Biology Commons^™

A Simple Method For Quantifying Blastema Growth In Regenerating Planarians, Natali Campillo , '25, Danielle Ireland, Yashvi Patel , '24, Eva-Maria S. Collins

Biology Faculty Works

Due to their strong regenerative capabilities, freshwater planarians are a well-suited model system for studying the effects of chemicals on stem cell biology and regeneration. After amputation, a planarian will regenerate the missing body parts within 1 to 2 weeks. Because planarians have a distinct head morphology that can be easily identified, head and eye regeneration has been a popular qualitative measure of toxicity. However, qualitative measures can only detect strong defects. Here, we present protocols for quantifying the rate of blastema growth to measure regeneration defects for assessment of chemical toxicity. Following amputation, a regenerative blastema forms at the …

Quantifying The Soundscape: How Filters Change Acoustic Indices, Emilia B. Hyland, Annie Schulz, John E. Quinn

Open Access Fund Publications

Monitoring biodiversity can be time consuming and costly. Automated recording units (ARUs) have rapidly emerged as an efficient and cost-effective tool for measuring biodiversity. Acoustic indices are one output from recordings from ARUs that can be quantified to serve as an ecological indicator for biodiversity. However, there is a lack of guidance on what acoustic filters to apply to these indices and when. To address this gap, we collected acoustic data from study locations spanning temperate and tropical forests, agricultural grasslands and croplands, and peri-urban development. We applied filters of 80, 500, 1000, and 2000 Hz to these data when …

Isolating Highly Specific Antibodies Against Cancer Target Hprt, Austin J. Hansen, Christopher J. Haynie, Kiara V. Whitley, Michelle Townsend, Abby Johnson, Hunter Lindsay, Laura Baird, Kim L. O'Neill

Library/Life Sciences Undergraduate Poster Competition 2023

Effective immunotherapeutic targeting of cancer cells requires identification of specific antigenic differences between cancerous and healthy cells. Hypoxanthine-guanine phosphoribosyltransferase (HPRT) is a cytoplasmic enzyme involved in the salvage pathway for DNA synthesis. Certain cancers (e.g., prostate and breast) upregulate and express HPRT on the cell membrane, making HPRT a potential cancer biomarker for cancer immunotherapies. Antibodies specific for unique cancer proteins are critical to develop targeted cancer immunotherapies. Using a yeast display library and cell sorting, we selected for high-affinity human single-chain (scFv) antibodies against HPRT that can be utilized in chimeric antigen receptor (CAR) T cell therapies and antibody-dependent …

Predicting The Impact Of Climate Change On The Distribution Of Rhipicephalus Sanguineus In The Americas, Marcos Sánchez Pérez, Teresa Patricia Feria-Arroyo, Crystian Sadiel Venegas Barrera, Carolina Sosa-Gutiérrez, Javier Torres, Katherine A. Brown, Guadalupe Gordillo Pérez

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Climate change may influence the incidence of infectious diseases including those transmitted by ticks. Rhipicephalus sanguineus complex has a worldwide distribution and transmits Rickettsial infections that could cause high mortality rates if untreated. We assessed the potential effects of climate change on the distribution of R. sanguineus in the Americas in 2050 and 2070 using the general circulation model CanESM5 and two shared socioeconomic pathways (SSPs), SSP2-4.5 (moderate emissions) and SSP2-8.5 (high emissions). A total of 355 occurrence points of R. sanguineus and eight uncorrelated bioclimatic variables were entered into a maximum entropy algorithm (MaxEnt) to produce 50 replicates per …

Myo19 Tethers Mitochondria To Endoplasmic Reticulum-Associated Actin To Promote Mitochondrial Fission, Stephen M. Coscia, Cameron P. Thompson, Qing Tang, Elana E. Baltrusaitis, Joseph A. Rhodenhiser, Omar A. Quintero, E. Michael Ostap, Melike Lakadamyali, Erika L. Holzbaur

Biology Faculty Publications

Mitochondrial homeostasis requires a dynamic balance of fission and fusion. The actin cytoskeleton promotes fission, and we found that the mitochondrially localized myosin, myosin 19 (Myo19), is integral to this process. Myo19 knockdown induced mitochondrial elongation, whereas Myo19 overexpression induced fragmentation. This mitochondrial fragmentation was blocked by a Myo19 mutation predicted to inhibit ATPase activity and strong actin binding but not by mutations predicted to affect the working stroke of the motor that preserve ATPase activity. Super-resolution imaging indicated a dispersed localization of Myo19 on mitochondria, which we found to be dependent on metaxins. These observations suggest that Myo19 acts …

Social Transmission Of Predator Information Through Referential Alarm Calls Within And Across Species, Carly Trebac

Honors Program: Senior Projects (Public)

Animals can encode information about a predator’s size, identity, or threat through alarm calls. This can provide referential information that can be used by individuals within and across species receiving the information. Referential alarm calls can encode information through changes in structure or rate of the call, and these variances in their call can elicit different responses, such as fleeing or mobbing, in conspecifics and heterospecifics. We aimed to investigate whether white-breasted nuthatch alarm calls can encode referential information and elicit different responses from conspecifics. Previous studies showed that a related species of nuthatch varies their call rate in the …

Ecological Boundaries And Constraints On Viable Eco-Evolutionary Pathways, Kyle E. Coblentz, John P. Delong

School of Biological Sciences: Faculty Publications

Evolutionary dynamics are subject to constraints ranging from limitations on what is physically possible to limitations on the pathways that evolution can take. One set of evolutionary constraints, known as ‘demographic constraints’, constrain what can occur evolutionarily due to the demographic or dynamical consequences of evolution leading to conditions that make populations susceptible to extinction. These demographic constraints can limit the strength of selection or the rates of environmental change populations can experience while remaining extant and the trait values a population can express. Here we further hypothesize that the population demographic and dynamic consequences of evolution also can constrain …

Molecular Peptide Grafting As A Tool To Create Novel Protein Therapeutics, Anton A. Komar

Biological, Geological, and Environmental Faculty Publications

The study of peptides (synthetic or corresponding to discrete regions of proteins) has facilitated the understanding of protein structure-activity relationships. Short peptides can also be used as powerful therapeutic agents. However, the functional activity of many short peptides is usually substantially lower than that of their parental proteins. This is (as a rule) due to their diminished structural organization, stability, and solubility often leading to an enhanced propensity for aggregation. Several approaches have emerged to overcome these limitations, which are aimed at imposing structural constraints into the backbone and/or sidechains of the therapeutic peptides (such as molecular stapling, peptide backbone …

Hypothalamic Menin Regulates Systemic Aging And Cognitive Decline, Lige Leng, Et. Al, Jingqi Yan, Jie Zhang

Biological, Geological, and Environmental Faculty Publications

Aging is a systemic process, which is a risk factor for impaired physiological functions, and finally death. The molecular mechanisms driving aging process and the associated cognitive decline are not fully understood. The hypothalamus acts as the arbiter that orchestrates systemic aging through neuroinflammatory signaling. Our recent findings revealed that Menin plays important roles in neuroinflammation and brain development. Here, we found that the hypothalamic Menin signaling diminished in aged mice, which correlates with systemic aging and cognitive deficits. Restoring Menin expression in ventromedial nucleus of hypothalamus (VMH) of aged mice extended lifespan, improved learning and memory, and ameliorated aging …

Is There A Link Between Male Gonopodium Size And Mating Strategies Amongst Fish In The Family Poeciliidae?, Ryen Hunsaker, Jerald B. Johnson

Library/Life Sciences Undergraduate Poster Competition 2023

Have different male mating strategies led to evolutionary changes in male gonopodium size?

Natural selection should act strongly on any traits that affect successful reproduction. Fish species in the family Poeciliidae (livebearers) have a unique form of reproduction.

College Of Natural Sciences Newsletter, February 2023, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 4, Issue 1

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3-4 Nobel Recipient Visits Campus
Page 4 Adopting the Pantry
Page 5 Growing a Recruitment Mindset
Page 6 February Outreach Events
Page 7 Media Coverage of CNS
Page 8 Open PRAIRIE Data
Page 9 54th Geography Convention, and Tom Loveland EROS Geography Scholarship
Page 10 Photos of Dr. Carolyn Bertozzi's Visit

Advances In Cartilage Tissue Engineering Using Bioinks With Decellularized Cartilage And Three-Dimensional Printing, Roxanne N. Stone, Jonathon C. Reeck, Julia Thom Oxford

Biology Faculty Publications and Presentations

Osteoarthritis, a chronic, debilitating, and painful disease, is one of the leading causes of disability and socioeconomic burden, with an estimated 250 million people affected worldwide. Currently, there is no cure for osteoarthritis and treatments for joint disease require improvements. To address the challenge of improving cartilage repair and regeneration, three-dimensional (3D) printing for tissue engineering purposes has been developed. In this review, emerging technologies are presented with an overview of bioprinting, cartilage structure, current treatment options, decellularization, bioinks, and recent progress in the field of decellularized extracellular matrix (dECM)–bioink composites is discussed. The optimization of tissue engineering approaches using …

Genomics Of Secondarily Temperate Adaptation In The Only Non-Antarctic Icefish, Angel G. Rivera-Colón, Niraj Rayamajhi, Bushra Fazal Minhas, Giovanni Madrigal, Kevin T. Bilyk, Veronica Yoon, Mathias Hüne, Susan Gregory, C. H.Christina Cheng, Julian M. Catchen

Department of Biology Faculty Scholarship and Creative Works

White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is …

Understanding The Factors Affecting The Quantity And Composition Of Street Litter: Implication For Management Practices, Alessandra Rossi, Meiyin Wu, Bernabas T. Wolde, Kevin W. Zerbe, Tsung Ta David Hsu, Ariane Giudicelli, Rosana Da Silva

Department of Biology Faculty Scholarship and Creative Works

Some urban areas have more litter than others. Understanding the reason for this is important not only for dealing with urban littering but also for marine water quality because approximately 80% of the world's marine litter originates on land. This study aimed to better understand the quality and quantity of litter on sidewalks along with the sampling site's socio-economic attributes to better discern why some areas have more/different litter than others and what, if any, are the implications for a more tailored waste management strategy. We surveyed twice each of the 35 sites we selected from the Lower Passaic River …

Dredged Sediments Contain Potentially Beneficial Microorganisms For Agriculture And Little Harmful Cyanobacteria, Megan A. Rúa, Ashley N. Julian, Louise Stevenson

Biological Sciences Faculty Publications

Abstract Introduction Soils worldwide are degrading, raising concerns about our ability to feed the growing global population. Soil amendments that can alleviate degradation are gaining attention. The application of sediments dredged from waterways to agricultural fields has increasing promise as a means for improving degraded soils. However, herbaceous plant species may have difficulty establishing on dredged material because of low nutrient availability, inhibitory levels of toxins, unsuitable moisture conditions and lack of microorganisms capable of ameliorating these characteristics. To counteract these issues, we sought to understand if the use of a cover crop would increase the abundance, diversity and function …

Predicting Fecal Indicator Bacteria Using Spatial Stream Network Models In A Mixed-Land-Use Suburban Watershed In New Jersey, Usa, Tsung Ta David Hsu, Danlin Yu, Meiyin Wu

Department of Biology Faculty Scholarship and Creative Works

Good water quality safeguards public health and provides economic benefits through recreational opportunities for people in urban and suburban environments. However, expanding impervious areas and poorly managed sanitary infrastructures result in elevated concentrations of fecal indicator bacteria and waterborne pathogens in adjacent waterways and increased waterborne illness risk. Watershed characteristics, such as urban land, are often associated with impaired microbial water quality. Within the proximity of the New York–New Jersey–Pennsylvania metropolitan area, the Musconetcong River has been listed in the Clean Water Act’s 303 (d) List of Water Quality-Limited Waters due to high concentrations of fecal indicator bacteria (FIB). In …

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. …

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 …

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 …

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 …

Link Between Energy Investment In Biosynthesis And Proteostasis: Testing The Cost–Quality Hypothesis In Insects, Taiwo Iromini, Xiaolong Tang, Kyara N. Holloway, Chen Hou

Biological Sciences Faculty Research & Creative Works

The Energy Requirement for Biosynthesis Plays an Important Role in an Organism's Life History, as It Determines Growth Rate, and Tradeoffs with the Investment in Somatic Maintenance. This Energetic Trait is Different between Painted Lady (Vanessa Cardui) and Turkestan Cockroach (Blatta Lateralis) Due to the Different Life Histories. Butterfly Caterpillars (Holometabolous) Grow 30-Fold Faster, and the Energy Cost of Biosynthesis is 20 Times Cheaper, Compared to Cockroach Nymphs (Hemimetabolous). We Hypothesize that Physiologically the Difference in the Energy Cost is Partially Attributed to the Differences in Protein Retention and Turnover Rate: Species with Higher Energy Cost May Have a Lower …

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 …

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 …

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 …