet and quizaloflop only affects flow of acetate into C37-39 trans-alkenes. Platensimycin has no effect on the flow of acetate into lipid pools in CCMP 1516. Though these results show precursors of acetate and bicarbonate are used in the synthesis of these neutral lipids, and through inhibitor studies I have identified many mechanisms vital to their synthesis, the biosynthetic pathway is yet unclear.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Grewal, Mandeep
- Description:
- Hydrophobic polymer lignin provides water proofing and structural integrity to cell wall which help plants adapt to terrestrial environment. Secretory peroxidases are thought to generate monolignol radicals that polymerize to form lignin. In Arabidopsis thaliana there are 73 secretory peroxidases .Identification of tissue, cellular, and subcellular location for individual peroxidases can help assigning their function. All secretory peroxidases contain signal peptide for entry into endomembrane system. Some peroxidases have hydrophobic carboxy-termini targeting to them to vacuole. Peroxidases lacking hydrophobic carboxy-terminal are targeted to wall. We tagged A. thaliana secretory peroxidase, AT2G34060, with yellow fluorescent protein. Plants transformed with this construct expressed AT2G34060 in the protoxylem cells of the roots of one to eight day old seedlings. AT2G34060 has a hydrophobic Carboxyterminal and aminotransferase domain. This peroxidase is located in vesicles arranged in a helical fluorescent pattern similar to microtubule pattern. Overexpression of AT2G34060 reduced the root length. A vesicular location and reduction in growth by overexpression suggests that AT2G43060 supports lignification by producing monolignol precursors through its putative aminotransferase ability. AT2G34060 may also be involved in deglycosylation of monolignols during their vesicular transport to the wall. The availability of monolignols may be a limiting factor in the lignification process. Therefore, a higher number of available monolignols may lead to shorter roots through higher lignification. Our work identifies a peroxidase that appears in cells undergoing lignifications and its subcellular location in vesicles is consistent with formation of lignin. Also, root shorting through overexpression is consistent with role in lignification.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Araujo Sariñana, Juan C.
- Description:
- Diabetes is one of the United States’ worst epidemics; the dangers associated with the disease can be both fatal and varied. The constant presence of high concentrations of glucose and free fatty acids (FFA) becomes a source of stress for cells, which results in programmed cell death (apoptosis). Our lab has identified a microRNA (miRNA), miR- 191, that may be involved in the stress response of pancreatic beta cells. miRNAs have been recognized as key regulators of the translation of messenger RNA (mRNA). miRNAs are involved in virtually all cellular processes, have the ability to target multiple genes, and play important roles in diseases such as cancer and diabetes. Previous research suggested that miR-191 is under the control of the pancreatic and duodenal homeobox 1 transcription factor (PDX-1) and of the neurogenic differentiation 1 transcription factor (NeuroD1), both of which are regulated in the presence of glucose. I have also observed that miR-191 is up-regulated when rat insulinoma cells (INS-1) are treated with glucose. Bioinformatic analysis suggests possible roles for miR-191 in regulating apoptotic genes. Inhibiting miR-191 in a UV-induced stress assay in insulinoma (INS-1) cells results in decreased cell death. Decreased cell death was also observed when miR-191 was knocked down in samples that were treated with 30 mM glucose and 0.5 mM palmitate. It is not yet clear how miR-191 is involved in the beta cell stress response but based on data presented here it appears that miR-191 is promoting apoptosis in response to stressful conditions.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Bergmann, Jean-Phillippe W.
- Description:
- Reproductive isolation is critical to speciation and therefore biodiversity. The immediate goal of such studies is to identify which barriers contribute most to overall reproductive isolation between species, in order to gain a broader understanding of the process of speciation. Mimulus guttatus and M. glaucescens have postzygotic barriers to hybridization, but their prezygotic barriers remain unstudied. I examined potential premating prezygotic barriers such as phenology, pollinator behavior and floral morphology, as well as possible post-pollination prezygotic barriers such as pollen adhesion, germination and pollen tube growth rates between species. We found no significant barriers to hybridization between species for any traits, although we did identify subtle differences in herkogamy and corolla tube width. We conclude that prezygotic barriers to reproduction between M. guttatus and M. glaucescens are weak, and contrast with evidence for postzygotic barriers such as reduced seed set and delayed flowering in hybrids. Additional research should focus on microhabitat preferences and a population genetic analysis to determine whether introgression can occur between natural populations.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Almasary, Areeje
- Description:
- Microorganisms can live in environments where macroscopic organisms cannot survive, such as in the extremely acidic geothermal Boiling Spring Lake (BSL) in Lassen Volcanic National Park, CA. BSL is an oligotrophic lake with thriving microbial populations whose carbon (C) sources are still poorly understood. In this study, I examined the possibility that allochthonous leaf litter (mostly pine needles) observed falling in the lake can fuel microbial production in BSL. Coniferous needles are known to be particularly difficult to colonize by microbes and have low decay rates, but no studies have examined the combined effects of low pH and high temperature on pine needle leaching and decomposition. In both lab- and field-based experiments, I found coniferous leaves had high decay rates during leaching and decomposition in BSL compared to those reported in the literature for other neutral pH and mesophilic lakes and streams. Thus, the acid and high temperatures appear to help condition the leaves and make their C more biologically available. I also found little difference in decay between fresh and dry leaves, but when needles were cut, I observed faster leaching rates and slower decomposition rates, suggesting the effects of mechanical weathering are important, possibly by degrading the waxy cuticle barrier. I also observed that leaves decayed more slowly in 0.2 μm-filtered BSL water, suggesting both native and introduced microbes contribute to leaf breakdown. Based upon bacterial growth experiments and recovery of an ascomycete fungus, both prokaryotes and eukaryotes seem to contribute to leaf decay. The addition of a nitrogen (N) source (yeast extract) enhanced prokaryote growth more than adding a simple carbon such as glucose, suggesting BSL is both C and nitrogen limited. I also used radioisotopes to assess primary and secondary production rates, and observed autotrophic growth was low, and dominated by chemoautotrophy, while heterotrophic uptake rates varied depending on the organic substrate used, and were highest for acetate. These results suggest that allochthonous carbon is important in fueling microbial production in the lake. I constructed a preliminary C budget for the lake by measuring leaf deposition and estimating other dissolved organic carbon (DOC) sources from BLS’s hydrologic budget.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Gottschalk Fisher, Erin
- Description:
- Vernal pool habitats have been significantly reduced by conversion to incompatible agriculture and urbanization. As a result, a number of vernal pool dependent species have become rare, including Colusa grass (Neostapfia colusana) and Greene’s tuctoria (Tuctoria greenei). This study examined the potential for introductions of the rare grasses into vernal pool habitats. To this end, four study sites were established, two sites for each species – one introduction site with restored or created vernal pools and one reference site with existing populations of the rare grass. The year prior to introductions, pool hydrology and reference populations were monitored and mapped to inform introduction success. Using seed and inflorescence packets, the species were introduced into the restored/created pools and, for comparison, reintroduction into the reference pools. For Greene’s tuctoria, germination and survivorship to reproduction occurred at both introduction and reintroduction pools. The introduction pools had significantly higher average percent germination (60%) than the reintroduction pools (35%), which may be a result of disturbance to the germination and early seedling stage at the reintroduction pools. Plants from seed packets had significantly higher vigor but showed a trend towards lower reproductive output compared to the plants growing from the higher-density inflorescence packets. In the second year, despite relatively low rainfall and only partial pool filling, the introduction pools supported over 2,000 second generation Greene’s tuctoria plants. For Colusa grass, germination occurred at both the introduction pools (13%) and reintroduction pools (23%); however only one plant survived to reproduce at the introduction pools while reintroduction pools had 40% survivorship to reproduction. Soil testing suggested that the low survivorship may be due to elevated salinity at the introduction pools. The differences between species and packet methods illuminated different paths to potential success in introducing new populations. The results of this research are imperative in informing recovery efforts for Colusa grass and Greene’s tuctoria populations as well as for other rare vernal pool plants.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Hoddick, Sarah
- Description:
- Emiliania huxleyi is a marine haptophyte alga known for its ability to generate large volumes of calcite coccoliths. It also synthesizes a unique suite of neutral lipid (PolyUnsaturated Long Chain Alkenes, Alkenones and Alkenoates, or PULCA), whose biosynthetic pathways are currently unknown. Like energy-storage triacylglycerides, which they replace, these lipids are packaged into lipid bodies (LBs), and a prior study used a proteomics screen of isolated LBs and endomembranes from E. huxleyi CCMP 1516 to generate a list of candidate proteins possibly associated with PULCA biosynthesis, mobilization, and catabolism. The goal of this thesis was to study gene expression these proteins under conditions of neutral lipid accumulation and degradation, including batch growth with addition of sodium bicarbonate, and during light-dark manipulations. I designed quantitative PCR (qPCR) primers for almost 120 genes identified by the proteomics screen, and optimized mRNA extraction, reverse transcription to cDNA, and qPCR. I confirmed neutral lipid accumulation during nutrient (phosphate) limitation in the light after sodium bicarbonate dosing, and catabolism during continuous darkness. I was able to quantify gene expression changes of many LB-associated genes, most with low expression values, as well as a number of control genes and other genes used in other studies. I observed several striking patterns of gene expression in the experiments. In the growth curve + bicarbonate experiment, many LB-associated genes likely related to acyl lipid biosynthesis showed 10-100-fold expression increases as neutral lipids accumulated. However, the timing of increases varied: some increased before bicarbonate addition, while others only after. In contrast, several genes for prenyl and sphingolipid pathways did not show such striking increases, and a few genes possibly related to acyl lipid catabolism decreased. Most genes associated with photosynthesis, structural proteins, and trafficking did not show significant changes, but several genes for carbohydrate metabolism also increased sharply, highlighting the likely connection between carbohydrate and lipid metabolism. In contrast, the light-dark experiment showed few large changes in expression, and several genes showed strong down-regulation, although patterns were not consistent. But because of the large numbers of time points and treatments in this experiment, I was only able to survey a few genes by qPCR, and these results are very tentative. In both experiments, I was able to quantify only a fraction of the LB-associated genes, due to the large effort necessary to screen genes by qPCR, and also due to degradation of mRNA stored at -80 oC. Although my study examined far more genes and time points than most qPCR studies, and I confirmed the likely role of acyl lipid biosynthesis pathways in PULCA production, an important outcome of this study is the need in future to use more comprehensive genome-wide techniques, such as RNA-seq, to evaluate the large numbers of genes likely involved in the pathways of neutral lipid biosynthesis.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Ervin, Bryan
- Description:
- In the pursuit of producing cleaner fuels, plant lignocellulose is a source of fermentable sugars that don’t compete with food production. Conversion of plant components, or lignocellulose, into biofuels typically requires hot and acidic pre-treatment conditions not suitable to most commercial fungal enzymes. In this work, I evaluated seven Ascomycota fungi associated with Boiling Springs Lake (BSL) in Lassen Volcanic National Park, a hot and acid environment, for utilization of lignocellulose material. Due to the conditions of BSL, I hypothesized these fungal isolates produce thermal/acidic stable enzymes. To test this, the fungi were screened for: growth on purified or natural components under hot, acid conditions; lignocellulose degradation genes with PCR; and, potential lignin degradation via a (per)oxidase assay. Growth analysis showed Acidomyces and Ochroconis growing >40 °C and pH <4; Aspergillus, Paecilomyces and Penicillium preferred cooler temperatures for acidic media but still grew above 40 °C; Phialophora only grew up to 27 °C under both acidic and neutral conditions; and Cladosporium showed a preference for cool, neutral conditions. The most promising material utilizers, Acidomyces, Ochroconis and Paecilomyces used cellobiose, xylan, pine and incense cedar needles for growth at 40 °C and pH 2. The remaining fungi used fewer materials. PCR results showed Acidomyces, Paecilomyces, and Ochroconis containing orthologs to known fungal lignocellulose degradation genes. Additionally, Acidomyces and Ochroconis showed extracellular (per)oxidase activity at 40 °C and pH 2. From these combined results, I concluded that Acidomyces, Ochroconis and Paecilomyces have potential for use in the pretreatment of lignocellulosic biofuels.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences
- Creator:
- Daniele, Ninette R.
- Description:
- Freshwater turtles worldwide are declining due to a variety of human caused impacts. The Western Pond Turtle (Emys marmorata) is native to the pacific coast of the North America and is also in decline. Many Western Pond Turtles live in human-modified habitats. The ecophysiology of this species in impacted habitats is largely unknown and blood profile baselines from healthy populations in natural habitats are lacking. Western Pond Turtles were sampled from a nature reserve (n=61) and wastewater treatment facility (n=37) and blood profiles were performed, which included determination of hematocrit and thirteen serum chemistry analytes. Baseline blood profiles for a subset of clinically healthy E. marmorata from a highly natural habitat were documented, including values for gravid females, with significant differences noted between males and females for 8 chemistries. Blood profiles were also compared between all sampled male turtles from the nature reserve and the wastewater facility populations; with significant differences found in ten blood analytes between populations at these habitats. The blood profile baselines from the nature reserve population will be helpful to wildlife veterinarians in evaluating disease in this species and possibly other Emydid turtles. Furthermore, the differences in blood profiles between populations suggest that turtles from altered habitats may have impacted physiologies and that blood profiles, with further study, may be useful in assessing the suitability of modified habitats. Managers may use this work in assessing the health of Western Pond Turtle populations and planning conservation strategies in altered landscapes.
- Resource Type:
- Thesis
- Campus Tesim:
- Chico
- Department:
- Biological Sciences