Author: Alex McNair

By: Philip Wang, Ryan Weaver, Geoffrey Hill

The food, pharmaceutical, and cosmetic industries are directing increasing attention to compounds with antioxidant properties. This interest arises from antioxidants’ capability to quench reactive oxygen species (ROS) such as H2O2 and O2-, which play a key role in aging and pathological conditions1. ROS attack bio-membranes and cause damage to lipids, proteins, and DNA2. Antioxidants prevent oxidative damage by reducing ROS and preventing the radical chain reactions that would otherwise lead to damage of cellular components. Animals internally synthesize many antioxidants, such as superoxide dismutase and glutathione, but can also obtain antioxidants from their diet.

Figure 1: Mortality of carotenoid-deficient and carotenoid-supplemented copepods for both the pro-oxidant exposure and control treatments shown with 95% upper and lower confidence levels.

Carotenoids are organic pigments synthesized by plants that are the source of red, orange, and yellow colors in many plants and animals. Carotenoids have antioxidant properties and can quench ROS by dispersing the radical’s energy into a solvent, as shown in many in vitro studies3. Increased dietary intake of carotenoids has been correlated with a variety of physiological benefits, such as increased immune function and increased pathogen resistance across multiple species4. Many scientists propose that the physiological benefits of increased carotenoid consumption arise from their antioxidant properties. However, evidence for carotenoids’in vivo antioxidant activity is contentious.

We used the marine copepod, Tigriopus californicus, to test the antioxidant properties of carotenoids in animal systems. In the wild, T. californicus obtains carotenoids by consuming algae. In the lab, T. californicus can be raised on a yeast diet to completely remove carotenoids from its system. Carotenoids can be reintroduced into the copepods by supplementing their yeast diet with powdered carotenoid. We fed 600 yeast-raised copepods either yeast or yeast with carotenoid supplement for 48 hours. We then placed half of them in a  100μM tert-butyl hydroperoxide (tBHP) solution to stimulate the production of ROS. After 24 hours of exposure, we counted copepods to assess mortality (Fig. 1).

The mortality data are promising and show that carotenoid-fed copepods had a lower mortality than carotenoid-deficient copepods in both the control and pro-oxidant exposure groups. However, there was no difference in mortality between the control groups and the pro-oxidant groups, a result that suggests our  concentration of pro-oxidant had no effect on the copepods’ mortality. We will repeat the experiment with a higher concentration of tBHP for a shorter amount of time to hopefully induce more oxidative damage in the exposure groups. We will also measure the amount of malondialdehyde using high performance lipid chromatography to quantify the level of lipid peroxidation in each group.

By: Benjamin King, Thorsten Knappenberger

The scientific community has been turning their focus to the watershed level when tackling sediment and pollution related issues. This paradigm shift has increased the number and size of the stream restoration projects that have been accomplished. However, there is a lack of data and inadequate attention given to the effectiveness of these restoration efforts.

In December 2015, an eroded reach of Parkerson Mill Creek was restored. The  tream bank degradation only took place on one side of the floodplain while the other side remained functional. Hence, the stream restoration was directed at only the degraded side. This reach now offers the unique opportunity to study the hydrology of a recently restored floodplain compared to a natural reference floodplain within the same reach.

To assess the hydrology of the restored and natural sides of the floodplain, we developed a groundwater-sampling plan in which four groundwater wells, evenly spaced at intervals of 20 feet, were established along a perpendicular transect within each floodplain. Each groundwater well was equipped with a groundwater-level sensor. The goal was to understand how rainfall, discharge volumes, and groundwater levels are interconnected and how groundwater levels differ between a recently restored floodplain (left floodplain) and a natural, reference floodplain (right floodplain). Results showed that groundwater moved more swiftly through the disturbed (restored) side of the reach due to a lack of established horizons within the soil profile. This result was predicted since this soil had been completely disrupted and had not been through the same weathering processes as the established, non-disturbed, bank of the stream. However, we noted that the restored floodplain has established vegetation and has been stable despite multiple storm events that have filled the stream to overflowing. Future restoration efforts should be pursued well after the initial work has been completed to understand better the healing process that a floodplain undergoes after being completely disturbed. Although traditionally limited by budget, these follow-up studies are needed to gain a full understanding of what is truly accomplished by a restoration effort.

By: Natalie Stephens, Christine Schnittka

Spatial visualization refers to one’s ability to mentally visualize, rotate, and transform objects. It is an important skill that helps with problem solving, with understanding and applying math and science concepts, and with engineering design. While the necessity for spatial skills is known, it is still not clear how to best infuse spatial thinking into primary education.

Applying spatial skills to the study of chemical molecular geometries makes it  ossible to identify and visualize molecular shapes to determine their chemical properties. The goal of this research was to determine if spatial recognition  oftware on a smartphone could help high school chemistry students develop  tronger spatial skills when applied to chemical molecular geometry. The software used was a free phone app, Aurasma. This app recognizes a designated picture,  alled a trigger image, and displays a 3D augmented reality model created by the designer. These 3D images can be designed and accessed by any user.

For this research, 3D images of 14 chemical molecular geometries were designed. Students in four chemistry classes at Southern High School (a pseudonym) were  iven access to traditional ball and stick models to learn the structures of the 14 molecules. The students had to identify the molecular geometries of these arious chemical compounds. Then, two classes, one regular and one advanced, were given access to trigger images and the Aurasma app to visualize the 3D tructures. The students using the app checked their guess of the molecular geometry and used the app to review the material.

All the students were given pre- and post- tests of their ability to identify the molecular geometries of chemical compounds. These evaluations were  uantitatively analysed to understand if the students with the added technology had an increase in their 3D chemical geometry skills over the group that just used traditional ball-and-stick models. Surveys were administered to determine whether participants used the app to review the material at home, and if they felt that the app helped them learn the material better than traditional physical models.

The advanced class that used the app had a statistically significant increase in heir test scores (p= 0.01) and they reported in their surveys that they believed the app helped them advance their understanding of molecular geometry. The  egular class had an increase in their test scores as well (p=0.12) but it was not as significant as the advanced chemistry class. Even though the advanced chemistry class had a greater increase in their test scores than the regular class, they did not report using the app more often. The advanced students’ willingness to learn and their higher level of fundamental understanding of molecular geometry allowed them to significantly improve their scores through the help of the Aurasma app.

Further research could examine if there is transfer of general spatial thinking skills from the advancement of the students’ chemical molecular geometry understanding. While this study gained some understanding about the benefits of utilizing the Aurasma app for molecular geometry, there are still many research opportunities to learn about spatial thinking and chemistry. 

By: Daniel Stubbs

Our project sought to develop a method for enabling smoothed particle hydrodynamics (SPH) to simulate fluid flow over a body using an inflow-outflow boundary condition that allows fluid to enter and to exit the computational domain.

With this boundary condition, inflow-outflow type simulations can benefit from the advantages SPH has over traditional computational fluid dynamics (CFD). For example, SPH is a particle-based method which, unlike traditional CFD, requires no grid mesh to be defined. Not requiring a mesh allows SPH to provide time savings and to handle simulations such as flow over complex shapes, mixing problems, or multiphase flow with relative ease. By giving SPH the ability to model the flow in and out of a domain accurately, SPH would naturally extend to a wider range of applications and would aid engineers as an efficient tool providing valuable insight into the intricate details of aerodynamic flows. Such insight would assist engineers in developing more efficient and capable designs.

Fig. 1: SPH simulation of a NACA0012 airfoil in an aerodynamic flow

This project began with an existing SPH simulation code already capable of simulating flow within a closed domain. The code was then extended by developing methods allowing for fluid particles to flow through the domain, leaving through an outlet and re-entering through an inlet. As part of this inflow outflow condition, methods were developed for resetting the particle properties upon exiting and re-entering the domain as well as for providing buffer regions at the outlet and inlet to ensure that the simulation would remain stable. Once these capabilities had been added to the simulation code, test cases were run on fundamental fluid dynamics problems such as flow over cylinders and airfoils. The results of these simulations were compared against widely available and accepted verification data.

Results from this project show that the inflow-outflow condition is working well, but that there are still some underlying issues within the core equations used in the simulation, particularly regarding boundary conditions and data extraction from solid boundaries. Figure 1 shows the aerodynamic flow around a two dimensional airfoil shape, which exemplifies the current capabilities of the simulation. The next steps for this project are to investigate the equations being used, to determine methods to improve the model’s accuracy, and to remove some of the shortcomings of the simulation in its current state. Future projects will seek to make the code capable of 3-D combustion reaction simulations as well as giving the code the ability to run on modern high-performance computing technologies such as multi-node supercomputers and GPU clusters.

Having developed a working method for allowing fluid to flow in and out of the computational domain in an SPH simulation, this project has laid the ground work and provided valuable lessons for future efforts with SPH. With this foundation in place, SPH is on course to be fully capable of simulating complex
fluid flow over any geometry, simple or complex, allowing insight into the fluid dynamics around shapes which challenge existing technology.

By: Da Sol Jung, Thankhoe A. Rants’o, Angela I. Calderón

Maca (Lepidium meyenii Walpers) is a plant cultivated in central Peru, and its root is a common active ingredient in the botanical dietary supplements for its effects on a variety of health issues such as sexual dysfunction, anemia, and cancer. The plant contains compounds that have cytotoxic and antioxidant activities, but information on the metabolism of the bioactive compounds is limited. The goal of this study was to identify Phase I and Phase II metabolites of the bioactive constituents of maca extracts, such as induction and inhibition of CYP3A4 and their interactions with anticancer drugs, for further study.

To predict the interactions of the maca compounds and their metabolites with anticancer drugs, Phase I and Phase II reactions of maca constituents were conducted, and the resulting metabolites were monitored and assessed for their increase in polarity and decrease in toxicity as well as possible inhibition of CYP3A4. Before performing the metabolic experiments, the permeability of the components was determined by incubating three different extracts in dichloromethane, methanol, and acidic methanol with buffer in a parallel artificial membrane permeability assay (PAMPA), which mimics the role of intestinal membrane. Then, the compounds were categorized into two groups: those that passively diffused across the membrane and those that did not. Both groups were incubated with human liver microsomes, phosphoric buffer at pH of 7.4, and nicotinamide adenine dinucleotide phosphate (NADPH) and/or uridine 5’-diphosphoglucuronic acid (UDPGA) to initiate Phase I and Phase II reactions and to obtain corresponding metabolites. Furthermore, for the Phase II experiment, alamethicin was added to the sample to activate UDPGA sequestered in the hepatocytes, and saccharolactone was added to inhibit glucuronidase, which reverses the Phase II reaction. The obtained metabolites of maca were analyzed with rapid resolution liquid chromatography, and their identity was confirmed via various layers by comparing obtained liquid chromatography (LC/MS) and mass spectrometry (MS/MS) data to previously published literature or database and elucidating the structure of a compound with ACD/Spectra software.

The permeability test illustrated that among twenty-seven known chemical constituents of maca, six chemical constituents showed high permeability—these compounds have passively diffused through the membrane from donor site to acceptor site—while other twenty-one constituents displayed low permeability. The second part of the experiment suggested the presence of twenty-three metabolites of maca chemical constituents, and further analysis with MS/MS, database, literature, and chemical software identified and confirmed eight metabolites produced via Phase I and Phase II reactions of maca extract. Among these eight metabolites, five metabolites were produced through hydrolysis and oxidation while three metabolites were produced through glucuronidation. While NMR analysis will provide further structural confirmation, a method to discern the compounds should be organized prior to the analysis, since botanical extract contains a wide range of compounds that are not necessarily bioactive or of interest. After finalizing the confirmation of produced metabolites, the samples will be tested for its possible inhibiting effect against CYP3A4 and will be incubated with and without anticancer drugs to observe the inhibition and interaction of the metabolites. The study provides a confirmed chemical profile of maca that may offer insight into active compounds that are known to be effective against cancer.

By: John Cook, Dr. Hari Narayanan and Dr. Jeff Overbey

The proliferation of affordable multi-touch devices over the last five years has brought the power of data visualization and interaction to the average
consumer. However, development and integration of pen-based input via new “smart stylus” tools has not resulted in data visualization applications that respond intelligently to markup and that enhance the naturalistic pen-and-paper interaction these tools are designed to replicate. The aim of this research is to create a system that provides natural pen-based data visualization and manipulation techniques and to evaluate it for feasibility and effectiveness against its touch-based “Windows, Icons, Menus, Pointer” (WIMP) counterparts. I have developed a spreadsheet application for the Apple iPad Pro that recognizes the pen gestures users would naturally use on a paper spreadsheet (circling, crossing out, highlighting, etc.; Figure 1) and maps them to their respective operations. The application also provides features typically offered by electronic spreadsheets (sorting, computation, etc.). 

For this project, I designed a user study in which fourteen undergraduate computing and liberal arts students first completed a number of gestures in isloation, then carried out a sequence of data manipulation tasks using both my application and its leading competitor, Microsoft Excel™. The former task provided data regarding the intuitiveness and usability of each naturalistic gesture, while the latter provided the same insights regarding the application and interaction scheme as a whole. An automatic time-stamping function collected timing data for the users’ interactions with each application, and an administered questionnaire provided qualitative feedback.

The results showed that the pen-based interactions yielded significant time savings over traditional WIMP interactions. On average, completing a set of data interaction tasks was two times faster using pen-based interactions (~5.5 versus 2.7 minutes). Unsurprisingly, previous experience with Excel™ was a predictor of
increased task-completion speed using pen-based techniques (27% faster). Interestingly, liberal arts students completed the tasks 17% faster than computing students. While all of the individual pen gestures were more efficient than their WIMP-based counterparts, some gestures stood out as particularly efficient. Basic arithmetic operations require multiple steps to complete in Excel™, but only two gestures using the pen-based system. As such, users completed these operations 88% faster using the pen-based techniques. Similarly, deletion and summation require multiple steps to complete using Excel™, and users completed these tasks 70% and 66% faster (respectively) using the pen-based techniques. The learning curve for the multiple-selection interaction was somewhat high using the WIMP system, and users completed this interaction 62 times faster using the pen-based system when performing the gesture in isolation.

Overall, the feedback from the questionnaire indicated that users found the pen-based interaction techniques more enjoyable, more intuitive (with the exception of a gesture to circle and paste), and easier to use (though users with a large amount of spreadsheet experience were understandably more comfortable using Excel™). This positive feedback, combined with the significant increase in user efficiency, indicates that a spreadsheet interface that implements pen-based gestural interaction techniques is quantitatively and qualitatively superior to a traditional WIMP-based interface. While no spreadsheet or other data manipulation applications that provide a pen-based gestural interface exist today, this study proves that such a system is both feasible and preferred by the end users.

Figure 1. Screenshot from the application displaying an example of a ‘cross out’ gesture to delete (left) and a line gesture to select (right).

By: Courtney Kloske, Sy Traore, Prem Kandel, Leonardo De La Fuente

Xylella fastidiosa (X. f.) is a bacterium that causes multiple lethal diseases in many economic crops including grapes, citrus, peach, plum, almond, coffee, pecan, and more recently olive. It was first described as Pierce’s disease in the grapevines of California vineyards. X. f. lives only in xylem vessels, which carry water and nutrients from the roots to the rest of the plant. Proliferation inside the xylem leads to formation of a biofilm that obstructs the plant’s vascular system, causing nutrient deprivation in the plant.

Previous research by our group showed that calcium increases the growth of the biofilm, and therefore, the virulence of the bacterium. Whole transcriptome analysis identified 17 X. f. genes that were consistently upregulated by calcium at different times, including 12 without an assigned function. One gene (PD0926) was selected and encodes for a hypothetical protein. The objective of this study was to determine the role of PD0926 in the virulence of X. f. To test its virulence, homologous recombination was used to cleanly delete the PD0926 and replace them with the chloramphenicol antibiotic resistance gene. Sequence verification was performed to verify successful knockout of the genes of interest in the X. f.
genome.

We successfully knocked out gene PD0926 in the WM11 and Temecula strains of X. f. These mutated strains will serve as a resource for performing further in vivo and in vitro testing. Microfluidic chambers will be used to test the biofilm formation of the mutated strain, and twitching motility will be observed. An in planta test will be performed to show the progression of the disease within a tobacco plant. These tests will help us understand the virulence of the mutated strain. With this knowledge, a more holistic view of the bacterium will help with potential eradication of this bacterium and its related diseases.

By: Trevor L. Cofer, Elizabeth A. Guertal, James Pitts

For many Alabama vegetable growers, fresh market tomatoes represent a significant source of income. Growers often apply high rates of potassium fertilizer at planting because it is thought to be needed to promote growth
and uniform ripening. Two tomato growers I spoke with before my project expressed concerns that the area around the stem of the fruit remained yellow throughout the season (called yellow shouldering). Since more potassium is required to color a tomato than to ensure full yield, if there is insufficient potassium at fruit set, the fruit will not color properly, no matter how long it stays on the plant.

The objective of this research was to examine rates and sources of potassium fertilizers and their effects on tomato growth, yield, and fruit quality. The one year study was conducted during the summer of 2016 at the Auburn University Chilton Research and Extension Center in Clanton, AL. The experiment was arranged in a completely randomized block design, with three replications of each treatment. Potassium was applied at bed formation at rates up to the soil test recommendation of 180 lbs K2O/A (0, 60, 90, 120, 150 and 180 lbs K20/A) and with four potassium sources (potassium chloride, potassium sulfate, potassium thiosulfate, and potassium magnesium sulfate), all readily available to growers. After two weeks of growth, plant height and stem diameter were measured weekly. At one and two months of growth, plant tissue samples were collected and analyzed for percent potassium. At harvest, fruit was counted, weighed, and categorized based on complete or incomplete ripening (via visual inspection). After harvest, soil samples were taken and analyzed for extractable potassium (Mehlich 1 extract).

Figure caption: Tomato affected by yellow shouldering.

We found that tomatoes receiving potassium before planting had greater potassium content in leaf tissue than those that were not fertilized with potassium. However, this did not translate to increased fruit yield, nor did it reduce the instances of yellow shouldering of the fruit. Leaf potassium was likely not high enough early in the growing season to promote uniform ripening. Neither the potassium source nor potassium rate significantly affected tomato yield or occurrences of yellow shouldering over the harvest period at the applied rates, although the potassium rate did significantly affect the plants’ height and stem diameter. A higher potassium rate promoted taller plants, whereas a lower potassium rate promoted increased stem girth. Soil test extractable potassium showed low to moderate extractable potassium, irrespective of potassium rate or source. Mean and median soil test extractable potassium of all plots was 64 and 60 lbs K2O/A, respectively. We tested soil from a similar tomato study on the same research station that had no instances of yellow shouldering and found 299 lbs K2O/A of extractable potassium, an extremely high value. Comparing results from the two studies, we concluded that although the potassium we applied was sufficient to maximize yield (which are how soil test recommendations are given) it was far from sufficient to promote uniform fruit ripening. Such information could help Alabama farmers evaluate their potassium application strategies based on soil testing recommendations.