The causative agent of malaria, Plasmodium spp., generated 608,000 deaths worldwide in 2022 according to the World Health Organization and disproportionately threatens endemic areas of Africa. Plasmodium sporozoites infect the host by entering the bloodstream through the skin following bites by female Anopheles mosquitoes. From there, sporozoites migrate to the liver and infect hepatocytes. A single sporozoite-infected hepatocyte is capable of producing thousands of merozoites, which go on to enter the bloodstream. Complete elimination of infected hepatocytes is necessary to achieve sterile protection. In order to observe adaptive and innate immune cell localization towards infected hepatocytes, we applied fluorescence microscopy on livers in a BALB/c rodent model of malaria. Naïve unvaccinated mice were infected with sporozoites of Plasmodium yoelii, a rodent malaria parasite. Two important cell populations are recruited to infected hepatocytes. The first are tissue resident memory CD8+ T cells (Trm), which are crucial in pre-erythrocytic protection. The second are Kupffer cells, which are specialized liver macrophages. To measure these adaptive and innate cell populations, respectively, we applied fluorescently-labeled antibodies to mark the parasite as well as Trms and Kupffer cells. After staining the collected liver tissue and imaging with a widefield fluorescent microscope, we visualized recruitment and measured immune cell proximity quantitatively within a region of interest of the area surrounding infected hepatocytes using microscopy imaging analysis software. This method will be used to test the hypothesis that Trms and Kupffer cells are induced following sporozoite challenge in the rodent malaria model.

Sambucus newtoni is a type of elderberry (Adoxaceae, Angiospermae) from the late Eocene epoch. It has not received much research attention since its discovery in the early 20th century. Researchers identify it based on its leaflets (parts of compound leaves), with other traits inferred from more modern Sambucus species. As a result, its flower morphology has remained unknown. Here, I contribute to our understanding of S. newtoni by describing an excellently preserved compression fossil of a floret (small flower) from a S. newtoni cluster of florets, a so-called cyme. The fossil was collected from lake deposits in the Florissant Formation, Colorado. I described and analyzed the specimen with a microscope and observed extremely well-preserved petals and anthers (male flower parts). The flower sits next to a fossilized fly specimen on the adjacent sedimentary rock layer. The close similarities of the flower of S. newtoni to that of the extant species S. javanica (Chinese elder) may help confirm recent common ancestry as originally suggested through comparisons of the leaflets. Further, improved understanding of S. newtoni through study of the new specimen may open the door to greater understanding of Sambucus evolutionary history as a whole.

Lithium-ion batteries (LIBs) are vital energy storage devices for electric vehicles (EVs). Conventionally, LIBs have planar electrodes that present trade-offs between energy and power (charge/discharge speed) due to ion diffusion limitations. EVs require a high energy battery to enable long mileage ranges while also being able to charge quickly (< 15 minutes). 3D battery electrodes can potentially overcome this trade-off, achieving both high energy and power by leveraging 3D structures that create fast ion transport pathways. However, a scalable manufacturing process for 3D electrodes is needed. We are investigating processes for this, and we need a method to characterize our 3D electrodes. There is no method to automatically quantify the features within these 3D structures, which is required for rapid, high quality analysis. By accurately measuring 3D electrode feature sizes, correlations between features and optimal battery performance can be determined. We hypothesize that fabricating fine 3D features (order of 10s of microns) will improve battery performance. To address this need, I have developed an image processing script that characterizes 3D electrode samples. I investigate how threshold values improve accuracy in comparison to manual measurements and am able to achieve < 10% error. I also connect the code’s feature size measurements to our manufacturing process operating conditions to inform how manufacturing conditions can be altered to precisely control feature sizes, which impact battery performance. We expect that higher operating frequencies for our manufacturing process will result in our target fine feature 3D electrodes, achieving high-performance Lithium-ion batteries. This material is based upon work supported by the U.S. Department of Energy’s Office of Energy Efficiency and Renewable Energy (EERE) under the Advanced Manufacturing Office (AMO) Award Number DE-EE0010226. The views expressed herein do not necessarily represent the views of the U.S. Department of Energy or the United States Government.
 

The antibiotic penicillin is highly effective at treating the STI syphilis, caused by the bacterium T. pallidum. However, the United States has seen increases in syphilis cases every year for the past 20 years; congenital syphilis cases have risen more than 219% from 2017 to 2021 and overall syphilis cases have risen 32% from 2020 to 2021. This situation demonstrates the need for an effective vaccine as current approaches are not working. The aim of this project is to utilize phage immunoprecipitation sequencing (PhIP-Seq) techniques to assist in the development of an effective vaccine in rabbits and eventually humans. To this end I have been using PhIP-Seq techniques to systematically profile the immune responses to vaccine candidates and T. pallidum infections in rabbits. When rabbits are immunized with a cocktail of three strains of the protein TprC we saw a protective immune response against treponemes (resulting in no viable treponemes) whereas an immunization with TprD saw reduced immune protection. I used PhIP-Seq methods - informed by next-generation sequencing (NGS) and differential expression analysis - to determine the epitope-specificity of antibodies in polyclonal serum samples from rabbits immunized with these vaccine candidates. Epitope-specificity comparisons between the resulting antibodies of the two immunogens can shed light on regions of these proteins critical for protection against treponemes. In the next few months I plan to integrate alanine scanning mutagenesis into the project to assess amino acid binding specificity and accurately identify crucial residues for antibody-binding. The fusion of scanning mutagenesis with PhIP-Seq will allow me and the other research scientists assisting with the project to refine of the effectiveness of our existing vaccine candidates.

As the world’s reliance on Lithium-ion batteries increases for technologies like electric vehicles, we need to improve battery performance. Traditional Lithium-ion batteries are composed of planar electrodes whose thickness can be optimized for energy capacity or charge rate (power). Thinner electrodes have a faster charge/discharge rate but low energy capacity while thicker electrodes have slow charge rates but higher energy capacity. Three-dimensional (3D) electrode structures that deviate from traditional planar electrodes can mitigate these trade-offs by allowing for fast ion transport while still maintaining a high ion quantity. One structure of interest due to its theoretical performance improvements shown in literature is a line patterned electrode. Line patterned electrodes have material and structural design features that greatly impact battery performance; it is therefore important to have methods to characterize and quantify features prior to battery testing. To rapidly and accurately analyze 3D line electrode feature sizes, we have developed an image processing code that analyzes cross-sectioned images of 3D line electrodes made from battery materials, enabling automated quantification of features such as line width, spacing and height. Cross-sectioned images are converted to black and white, which can then be processed by a function to detect the line edges and calculate the feature sizes. The results of our image processing code were compared to manual measurements to quantify accuracy. We draw connections between 3D line patterned electrode features and Lithium-ion battery performance to demonstrate how 3D electrode structures can be tuned to improve performance. This material is based upon work supported by the U.S. Department of Energy’s Office of Energy Efficiency and Renewable Energy (EERE) under the Advanced Manufacturing Office (AMO) Award Number DE-EE0009112. The views expressed herein do not necessarily represent the views of the U.S. Department of Energy or the United States Government.

The Strand Lab Benzene Team quanitified the removal of benzene by a genetically modified plant (2E1 pothos ivy) under concentrations similar to home environments. The objective is to make this houseplant available to the public and develop a practical home biofilter that uses a genetically modified (GM) houseplant. The development of a genetically modified pothos ivy with the 2E1 gene provides means to degrade volatile organic compounds (VOC), for example, benzene. My partner developed extraction procedures while I developed the analysis procedures for influent and effluent samples concentrating benzene so that analysis could be done by injection of the concentrated extracts on gas chromatography with flame ionization detection (GC-FID). I created calibration curves with external standards to help quantify the concentration of benzene within a sample. GC-FID was used to measure benzene area peaks for both the influent and effluent samples from which benzene concentrations in conjunction with the standard curves could be calculated. Our findings reveal a 65% removal of benzene by the A9 transformant of pothos ivy containing the cytochrome P450 2E1. The wild-type plant showed no significant benzene removal. The development of this GM houseplant offers a promising solution for indoor air purification, potentially mitigating health risks associated with the exposure of benzene and other VOCs. Furthermore, the potential commercialization of GM houseplants could influence the biotech industry to expand the application of biofilters beyond the home environment such as office spaces, schools, and hospitals. 

Land plants have evolved the ability to uptake silicon from the soil and deposit it as silica-based structures called phytoliths in their tissues. Phytoliths are hypothesized to play a variety of roles in plants including contributing to structural support, defense against abiotic stressors such as drought, and herbivore deterrence. Grasses (Family Poaceae) in particular are known for their high silica concentrations of up to 40% of dry mass. We are investigating whether or not high silica concentrations are more common in grassland species and are associated with C4 photosynthesis. This directly tests the “C4-grazer hypothesis,” which states that, compared to other species, C4 grasses (i.e., those with adaptations allowing more efficient photosynthesis under hot and dry conditions relative to the ancestral C3 photosynthesis) have evolved increased silica accumulation as a response to ungulate herbivory in grassland environments. Using material from herbariums across the world, we have prepared 482 grass leaf samples for analysis. Our samples derive from approximately 200 species from all 12 subfamilies of Poaceae. These samples are analyzed using a portable X-ray fluorescence spectrometer to measure silicon concentration, which serves as a proxy for accumulated silica. To do so, we have established a custom calibration and protocol for measurements. Preliminary results show that high silica concentrations have evolved in a range of grasses, including species occupying both open grasslands and shady forest habitats, and both C3 and C4. This suggests that the mechanisms and influences on silica accumulation may depend not only on photosynthetic pathway and herbivory pressure, but may also depend on other evolutionary and environmental factors. Overall, this research will improve our understanding of how grasses adapt to stressors that will worsen under climate change, and how grasses might contribute to global carbon-silicon cycling.

Phytoliths are silica bodies inside and around plant cell which hold crucial evolutionary insights into the grass family, Poaceae. This study focuses on phytolith morphology within the PACMAD group, consisting of the Poaceae subfamilies Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae. By examining over 1,500 phytoliths across 114 extant species within these subfamilies, we aim to identify patterns in the distribution and abundance of specific phytolith morphologies, so-called morphotypes. This analysis could help deepen our understanding of both phytolith morphotypes as potential indicators of evolutionary relationships within grasses. We can also use these patterns to determine the taxonomic affinities of fossil phytoliths, which allows us to trace the evolutionary history of grasses in the fossil record. Additionally, we focus on the evolution of C4 photosynthesis, a key adaptation in grasses to dry and hot climates; specifically, how we can use phytolith morphology as an indicator for this evolutionary trait in the fossil record. Through comparative analyses within and beyond the PACMAD clade, we aim to compare phytoliths from modern C3 and C4 grasses to gain a better understanding of the differences between phytoliths from grasses with the two photosynthetic pathways and apply it to fossil phytoliths to better understand when C4 grasses evolved and spread. Furthermore, we emphasize the significance of this research in the context of climate change. By linking phytolith morphotypes to the climatic preferences of extant grasses and applying this information to the fossil record, we can trace past climatic shifts and patterns, learning how grasses adapted to environmental changes. Our preliminary results so far show that there are distinct patterns in phytolith morphology across PACMADs, although, at the genus and species level, there is an overlap in morphological traits that we hope to address with increased data.

As the climate changes, we are beginning to see the impacts on a global scale. In order to understand how our landscapes will change with future warming, we can look back to see how landscapes were impacted by past warm, variable climates. This project looks to understand how climate variability in the Middle Miocene is expressed in terrestrial sedimentary records. Using X-ray fluorescence (XRF) analysis, we created a high-resolution elemental geochemical profile of sediment samples from Clarkia, ID (~16 Ma). From XRF, elemental concentrations for a host of elements, including Ca, Fe, K, Mn, Sr, Ti, Zn, and Zr, were calculated. Some elements, notably Ca, showed long-term trends but also sections of shorter-term cyclic variability. It is possible that this variability reflects changes in basin weathering rates of Ca-bearing minerals as a function of climate change occurring on timescales of tens to hundreds of thousands of years. Alternatively, Ca concentrations may reflect changes to precipitation of Ca-bearing minerals within the ancient lake, responding to algal productivity. These hypotheses are tested using X-ray diffraction (XRD) to identify minerals and their crystalline structures as well as characterizing the elemental trends from an additional site, Clarkia’s P-40. Understanding the depositional history of the Clarkia lakebeds aids our understanding in how climate impacts Miocene landscapes.

The latest Eocene Florissant Formation (deposited ~34 million years ago) contains a rich flora and fauna that has received much study by paleobotanists since the 19th century. However, several questions about the ecology and evolution of biota are outstanding and much material remains to be studied. Using observations from a high-definition compound microscope, dichotomous keys, and published literature, I seek to directly analyze and identify an unidentified fossil of a latest Eocene angiosperm, gain a comprehensive view of their surrounding habitat, and contribute to a better understanding of plant-pollinator relationships in the Florissant region. The fossilized angiosperm flower I am studying was collected by Judge Junius Henderson from lacustrine deposits of the Florissant Formation (in modern day Teller County, Colorado). It is a compression fossil with perfectly preserved petals and anthers, providing a rare opportunity for detailed analysis of its anatomy. The rock additionally contains the abdominal region of an insect, which I will attempt to place taxonomically to draw inferences about its ecological role in the Florissant ecosystem. My preliminary studies suggest that the fossil flower belongs to the extinct species Phenanthera petalifera (family unknown)- originally described by Theodore Cockerell in the early 20th century- due to matching dimensions, spatulate appendages, and two-lobed stamens exerted beyond the calyx. The insect is harder to place due to incomplete preservation, but anatomy suggests Aeschneta larvata, a bee fly (family bombyliidae), or a similar insect in order Diptera; I will explore the prominence of these possibilities. Documenting the diversity of plants and potential pollinators in ancient ecosystems existing during past warm climates is crucial for understanding how plant-pollinator relationships might change as anthropogenic warming causes shifts and losses in plant-pollinator niches.