Digital Commons Network^™

Mmappr2: An Improved Bioinformatics Approach To Find Novel Genes, Aiden Cardall, Jonathon T. Hill, Kyle Johnsen, Connor Ward, Maliha Tasnim, Jared Taylor

Library/Life Sciences Undergraduate Poster Competition 2024

Introduction

• New genes are commonly found by randomly inducing mutations in model organisms.

• Mapping the mutations to the genome to find novel genes is difficult, time-consuming, and expensive.

• We created a bioinformatics program, MMAPPR, to automate this process.

• Here, we introduce a new algorithm, MMAPPR2, which requires little to no bioinformatics knowledge to use.

• MMAPPR2 makes several improvements that allow it to identify genes more rapidly and precisely.

• MMAPPR2 will aid the rapid identification of genes in a wide range of species and developmental systems.

Determining The Role Of Noncoding Insertion And Deletion Mutations In Lung Cancer, Zachary Everton, Matthew H. Bailey

Library/Life Sciences Undergraduate Poster Competition 2024

Background

● Cancer is a disease in which cells grow and divide at an uncontrolled rate and cause damage to surrounding tissue and is caused by mutations in the cells’ DNA.

● Though some cancer-causing mutations are inherited from parents, most cancer-causing mutations emerge over the course of a person’s life and are localized to the tumor. These localized mutations are also known as somatic mutations.

● The human genome is over 6.27 billion base pairs long and cannot be read from end to end; instead it is read in small pieces that are aligned to best-matching sequences in the …

Utilizing Ai Integrated Neuroimaging Technology To Expand Upon Machine Learning In Positron Emission Tomography Technology With The Aim Of Detecting Amyloid Beta Biomarkers Early In The Onset Of Alzheimer's., Ethan S. Terman

Undergraduate Research Posters

Early intervention in Alzheimer's is vital for treatment. The earlier a professional can detect symptoms and make a diagnosis the earlier a prognosis can be implemented. With the prevalence of data in our day-to-day world combined with Artificial intelligence (AI), utilizing both for machine learning can pave the way for more accurate and efficient detection of Alzheimer's and other neurodegenerative diseases. AI combined with Machine learning (ML) increases diagnostic efficiency and reduces human errors, making it a valuable resource for physicians and clinicians alike. With the increasing amount of data processing and image interpretation required, the ability to use AI …

Bioinformatics Lab: A Course-Based Undergraduate Research Experience Curriculum, Kristen M. Deangelis, Mallory Choudoir, Ashley Eng, Maureen A. Morrow

Microbiology Educational Materials

This is a computer lab course intended to give students technical and practical experience in analyzing sequencing data. We focus on bacterial genomes from recently isolated bacteria, so there is a possibility of discovery of new microbial diversity. Collaborative learning will be encouraged, but students will work individually to assemble, annotate, and analyze a bacterial genome.

Each week will begin with a review on the topic to be covered for that week. When applicable, there will be pre-recorded lectures to introduce lab topics, and students are expected to have watched these before coming to class. Our time in class will …

Analysis Of Ab Initio Protein Structure Prediction Methods, Maytha Alshammari, Jing He

College of Sciences Posters

Protein structure prediction produces atomic models of three-dimensional structure of a protein from its amino acid sequence. Understanding the function mechanism of proteins requires knowledge of three-dimensional structures. When developing new enzymes and drugs, it's essential to understand the structure of the target protein. In this study, we analyze models predicted using two ab initio protein structure prediction methods, trRosetta and Quark. A set of thirty protein chains was used to evaluate the effectiveness of the methods. The thirty chains were collected from Protein Data Bank (June – November, 2020). The length and the relative position of the predicted secondary …

Respire: A Technological Tool To Navigate Mechanical Ventilation In Patient Care And Educational Settings, Swara Chokshi

Undergraduate Research Posters

Around the world, more than 20 million patients rely on mechanical ventilators annually; however, not enough individuals understand how to operate ventilators, posing a risk to the health of many. Moreover, it is increasingly difficult to determine optimal mechanical ventilator settings in a timely fashion, especially in low-resource countries and critical care areas. Respire is a mobile application that bridges this gap in a twofold manner: it is designed to assist healthcare workers around the world navigate and use mechanical ventilators effectively as well as educate the general public about mechanical ventilation. Respire offers a user-friendly yet educational interface that …

Structural Analysis Of Predicted Proteins Using Alphafold, Brydon P. Wall

Undergraduate Research Posters

The function of around 67% of predicted proteins from genes in Mycobacteriophage CheetoDust can not be confidently predicted using traditional techniques and can only be functionally labeled “hypothetical proteins”. However, a new approach using AlphaFold, an artificial intelligence tool to generate a structural prediction from a sequence, can take advantage of structurally conserved regions that were previously obfuscated to gain new insights and visualize data in new ways.

Since amino acid sequences are more conserved than its corresponding DNA sequence, amino acid sequences are used when predicting the function of the corresponding translated protein. Until recently, predicting structure from an …

Survey Of Visual Opsin Evolution Across Caddisflies (Insecta: Trichoptera), Ashlynn Powell, Jacqueline Heckenhauer, Steffen Pauls, Paul Frandsen

Library/Life Sciences Undergraduate Poster Competition 2022

Caddisflies are a highly diverse order of aquatic insects. As eggs, larvae, and pupae, they occupy freshwater habitats, while as adults, they are generally aerial and terrestrial¹. Such varied environments call for a flexible and complex visual system. Visual systems are controlled by light-sensing molecules called opsins, which are categorized by the wavelength of light they are most sensitive to². In insects, these categories are:

• Long wavelength (LW)
• Short wavelength (SW)
• Ultraviolet wavelength (UV)

Adaptive duplication of opsin genes is the primary mechanism of evolution that allows for greater visual capacity³. While opsins have …

Does Bathing After Sexual Assault Or Time Elapsed Have A Greater Effect On The Development Of Codis Eligible Dna Profiles?, Emily Black, Sam Payne, Julie Valentine, Leslie Miles

Library/Life Sciences Undergraduate Poster Competition 2022

Which has a greater effect on the development of CODIS eligible DNA profiles from SAKs – bathing/showering status of the victim or time between the assault and examination?

Male And Female Victims Experience Different Types Of Sexual Assault, Carolyn Allen, Samuel Payne, Julie Valentine

Library/Life Sciences Undergraduate Poster Competition 2022

Intro:

• Sexual assault kits (SAKs) contain forensic evidence and are collected following an assault
• Most research on SAK processing has been done with combined male and female assaults
• 10% of victims are male
• There is lots of research on female victims, but very little research on male victims

Eeg As Successful Diagnostic Tool For Immune Effector Cell Associated Neurotoxicity Syndrome, Daniel Jones, Christine Eckhardt, Haoqi Sun, Ryan Tesh, Brandon Westover

Library/Life Sciences Undergraduate Poster Competition 2022

CAR T cell therapy was first proven effective in 2013¹ for the treatment of certain cancer s . However, its widespread adoption is still hindered by side effects like immune effector cell associated neurotoxicity syndrome (ICANS). Current research aims to better predict, diagnose, and treat ICANS so that CAR T cell therapy can be more widely applied. Although prior studies have attempted to identify an objective biomarker of ICANS² , current practice relies on clinical assessment to diagnose ICANS. We hypothesize that qualitative features of the EEG may be utilized to develop a physiological grading system of the …

Beyond Safe Harbor: Risk Of Exposing Location In De-Identified Clinical Data, Alfred J. Anzalone, Carol Reynolds Geary, James C. Mcclay

Posters and Presentations: Neurological Sciences

The use of de-identified EHR data for clinical and translational research has increased significantly since the HIPAA Privacy Rule De-Identification standards went into effect -Inclusion of SDOH measures in de-identified research is increasing as well, which presents an inherent risk of re-identifying PHI (primarily location units smaller than the state) -Data warehouse architecture and institutional policies need to recognize the risk associated with providing multiple location-based indices -Research interests are secondary to privacy concerns throughout biomedical research, but particularly in de-identified research, which is intended to promote more secure access to EHR data while allowing for expedient access (fewer institutional …

Maintenance Of Onc Terminology For I2b2 Metadata, James Campbell, Alfred J. Anzalone, Jay Pedersen, James C. Mcclay

Posters and Presentations: Emergency Medicine

ONC terminologies are constantly adding new content and deactivating existing codes. The University of Nebraska Medical Center (UNMC) deploys three primary code sets that require regular updating to support research: SNOMED CT, RXNORM / NDC, and LOINC. A problem across the i2b2 community is keeping these terminologies up-to-date and loading them into i2b2 for timely analysis of EHR data. We have developed tool kits for rapid deployment of SNOMED CT metadata and will be extending the work to RXNORM/NDC and LOINC.

Multi-Label Model For Toxicity Prediction, Xiu Huan Yap, Michael L. Raymer

Symposium of Student Research, Scholarship, and Creative Activities Materials

Most computational predictive models are specifically trained for a single toxicity endpoint. Since more than 1300 toxicity assays have been reported in the TOXCAST dashboard, achieving high coverage over this growing number of toxicity endpoints remains challenging. Furthermore, single-endpoint models lack the ability to learn dependencies between endpoints, such as those targeting similar biological pathways, which may be used to boost model performance. In this study, we characterize the performance of 3 multi-label classification (MLC) models, namely Classifier Chains (CC), Label Powersets (LP) and Stacking (SBR), on Tox21 challenge data. These MLC models employ the Problem Transformation approach, which is …

Cylindrical Similarity Measurement For Helices In Medium-Resolution Cryo-Electron Microscopy Density Maps, Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He

College of Sciences Posters

Cryo-electron microscopy (cryo-EM) density maps at medium resolution (5-10 Å) reveal secondary structural features such as α-helices and β-sheets, but they lack the side chains details that would enable a direct structure determination. Among the more than 800 entries in the Electron Microscopy Data Bank (EMDB) of medium-resolution density maps that are associated with atomic models, a wide variety of similarities can be observed between maps and models. To validate such atomic models and to classify structural features, a local similarity criterion, the F1 score, is proposed and evaluated in this study. The F1 score is theoretically normalized to a …

Statistical Analysis Of Social Network Change, Teresa D. Schmidt

Systems Science Friday Noon Seminar Series

We explore two statistical methods that infer social network structures and statistically test those structures for change over time: regression-based differential network analysis (R-DNA) and information theory-based differential network analysis (I-DNA). RDNA is adapted from bioinformatics and I-DNA employs reconstructability analysis. Both methods are used to analyze Medicaid claims data from one-year periods before and after the formation of the Health Share of Oregon Coordinated Care Organization (CCO). We hypothesized that Health Share’s CCO formation would be followed by several changes in the healthcare delivery network.

Application of R-DNA and I-DNA to claims data involves three steps: (a) the inference …

Using Non Stem-Cells To Understand Early Tumor Growth, Jake Hogan, Heiko Enderling, Joel Brown, Robert A. Gatenby

Library/Life Sciences Undergraduate Poster Competition 2018

Tumors of similar size and shape can exhibit different responses to the same treatment. Targeted therapy aims to better treat these tumors by classifying them according to genotypic traits. A better understanding of how tumor traits such as non-stem cells influence tumor growth could improve targeted therapy. We hypothesize that the production of non-stem cells may aid tumor growth in avascular tumors (tumors lacking blood vessels).

2018 Annual Report, Christopher C. Witt

Annual Reports

In 2018, the Museum of Southwestern Biology (MSB) has continued to improve its profile and impacts, both on the University of New Mexico campus and in the international scientific community. Its collections serve as scientific infrastructure that enhances research, teaching, community service, and public outreach. The MSB is part of the UNM Department of Biology, and the missions of the MSB and the Department are synergistic. MSB houses extensive and rapidly growing collections representing biodiversity of world, primarily from the last halfcentury. MSB has outstanding collections from New Mexico and western North America, but it also has substantial holdings from …

Isolation Of A Novel Phage Otoolekemple52, Thomas O. Raymond

Undergraduate Research Posters

A bacteriophage is a virus capable of infecting bacteria like ubiquitous soil-dwelling genus Bacillus. Within the Bacillus genus, there is the “ACT family” made up of B. thuringiensis, B. cereus, and B. anthracis, which are highly related but with different pathogenic characteristics. Because of this, phages isolated using a species in this group may have a broad host range encompassing several species from Bacillus. Since B. cereus and B. anthracis can result in fatal to mild sickness in humans, the non-pahtogenic B. thuringiensis kurstaki was used to discover and characterize novel phages. The phage OTooleKemple52 was isolated …

Evolution Of Protein Complexes In Bacterial Species, Shwetha Hara Sridhar, Wedad Albalawi, Peter Uetz

Undergraduate Research Posters

Protein complexes are composed of two or more associated polypeptide chains that may have different functions. Protein complexes play a critical role for all processes in life and are considered as highly conserved in evolution. In previous studies, protein complexes from E. coli or Mycoplasma pneumoniae have been characterized experimentally, revealing that a typical bacterial cell has on the order of 500 protein complexes. Using gene homology (orthology), these experimentally-observed complexes can be used to predict protein complexes across many species of bacteria. Surprisingly, the majority of protein complexes is not conserved, demonstrating an unexpected evolutionary flexibility.

The current research …

Bioinformatics And Biomedical Engineering, Francisco Ortuño, Ignacio Rojas, Kathryn Dempsey Cooper, Sachin Pawaskar, Hesham Ali

Faculty Books and Monographs

Editors: Francisco Ortuño, Ignacio Rojas

Chapter, Identification of Biologically Significant Elements Using Correlation Networks in High Performance Computing Environments, co-authored by Kathryn Dempsey Cooper, Sachin Pawaskar, and Hesham Ali, UNO faculty members.

The two volume set LNCS 9043 and 9044 constitutes the refereed proceedings of the Third International Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, held in Granada, Spain in April 2015. The 134 papers presented were carefully reviewed and selected from 268 submissions. The scope of the conference spans the following areas: bioinformatics for healthcare and diseases, biomedical engineering, biomedical image analysis, biomedical signal analysis, computational genomics, computational …

Art Or Science?, Allison Marsh

Section 3: Imaging the Fast Moving

No abstract provided.

Integrating Phage Therapy Into Western Medicine, Jacob B. Jaminet

Undergraduate Research Posters

The World Health Organization has described the rise of antibiotic use as a “global heath security emergency” (who.int). With the growing concern about antibiotic resistant bacteria, there has been an increased interest in bacteriophages. Bacteriophages are high-specific viruses that only infect bacteria. The use of bacteriophages medicinally to treat bacteria is called phage therapy. Research in phage therapy gained momentum until the introduction of antibiotics. While the USA and other Western countries accepted antibiotics, the Soviet Union and their satellite nations still continued to research phages. Since the funding for research was supplied by the Soviet military, the results of …

Conclusion Panel, Allison Marsh

Section 6: Conclusion

No abstract provided.

Mapping The Ocean Frontier, Allison Marsh

Section 4: Imaging the Concealed

No abstract provided.

Spotlight On Usc: South Carolina Institute For Anthropology And Archaeology, Allison Marsh

Section 4: Imaging the Concealed

No abstract provided.

Seeing With Sound, Allison Marsh

Section 4: Imaging the Concealed

No abstract provided.

World Ocean Floor, Courtesy Of The Library Of Congress, Allison Marsh

Section 4: Imaging the Concealed

No abstract provided.

Marie Tharp At Her Drafting Table, Courtesy Of The Lamont-Doherty Earth Observatory, Earth Institute, Columbia University, Allison Marsh

Section 4: Imaging the Concealed

No abstract provided.

Why Do We Collect?, Allison Marsh

Section 2: Imaging the Microscopic

No abstract provided.