Life Sciences Commons^™

Determinants And Mechanisms Of The Low Fusogenicity And High Dependence On Endosomal Entry Of Omicron Subvariants, Panke Qu, John P Evans, Chaitanya Kurhade, Cong Zeng, Yi-Min Zheng, Kai Xu, Pei-Yong Shi, Xuping Xie, Shan-Lu Liu

Faculty, Staff and Student Publications

The rapid spread and strong immune evasion of the SARS-CoV-2 Omicron subvariants has raised serious concerns for the global COVID-19 pandemic. These new variants exhibit generally reduced fusogenicity and increased endosomal entry pathway utilization compared to the ancestral D614G variant, the underlying mechanisms of which remain elusive. Here, we show that the C-terminal S1 mutations of the BA.1.1 subvariant, H655Y and T547K, critically govern the low fusogenicity of Omicron. Notably, H655Y also dictates the enhanced endosome entry pathway utilization. Mechanistically, T547K and H655Y likely stabilize the spike trimer conformation as suggested by increased molecular interactions in structural modeling and enhanced …

Cedar: Incorporating Cell Type Hierarchy Improves Cell Type-Specific Differential Analyses In Bulk Omics Data, Luxiao Chen, Ziyi Li, Hao Wu

Faculty, Staff and Student Publications

Bulk high-throughput omics data contain signals from a mixture of cell types. Recent developments of deconvolution methods facilitate cell type-specific inferences from bulk data. Our real data exploration suggests that differential expression or methylation status is often correlated among cell types. Based on this observation, we develop a novel statistical method named CeDAR to incorporate the cell type hierarchy in cell type-specific differential analyses of bulk data. Extensive simulation and real data analyses demonstrate that this approach significantly improves the accuracy and power in detecting cell type-specific differential signals compared with existing methods, especially in low-abundance cell types.

Prognostic Significance Of Acellular Mucin In Patients Undergoing Cytoreductive Surgery And Hyperthermic Intraperitoneal Chemotherapy (Crs/Hipec) For Appendiceal Neoplasms, Derek J Erstad, Kristen A Robinson, Karen Beaty, Safia Rafeeq, Yi-Ju Chiang, Kanwal Raghav, John P Shen, Michael J Overman, Wai Chin Foo, Melissa W Taggart, Paul F Mansfield, Richard E Royal, Keith F Fournier, Christopher P Scally

Faculty, Staff and Student Publications

Introduction: Appendiceal neoplasms have a propensity for peritoneal dissemination. The standard of care for select individuals is CRS/HIPEC. In the current 8th AJCC Staging system, a finding of only intraperitoneal acellular mucin (M1a) is classified as Stage IVa. There is concern that the current AJCC system may over-stage patients.

Methods: This was a single-institution retrospective review of 164 cases of mucinous appendiceal neoplasm. Patients undergoing CRS/HIPEC with M1a disease were compared to patients with peritoneal deposits containing tumor cells (well-differentiated adenocarcinoma; low-grade mucinous carcinoma peritonei-M1b,G1). Overall and recurrence-free survival were assessed.

Results: Median age was 51 years, 70% were female, …

Recovering False Negatives In Crispr Fitness Screens With Jloe, Merve Dede, Traver Hart

Faculty, Staff and Student Publications

It is widely accepted that pooled library CRISPR knockout screens offer greater sensitivity and specificity than prior technologies in detecting genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the assumption that CRISPR screens are saturating has been largely untested. Through integrated analysis of screen data in cancer cell lines generated by the Cancer Dependency Map, we show that a typical CRISPR screen has a ∼20% false negative rate, in addition to library-specific false negatives. Replicability falls sharply as gene expression decreases, while cancer subtype-specific genes within a tissue show distinct profiles compared …

Allosteric Autoregulation Of Dna Binding Via A Dna-Mimicking Protein Domain: A Biophysical Study Of Znf410-Dna Interaction Using Small Angle X-Ray Scattering, Gundeep Kaur, Ren Ren, Michal Hammel, John R Horton, Jie Yang, Yu Cao, Chenxi He, Fei Lan, Xianjiang Lan, Gerd A Blobel, Robert M Blumenthal, Xing Zhang, Xiaodong Cheng

Faculty, Staff and Student Publications

ZNF410 is a highly-conserved transcription factor, remarkable in that it recognizes a 15-base pair DNA element but has just a single responsive target gene in mammalian erythroid cells. ZNF410 includes a tandem array of five zinc-fingers (ZFs), surrounded by uncharacterized N- and C-terminal regions. Unexpectedly, full-length ZNF410 has reduced DNA binding affinity, compared to that of the isolated DNA binding ZF array, both in vitro and in cells. AlphaFold predicts a partially-folded N-terminal subdomain that includes a 30-residue long helix, preceded by a hairpin loop rich in acidic (aspartate/glutamate) and serine/threonine residues. This hairpin loop is predicted by AlphaFold to …

“Exploring The Advantages And Disadvantages Of Universal Electronic Medical Records”, Zachary Mcclenny

Honors Theses

A universal electronic medical record (EMR) is a platform where all of a patient's medical information, history, and data is stored and maintained by providers over time. A universal platform allows all of the medications, tests, procedures, labs, scans, notes, and any other clinical information for that patient to be kept in a record for any provider to view and make changes to while under their care. Although in the United States today, as well as many other countries, EMRs are owned and operated by privately ran businesses and institutions. Only the private institutions that have access to the EMR …

Which Factors Influence Consumer Organic Specialty Bakery Product Taste Ratings?, Tatiana Drugova, Kynda R. Curtis

All Current Publications

In this fact sheet, we compare consumer taste ratings for organic and conventional specialty bakery products and analyze what factors explain the differences. These products are typically consumed for pleasure and are more expensive than mainstream baked goods. However, consumers have high quality expectations, including taste, which may be an issue if not satisfactory. Understanding factors that impact consumer taste rating for organic specialty bakery products can help identify what might be done to improve taste perceptions/expectations and the success of organic specialty bakery/pastry products.

Who Values Organic Specialty Bakery Products?, Tatiana Drugova, Kynda R. Curtis

All Current Publications

In this fact sheet, we examine differences in socio-demographics and lifestyle choices between those who view organic as important when purchasing specialty bakery products and those who don’t, with the aim to identify a target market of consumers who prefer organic specialty bakery products. Additionally, we evaluate other important product attributes to consumers seeking organic specialty bakery products. Consumer taste ratings for organic and conventional specialty bakery products are compared for those who value organics and those who don’t to evaluate the impact of taste beliefs on consumer demand for organic specialty bakery products.

Abundance Of Halyomorpha Halys (Hemiptera: Pentatomidae) And Megacopta Cribraria (Hemiptera: Plataspidae) In Soybean In Areas With Few Previous Sightings In Tennessee, Kaushalya G. Amarasekare, Richard H. Link

Agricultural and Environmental Sciences Faculty Research

Halyomorpha halys (Stål) and Megacopta cribraria (Fabricius) are two exotic invasive pests that have invaded the United States in recent years. Halyomorpha halys can damage various fruits, vegetables, and field crops, such as soybean and corn, while Megacopta cribraria only attacks soybean and kudzu, a weed species. They are currently found in southeastern states and threaten soybean and other crops grown in the region. This study evaluated the seasonal abundance of H. halys and M. cribraria in soybeans in 2016 and 2017 in two counties in the central region of Tennessee, where both species had either a few sightings or …

Can Tilt Be Used To Teach Study Tactics? A Case Study In A Biology Classroom, Anne Jacobs

Perspectives In Learning

Recently, there has been a movement encouraging instructors in higher education to use the Transparency in Teaching and Learning (TILT) framework when designing assignments. This framework helps instructors clarify their expectations and evaluation criteria. Making assignments more transparent may result in greater student success. However, it is less clear how this framework can be applied to classes that use exams as a main method of assessing student learning. One option might be to use a TILTed assignment to introduce students to learning tools to improve their studying. I did this by giving students in an introductory biology class an assignment …

Salty Genes: Rapid Discovery Of Salt Tolerance Genes In The Bacteria Kushneria, Andrew Jenkins, Brent Nielson, Jonathon T. Hill

Library/Life Sciences Undergraduate Poster Competition 2023

1st place poster design

Global rising levels of soil salinity have led researchers to seek microbial solutions to increase agricultural plant viability in high salt soils.

Kushneria increases growth of inoculated alfalfa in high salt soils, but little is known about how Kushneria survives in these environments1 or how it can be used to reduce the economic burden of salted soil.

Coloration Strategies In Sympatric Vietnamese Damselflies, Eva J. Driggs, Seth M. Bybee

Library/Life Sciences Undergraduate Poster Competition 2023

Odonates (dragonflies and damselflies) have evolved vibrant coloration for various reasons. Odonates use color signals to identify their own species from others and potential mates. Some Odonates use blue color to blend into the water while others are only active when their color can best be seen. Different selective pressures will evolve a specific color strategy. Color is a key to understanding the evolutionary pressures for damselflies. Color has not been studied in depth for Vietnamese Odonates, even though Vietnam is a top 15 biodiversity hotspot. We hope to better understand color evolution in Vietnamese damselflies and the role …

Differential Impacts Of Cereal And Protein Sources Fed To Pigs After Weaning On Diarrhoea And Faecal Shedding Of Escherichia Coli, Production, And Total Tract Apparent Digestibility, John R. Pluske, Bruce P. Mullan, Jae Cheol Kim, David J. Hampson

Animal production and livestock research articles

Different cereal types, in combination with different protein sources, are fed to pigs after weaning, but their interactions and possible implications are not well researched. In this study, 84 male weaned piglets were used in a 21-day feeding trial to investigate the effects of feeding either medium-grain or long-grain extruded rice or wheat, in a factorial combination with protein sources of either vegetable or animal origin, on postweaning performance, shedding of β–haemolytic Escherichia coli, and the coefficient of total tract apparent digestibility (CTTAD). Pigs fed either rice type performed the same (p > 0.05) as wheat-fed pigs after weaning. The use …

Getting To The Root Of Tree Soil Microbiome Sampling, Sarah Addison, Megan A. Rua, Simeon Smaill, Kaitlyn Daley, Brajesh Singh, Steve Wakelin

Biological Sciences Faculty Publications

Microbiomes play critical roles in host functioning and therefore there is increasing interest in the microbiome assembly of plants. However, sampling strategies for long-lived perennial trees need to be standardised to produce robust data that accurately represents the microbiome over time. This issue is currently unresolved because there is little evidence indicating which portion of perennial tree species (e.g., root region or surrounding soil) is the best to sample to produce the most accurate measure of microbiome communities. Our aim was to sample different compartments of a plant’s belowground microbiome to identify the optimal sampling strategy to account for the …

Split And Join: An Efficient Approach For Simulating Stapled Intestinal Anastomosis In Virtual Reality, Di Qi, Suvranu De

Engineering Faculty Articles and Research

Colorectal cancer is a life-threatening disease. It is the second leading cause of cancer-related deaths in the United States. Stapled anastomosis is a rapid treatment for colorectal cancer and other intestinal diseases and has become an integral part of routine surgical practice. However, to the best of our knowledge, there is no existing work simulating intestinal anastomosis that often involves sophisticated soft tissue manipulations such as cutting and stitching. In this paper, for the first time, we propose a novel split and join approach to simulate a side-to-side stapled intestinal anastomosis in virtual reality. We mimic the intestine model using …

Evaluating Metabolic And Genomic Data For Predicting Grain Traits Under High Night Temperature Stress In Rice, Ye Bi, Rafael Massahiro Yassue, Puneet Paul, Balpreet Kaur Dhatt, Jaspreet Sandhu, Phuc Thi Do, Harkamal Walia, Toshihiro Obata, Gota Morota

Department of Agronomy and Horticulture: Faculty Publications

The asymmetric increase in average nighttime temperatures relative to increase in average daytime temperatures due to climate change is decreasing grain yield and quality in rice. Therefore, a better genome-level understanding of the impact of higher night temperature stress on the weight of individual grains is essential for future development of more resilient rice. We investigated the utility of metabolites obtained from grains to classify high night temperature (HNT) conditions of genotypes, and metabolites and single-nucleotide polymorphisms (SNPs) to predict grain length, width, and perimeter phenotypes using a rice diversity panel. We found that the metabolic profiles of rice genotypes …

Use Of Organic Acid Mixtures Containing 2-Hydroxy-4-(Methylthio) Butanoic Acid (Hmtba) To Mitigate Salmonella Enterica, Shiga Toxin-Producing Escherichia Coli (Stec) And Aspergillus Flavus In Pet Food Kibbles, Aiswariya Deliephan, Janak Dhakal, Bhadriraju Subramanyam, Charles G. Aldrich

Department of Food Science and Technology: Faculty Publications

Post-processing operations of extruded pet food kibbles involve coating the product with fats and flavorings. These processes increase the risk for cross-contamination with food-borne pathogens such as Salmonella and Shiga toxin-producing Escherichia coli (STEC), and mycotoxin-producing molds such as Aspergillus spp. after the thermal kill step. In this study, the antimicrobial effects of two types of organic acid mixtures containing 2-hydroxy-4-(methylthio) butanoic acid (HMTBa), Activate DA™ and Activate US WD-MAX™, against Salmonella enterica, STEC and Aspergillus flavus when used as a coating on pet food kibbles were evaluated. Using canola oil and dry dog digest as fat and flavor …

The Tfiis N-Terminal Domain (Tnd): A Transcription Assembly Module At The Interface Of Order And Disorder, Katerina Cermakova, Vaclav Veverka, H Courtney Hodges

Faculty, Staff and Students Publications

Interaction scaffolds that selectively recognize disordered protein strongly shape protein interactomes. An important scaffold of this type that contributes to transcription is the TFIIS N-terminal domain (TND). The TND is a five-helical bundle that has no known enzymatic activity, but instead selectively reads intrinsically disordered sequences of other proteins. Here, we review the structural and functional properties of TNDs and their cognate disordered ligands known as TND-interacting motifs (TIMs). TNDs or TIMs are found in prominent members of the transcription machinery, including TFIIS, super elongation complex, SWI/SNF, Mediator, IWS1, SPT6, PP1-PNUTS phosphatase, elongin, H3K36me3 readers, the transcription factor MYC, and …

Uncovering Novel Regulators Of Memory Using C Elegans Genetic And Genomic Analysis, Katie L Brandel-Ankrapp, Rachel N Arey

Faculty, Staff and Students Publications

How organisms learn and encode memory is an outstanding question in neuroscience research. Specifically, how memories are acquired and consolidated at the level of molecular and gene pathways remains unclear. In addition, memory is disrupted in a wide variety of neurological disorders; therefore, discovering molecular regulators of memory may reveal therapeutic targets for these disorders. C. elegans are an excellent model to uncover molecular and genetic regulators of memory. Indeed, the nematode's invariant neuronal lineage, fully mapped genome, and conserved associative behaviors have allowed the development of a breadth of genetic and genomic tools to examine learning and memory. In …

Data On Data: An Analysis Of Data Usage And Analytics In The Agricultural Supply Chain, Lourival Carmo Monaco Neto, Brady Brewer, Allan Gray

Department of Agricultural Economics Faculty Publications

The amount of data being collected throughout the agricultural supply chain has increased in both volume and velocity. All signs indicate that this will only increase as data collection technologies become more cost effective and prevalent throughout the supply chain. Previous work in this area has focused on data collection at the farm level. Our study focuses on data that originates at five different stages of the agricultural supply chain off the farm and how these stages view their firm's data collection and analysis efforts. We find that there is heterogeneity in the data collection efforts and analysis across the …

Analysis Of Acquired Resistance Mechanisms To Osimertinib In Patients With Egfr-Mutated Advanced Non-Small Cell Lung Cancer From The Aura3 Trial, Juliann Chmielecki, Tony Mok, Yi-Long Wu, Ji-Youn Han, Myung-Ju Ahn, Suresh S Ramalingam, Thomas John, Isamu Okamoto, James Chih-Hsin Yang, Frances A Shepherd, Krishna C Bulusu, Gianluca Laus, Barbara Collins, J Carl Barrett, Ryan J Hartmaier, Vassiliki Papadimitrakopoulou

Faculty, Staff and Student Publications

Osimertinib, an epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI), potently and selectively inhibits EGFR-TKI-sensitizing and EGFR T790M resistance mutations. This analysis evaluates acquired resistance mechanisms to second-line osimertinib (n = 78) in patients with EGFR T790M advanced non-small cell lung cancer (NSCLC) from AURA3 (NCT02151981), a randomized phase 3 study comparing osimertinib with chemotherapy. Plasma samples collected at baseline and disease progression/treatment discontinuation are analyzed using next-generation sequencing. Half (50%) of patients have undetectable plasma EGFR T790M at disease progression and/or treatment discontinuation. Fifteen patients (19%) have >1 resistance-related genomic alteration; MET amplification (14/78, 18%) and EGFR C797X mutation …

Parasitoid Wasps Of The Invasive Brown Marmorated Stink Bug In Utah, Zachary R. Schumm, Kate V. Richardson, Mark Cody Holthouse, Yota Mizuno, Diane G. Alston, Lori R. Spears

All Current Publications

The brown marmorated stink bug (BMSB, Halyomorpha halys Stål), an invasive insect from eastern Asia, is causing nuisance problems and agricultural damage in northern Utah. Insecticide applications to control this pest are not sustainable, and therefore the focus is on biological control through the use of parasitoid wasps that sting and kill stink bug eggs. Surveys are underway in Utah to search for Samurai wasp (Trissolcus Japonicus [Ashmead]), a parasitoid wasp native to BMSB’s home range that has been found in 12 U.S. States, and is highly effective at killing BMSB eggs. While Samurai wasp has not been found, …

Why The Delay In Recognizing Terrestrial Obligate Cave Species In The Tropics?, Francis G. Howarth

International Journal of Speleology

“Nothing could possibly live there!” They believed. Indeed, until recently, few specialized cave- adapted animals were known from volcanic, tropical, or oceanic island caves, and plausible theories had been put forward to explain their absence. But assume nothing in science! One must illuminate, explore, and survey habitats before declaring them barren. Our understanding of cave biology changed dramatically about 50 years ago following the serendipitous discovery of cave-adapted terrestrial arthropods in Brazil and on the young oceanic islands of the Galápagos and Hawai‘i. These discoveries and subsequent studies on the evolutionary ecology of cave animals have revealed a remarkable hidden …

Ultrasound-Assisted Air-Jet Spinning Of Silk Fibroin-Soy Protein Nanofiber Composite Biomaterials., Futian Yang, Fang Wang, Janine Mazahreh, Xiao Hu

College of Science & Mathematics Departmental Research

Ultrasound utilizes a non-radiation technology that can meet modern standards to gain access to cheap, reliable and sustainable modern energy. Ultrasound technology can be implemented in the field of biomaterials for its exceptional potential in controlling the shape of nanomaterials. This study presents the first example of the production of soy and silk fibroin protein composite nanofibers in various ratios via combining ultrasonic technology with air-spray spinning. Characterization of ultrasonic spun nanofibers was performed by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), X-ray powder diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetric (TG) analysis, water contact angle, water retention, enzymatic …

Ambient Electromagnetic Radiation As A Predictor Of Honey Bee (Apis Mellifera) Traffic In Linear And Non-Linear Regression: Numerical Stability, Physical Time And Energy Efficiency, Vladimir Kulyukin, Daniel Coster, Anastasiia Tkachenko, Daniel Hornberger, Aleksey V. Kulyukin

Computer Science Faculty and Staff Publications

Since bee traffic is a contributing factor to hive health and electromagnetic radiation has a growing presence in the urban milieu, we investigate ambient electromagnetic radiation as a predictor of bee traffic in the hive’s vicinity in an urban environment. To that end, we built two multi-sensor stations and deployed them for four and a half months at a private apiary in Logan, Utah, U.S.A. to record ambient weather and electromagnetic radiation. We placed two non-invasive video loggers on two hives at the apiary to extract omnidirectional bee motion counts from videos. The time-aligned datasets were used to evaluate 200 …

Kras-Mutant Lung Cancer: Targeting Molecular And Immunologic Pathways, Therapeutic Advantages And Restrictions, Nastaran Karimi, Seyed Javad Moghaddam

Faculty, Staff and Student Publications

RAS mutations are among the most common oncogenic mutations in human cancers. Among RAS mutations, KRAS has the highest frequency and is present in almost 30% of non-small-cell lung cancer (NSCLC) patients. Lung cancer is the number one cause of mortality among cancers as a consequence of outrageous aggressiveness and late diagnosis. High mortality rates have been the reason behind numerous investigations and clinical trials to discover proper therapeutic agents targeting KRAS. These approaches include the following: direct KRAS targeting; synthetic lethality partner inhibitors; targeting of KRAS membrane association and associated metabolic rewiring; autophagy inhibitors; downstream inhibitors; and immunotherapies and …

Integrating Theatre And Biology: How Embodied Performance Can Enhance Empathy Among College Science Students, Annika C. Speer, Begona Echeverria

The Transdisciplinary STEAM+ Journal

In these field notes, we examine the integration of the arts into a 20-person honors biology seminar at UC Riverside “Beyond Science: Being Humane Amid Human Rights Crises.” We held a four-hour workshop to examine the ways in which performance and theatrical storytelling can enhance science learning. The workshop provided a unique avenue for exploring how human activities result in downward consequences including refugee displacement, one of the course objectives. In addition to the workshop, we conducted surveys and a focus group with the students to better understand their experience incorporating the arts into their science class. A key concept …

Dear Duck-Billed Platypus, Michael J. Leach Dr

The Transdisciplinary STEAM+ Journal

This piece is a concrete poem that both shows and describes the platypus (Ornithorhynchus anatinus).

Light Leaf: Observations Of Leaves In Light, Paul Kelley

The Transdisciplinary STEAM+ Journal

For me, spending time in isolation yielded some interesting findings, as I began to closely observe the various leaves that engulf my backyard. Every new day brought with it a new detail, a subtlety with every shift in light, revealing an endless array of abstractions, textures and colors. I was seeing the hidden life of leaves dancing in the sunlight. Naturally, I began documenting my observations.

Students Arts Participation Increases Stem Motivation Via Self-Efficacy, Stephen M. Dahlem

The Transdisciplinary STEAM+ Journal

This work found that there exists a correlation between student motivation in science, technology, engineering and mathematics (STEM) and student participation in the arts during high school with self-efficacy being a mediator. STEM is an important component of student success from a broad, national, perspective, as well as from a domain-specific point of view. The results of this work may provide aid to teachers, parents, administrators, and even students seeking to find ways to increase student motivation and performance in the STEM subjects. Additionally, this work may be of interest to advocates of the arts. This quantitative correlational study was …