Predicting complex phenotype-genotype relationships in grasses: A systems genetics approach

Ficklin, Stephen Patrick Clemson University 2013 해외박사(DDOD)

It is becoming increasingly urgent to identify and understand the mechanisms underlying complex traits. Expected increases in the human population coupled with climate change make this especially urgent for grasses in the Poaceae family because these serve as major staples of the human and livestock diets worldwide. In particular, Oryza sativa (rice), Triticum spp. (wheat), Zea mays (maize), and Saccharum spp. (sugarcane) are among the top agricultural commodities. Molecular marker tools such as linkage-based Quantitative Trait Loci (QTL) mapping, Genome-Wide Association Studies (GWAS), Multiple Marker Assisted Selection (MMAS), and Genome Selection (GS) techniques offer promise for understanding the mechanisms behind complex traits and to improve breeding programs. These methods have shown some success. Often, however, they cannot identify the causal genes underlying traits nor the biological context in which those genes function. To improve our understanding of complex traits as well improve breeding techniques, additional tools are needed to augment existing methods. This work proposes a knowledge-independent systems-genetic paradigm that integrates results from genetic studies such as QTL mapping, GWAS and mutational insertion lines such as Tos17 with gene co-expression networks for grasses--in particular for rice. The techniques described herein attempt to overcome the bias of limited human knowledge by relying solely on the underlying signals within the data to capture a holistic representation of gene interactions for a species. Through integration of gene co-expression networks with genetic signal, modules of genes can be identified with potential effect for a given trait, and the biological function of those interacting genes can be determined.

Identification of ubiquilin-1 as a neuronal nicotinic acetylcholine receptor subunit-interacting protein: Role in regulation of surface receptors

Ficklin, Mary Beth Duke University 2006 해외박사(DDOD)

Neuronal nicotinic acetylcholine receptors (nAChRs) play important roles in both the peripheral and central nervous systems. Considerable effort has been made to understand the molecular structure, physiology, and pharmacology of neuronal nAChRs. Less progress has been made, however, in resolving the cellular events and molecular mechanisms that guide the assembly and trafficking of neuronal nAChRs to the surface membrane. Here, we describe the identification of ubiquilin-1 as a nAChR subunit-interacting protein. We describe a role for ubiquilin-1, a ubiquitin-like protein with the capacity to interact with both the proteasome and ubiquitin ligases, in regulating surface expression of neuronal nAChRs. Ubiquilin-1 interacts with unassembled alpha3 and alpha4 subunits when coexpressed in heterologous cells and interacts with the endogenous nAChR subunits in neurons. Coimmunostaining shows that the interaction of ubiquilin-1 with the alpha3 subunit draws the receptor subunit and proteasome into a complex. Coexpression of ubiquilin-1 and neuronal nAChRs in heterologous cells dramatically reduces the expression of the receptors on the cell surface. In cultured superior cervical ganglion neurons, expression of ubiquilin-1 abolishes nicotine-induced upregulation of nAChRs, a process recently suggested to act through increased assembly and maturation of receptor subunits into functional pentameric receptors. Taken together, these data suggest that ubiquilin-1 limits the availability of unassembled nAChR subunits for further assembly and trafficking by drawing them to the proteasome. This provides a role for ubiquilin-1 in regulating surface expression of neuronal nAChRs, in particular nicotine-induced upregulation of surface receptors.

Modeling the Impacts of Climate Change on Hydrology and Agricultural Pollutant Runoff in California's Central Valley

Ficklin, Darren L University of California, Davis 2010 해외박사(DDOD)

Quantifying the hydrologic and agricultural pollutant runoff response to an increased atmospheric CO2 concentration and climate change is critical for proper management of water resources within agricultural systems. This research takes this challenge by simulating the effects of climate change on the hydrologic cycle and agricultural pollutant transport in the Central Valley of California using the Soil and Water Assessment Tool (SWAT) water quality model and the HYDRUS soil water transport model. Specifically, changes in hydrology (streamflow, surface runoff, groundwater recharge, evapotranspiration, and irrigation water use) and agricultural pollutant runoff (sediment, nitrate, phosphorus, chlorpyrifos, and diazinon) were assessed. For the first three studies, hydrological responses were modeled in the San Joaquin River watershed using variations of atmospheric CO2 (550 and 970 ppm), temperature (+1.1 and +6.4°C), and precipitation (0%, +/-10%, and +/-20%) based on Intergovernmental Panel on Climate Change projections. The fourth study used a calibration and an uncertainty analysis technique for the calibration of the Sacramento River watershed. This study confirmed that SWAT was able to capture the large amount of uncertainty within the Sacramento River watershed and successfully simulate streamflow, sediment, nitrate, chlorpyrifos and diazinon loads. The final study uses a novel stochastic climate change analysis technique to bracket the 95% confidence interval of potential climate changes. For all studies, increases in precipitation generally changed the hydrological cycle and agricultural runoff proportionally, where increases in precipitation resulted in increases in surface runoff and thus agricultural runoff and vice-versa. Also, for all studies, increasing temperature caused a temporal shift in plant growth patterns and redistributed evapotranspiration and irrigation water demand earlier in the year. This lead to an increase in streamflow during the summer months compared to the present-day climate due to decreased irrigation demand. Increasing CO2 concentration to 970 ppm and temperature by 6.4°C in the San Joaquin River watershed caused watershed-wide average evapotranspiration, averaged over 50 simulated years, to decrease by 37.5%, resulting in increases of water yield by 36.5% and stream flow by 23.5% compared to the present-day climate. Solely increasing CO2 concentration in the San Joaquin River watershed resulted in an increase in nitrate, phosphorus, and chlorpyrifos yield by 4.2, 7.8, and 6.4%, respectively, and a decrease in sediment and diazinon yield by 6.3 and 5.3%, respectively, in comparison to the presentday reference scenario. Only increasing temperature reduced yields of all agricultural runoff components. Elevating atmospheric CO 2 concentrations generally decreased groundwater recharge under almonds, alfalfa, and tomatoes in the San Joaquin Valley due to decreased evapotranspiration resulting in decreased irrigation water use. Increasing average daily temperature by 1.1 and 6.4°C and atmospheric CO2 concentration to 550 and 970 ppm led to a decrease in cumulative groundwater recharge for most scenarios. For the final study, 95% confidence interval (CI) results from stochastic climate change simulations indicate that streamflow (3% for the upper CI limit, 9.5% for the lower CI limit) and sediment runoff (20% for the upper CI limit, 26% for the lower CI limit) in the Sacramento River watershed is more likely to decrease under climate changes compared to present-day, while the increase and decrease for nitrate runoff was found to be equal (13% for the upper CI limit, 13% for the lower CI limit). For the San Joaquin River watershed, streamflow slightly decreased under climate change (27% for the upper CI limit, 28% for the lower CI limit), while sediment (73% for the upper CI limit, 49% for the lower CI limit) and nitrate (28% for the upper CI limit, 26% for the lower CI limit) increased compared to present-day climate. Comparisons of watershed sensitivities indicate that San Joaquin River watershed is more sensitive to climate changes than the Sacramento River watershed largely due to differences in land use and soil properties. This research improves the understanding between climate change and hydrology and agricultural pollutant runoff within the Central Valley of California. Theses climate change analyses may be used by water resource managers to evaluate the potential effects of climate change.