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- Creator:
- Carlin, Joseph A.
- Description:
- Extreme episodic events have the capacity to transport large amounts of terrestrial material to the coastal ocean. While estuaries and deltas are typically thought to trap most of this material, some escapes these coastal features and is transported to distal depocenters along the continental shelf. Distal shelf depocenters can act as the ultimate sink for event deposits, yet event sedimentation and the impact of terrestrial carbon burial within these shelf deposits remains understudied. Therefore, this study investigated event sedimentation within the Texas Mud Blanket (TMB), a distal shelf depocenter of the Brazos River located in the northwestern Gulf of Mexico. Using a core that was collected from the TMB during a months-long elevated discharge event in late 2015 to early 2016 we applied a multi-proxy approach to delineate the event deposit. We utilized physical sediment properties (fabric, texture, and bulk density), radioisotopes (7Be and 210Pb), and organic geochemical properties (ẟ13C, C/N, and lignin-phenols) to identify a 10 cm event layer at the surface of the core. Within this 10 cm layer, we also distinguished two sub-layers associated with separate extreme discharge periods in the winter and spring, respectively. Using these event layer characteristics, we identified three other earlier potential event deposits in the core that we have attributed to events in 2010, 2007, and 2000–2001. From these results, this study has demonstrated that the TMB may be an archive for event deposits over multi-decadal time periods, in particular the transition from periods of prolonged drought to extreme wetness associated with the Brazos River. This event-dominated sedimentation regime can enhance long-term carbon burial, potentially increasing current estimates of carbon burial significantly in the TMB and other similar distal shelf depocenters. Ultimately this study highlights the potential for distal shelf depocenters as organic carbon burial “hotspots,” and postulates that this role may expand in the future as climate change increases the intensity and frequency of extreme events.
- Resource Type:
- Article
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Paig-Tran, E.W. Misty, Lowe, Andrew, Walker, Sean, and Walter, Ryan P.
- Description:
- The cory catfishes (Callichthyidae) are small, South American armored catfishes with a series of dermal scutes that run the length of the fish from posterior to the parieto-supraoccipital down to the caudal peduncle. In this study, we explore the anatomy and functional performance of the armored scutes in the three-striped cory catfish, Corydoras trilineatus . The lateral surface has a dorsal and a ventral row of scutes that interact at the horizontal septum. The scutes have little overlap with sequential posterior scutes (~33% overlap) and a deep ridge in the internal surface that connects to the underlying soft tissue. The internal surface of C. trilineatus scutes is stiffer than the external surface, contrary to the findings in a related species of cory catfish, C. aeneus , which documented a hypermineralized, enamel-like, non- collagenous, hyaloine layer along the external surface of the scute. Clearing and staining of C. trilineatus scutes revealed that the scutes have highly mineralized (~50% mineralization) regions embedded in be- tween areas of low mineralization along the posterior margin. Puncture tests showed that posterior scutes were weaker than both anterior and middle scutes, and scutes attached to the body required 50% more energy to puncture than isolated scutes. Corydoras trilineatus has the strongest armor in areas critical for protecting vital organs and the external armored scute receives synergistic benefits from interactions to the soft underlying tissue, which combine to provide a tough protective armor that still allows for flexible mobility.
- Resource Type:
- Article
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Ramirez, Maria Soledad
- Description:
- Acinetobacter baumannii is a multidrug resistant nosocomial pathogen that shows an outstanding ability to undergo genetic exchange, thereby acquiring different traits that contribute to its success. In this work, we identified genetic features of an indigo-pigmented A. baumannii strain (Ab33405) that belongs to the clonal complex CC113B/CC79P. Ab33405 possesses a high number of genes coding for antibiotic resistance and virulence factors that may contribute to its survival, not only in the human host, but also in the hospital environment. Thirteen genes conferring resistance to different antibiotic families (trimethoprim, florfenicol, β-lactams, aminoglycosides and sulfonamide) as well as the adeIJK genes and the capsule locus (KL) and outer core locus (OCL) were identified. Ab33405 includes 250 unique genes and a significant number of elements associated with Horizontal Gene Transfer, such as insertion sequences and transposons, genomic islands and prophage sequences. Also, the indigo-pigmented uncommon phenotype that could be associated with the monooxygenase or dioxygenase enzyme coded for by the iacA gene within the iac cluster was probably conferred by insertion of a 18-kb DNA fragment into the iacG gene belonging to this cluster. The Ab33405 genome includes all type VI secretion system genes and killing assays showed the ability of Ab33045 to kill Escherichia coli. In addition, Ab33405 can modulate susceptibility antibiotics when exposed to blue light.
- Resource Type:
- Article
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Paig-Tran, Erin
- Description:
- Solid-liquid filtration is a ubiquitous process found in industrial and biological systems. Although implementations vary widely, almost all filtration systems are based on a small set of fundamental separation mechanisms, including sieve, cross-flow, hydrosol, and cyclonic separation. Anatomical studies showed that manta rays have a highly specialized filter-feeding apparatus that does not resemble previously described filtration systems. We examined the fluid flow around the manta filter-feeding apparatus using a combination of physical modeling and computational fluid dynamics. Our results indicate that manta rays use a unique solid-fluid separation mechanism in which direct interception of particles with wing-like structures causes particles to “ricochet” away from the filter pores. This filtration mechanism separates particles smaller than the pore size, allows high flow rates, and resists clogging.
- Resource Type:
- Article
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Zacherl, Danielle
- Description:
- Worldwide, artificially armored shorelines can dominate available estuarine habitat. Increases in artificial substrata in southern California, USA, coincide with increased abundances of nonindigenous species. The US west coast Olympia oyster, Ostrea lurida, may be particularly sensitive to changes in natural habitat availability and recently experienced large-scale declines in abundance. Simultaneously, the non-indigenous and often invasive Pacific oyster, Crassostrea gigas, has been introduced along the US West Coast, including into southern California estuaries where its impact is unstudied. We recorded C. gigas and O. lurida densities from October 2010 through July 2017 throughout southern California on several habitat types and as a function of tidal elevation as a critical baseline for evaluating impacts of C. gigas. Ostrea lurida was present in higher proportions than C. gigas in hard substrate-dominated habitats, whether natural or human-introduced. A strong zonation pattern emerged; C. gigas achieved its maximum density above +0.4 m MLLW versus O. lurida at or below +0.2 m MLLW. These data reveal the optimal tidal elevation for placement of a restored O. lurida bed and establish a critical baseline and techniques for evaluating future changes in oyster density.
- Resource Type:
- Article
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
6. Enhancing Learning Power through First-Year Experiences for Students Majoring in STEM Disciplines
- Creator:
- Koch, Robert
- Description:
- Academic programs targeted for first-time students can help their persistence in STEM majors. Our project, ASCEND STEM, included three first-year experiences (FYEs) designed to offer students the skills that would help them successfully traverse potential barriers to academic success. In the FYEs, we sought to strengthen the learning power, improve the academic achievements, and increase the postsecondary success of first-time, full-time freshmen majoring in a STEM discipline. Two models of FYE were offered in three settings—two scenarios were for engineering majors and the third for science and mathematics majors. Both models tested whether the offering of literacy skill building in the context of discipline knowledge acquisition strengthened learning power (as measured by the Effective Lifelong Learning Inventory) and asked whether this could affect academic success and persistence within the STEM major. We found that either model one, integrating literacy skill building and discipline-based concepts into a single course (the approach used in science and math), or model two, pairing a literacy skill building course with either a discipline-based course or a special group support program (the approach used in engineering), improved learning power. Increases in learning power were a valid predictor of improved grades and persistence in engineering where a highquality control group was available.
- Resource Type:
- Article
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Schenk, H. Jochen
- Description:
- Premise of the Study Xylem sap in angiosperms moves under negative pressure in conduits and cell wall pores that are nanometers to micrometers in diameter, so sap is always very close to surfaces. Surfaces matter for water transport because hydrophobic ones favor nucleation of bubbles, and surface chemistry can have strong effects on flow. Vessel walls contain cellulose, hemicellulose, lignin, pectins, proteins, and possibly lipids, but what is the nature of the inner, lumen‐facing surface that is in contact with sap? Methods Vessel lumen surfaces of five angiosperms from different lineages were examined via transmission electron microscopy and confocal and fluorescence microscopy, using fluorophores and autofluorescence to detect cell wall components. Elemental composition was studied by energy‐dispersive X‐ray spectroscopy, and treatments with phospholipase C (PLC) were used to test for phospholipids. Key Results Vessel surfaces consisted mainly of lignin, with strong cellulose signals confined to pit membranes. Proteins were found mainly in inter‐vessel pits and pectins only on outer rims of pit membranes and in vessel‐parenchyma pits. Continuous layers of lipids were detected on most vessel surfaces and on most pit membranes and were shown by PLC treatment to consist at least partly of phospholipids. Conclusions Vessel surfaces appear to be wettable because lignin is not strongly hydrophobic and a coating with amphiphilic lipids would render any surface hydrophilic. New questions arise about these lipids and their possible origins from living xylem cells, especially about their effects on surface tension, surface bubble nucleation, and pit membrane function.
- Resource Type:
- Article
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Stapp, Paul
- Description:
- In late 2009, the Catalina Island Conservancy began using fertility control to replace periodic removals to manage an introduced population of American bison (Bison bison) on the island. Through the application of the immunocontraceptive vaccine porcine zona pellucida (PZP), population growth was slowed within 1 year, and halted over time. In response to lingering questions about the use of PZP to manage large, free-ranging wildlife populations, we sought to determine the reversibility of PZP by ceasing the annual application to a subset of 15 bison cows and monitoring for subsequent calf arrival, and to document changes in the timing and length of the breeding season in response to PZP by monitoring breeding behavior and assessing fecal progesterone (FP) levels for all 60 resident cows over a 13-month period. As of June 2017, no new calves had been observed on the island, suggesting that, following repeated annual treatment with PZP (3 or 4 years), bison do not resume normal reproduction for at least 4 or 5 years, and that fewer treatments would be advisable if a faster return to fertility is desired. Based on observations of bull and cow behavior, and FP levels, cows displayed estrous cycles consistently throughout the study period, indicating that bison may ovulate year-round when conception and its consequences, e.g., lactation and presence of calves, are blocked. Because there is little evidence that an extended breeding season would negatively impact the health of bulls or result in large numbers of out-of-season births on Catalina, PZP appears to be a highly effective tool for managing the population of introduced bison on the island. However, the extended period of contraception and breeding activity of both cows and bulls may make PZP less suitable in high-latitude, predator-rich environments where bison conservation remains a top priority.
- Resource Type:
- Article
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Schenk, H. Jochen
- Description:
- Vascular plants transport water under negative pressure without constantly creating gas bubbles that would disable their hydraulic systems. Attempts to replicate this feat in artificial systems almost invariably result in bubble formation, except under highly controlled conditions with pure water and only hydrophilic surfaces present. In theory, conditions in the xylem should favor bubble nucleation even more: there are millions of conduits with at least some hydrophobic surfaces, and xylem sap is saturated or sometimes supersaturated with atmospheric gas and may contain surface-active molecules that can lower surface tension. So how do plants transport water under negative pressure? Here, we show that angiosperm xylem contains abundant hydrophobic surfaces as well as insoluble lipid surfactants, including phospholipids, and proteins, a composition similar to pulmonary surfactants. Lipid surfactants were found in xylem sap and as nanoparticles under transmission electron microscopy in pores of intervessel pit membranes and deposited on vessel wall surfaces. Nanoparticles observed in xylem sap via nanoparticle-tracking analysis included surfactant-coated nanobubbles when examined by freeze-fracture electron microscopy. Based on their fracture behavior, this technique is able to distinguish between dense-core particles, liquid-filled, bilayer-coated vesicles/liposomes, and gas-filled bubbles. Xylem surfactants showed strong surface activity that reduces surface tension to low values when concentrated as they are in pit membrane pores. We hypothesize that xylem surfactants support water transport under negative pressure as explained by the cohesion-tension theory by coating hydrophobic surfaces and nanobubbles, thereby keeping the latter below the critical size at which bubbles would expand to form embolisms.
- Resource Type:
- Article
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Hoese, William
- Description:
- Background: Evolutionary trees illustrate relationships among taxa. Interpreting these relationships requires developing a set of “tree-thinking” skills that are typically included in introductory college biology courses. One of these skills is determining relationships among taxa using the most recent common ancestor, yet many students instead use one or more alternate strategies to determine relationships. Several alternate strategies have been well documented and these include using superficial similarity, proximity at the tips of a tree, or the fewest intervening nodes in the tree to group taxa. Results: We administered interviews (n = 16) and pencil-and-paper questionnaires (n = 205), and constructed a valid and reliable assessment that measured how well students determined relationships among taxa on an evolutionary tree. Our questions asked students to consider a focal taxon and identify which of two additional taxa is most closely related to it. We paired the use of most recent common ancestor with one of three alternative strategies (i.e., similarity, proximity, or node-counting) to explicitly test students’ understanding of the relationships among the taxa on each tree. Conclusions: Our assessment enables us to identify students who are effectively distracted by an alternative strategy, those who use the most recent common ancestor inconsistently, or who are guessing in order to determine relationships among taxa. Our 18-question tool (see Additional file 1) can be used for formative assessment of student understanding of how to interpret relationships on evolutionary trees. Because our assessment tests for the same skill throughout, students who answer incorrectly, even once, likely have an incomplete understanding of how to determine relationships on evolutionary trees and should receive follow-up instruction.
- Resource Type:
- Article
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Walker, Kimberly Mae
- Description:
- Ostrea lurida’s potential role as a foundation species has not been explored, so little is understood about ecosystem services produced by ongoing restoration efforts for the United States’ only native oyster species on the west coast. Further, the effectiveness of different techniques for restoring Olympia oyster beds has not been systematically evaluated. The most common technique is augmenting available habitat by adding dead shell onto mudflats and allowing remnant oysters to seed the shell with spat; shell has been added at varying thicknesses, either consolidated in bags or simply placed loose onto the mudflat. Here, I explored the effects of different combinations of Olympia oyster restoration techniques (varying the thickness of constructed shell beds using loose versus bagged oyster shell) on invertebrate abundance, diversity, and community composition. Twenty-five oyster beds were established in Newport Bay, Orange County, California in June 2010. Five beds were not augmented with any shell and were used as control plots. The other twenty beds were randomly assigned to be constructed using dead oyster shell at thicknesses of 12 cm or 4 cm using shell bagged in jute or loose shell (n= 5 replicates per treatment). Visual inspection of MDS plots and results from ANOSIM indicated after one year a significant shift in community composition of the oyster beds versus the control plots, with trends in differences of the thick beds and thin-bagged beds. However, the density of most invertebrate species changed over time and bagging of the shell in some cases also mattered. Amphipods, polychaetes and oligochaetes all declined significantly on some treatment plots over the study period, but not because of shell enhancements. Bivalves, gastropods and isopods all increased over the study period with trends towards increases on the thicker beds and thin-bagged beds, although insignificant. Results could inform future restoration efforts for this species and establish ecosystem services provided by O. lurida as a foundation species.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Carter, Ariel L.
- Description:
- Adult California grunion, Leuresthes tenuis, spawn on sandy beaches during spring high tides. Embryos develop within the sand enclosed in the chorion, which must be strong enough to protect the embryo but also allow rapid hatching. Grunion embryos are competent to hatch at 8 days post-fertilization (dpf) at 20°C, but require agitation in seawater to hatch, and can delay hatching up to 30 dpf. I hypothesized that chorions of fertilized eggs would require more force to break than chorions of unfertilized eggs because of hardening of the chorion at fertilization, and that chorions would require more force to break during normal incubation (10 dpf) than after extended incubation (28 dpf) due to degradation over time. Gametes were collected from grunion in March-July 2013- 2015. Eggs were fertilized and embryos were incubated in the laboratory at 20°C for up to 30 dpf. Mean crushing force (N) did not differ significantly between unfertilized and fertilized eggs except for 1 of 9 collection dates when it was significantly greater in fertilized eggs. Thus, the hardness of grunion chorions apparently does not increase at fertilization. Mean crushing force did not differ significantly between 10 dpf and 28 dpf but decreased significantly over the 28 days of incubation in 7 of 14 clutches. I used hydrophobic interaction column chromatography to partially purify the choriolytic enzyme, which allows the embryo to hatch from the chorion, and enzyme kinetics parameters were estimated. The Vmax was 0.045 ± 0.003 ΔA280 min-1 mg-1 protein and the Km value was 0.652 ± 0.111 mg casein ml-1 .
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Burdi, Christina Elizabeth
- Description:
- Rocky intertidal grazers with similar morphologies and ecological habitats likely compete for food and space. Two intertidal limpets Lottia scabra and L. conus (Gastropoda: Lottidae), are alike in their morphology and overlap in range in southern California. Despite both species being common in this region, little has been published on L. conus since it was described in 1945, thus comparisons of L. conus to L. scabra are minimal. Limited descriptions and dorsal shell plasticity contribute to inaccurate identifications; therefore any potential interactions between these species remain unstudied. I evaluated published and unpublished shell differences between L. conus and L. scabra to determine whether shell diagnoses could distinguish between species. To ensure accurate identifications, species-specific mitochondrial 16S ribosomal DNA primers were successfully designed and applied using a PCR-based assay. Sequencing of selected individuals with nuclear (ITS-1) DNA confirmed that the mitochondrial and nuclear markers agree in their identification. Measured shell features were significantly different between L. conus and L. scabra, however, the range in these characteristics overlapped considerably, which contributed to misidentifications. Qualitative diagnoses also contradicted published distinctions. My results indicated that L. conus has a wider range of morphologies than previously recognized, some of which are indistinguishable from L. scabra, and can only be reliably identified with molecular techniques. Furthermore, I found that non-lethal sampling of foot mucus could be used in the field for iii species identification for future studies on the potential ecological interactions between L. scabra and L. conus. This technique has considerable potential for a variety of molluscan studies while reducing organism mortality.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Lam, Caroline
- Description:
- In the unicellular green alga Chlamydomonas reinhardtii, the D1 protein, which is the main electron acceptor of photosystem II, is encoded by the chloroplastic psbA gene. Translation of D1 is regulated by a set of nuclear-encoded RNA-binding proteins (RB38, RB47, RB55, and RB60), which form a complex and interact with a stem-loop structure in the 5’-untranslated region of the psbA mRNA. Earlier work showed that the genes that encode two of these RNA-binding proteins, rb38 and rb60, as well as the psbO gene, which encodes the OEE1 protein within the Oxygen Evolving Complex, are regulated by red light. This red-light induction involves calmodulin (CaM), a ubiquitous calciumbinding protein that is found in all eukaryotic cells. Thus, it was hypothesized that calcium (Ca2+) would also be involved in this red-light signaling pathway. To test this hypothesis, cells that were grown in the dark in Ca2+-free media were either exposed to varying amounts of Ca2+ or the Ca2+-channel inhibitors, nifedipine and neodymium (Nd3+), in the presence of Ca2+. Treatment with Ca2+ had a dose-dependent effect on rb38, rb60, and psbO mRNA accumulation, but not on rb47 accumulation, with maximal accumulation occurring in response to 10-6 M free Ca2+. This Ca2+-induced accumulation was reduced with the addition of the Ca2+ inhibitors. A similar pattern was not however reflected in the protein levels. RB38, RB47, RB60, and OEE1 accumulated equally across all treatments. An increase in psbA mRNA accumulation was seen only after darkgrown cells were treated with Ca2+ concentrations above 10-5 M, and no change was recognized after a 10-6 M treatment or in presence of the inhibitors. Both Ca2+ and the inhibitors did however affect D1 accumulation, with the inhibitors reducing the increase that was recognized after a 10-6 M Ca2+ treatment. While this study adds to our understanding of Ca2+ acting as a secondary messenger in the red-light signaling pathway, and presents some interesting implications on future work in red-light signaling and D1 synthesis in C. reinhardtii, more research however is needed to dissect the pathway fully.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Ott, Christopher Michael
- Description:
- Apolipoprotein E (apoE) is a crucial protein involved with cholesterol homeostasis and is a genetic risk factor for Alzheimer’s disease. Apomine and simvastatin are potent cholesterol-reducing compounds that mediates their actions through inhibition of HMGCoA-reductase, the rate-limiting enzyme in cholesterol synthesis. We hypothesize that these two compounds increase apoE secretion from human HepG2 liver hepatocyte cells to capture cholesterol from extracellular sources to compensate for their sterol-deprived state. Treatment of HepG2 liver hepatocyte cells with apomine in serum-free medium leads to a significant increase in secreted apoE that is suppressed in the presence of LDL cholesterol added to the culture medium. Consistent with our hypothesis, we found that Apomine and simvastatin increase expression of apoE along with the lipid membrane receptors: LDLR and ApoER2. These results indicate that the presence of cholesterol in the growth medium suppresses the cell’s drive to search for cholesterol through increased apoE secretion. Moreover, the results suggest that increase in apoE expression by apomine and simvastatin is dependent upon SREBP2, responsible for cellular cholesterol regulation. This novel regulation of apoE expression by apomine is relevant to the fields of Alzheimer’s disease and other cholesterol homeostasis related processes.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Wieber, Emily Nguyen
- Description:
- The purpose of this study was 1) to measure fruit yield of navel orange trees and the plants’ physiological responses to regulated deficit irrigation (RDI) and 2) to determine if plant-based measures, including stem water potentials (stem), sap flow (SF), and daily trunk diameter fluctuations (TDF) could be easily used to indicate citrus water need using minimal instruments. The study was conducted in 2014/15 at the Citrus Experiment Station at the University of California, Riverside, and consisted of one control and three deficit irrigation treatments. Control trees were irrigated to replace 100% of water lost due to crop evapotranspiration (ETc). During the early fruit growth period (mid-May to mid-July), RDI1 and RDI3 trees were subjected to 25% of ETc. During fruit maturity period (mid-October to mid-December), RDI2 and RDI3 trees were subjected to 75% of ETc. At all other times, irrigation was 100% of ETc. All RDI treatments resulted in lower yield and higher percentage of small oranges than the control, but the yield effects were only significant for RDI1 and the size effect only for RDI1 and RDI3. Total water savings were 19% for RDI1, 2% for RDI2, and 21% for RDI3. Considering the benefits of water savings and the potential loss/gain in gross revenues, RDI3 and RDI2 were better irrigation strategies than RDI1. Of the plant-based parameters, the labor-intensive discontinuous stem had the highest signal intensity for water stress, while the continuous measurements using plant sensors failed to detect water stress consistently.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Fawaz, Allia A.
- Description:
- Evolutionary trees present hypotheses of the relationships among taxa. Some undergraduate biology students have trouble properly interpreting relationships on these trees; instead of using the most recent common ancestor (MRCA), many students use alternative strategies such as tip proximity, node counting, or morphological similarity to determine relationships. I designed questions to examine these alternative strategies and the use of the MRCA strategy to measure the most commonly, and the most consistently, used strategies by students in college introductory biology. I developed three highly reliable multiple-choice questionnaires, with each of the four possible answers for a question indicating the use of a different strategy (Cronbach’s α = 0.83; α = 0.89; α = 0.89). I administered the questionnaires to undergraduate students in their first core biology class after they received instruction on reading evolutionary trees (n = 197; n = 115; n = 97). Some students’ alternative strategy use was consistent. Students were much more likely to choose answers consistent with the tip proximity and node counting strategies than the morphological similarity strategy. The students looked at the expected areas for their chosen strategy when taking the questionnaire using eye-tracking equipment. Over 53% of the students missed at least one question on the questionnaires. The taxa and tree structure may have influenced the students’ use of the alternative strategies on the questionnaires. These questionnaires allow us to understand how students determine evolutionary relatedness among species and can help instructors of biology courses improve students’ understanding of evolutionary trees.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Lopez, Christina
- Description:
- Multidrug resistant Acinetobacter baumannii, a common etiologic agent of severe nosocomial infections in compromised hosts, usually harbors aac(6’)-Ib. This gene codes for an aminoglycoside acetyltransferase that modifies amikacin and other aminoglycosides of clinical relevance. The goal of this work was to interfere with expression of this resistance gene and induce susceptibility to amikacin in resistant pathogens. In vitro translation assays led to the identification of an antisense oligodeoxynucleotide (ODN4) that targets the initiation of translation region of aac(6’)- Ib mRNA. An isosequential nuclease-resistant chimeric oligomer composed of 2’,4’- bridged nucleic acid-NC (BNANC) residues and deoxynucleotides (BNANC -DNA) covalently bound to the cell-penetrating peptide (RXR)4XB (where “X” and “B” stand for 6-aminohexanoic acid and β-alanine, respectively). This compound, called CPPBD4, inhibited translation at similar levels observed with ODN4. Addition of a combination of Amikacin and CPPBD4 to a culture of an Acinetobacter baumannii clinical strain harboring aac(6’)-Ib resulted in growth inhibition indicating that CPPBD4 reached the cytosol and interfere with the expression of the resistance enzyme.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Quick, Donald Delliemer
- Description:
- Much of Southern California experiences a Mediterranean climate, with long, hot summers and cool, wet winters. Characteristic plants include the deeply-rooted shrubs collectively known as chaparral. Such species, including Malosma laurina (Laurel Sumac, Family Anacardiaciae) and Heteromeles arbutifolia (Toyon, Family Rosaceae), have the ability to tap cool, deep waters. Chaparral species face severe drought stress during the summer, which can be quantified in measurements of water status. Measuring water status continuously in situ can prove challenging, partially because some instruments are extremely sensitive to the extreme temperature gradients experienced by chaparral shrubs during the summer, and often require complex protocols for installation and maintenance. This study was conducted to develop two methods, stem psychrometry and measuring air flow into xylem, for using plant water status sensors on deeply-rooted chaparral shrubs. It was found that temperature gradients in large basal stems caused by ascent of cool xylem sap from deep soil layers can lead stem psychrometers to report overly-negative water potential readings midday. Attempts to correct for these temperature effects turned out to be unsuccessful, leading to a recommendation to install psychrometers on smaller branches up high. Air flow into xylem occurs during embolism spread or repair, possibly as stable nanobubbles are pulled through pit membranes, driven by the pressure gradient between air and xylem sap, and subsequently dissolved into the iii xylem sap. Using a liquid flow gauge to measure air flow into xylem, one set of measurements out of many attempts was completed, demonstrating the validity of the approach.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
- Creator:
- Wen, Chiaokai
- Description:
- LH14E is a novel small molecule, which may induce cell cycle arrest by inhibiting the Wnt/β-catenin signaling pathway. The canonical Wnt signaling pathway is important in cancer, developmental biology, and normal cellular functions. Despite extensive efforts, the field has yet to successfully develop effective small-molecule that can inhibit progression of β-catenin-related cancers in the clinic. In this study, I demonstrate a new cell cycle arrest compound which acts on the β-catenin signaling pathway. The small-molecule LH14E reduced β-catenin protein levels by 60% and inhibited β-catenin transcriptional activity by 37% in HeLa human cervical cancer cells. Under treatment with LH14E, CCND1 gene expression was reduced by 39%. LH14E also reduced cell numbers to 60% of control, indicating a reducing in the rate of cell proliferation. The effects of LH14E on the cell growth rate in serum-free medium was comparable to Cisplatin and Mitomycin C, two well-studied first-line chemotherapy drugs. I also found evidence that LH14E reduced mitochondrial activity in HeLa cells. The evidence presented here supports LH14E’s potential as a cancer therapeutic and prompts further investigation of LH14E in vivo.
- Resource Type:
- Masters Thesis
- Campus Tesim:
- Fullerton
- Department:
- Department of Biological Sciences
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