Tag: The Bonds that Make Us

Ensembles link RNA thermodynamics and molecular evolution

Presenter(s): Daria Wonderlick—Biochemistry

Faculty Mentor(s): Mike Harms

Session 5: The Bonds that Make Us

Designing better biomolecules is a long-standing goal for biochemists . Doing so requires a rigorous understanding of how the sequence of a biomolecule determines its properties . Sequence changes, known as mutations, alter these properties and drive the natural evolutionary process . If we can accurately predict how mutations impact biomolecular properties, we can engineer novel biomolecules for applications in medicine, energy, and technology . Predicting a mutational effect is challenging, however, because the effect often depends on the presence of other mutations . Previous work in the Harms lab suggests that some of these mutational interactions emerge from a thermodynamic property of biomolecules—the ensemble . A biomolecule’s ensemble is the collection of interchanging structures it can adopt . A mutation may impact any structure in the ensemble, and its effect arises from perturbations to the relative populations of these structures . Mutations will have different effects depending on the degree to which other mutations have redistributed the ensemble . To mechanistically understand how the ensemble mediates mutational interactions, I am characterizing the effects of five mutations alone and in combination on a magnesium- and adenine-binding RNA molecule with a simple four-structure ensemble . By measuring the amount of a fluorescent adenine analog bound in the presence of varying magnesium concentrations, I can detect the effect of mutations on each of the four structures in this ensemble . The simplicity of this system will provide detailed mechanistic insight into the relationship between ensembles and mutations that can be used to improve the mutational predictions required for successful biomolecule design .

Quantification of Point Defects in Perovskite Solar Cells

Presenter(s): Nicole Wales—Chemistry and Physics

Faculty Mentor(s): Mark Lonergan, Zack Crawford

Session 5: The Bonds that Make Us

In order to improve perovskite solar cell efficiency, it is necessary to minimize defects within the perovskite absorber layer, which may include crystallographic point defects . By understanding how these defects form and contribute to the material’s electronic structure, we will gain insight into routes of Shockley-Read-Hall recombination and associated efficiency loss . Theoretical studies have credited some point defects with the production of energy trap states within the bandgap. As such, we aim to measure and describe the nature and formation of traps in real materials. External quantum efficiency measurements are used to describe a gaussian distribution of traps . Additionally, capacitance techniques are applied with the added advantage of increased sensitivity to the absorber layer . However, capacitance techniques are complicated by the hysteretic perovskite system, which is discussed . The samples used in this study include methylenediammonium dichloride- stabilized alpha-formamidinium lead triiodide, a perovskite with interstitially incorporated chloride . External quantum efficiency measurements showed lower defect densities compared to devices of different compositions, however, one sample did show a small signal with a defect transition energy of 1 .08 ± 0 .01 eV . Findings may point to material suppression of sub-gap defects associated with methylenediammonium dichloride-stabilization compared to alternative compositions . It will be interesting to determine if methylenediammonium dichloride is the source of defect suppression in these samples . To understand how the composition might affect defect states, it will also be necessary to take measurements of other stabilizing agents with different compositions .

Ultrathin Iridium Oxide Catalyst on a Conductive Support for the Oxygen Evolution Reaction in Acid

Presenter(s): Nathan Stovall—Chemistry

Faculty Mentor(s): Shannon Boettcher, Raina Krivina S

ession 5: The Bonds that Make Us

Anthropogenic climate change has driven interest in the research and development of clean
energy alternatives . Great advancements in renewable energy production have been made, but its intermittent nature requires the development of a large-scale storage technology . Water electrolysis is a promising solution to the storage dilemma, via the state-of-the-art proton exchange membrane (PEM) electrolyzers that can convert renewable energy into hydrogen fuel . However, the acidic operating conditions of PEM cells results in slow kinetics of the oxygen evolution reaction (OER) . Iridium oxide is the only catalyst capable of withstanding these harsh conditions, but its low abundance and high costs limit large-scale implementation . My research focuses on designing a novel sub-monolayer-thick iridium oxide catalyst on an inexpensive conductive support that would allow to decrease iridium loading while maximizing activity . We have developed a novel synthetic method for adhering a cheap commercially available iridium precursor (IrCODCl dimer) to the surfaces of inexpensive acid-stable metal oxide nanoparticles . The mechanism of the assembly was investigated with UV-vis spectroscopy, X-ray photoelectron spectroscopy, and NMR . We discovered that the dimer attaches in a surface-limited manor allowing for precise control over the catalyst’s thickness . The determination of the mass loadings was accomplished via x-ray fluorescence and ex-situ inductively coupled plasma induced mass spectroscopy . Electrochemical measurements conducted in pH 1 have shown exceptionally high intrinsic activity at significantly reduced mass loadings . We are currently working on improving the catalyst’s stability which might in the future allow for industrial-scale implementation of water electrolysis as renewable energy storage .

Polycomb Repressive Complex 2 Ensures Robust Skeletal Growth and Patterning During Zebrafish Fin Regeneration

Presenter(s): Bryson Tyler Ricamona—Biology

Faculty Mentor(s): Scott Stewart, Kryn Stankunas

Session 5: The Bonds that Make Us

After amputation zebrafish regenerate their fins back to the correct size and shape . Fin bone regeneration is driven by an endogenous “stem cell” population generated by dedifferentiation of mature osteoblasts at the amputation site . The resulting osteo-progenitors both self-renew and re-differentiate until regeneration is complete . Yet it is unknown how mature osteoblasts reprogram and change gene expression patterns upon dedifferentiation . Recent in mammal work links chromatin function and covalent modification of histones to cellular potency and differentiation . Ezh1 and Ezh2 are key subunits of Polycomb Repressive Complex 2 (PRC2) that tri-methylates lysine 27 of histone H3 (H3K27me3) to maintain repressed states of developmental regulatory genes in mammals . To test if PRC2 is required for dedifferentiation during fin regeneration we analyzed regeneration in ezh1 and ezh2 mutant zebrafish . Here we show that, although ezh1-/-; ezh2+/- mutant fins regenerated largely to the same size as wildtype, they display notable defects in bone patterning . These defects, including the formation of large bony plates and the fusion of adjacent rays occur within 5 days post-amputation suggesting PRC2 is needed for a relatively early phase of regeneration . Such defects are exacerbated when PRC2 mutants are subjected to a second round of amputation in the regenerated region, possibly due to an increased amount of cells with abnormal H3K27me3 levels leading to dysregulation of gene expression . This suggests that PRC2 is a necessary regulator in the lineage specific osteoblast pathway during regeneration due to observations of abnormal bony ray morphology .

Utilizing Behavioral and Molecular Techniques to Study Gap Junction Channels in Developing Zebrafish

Presenter(s): Laura Reich—Biology

Faculty Mentor(s): Rachel Lukowicz, Adam Miller

Session 5: The Bonds that Make Us

Animal behavior requires coordination between the nervous and muscular systems . These systems communicate at specialized subcellular structures, found within and between systems, that allow the cells to coordinate their activity to achieve movement . One type of communication arises from gap junction channels (GJCs), which are built by the Connexin (Cx) family of proteins that allow for direct ionic and small molecule exchange between interconnected cells . The GJC family is large with up to 20 individual genes encoded in the human genome . Given this complexity, it is unknown how individual Cxs contribute to behavior . We are using the embryonic zebrafish to address this question due to its rapid development, genetic access, and its first behavior, spontaneous coiling, which requires GJCs . We first identified Cxs that were likely to contribute to coiling using a combination of RNA-seq and RNA detection in vivo and found a previously uncharacterized Cx, Cx46 .8, expressed in slow muscle fibers . To understand Cx46 .8’s involvement in coiling, we developed an automated behavioral tracking system, using DeepLabCuts (DLC), to track movement during spontaneous coiling . Using this system, we found that animals lacking Cx46 .8 have defects in coiling, indicating that we have identified a novel Cx that contributes to behavior . Further experimentation will utilize DLC, in addition to molecular techniques, to unravel the molecular and functional mechanisms of Cx46 .8 and other Cxs that contribute to GJC communication in behavior .

Anaerobic digestion of wastewater sludge in the atmospheric gases of Mars

Presenter(s): Alexandria Montgomery—Biology

Faculty Mentor(s): Tyler Radniecki, Ashley Berninghaus

Session 5: The Bonds that Make Us

Proposed future missions to send humans to Mars for long term exploration require the development of improved waste management technology in space and increased reliable energy for running necessary systems . In this study, the potential of methanogenic bacteria from wastewater sludge
to be a source of biomethane in the atmospheric composition of Mars was explored . Bottles of wastewater containing methanogens were prepared anaerobically and sparged with either nitrogen or a martian gas mixture and their biogas production was tracked and compared over time . Research findings proving high survivalbiltiy rates of the bacteria and high metabolic function under these extreme conditions suggest anaerobic digestion of mission waste to be a viable solution for recycling human waste and producing biomethane for the production of energy .

Stem Cell Research

Presenter(s): Aryanna Entezari-Schweiger—Human Physiology

Session 5: The Bonds that Make Us

Imagine having the ability to transplant organs without rejection, create medications without requiring human trials and extend a humans life . Stem cells give researchers exactly that! These cells have proven their ability to cure the incurable, learn about the effects of drugs, and understand the developmental process of humans . Stem cells have already cured people with seemingly “incurable” medical conditions such as Alzeihmers, spinal cord injuries and diabetes so investment into stem cell research should be a research priority . Embryonic stem cells are harvested from undifferentiated embryos early in development and inserted into damaged tissues to differentiate into healthy, functioning cells . However, with the moral implications about embryonic stem cells, scientists have turned to reprogramming adult stem cells to further their research . Adult stem cells can be harvested and reprogrammed into pluripotent stem cells and used for therapeutic purposes or medical research . With over 50 years of stem cell research, society should be seeing greater medical advancements . Unfortunately, stem cell research is not commonly funded by wealthy private institutions but rather from limited federal funds . Stem cell research is one of the youngest fields of research that has great promise of treatment and cure for the most common diseases in the world . Through continued intensive research, findings become more and more conclusive and have proved to have a widespread use . Stem cell research should be a front runner in medical laboratories in hopes of enhancing medical treatment .

Metal-Ligand Bond Dynamics in Metal-Organic Frameworks Confirmed by Variable Temperature Vibrational Spectroscopy

Presenter(s): Stacey Andreeva—Chemistry

Faculty Mentor(s): Carl Brozek

Session 5: The Bonds that Make Us

Dynamic chemical bonds reversibly break and reform with minimal heat, light, or pressure . This type of bonding is responsible for the basic mechanism of crystallization for many material systems because erroneous bond formation can be corrected through facile reversal until the material settles into the most favorable crystalline phase . A particularly important class of crystalline materials that emerge from this dynamic process are metal-organic frameworks (MOFs) . MOF architecture is dependent on two building blocks: the metal ions or metal clusters and the organic ligands that bridge the metals . For the past two decades, MOFs have been viewed as rigid structures, but we propose that even after formation, MOFs contain metal-ligand bonds that remain dynamic such that the crystalline structure contains mixtures of partially bound and unbound arrangements . We hypothesize that metal-carboxylate bonds— which constitute the majority of MOFs—are especially dynamic, with large fraction of these bonds existing in unbound states . To understand this metal- ligand interaction, our research focuses on monitoring the changes in the vibrational frequencies as a function of temperature . Variable temperature vibrational spectroscopy shows a lowering in energy of the stretches associated with these dynamic bonds at increased temperatures, indicative of bond weakening . By understanding this relationship, more general insights can be made regarding important material behavior such as crystallization and self-healing responsiveness. Insight into their labile nature would provide a predictive model their growth mechanism and inspire important applications such as the use of MOF for self-healing membranes .