Systematic proteomic strategies to map the human signaling landscape

Thesis (Ph.D.)--University of Washington, 2016-05

Elucidating the cis-regulatory landscape of retinal development and regeneration

Thesis (Ph.D.)--University of Washington, 2016-04

Genetic effects of chronic habitat fragmentation on tree species: the case of Sorbus aucuparia in a deforested Scottish landscape

Sustainable forest restoration and management practices require a thorough understanding of the influence that habitat fragmentation has on the processes shaping genetic variation and its distribution in tree populations. We quantified genetic variation at isozyme markers and chloroplast DNA (cpDNA), analysed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in severely fragmented populations of Sorbus aucuparia (Rosaceae) in a single catchment (Moffat) in southern Scotland. Remnants maintain surprisingly high levels of gene diversity (H-E) for isozymes (H-E = 0.195) and cpDNA markers (H-E = 0.490). Estimates are very similar to those from non-fragmented populations in continental Europe, even though the latter were sampled over a much larger spatial scale. Overall, no genetic bottleneck or departures from random mating were detected in the Moffat fragments. However, genetic differentiation among remnants was detected for both types of marker (isozymes Theta(n) = 0.043, cpDNA Theta(c) = 0.131; G-test, P-value < 0.001). In this self-incompatible, insect-pollinated, bird-dispersed tree species, the estimated ratio of pollen flow to seed flow between fragments is close to 1 (r = 1.36). Reduced pollen-mediated gene flow is a likely consequence of habitat fragmentation, but effective seed dispersal by birds is probably helping to maintain high levels of genetic diversity within remnants and reduce genetic differentiation between them.

Cardiac expression of the cystic fibrosis transmembrane conductance regulator involves novel Exon 1 usage to produce a unique amino-terminal protein

Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a chloride channel present in many cells. In cardiomyocytes, we report that multiple exon 1 usage and alternative splicing produces four CFTR transcripts, with different 5'-untranslated regions, CFTRTRAD-139, CFTR-1C/-1A, CFTR-1C, and CFTR-1B. CFTR transcripts containing the novel upstream exons (exons -1C, -1B, and -1A) represent more than 90% of cardiac expressed CFTR mRNA. Regulation of cardiac CFTR expression, in response to developmental and pathological stimuli, is exclusively due to the modulation of CFTR-1C and CFTR-1C/-1A expression. Upstream open reading frames have been identified in the 5'-untranslated regions of all CFTR transcripts that, in conjunction with adjacent stem-loop structures, modulate the efficiency of translation initiation at the AUG codon of the main CFTR coding region in CFTRTRAD-139 and CFTR-1C/-1A transcripts. Exon(-1A), only present in CFTR-1C/-1A transcripts, encodes an AUG codon that is in-frame with the main CFTR open reading frame, the efficient translation of which produces a novel CFTR protein isoform with a curtailed amino terminus. As the expression of this CFTR transcript parallels the spatial and temporal distribution of the cAMP-activated whole-cell current density in normal and diseased hearts, we suggest that CFTR-1C/-1A provides the molecular basis for the cardiac cAMP-activated chloride channel. Our findings provide further insight into the complex nature of in vivo CFTR expression, to which multiple mRNA transcripts, protein isoforms, and post-transcriptional regulatory mechanisms are now added.

Tertiapin-Q blocks recombinant and native large conductance K+ channels in a use-dependent manner

Tertiapin, a short peptide from honey bee venom, has been reported to specifically block the inwardly rectifying K+ (Kir) channels, including G protein-coupled inwardly rectifying potassium channel (GIRK) 1 + GIRK4 heteromultimers and ROMK1 homomultimers. In the present study, the effects of a stable and functionally similar derivative of tertiapin, tertiapin-Q, were examined on recombinant human voltage-dependent Ca2+-activated large conductance K+ channel (BK or MaxiK; alpha-subunit or hSlo1 homomultimers) and mouse inwardly rectifying GIRK1 + GIRK2 (i.e., Kir3.1 and Kir3.2) heteromultimeric K+ channels expressed in Xenopus oocytes and in cultured newborn mouse dorsal root ganglion (DRG) neurons. In two-electrode voltage-clamped oocytes, tertiapin-Q (1-100 nM) inhibited BK-type K+ channels in a use- and concentration-dependent manner. We also confirmed the inhibition of recombinant GIRK1 + GIRK2 heteromultimers by tertiapin-Q, which had no effect on endogenous depolarization- and hyperpolarization-activated currents sensitive to extracellular divalent cations (Ca2+, Mg2+, Zn2+, and Ba2+) in defolliculated oocytes. In voltage-clamped DRG neurons, tertiapin-Q voltage- and use-dependently inhibited outwardly rectifying K+ currents, but Cs+-blocked hyperpolarization-activated inward currents including I-H were insensitive to tertiapin-Q, baclofen, barium, and zinc, suggesting absence of functional GIRK channels in the newborn. Under current-clamp conditions, tertiapin-Q blocked the action potential after hyperpolarization (AHP) and increased action potential duration in DRG neurons. Taken together, these results demonstrate that the blocking actions of tertiapin-Q are not specific to Kir channels and that the blockade of recombinant BK channels and native neuronal AHP currents is use-dependent. Inhibition of specific types of Kir and voltage-dependent Ca2+-activated K+ channels by tertiapin-Q at nanomolar range via different mechanisms may have implications in pain physiology and therapy.

Fossil biotas from the Okanagan Highlands, southern British Columbia and northeastern Washington State: climates and ecosystems across an Eocene landscape

The late Early to early Middle Eocene Okanagan Highlands fossil sites, spanning -1000 km north-south (northeastern Washington State, southern British Columbia) provide an opportunity to reconstruct biotic communities across a broad upland landscape during the warmest part of the Cenozoic. Plant taxa from these fossil sites are characteristic of the modern eastern North American deciduous forest zone, principally the mixed mesophytic forest, but also include extinct taxa, taxa known only from eastern Asian mesothermal forests, and a small number of taxa restricted to the present-day North American west coast coniferous biome. In this preliminary report, paleoclimates and forest types are reconstructed using collections from Republic in Washington State, USA., and Princeton, Quilchena, Falkland, McAbee, Hat Creek, Horsefly, and Driftwood Canyon in British Columbia, Canada. Both leaf margin analysis (LMA) and quantitative bioclimatic analysis of identified nearest living relatives of megaflora indicated upper microthermal to lower mesothermal moist environments (MAT -10-15 degrees C, CMMT > 0 degrees C, MAP > 100 cm/year). Some taxa common to most sites suggest cool conditions (e.g., Abies, other Pinaceae; Alnus, other Betulaceae). However, all floras contain a substantive broadleaf deciduous element (e.g., Fagaceae, Juglandaceae) and conifers (e.g., Metasequoia) with the bioclimatic analysis yielding slightly higher MAT than LMA. Thermophilic (principally mesothermal) taxa include various insects, the aquatic fern Azolla, palms, the banana relative Ensete, taxodiaceous conifers, Eucommia and Gordonia, taxa which may have occurred near their climatic limits. The mixture of thermophilic and temperate insect and plant taxa indicates low-temperature seasonality (i.e., highly equable climate).

Spin-charge conductance in nanoscale electronic devices

We introduce a spin-charge conductance matrix as a unifying concept underlying charge and spin transport within the framework of the Landauer-Buttiker conductance formula. It turns out that the spin-charge conductance matrix provides a natural and gauge covariant description for electron transport through nanoscale electronic devices. We demonstrate that the charge and spin conductances are gauge invariant observables which characterize transport phenomena arising from spin-dependent scattering. Tunnelling through a single magnetic atom is discussed to illustrate our theory.