STEM Foundry

Students in my lab will be able to choose from within a variety of projects. In one project we are aiming to characterize the molecular basis of bacteriophage-host interactions, including the bacteriophage lifestyle. A different project seeks to identify microorganisms with high tolerance or resistance to UV radiation and reactive oxygen species. We aim to evaluate this resistance and characterize possible mechanisms of resistance. A third microbiology project involves the development of biosensors (eg. bacteria) to sense pollutants in the environment such as metals or inorganic pollutants such as nitrates. Lastly, a solely bioinformatic project uses comparative genomics to annotate genes in the insulin signaling pathway of Drosophila species as part of a large collaboration. This project aims to better understand the evolution and function of metabolic pathways in eukaryotic organisms.

Conservation of migratory songbirds can be particularly challenging as it these animals require three distinct habitats for successful completion of their life cycle: breeding habitat, wintering habitat, and migratory habitat. The migratory phase of the life cycle of these animals may be the most critical as migratory behavior is physiologically stressful and dangerous. This was clearly demonstrated by a mass migratory songbird die-off that occurred in early Sept. 2020 the southwestern United States. Thousands of dead migrating birds were found over the span of just a few days. It is thought that this die-off was a result of a lethal combination of drought conditions reducing food availability, poor air quality caused by wildfires, and a freak snow storm. Migratory banding stations can provide valuable information to better understand the threats that migratory birds face on route to and from their breeding grounds. Migratory songbirds will be captured from field sites in areas heavily used by migrating birds in the area. We will use mist-nets to capture the birds and take various measurements to determine overall physiological condition of the birds. Birds will then be released to continue their migration.

This project focuses on mapping the local distribution of a rare lizard, the Colorado Checkered Whiptail (Aspidoscelis neotesselatus), as well as quantifying possible threats to its local persistence. The species is considered a species of conservation priority by the Colorado State Parks and Wildlife department, despite high levels of abundance within urban areas in Pueblo County. Because these urban populations have not previously been documented or studied, potential benefits and threats of urbanization have not been quantified for the persistence of lizard populations. A. neotesselatus is a parthenogenetic, asexually reproducing species. Like many similar, asexual species within the genus Aspidoscelis, it appears to thrive in disturbed areas. However, animals living in disturbed areas which are also highly urban may also be susceptible to anthropogenic stressors, including high levels of mesopredators. Increased predator-pressure in Pueblo County is most likely caused by feral cats, but could also include higher densities of natural predators such as raccoons, ravens, and coyotes that are known to aggregate around areas with increased irrigation and increased food sources. Here, we will quantify numbers of lizards across a gradient of urban-natural areas while also quantifying tail drops as a measure of predator attacks. Similarly, we will quantify external and internal parasite loads and differences in white blood cell profiles, as measures of stress. We hypothesize that the lizards in the most urban areas will exhibit higher levels of predator attacks and physiological stress than lizards in natural areas.

The objectives of this proposal are two-fold. First, to explore the synthetic generation of new organofluorine compounds from two important classes of naturally occurring materials, phenols and alkenes and more specifically using resorcinol and limonene and derivatives. The approach will use electrophilic fluorinations to explore these reactions. It is anticipated that these new compounds will be biologically active; this aspect will be explored as appropriate. Secondly, the project will engage two students doing research in the summer and fall semesters. The students will be fully engaged in all aspects of the research including synthesis, isolation, purification, and structural identification. They will make use of many instrumental spectroscopic and chromatographic techniques. Ultimately it is anticipated that the research will lead to professional presentations and publications.

The treatment of human diseases is a major public health concern that relies heavily on the existence of effective and safe medicines. However, the rate at which successful drugs are discovered is often constrained by the availability of synthetic methods capable of generating novel molecular scaffolds. Given this challenge, one of the primary goals of modern organic chemistry is to develop innovative reactions that can be applied in drug discovery. An important consideration in the design of new transformations is the ability to turn inexpensive building blocks into value-added products. Hydrocarbons derived from crude oil, such as alkenes, alkynes, are one such class of building blocks; however, they often lack the requisite polar functional groups that typically dominate interactions between pharmaceutical agents and their biological targets. The primary objective of the proposed research is to develop new carbon–boron (C–B) bond-forming carboboration reactions of alkenes and alkynes. C–B bonds are versatile functional handles that serve as a gateway to polar functional groups commonly found in medicines, such as amines and ethers. Central to the proposal will be the application of transition metal catalysis to achieve the desired transformations. A secondary goal is to study the mechanisms of the new reactions we develop to further our understanding of the underlying catalysis and to provide insight that will be of broad interest in the field. Students joining on this project can expect to learn the fundamentals of organic synthesis and method development, the foundations of catalysis, and key principles in transition metal reactivity. Students will also gain experience with cutting edge instrumentation and lab techniques. It is anticipated that this research will lead to publications in peer-reviewed scientific journals.

The overall scientific goal of this proposal is to investigate if a protein, Disulfide Bond Forming Enzyme (DBF) has the ability to rearrange incorrectly made disulfide bonds within γ-crystallin protein aggregates, the causative agent of cataracts. Cataracts are the leading cause of blindness worldwide and account for over 51% of all visual impairments¹. γ-crystallins are the primary structural proteins in the eye lens. Normally these proteins exist as single entities called monomers that have a size of ~20 kDa. However, they can assemble into larger complexes such as dimers (2 proteins, ~40 kDa) or larger complexes known as γ-crystallin aggregates. Cataracts are ultimately caused when these larger protein complexes cannot be reverted back to their monomeric components. One example of the irreversibility of the γ-crystallin proteins are when strong disulfide bonds are formed between different proteins. These intermolecular disulfide bonds are covalent, irreversible interactions between different proteins, that inhibit their ability to disassemble back to their monomeric form. This type of disulfide-mediated aggregation is not unique to cataracts but has also been observed in other diseases such as Alzheimer’s, Amyotrophic lateral sclerosis (ALS), Parkinson’s as well as certain cancers².

1. Khairallah, M. et al. Number of People Blind or Visually Impaired by Cataract and in World Regions, 1990 to 2010. Invest Ophth & Vis Scie. 2015, 56: 6762-6769.
    2. Bechtel, T., Weerapan, E., From structure to redox: the diverse functional roles of disulfides and implications in disease. Proteomics. 2017, 17: pmic.201600391.

The broad objective of this project is to find relationships between instructors' as well as students' behaviors and the specific tasks provided by laboratory activities. In addition, the project's specific aims include finding the usefulness of task analysis to create profiles of laboratory activities. Students' involvement in the research will involve becoming familiar with the analytical instruments used to investigate in-class behavior as well as task analyses, and mentoring will include introducing STEM students to chemistry and/or STEM education research regardless of experience in the area, where they will use their subject matter expertise and experience to provide insight into the data. They will also be trained on the use of statistical software as necessary as well as introduced to theoretical frameworks used for the analysis. Their products will include presentations in symposia (in-campus or out-campus as possible) as well as authorship credit in a future publication.

Treatment of Penicillium fellutanum with different metals and sugars changes the expression of enzymes in P. fellutanum. These enzymes are part of a system of energy regulation and storage. The enzymes are also suspected to act on the remodeling of the surface of P. fellutanum. This project uses Atomic Force Imaging and Bioanalytical techniques to determine which enzymes are increased by which metals and sugars. Correlations and models will be developed in the process of determining which factors have the greatest influence on the surface remodeling of the fungus.

Treatment of Saccharomyces cerevisiae with cadmium and selenite results in the formation of fluorescent complexes in the yeast cells. The mechanism for this formation of "quantum dots" is poorly understood. This research aims to look at the formation of these complexes and determine which enzymes are responsible for the creation of the complexes.

Hot Mix Asphalt (HMA) is one of the primary components of roadway pavement. HMA is a mixture of stone aggregates, asphalt binders, and some additives. On the other hand, in our day-to-day life plastics are an essential component. Every year, human produces over 35 million tons of plastics, where only 10% gets recycled, though the material can be employed as a strong structural component. To this end, in the current research, the students will work in a newly developed technique of employing waste plastics, unusable single-use rPE plastic such as grocery bags and shrink-wrap film that is destined for the landfill, as one of the HMA pavement components. The research going to present the technical aspects of mixing waster plastic in HMA and the pavement performance data. The data from the field, as well as the laboratory, shows that waste plastic can be used as a strong recycled material without reducing the pavement performance indicators.

Transportation is the largest branch of civil engineering. It includes all aspects of surface, water, air, marine, and pipe transportation. Highway geometry, pavement materials, traffic analysis, traffic safety, railway engineering, Hyperloop transportation, etc. are the focus areas of research at the CSU Pueblo. The Southern Colorado Institute of Transportation Technology (SCITT) was established in 2022 through a partnership between the state of Colorado and CSU Pueblo. The role of the SCITT is to conduct and facilitate education, training, and research on issues related to the safety, security, and innovation of railroad, ground, and intermodal transportation and general issues related to transportation problems in the state. The institute also serves as an information exchange and depository for the most current information pertaining to transportation education, research, and related issues, including the economic development of transportation technology in Colorado and nationwide. Students are to be educated, trained and exposed to different areas of transportation based on their interests and career focus.

In the 1990’s a portion of one guide way was selected to be the location of a new impact wall at the Transportation Technology Center, which would allow testing to be done on the crashworthiness of rail vehicles. The impact wall itself is a large reinforced concrete barrier that was built directly on top of an existing guideway in order to use the guideway structure to sustain forces from impacts. This guideway track is approximately 2,500 feet long and slopes down toward the impact wall with a gradient of 0.86 percent. The guideway leading to the impact wall has had a railroad track built on it to allow rail vehicles enough space to gain speed before reaching the impact wall. Many different types of impact tests can be conducted using the impact wall at the TTC. Some of these tests include:

• Passenger rail vehicle crashworthiness testing
• Crash Energy Management (CEM) component testing
• Tank car puncture resistance testing
• Fuel tank puncture resistance testing

In an effort to expand the testing capabilities of the TTC, this project aims to modify the impact track to allow road vehicles to run along the guideway into the impact wall. This will allow impact testing of road vehicles to be done in addition to rail vehicles. Students working on this project will gain analysis and design experience of the impact wall. In addition, the abovementioned testing and research of different impact testing will also be explored.

The Transportation Testing Center (TTC) in Pueblo is the only federally-owned railway research and testing center in the country. It is also the largest railway testing facility in the world with over 50 miles (80 km) of test tracks. Test tracks are used for rolling stock prototype testing, type testing, homologation, and research. The site is planning for a dynamic load test frame of 1500 kip structural capacity with 2 hydraulic actuators. This frame will be used for high-impact dynamic load that may occur in high-speed rail truck. The project consists of engineering investigation of possible load, structural materials, possible distresses, and finally designing the structural components of the frame capable of running dynamic load tests on rail trucks. Student will gain research skill as well as real-life engineering analysis and design skill.

Wooden is the most popular option considering the different tying options in railroad construction. Wooden ties are hardwood and offers sturdiness and durability. Untreated hardwood rots somewhat easily when exposed to the elements. To prevent this, suppliers typically treat wooden ties with creosote. Still though, wooden tie in rail tracks undergo continuous degradation due to fatigue loading and aging. MxV Rails (one of the most famous railway-based research companies in the nation) already developed a numerical index rating protocol. This research aims to use the protocol to monitor the health of wooded tie over a 5-year period. Another aim of the research is to understand how a wood tie in the middle of a railway track may or may not affect the surrounding 5 wood ties in each direction. This research will help the rail agency to decide how to keep these wooded ties in better condition to support the overall quality of the railway track.

Creating a viable low-cost alternative to existing lower extremities exoskeletons. Namely, such commercially available exoskeletons cost from $80K to $180K. We are trying to create such devices for much less. We have a first prototype that may need to be fully redesigned. There are a few directions that this project can take. Including dealing with the hardware design, control system, and AI in decision making and how long and fast the next step is.

The Ionic Polymer Metal Composite (IPMC) is a synthetic composite material that can exhibit extreme part deformation under a low electric field. The applications of these artificial muscles range from robotics and biomedical to environmental sciences. These polymeric muscles work in air, underwater, or any polar fluid such as blood. The proposed work is to study the response of IPMC in different work environments. This work includes an experimentally studying the effect of work environment polarity on the IPMC strip deflection. In addition, this study will also consider the effect of the concertation of polar fluids.

In the field of computer vision, semantic segmentation is one of the key problems to understanding the scene at a high-level. Inferring knowledge from imagery has many applications, such as autonomous driving, human-computer interaction, virtual reality, etc. In this project, a special deep learning architecture based on the state-of-the-art semantic segmentation algorithm U-net is developed. One application will be the detection, localization, and classification of (asphalt paving or concrete) road cracks. Other applications of image segmentation will be investigated.

This project suggests developing an AI-based model to recognize fire in the forest using Satellite imagery. A supervised Convolutional Neural Network (CNN) will be designed and trained to classify images into two classes (Fire and NoFire). The training patterns (Images) will be created using the imagery captured by satellite forest images with superimposed synthetic fire images to create an adequate number of training patterns (examples). To more accurately depict the behavior of potential fires, we need to study wind patterns, fire behavior, and seasonal changes in selected test areas along with gathering the base images.

This project will explore the scientific and mathematical determination of the shape of the earth, still ongoing. It will focus on the data collection and analysis in the Struve Geodetic Arc Survey. This Survey was led by astronomer Frederick Wilhelm Struve over the years 1816-1855 and over 2820 kilometers through 10 countries from Ukraine to Norway. Thirty-four of the 265 station points in 258 main measured triangles are designated as UNESCO World Heritage Sites. These sites honor the outstanding international cooperation leading to great advances in knowledge of the earth's shape and size and topographical mapping techniques. The mentor visited two of these sites in 2021-22.