Chemistry and Biochemistry Faculty Works
https://scholarsbank.uoregon.edu/xmlui/handle/1794/9991
2024-03-29T11:16:03ZAncient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation
https://scholarsbank.uoregon.edu/xmlui/handle/1794/29015
Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation
Short, Aidan W.; Streisfeld, Matthew A.
The reuse of old genetic variation can promote rapid diversification in evolutionary radiations, but in most cases, the historical events
underlying this divergence are not known. For example, ancient hybridization can generate new combinations of alleles that sort into
descendant lineages, potentially providing the raw material to initiate divergence. In the Mimulus aurantiacus species complex, there is
evidence for widespread gene flow among members of this radiation. In addition, allelic variation in the MaMyb2 gene is responsible
for differences in flower color between the closely related ecotypes of subspecies puniceus, contributing to reproductive isolation by
pollinators. Previous work suggested that MaMyb2 was introgressed into the red-flowered ecotype of puniceus. However, additional
taxa within the radiation have independently evolved red flowers from their yellow-flowered ancestors, raising the possibility that
this introgression had a more ancient origin. In this study, we used repeated tests of admixture from whole-genome sequence data
across this diverse radiation to demonstrate that there has been both ancient and recurrent hybridization in this group. However,
most of the signal of this ancient introgression has been removed due to selection, suggesting that widespread barriers to gene flow
are in place between taxa. Yet, a roughly 30 kb region that contains the MaMyb2 gene is currently shared only among the red-flowered
taxa. Patterns of admixture, sequence divergence, and extended haplotype homozygosity across this region confirm a history
of ancient hybridization, where functional variants have been preserved due to positive selection in red-flowered taxa but lost in
their yellow-flowered counterparts. The results of this study reveal that selection against gene flow can reduce genomic signatures of
ancient hybridization, but that historical introgression can provide essential genetic variation that facilitates the repeated evolution
of phenotypic traits between lineages.
12 pages
2023-06-05T00:00:00ZComparison of fractal and grid electrodes for studying the effects of spatial confinement on dissociated retinal neuronal and glial behavior
https://scholarsbank.uoregon.edu/xmlui/handle/1794/28997
Comparison of fractal and grid electrodes for studying the effects of spatial confinement on dissociated retinal neuronal and glial behavior
Moslehi, Saba; Rowland, Conor; Smith, Julian H.; Griffiths, Willem; Watterson, William J.; Niell, Cristopher M.; Alemán, Benjamín J.; Perez, Maria-Thereza; Taylor, Richard P.
Understanding the impact of the geometry and material composition of electrodes on the survival
and behavior of retinal cells is of importance for both fundamental cell studies and neuromodulation
applications. We investigate how dissociated retinal cells from C57BL/6J mice interact with electrodes
made of vertically-aligned carbon nanotubes grown on silicon dioxide substrates. We compare
electrodes with different degrees of spatial confinement, specifically fractal and grid electrodes
featuring connected and disconnected gaps between the electrodes, respectively. For both electrodes,
we find that neuron processes predominantly accumulate on the electrode rather than the gap
surfaces and that this behavior is strongest for the grid electrodes. However, the ‘closed’ character of
the grid electrode gaps inhibits glia from covering the gap surfaces. This lack of glial coverage for the
grids is expected to have long-term detrimental effects on neuronal survival and electrical activity. In
contrast, the interconnected gaps within the fractal electrodes promote glial coverage. We describe
the differing cell responses to the two electrodes and hypothesize that there is an optimal geometry
that maximizes the positive response of both neurons and glia when interacting with electrodes.
18 pages
2022-10-20T00:00:00ZAging and sperm signals alter DNA break formation and repair in the C. elegans germline
https://scholarsbank.uoregon.edu/xmlui/handle/1794/28989
Aging and sperm signals alter DNA break formation and repair in the C. elegans germline
Toraason, Erik; Adler, Victoria L.; Libuda, Diana E.
Female reproductive aging is associated with decreased oocyte quality and fertility. The
nematode Caenorhabditis elegans is a powerful system for understanding the biology of
aging and exhibits age-related reproductive defects that are analogous to those observed in
many mammals, including dysregulation of DNA repair. C. elegans germline function is influenced
simultaneously by both reproductive aging and signals triggered by limited supplies
of sperm, which are depleted over chronological time. To delineate the causes of DNA repair
defects in aged C. elegans germlines, we assessed both DNA double strand break (DSB)
induction and repair during meiotic prophase I progression in aged germlines which were
depleted of self-sperm, mated, or never exposed to sperm. We find that germline DSB
induction is dramatically reduced only in hermaphrodites which have exhausted their endogenous
sperm, suggesting that a signal due specifically to sperm depletion downregulates
DSB formation. We also find that DSB repair is delayed in aged germlines regardless of
whether hermaphrodites had either a reduction in sperm supply or an inability to endogenously
produce sperm. These results demonstrate that in contrast to DSB induction, DSB
repair defects are a feature of C. elegans reproductive aging independent of sperm presence.
Finally, we demonstrate that the E2 ubiquitin-conjugating enzyme variant UEV-2 is
required for efficient DSB repair specifically in young germlines, implicating UEV-2 in the
regulation of DNA repair during reproductive aging. In summary, our study demonstrates
that DNA repair defects are a feature of C. elegans reproductive aging and uncovers parallel
mechanisms regulating efficient DSB formation in the germline.
29 pages
2022-11-07T00:00:00ZLigand field tuning of d-orbital energies in MOF clusters
https://scholarsbank.uoregon.edu/xmlui/handle/1794/28975
Ligand field tuning of d-orbital energies in MOF clusters
Diamond, Brian; Payne, Lillian; Hendon, Christopher
Linker functionalization is a common route used to affect the electronic and catalytic properties of
metal-organic frameworks. By either pre- or post-synthetically installing linkages with differing
linker moieties the band gap, workfunction, and exciton lifetimes have been shown to be affected.
One overlooked aspect of linker functionalization, however, has been the impact on the metal dorbital
energies to which they are bound. The ligand field differences should result in substantial
changes in d-splitting. In this study we use DFT to study the energetics of d-orbital energy tuning
as a function of linker chemistry. We offer a general descriptor, linker pKa, as a tool to predict the
resultant d-splitting in MOFs. Our calculations reveal that simple functionalizations can affect the
d-energies by up to 2 eV and illustrate the significance of this band modularity using four
archetypal MOFs: UiO-66, MIL-125, ZIF-8, and MOF-5. Together, we show that linker
functionalization dramatically affects d-energies in MOF clusters and highlight that linker
functionalization is a useful route for fine-tuning band edges centered on the metals, rather than
linkers themselves.
20 pages
2023-04-12T00:00:00Z