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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