Digital Commons Network^™

Remembering Paul Johnsgard, Linda R, Brown, Josef Kren

Zea E-Books Collection

Paul A. Johnsgard (1931–2021) was a friend of many, an artist, prolific author, teacher, and humble admirer of all living creatures. It was impossible to find someone at Nebraska Audubon Society or Nebraska Ornithologists’ Union meetings who did not know Paul Johnsgard. His more than 100 published books made him known not just in a community of ornithologists, birdwatchers, and bird lovers in the United States but also abroad. He was a world-renowned ornithologist and naturalist who remained deeply embedded in his local culture and its prairie environment.

We invited about 75 people to write a short memory of Paul. …

The Role Of Preproglucagon Peptides In Regulating Β-Cell Morphology And Responses To Streptozotocin-Induced Diabetes, Deanna M. Arble, Chelsea R. Hutch, Hannah Hafner, Daria Stelmak, Kyle Leix, Joyce Sorrell, Joshua W. Pressler, Brigid Gregg, Darleen A. Sandoval

Biological Sciences Faculty Research and Publications

Insulin secretion from β-cells is tightly regulated by local signaling from preproglucagon (Gcg) products from neighboring α-cells. Physiological paracrine signaling within the microenvironment of the β-cell is altered after metabolic stress, such as high-fat diet or the β-cell toxin, streptozotocin (STZ). Here, we examined the role and source of Gcg peptides in β-cell function and in response to STZ-induced hyperglycemia. We used whole body Gcg null (Gcg^Null) mice and mice with Gcg expression either specifically within the pancreas (Gcg^ΔPanc) or the intestine (Gcg^ΔIntest). With lower doses of STZ exposure, insulin levels were …

Acclimation And Hardening Of A Slow-Growing Woody Species Emblematic To Western North America From In Vitro Plantlets, Peggy Martinez, Marcelo Serpe, Rachael Barron, Sven Buerki

Biology Faculty Publications and Presentations

Premise: Determining the tolerance of plant populations to climate change requires the development of biotechnological protocols producing genetically identical individuals used for genotype-by-environment experiments. Such protocols are missing for slow-growth, woody plants; to address this gap, this study uses Artemisia tridentata, a western North American keystone shrub, as model.

Methods and Results: The production of individual lines is a two-step process: in vitro propagation under aseptic conditions followed by ex vitro acclimation and hardening. Due to aseptic growth conditions, in vitro plantlets exhibit maladapted phenotypes, and this protocol focuses on presenting an approach promoting morphogenesis for slow-growth, woody species. …

Phase Separation In Biology And Disease; Current Perspectives And Open Questions, Steven Boeynaems, Shasha Chong, Jörg Gsponer, Liam Holt, Dragomir Milovanovic, Diana M. Mitrea, Oliver Mueller-Cajar, Bede Portz, John F. Reilly, Christopher D. Reinkemeier, Benjamin R. Sabari, Serena Sanulli, James Shorter, Emily M. Sontag, Lucia Strader, Jeanne Stachowiak, Stephanie C. Weber, Michael R. White, Huaiying Zhang, Markus Zweckstetter, Shana Elbaum-Garfinkle, Richard Kriwacki

Biological Sciences Faculty Research and Publications

In the past almost 15 years, we witnessed the birth of a new scientific field focused on the existence, formation, biological functions, and disease associations of membraneless bodies in cells, now referred to as biomolecular condensates. Pioneering studies from several laboratories supported a model wherein biomolecular condensates associated with diverse biological processes form through the process of phase separation. These and other findings that followed have revolutionized our understanding of how biomolecules are organized in space and time within cells to perform myriad biological functions, including cell fate determination, signal transduction, endocytosis, regulation of gene expression and protein translation, and …

A Trial Of Fire And Ice: Assessment Of Control Techniques For Pyrus Calleryana Invasion Of Grasslands In Southwestern Ohio, Usa, Margaret E. Maloney, Eric B. Borth, Grace Dietsch, Mary C. Lloyd, Ryan W. Mcewan

Biology Faculty Publications

Pyrus calleryana (Callery pear) is an invasive plant that threatens ecosystems in the eastern United States. We investigated the efficacy of various control techniques on P. calleryana invasion in grasslands. Treatments were applied to (a) P. calleryana stems that had experienced mowing annually for several years and were sprouting (n = 100 stems; “trees-sprouting”) and (b) stems that had established ca. 10 years earlier, had never been cut, and were single-stemmed trees (n = 40 stems; “trees-intact”). In both experiments, existing stems were cut and randomly assigned one of the following treatments: cut only (control), burning, freezing, or herbicide, and …

Six Decades Of North American Bird Banding Records Reveal Plasticity In Migration Phenology, Kyle G. Horton, Sara R. Morris, Benjamin M. Van Doren, Kristen M. Covino

Biology Faculty Works

1. The timing of avian migration has evolved to exploit critical seasonal resources, yet plasticity within phenological responses may allow adjustments to interannual resource phenology. The diversity of migratory species and changes in underlying resources in response to climate change make it challenging to generalize these relationships.
2. We use bird banding records during spring and fall migration from across North America to examine macroscale phenological responses to interannual fluctuations in temperature and long-term annual trends in phenology.
3. In total, we examine 19 species of North American wood warblers (family Parulidae), summarizing migration timing from 2,826,588 banded birds from 1961 to 2018 …

Hyperdontia In The Paraguayan Martha's Marked Gecko (Homonota Marthae: Phyllodactylidae: Squamata), Juan D. Daza, Emma C. Krakoski, Tony Gamble, Aaron M. Bauer

Biological Sciences Faculty Research and Publications

No abstract provided.

Adult And Regenerating Planarians Respond Differentially To Chronic Drug Exposure, Kevin Bayingana , '23, Danielle Ireland, Elizabeth Rosenthal , '23, Christina Rabeler, Eva-Maria S. Collins

Biology Faculty Works

There is a lack of data on the effects of chronic exposure to common drugs and stimulants on the developing nervous system. Freshwater planarians have emerged as a useful invertebrate model amenable to high-throughput behavioral phenotyping to assay chemical safety in adult and developing brains. Here, we leverage the unique strength of the system to test in parallel for effects on the adult and developing nervous system, by screening ten common drugs and stimulants (forskolin, clenbuterol, LRE-1, MDL-12,330A, adenosine, caffeine, histamine, mianserin, fluoxetine and sertraline) using the asexual freshwater planarian Dugesia japonica. The compounds were tested up to 100 …

Recent Advances In Centrifugal Spinning And Their Applications In Tissue Engineering, Shaik Merkatur Hakim Marjuban, Musfira Rahman, Syeda Sharmin Duza, Mohammad Boshir Ahmed, Dinesh K Patel, Md Saifur Rahman, Karen Lozano

Faculty, Staff and Student Publications

Over the last decade, researchers have investigated the potential of nano and microfiber scaffolds to promote wound healing, tissue regeneration, and skin protection. The centrifugal spinning technique is favored over others due to its relatively straightforward mechanism for producing large quantities of fiber. Many polymeric materials have yet to be investigated in search of those with multifunctional properties that would make them attractive in tissue applications. This literature presents the fundamental process of fiber generation, and the effects of fabrication parameters (machine, solution) on the morphologies such as fiber diameter, distribution, alignment, porous features, and mechanical properties. Additionally, a brief …

Psf Sampling In Fluorescence Image Deconvolution, Eric A. Inman

Master's Theses

All microscope imaging is largely affected by inherent resolution limitations because of out-of-focus light and diffraction effects. The traditional approach to restoring the image resolution is to use a deconvolution algorithm to “invert” the effect of convolving the volume with the point spread function. However, these algorithms fall short in several areas such as noise amplification and stopping criterion. In this paper, we try to reconstruct an explicit volumetric representation of the fluorescence density in the sample and fit a neural network to the target z-stack to properly minimize a reconstruction cost function for an optimal result. Additionally, we do …

Profiling Disease-Selective Drug Targets: From Proteomics To Ligandomics, Prabuddha Waduge, Hong Tian, Keith A Webster, Wei Li

Faculty, Staff and Students Publications

Despite advancements in omics technologies, including proteomics and transcriptomics, identification of therapeutic targets remains challenging. Ligandomics recently emerged as a unique technology of functional proteomics for global profiling of cell-binding protein ligands. When applied to diseased versus healthy vasculatures, comparative ligandomics systematically maps novel disease-restricted ligands that allow selective targeting of pathological but not physiological pathways, providing high efficacy with intrinsic safety. In this review, we discuss the potential of cellular ligands as therapeutic targets and summarize the development of ligandomics. We further compare the advantages and limitations of different omics technologies for drug target discovery and discuss target selection …

Crispr/Cas9 Screen Uncovers Functional Translation Of Cryptic Lncrna-Encoded Open Reading Frames In Human Cancer, Caishang Zheng, Yanjun Wei, Peng Zhang, Longyong Xu, Zhenzhen Zhang, Kangyu Lin, Jiakai Hou, Xiangdong Lv, Yao Ding, Yulun Chiu, Antrix Jain, Nelufa Islam, Anna Malovannaya, Yun Wu, Feng Ding, Han Xu, Ming Sun, Xi Chen, Yiwen Chen

Faculty, Staff and Students Publications

Emerging evidence suggests that cryptic translation within long noncoding RNAs (lncRNAs) may produce novel proteins with important developmental/physiological functions. However, the role of this cryptic translation in complex diseases (e.g., cancer) remains elusive. Here, we applied an integrative strategy combining ribosome profiling and CRISPR/Cas9 screening with large-scale analysis of molecular/clinical data for breast cancer (BC) and identified estrogen receptor α-positive (ER+) BC dependency on the cryptic ORFs encoded by lncRNA genes that were upregulated in luminal tumors. We confirmed the in vivo tumor-promoting function of an unannotated protein, GATA3-interacting cryptic protein (GT3-INCP) encoded by LINC00992, the expression of which was …

Failure Of Nasal Defect Closures Following The Use Of Continuous Positive Airway Pressure, Yelena Dokic, Emily Powell, John Kohorst, Ikue Shimizu

Faculty, Staff and Students Publications

In this paper, we report a case series of three patients who developed nasal tip necrosis following Mohs micrographic surgery (MMS), complicated by the concomitant use of a continuous positive airway pressure (CPAP) machine for sleep apnea.

Safeguarding Sandalwood: A Review Of Current And Emerging Tools To Support Sustainable And Legal Forestry, Ellyse Bunney, Francesca A. Mcinerney, Eleanor Dormontt, Arif Malik, Nina Welti, David Wilkins, Malcolm Plant, Dhanushka S. Hettiarachchi, Darren Thomas, Ashley Dowell, Tresa Hamalton, Andrew J. Lowe

Research outputs 2022 to 2026

Societal Impact Statement: Sandalwood and other high value tree species are under significant threat from illegal harvest. Illegal logging is an increasing problem contributing to deforestation, biodiversity loss, human rights abuses and funding transnational crime. Successful prosecution of illegal logging is hindered by a lack of methods to provide evidence of the origin of timber. New analytical techniques have been developed to trace timber back to its source. These methods, together with the establishment of sustainable sources of forest resources, can help protect vulnerable species by providing evidence to prosecute illegal harvest and ensure that commercially available forest products come …

Chromosome-Length Assembly Of The Baikal Seal (Pusa Sibirica) Genome Reveals A Historically Large Population Prior To Isolation In Lake Baikal, Aliya Yakupova, Andrey Tomarovsky, Azamat Totikov, Violetta R. Beklemisheva, Maria Logacheva, Polina Perelman, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Natalya A. Serdyukova, Michael Rayko, Tatiana Bulyonkova, Nikolay Cherkasov, Vladimir Pylev, Vladimir Peterfeld, Aleksey Penin, Elena Balanovska, Alla L. Lapidus, Dna Zoo Consortium, Stephen James O'Brien, Alexander S. Graphodatsky, Klaus-Peter Koepfli, Sergey Kliver

Biology Faculty Articles

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied …

“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 …

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 …

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 …

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 …

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 …

Detection And Capture Of Nitrogen Fixing Bacteria From Soil And Roots Using Plant Specific Lectins, Alana Horton

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Diazotrophs increase plant productivity by providing ammonia directly to plants in the rhizosphere or through association with the roots (Sun et al., 2021). Leveraging diazotrophs can aid in the reduction or application of harmful synthetic nitrogen fertilizers. This thesis aims to use plant root proteins, or lectins, to more rapidly recover viable diazotrophs that are likely to associate with crops. In this study, lectins, are used to recover bacteria from bulk soil by taking advantage of the binding relationship between lectins and bacterial cell surface polysaccharides. When commercially-available lectins were used with a magnetic pulldown to separate the lectin, bacterial …

How Administration Stakes And Settings Affect Student Behavior And Performance On A Biology Concept Assessment, Crystal Uminski, Joanna K. Hubbard, Brian A. Couch

School of Biological Sciences: Faculty Publications

Biology instructors use concept assessments in their courses to gauge student understanding of important disciplinary ideas. Instructors can choose to administer concept assessments based on participation (i.e., lower stakes) or the correctness of responses (i.e., higher stakes), and students can complete the assessment in an in-class or out-of-class setting. Different administration conditions may affect how students engage with and perform on concept assessments, thus influencing how instructors should interpret the resulting scores. Building on a validity framework, we collected data from 1578 undergraduate students over 5 years under five different administration conditions. We did not find significant differences in scores …

Editorial: Community Series In Tools, Techniques, And Strategies For Teaching In A Real-World Context With Microbiology, Volume Ii, Davida S. Smyth, Nicole A. Broderick, Carlos C. Goller

All Faculty Scholarship (Archived)

This Research Topic is the second volume in the Community Series Tools, Techniques, and Strategies for Teaching in a Real-World Context with Microbiology. Making microbiology relevant to our students increases student engagement with science, which could not be more important as we emerge from the COVID-19 pandemic. We have learned much during this period as we adapted and modified our learning environments and strategies, all while demonstrating the many ways microbes impact our world beyond disease. Placing microbes at center stage leads to engaging and exciting curricula and assignments. Microbes also are wonderful tools as they are easy to manipulate …

Effects Of B4galnt1 Expression On Metastatic Phenotype And Response To Treatment In Osteosarcoma Cell Lines, Fatemeh Zareihajiabadi

Annual Research Symposium

No abstract provided.

Diverse Marine T4-Like Cyanophage Communities Are Primarily Comprised Of Low-Abundance Species Including Species With Distinct Seasonal, Persistent, Occasional, Or Sporadic Dynamics, Emily Dart, Jed A. Fuhrman, Nathan A. Ahlgren

Biology

Cyanophages exert important top-down controls on their cyanobacteria hosts; however, concurrent analysis of both phage and host populations is needed to better assess phage-host interaction models. We analyzed picocyanobacteria Prochlorococcus and Synechococcus and T4-like cyanophage communities in Pacific Ocean surface waters using five years of monthly viral and cellular fraction metagenomes. Cyanophage communities contained thousands of mostly low-abundance (<2% relative abundance) species with varying temporal dynamics, categorized as seasonally recurring or non-seasonal and occurring persistently, occasionally, or sporadically (detected in ≥85%, 15-85%, or <15% of samples, respectively). Viromes contained mostly seasonal and persistent phages (~40% each), while cellular fraction metagenomes had mostly sporadic species (~50%), reflecting that these sample sets capture different steps of the infection cycle-virions from prior infections or within currently infected cells, respectively. Two groups of seasonal phages correlated to Synechococcus or Prochlorococcus were abundant in spring/summer or fall/winter, respectively. Cyanophages likely have a strong influence on the host community structure, as their communities explained up to 32% of host community variation. These results support how both seasonally recurrent and apparent stochastic processes, likely determined by host availability and different host-range strategies among phages, are critical to phage-host interactions and dynamics, consistent with both the Kill-the-Winner and the Bank models.

Plant Species’ Capacity For Range Shifts At The Habitat And Geographic Scales: A Trade-Off-Based Framework, Bailey H. Mcnichol, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

Climate change is causing rapid shifts in the abiotic and biotic environmental conditions experienced by plant populations, but we lack generalizable frameworks for predicting the consequences for species. These changes may cause individuals to become poorly matched to their environments, potentially inducing shifts in the distributions of populations and altering species’ habitat and geographic ranges. We present a trade-off-based framework for understanding and predicting whether plant species may undergo range shifts, based on ecological strategies defined by functional trait variation. We define a species’ capacity for undergoing range shifts as the product of its colonization ability and the ability to …

Acetylcholinesterase Activity Staining In Freshwater Planarians, Christina Rabeler, Taixi Gong , '24, Danielle Ireland, O. Cochet-Escartin, Eva-Maria S. Collins

Biology Faculty Works

The serine hydrolase acetylcholinesterase (AChE) is an important neuronal enzyme which catalyzes the hydrolysis of the neurotransmitter acetylcholine and other choline esters. The breakdown of acetylcholine by AChE terminates synaptic transmission and regulates neuromuscular communication. AChE inhibition is a common mode of action of various insecticides, such as carbamates and organophosphorus pesticides. Freshwater planarians, especially the species Dugesia japonica, have been shown to possess AChE activity and to be a suitable alternative model for studying the effects of pesticides in vivo. AChE activity can be quantified in homogenates using the Ellman assay. However, this biochemical assay requires specialized equipment …

Drug-Like Small Molecules That Inhibit Expression Of The Oncogenic Microrna-21, Matthew D Shortridge, Bhawna Chaubey, Huanyu J Zhang, Thomas Pavelitz, Venkata Vidadala, Changyan Tang, Gregory L Olsen, George A Calin, Gabriele Varani

Faculty, Staff and Student Publications

We report the discovery of drug-like small molecules that bind specifically to the precursor of the oncogenic and pro-inflammatory microRNA-21 with mid-nanomolar affinity. The small molecules target a local structure at the Dicer cleavage site and induce distinctive structural changes in the RNA, which correlate with specific inhibition of miRNA processing. Structurally conservative single nucleotide substitutions eliminate the conformational change induced by the small molecules, which is also not observed in other miRNA precursors. The most potent of these compounds reduces cellular proliferation and miR-21 levels in cancer cell lines without inhibiting kinases or classical receptors, while closely related compounds …

Deepbend: An Interpretable Model Of Dna Bendability, Samin Rahman Khan, Sadman Sakib, M Sohel Rahman, Md Abul Hassan Samee

Faculty, Staff and Students Publications

The bendability of genomic DNA impacts chromatin packaging and protein-DNA binding. However, we do not have a comprehensive understanding of the motifs influencing DNA bendability. Recent high-throughput technologies such as Loop-Seq offer an opportunity to address this gap but the lack of accurate and interpretable machine learning models still remains. Here we introduce DeepBend, a convolutional neural network model with convolutions designed to directly capture the motifs underlying DNA bendability and their periodic occurrences or relative arrangements that modulate bendability. DeepBend consistently performs on par with alternative models while giving an extra edge through mechanistic interpretations. Besides confirming the known …

Transcriptome, Proteome, And Protein Synthesis Within The Intracellular Cytomatrix, Tattym E Shaiken, Sandra L Grimm, Mohamad Siam, Amanda Williams, Abdol-Hossein Rezaeian, Daniel Kraushaar, Emily Ricco, Matthew J Robertson, Cristian Coarfa, Antrix Jain, Anna Malovannaya, Fabio Stossi, Antone R Opekun, Alyssa P Price, Julien Dubrulle

Faculty, Staff and Students Publications

Despite the knowledge that protein translation and various metabolic reactions that create and sustain cellular life occur in the cytoplasm, the structural organization within the cytoplasm remains unclear. Recent models indicate that cytoplasm contains viscous fluid and elastic solid phases. We separated these viscous fluid and solid elastic compartments, which we call the cytosol and cytomatrix, respectively. The distinctive composition of the cytomatrix included structural proteins, ribosomes, and metabolome enzymes. High-throughput analysis revealed unique biosynthetic pathways within the cytomatrix. Enrichment of biosynthetic pathways in the cytomatrix indicated the presence of immobilized biocatalysis. Enzymatic immobilization and segregation can surmount spatial impediments, …