Biology Commons^™

Rebuild The Academy: Supporting Academic Mothers During Covid-19 And Beyond, Robinson W. Fulweiler, Sarah W. Davies, Jennifer F. Biddle, Amy J. Burgin, Emily H.G. Cooperdock, Torrance C. Hanley, Carly D. Kenkel, Amy Marcarelli, Catherine M. Matassa, Talea L. Mayo, Lory Z. Santiago-Vàzquez, Nikki Traylor-Knowles, Maren Ziegler

Michigan Tech Publications, Part 1

The issues facing academic mothers have been discussed for decades. Coronavirus Disease 2019 (COVID-19) is further exposing these inequalities as womxn scientists who are parenting while also engaging in a combination of academic related duties are falling behind. These inequities can be solved by investing strategically in solutions. Here we describe strategies that would ensure a more equitable academy for working mothers now and in the future. While the data are clear that mothers are being disproportionately impacted by COVID-19, many groups could benefit from these strategies. Rather than rebuilding what we once knew, let us be the architects of …

Long-Read Assembly Of A Great Dane Genome Highlights The Contribution Of Gc-Rich Sequence And Mobile Elements To Canine Genomes, Julia V. Halo, Amanda L. Pendleton, Feichen Shen, Aurélien J. Doucet, Thomas Derrien, Christophe Hitte, Laura E. Kirby, Bridget Myers, Elzbieta Sliwerska, Sarah Emery, John V. Moran, Adam R. Boyko, Jeffrey M. Kidd

Biological Sciences Faculty Publications

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of …

An Analysis Of Extraction Efficiencies Of Various Swabs On Sperm Recovery, Lindsey Campany

Graduate Student Research Symposium

With advancements in the DNA technology and methodology, more complete DNA profiles can be obtained. Extraction procedures and their reagents have been optimized for maximal DNA yield, but the cotton swab used and provided for sexual assault examinations has not advanced. Despite research suggesting the cotton swab’s absorbent nature and its inclination to retain cellular material, the field of forensic nursing has not yet implemented another swab.

Three swabs that this research will be evaluating are nylon flocked swabs, cotton swabs, and the cytobrush swab. The nylon flocked and cotton swabs have been studied for their efficiency, but no studies …

A Caenorhabditis Elegans Behavioral Assay Distinguishes Early Stage Prostate Cancer Patient Urine From Controls., Morgan Thompson, Noemi Sarabia Feria, Ally Yoshioka, Eugene Tu, Fehmi Civitci, Suzanne Estes, Josiah T. Wagner

Biology Faculty Publications and Presentations

Current methods for non-invasive prostate cancer (PrCa) detection have a high false-positive rate and often result in unnecessary biopsies. Previous work has suggested that urinary volatile organic compound (VOC) biomarkers may be able to distinguish PrCa cases from benign disease. The behavior of the nematode has been proposed as a tool to take advantage of these potential VOC profiles. To test the ability of Bristol N2 to distinguish PrCa cases from controls, we performed chemotaxis assays using human urine samples collected from men screened for PrCa. Behavioral response of nematodes towards diluted urine from PrCa cases were compared to controls …

A Multiplexed, Automated Evolution Pipeline Enables Scalable Discovery And Characterization Of Biosensors, Brent Townshend, Joy S. Xiang, Gabriel Manzanarez, Eric J. Hayden, Christina D. Smolke

Biology Faculty Publications and Presentations

Biosensors are key components in engineered biological systems, providing a means of measuring and acting upon the large biochemical space in living cells. However, generating small molecule sensing elements and integrating them into in vivo biosensors have been challenging. Here, using aptamer-coupled ribozyme libraries and a ribozyme regeneration method, de novo rapid in vitro evolution of RNA biosensors (DRIVER) enables multiplexed discovery of biosensors. With DRIVER and high-throughput characterization (CleaveSeq) fully automated on liquid-handling systems, we identify and validate biosensors against six small molecules, including five for which no aptamers were previously found. DRIVER-evolved biosensors are applied directly to regulate …

A Microbiome Engineering Framework To Evaluate Rhizobial Symbionts Of Legumes, Kenjiro W. Quides, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background

For well over a century, rhizobia have been recognized as effective biofertilizer options for legume crops. This has led to the widespread use of rhizobial inoculants in agricultural systems, but a recurring issue has emerged: applied rhizobia struggle to provide growth benefits to legume crops. This has largely been attributed to the presence of soil rhizobia and has been termed the ‘rhizobial competition problem.’

Scope

Microbiome engineering has emerged as a methodology to circumvent the rhizobial competition problem by creating legume microbiomes that do not require exogenous rhizobia. However, we highlight an alternative implementation of microbiome engineering that focuses …

Effects Of Varying Heat Indexes On Habitat Utilization And Behavior On Captive Red-Ruffed Lemurs (Varecia Rubra), Jeffrey Gammon

The Pegasus Review: UCF Undergraduate Research Journal

The two captive red-ruffed lemurs (Varecia rubra) at the Central Florida Zoo experienced a more temperate climate and utilized a differing habitat than they would in their native range, Madagascar. Proper management of the species in captivity is crucial for its long-term survival as they are critically endangered. Over a four month period, heat index temperature, lemur behavior, and habitat utilization data were collected via an instantaneous scan sample. Variables were analyzed to characterize how variations in heat index alter habitat utilization and behavior of the captive lemurs. As the heat index increased, habitat use became more restricted …

Scc-Civic-Pg Track B: Data And Tools To Build Resilience In Western Gateway And Natural Amenity Region Communities, Jordan Smith

Funded Research Records

No abstract provided.

Neglected Nematodes: The Neurolenin Solution, Kevin M. Shea, Steven Williams

Chemistry: Faculty Publications

Over 1 billion people worldwide are affected by Neglected Topical Diseases (NTDs). This group of pathogens encapsulates viruses, bacteria and parasites, and disproportionately affects the world’s poorest and most vulnerable communities in Africa, Asia and Latin America. Lymphatic Filariasis (LF) is an NTD caused by a parasitic nematode infection. The larvae of these filarial nematode worms are transmitted via mosquito bites and disrupt the functioning of the infected individual’s lymphatic system. LF can be caused by three types of filarial worms, Wuchereria bancrofti, Brugia malayi and Brugia timori, which are transmitted by the Culex, Anopheles and Aedes mosquito families. Symptomatic …

Phenology Of Antler Casting And Occurrence Of Late-Breeding In Nebraska White-Tailed Deer, Brian C. Peterson, Patrick D. Farrell, Dave Fehlhafer, Miranda C. Reinson, Dustin H. Ranglack

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

White-tailed deer (Odocoileus virginianus) in Nebraska primarily breed in November (stimulated by photoperiod), but this season extends into December and January for unfertilized females and healthy fawns reaching the appropriate breeding weight by winter. Variation in the typical mating period can be attributed to geographic region, skewed sex ratios, and fawns reaching sexual maturity during their first year of birth. During April of 2019, we observed late season breeding by a male white-tailed deer in the central Platte River valley and documented late antler casting for this same late-copulating male. An additional male was observed in April of …

Gene Variants Of Coagulation Related Proteins That Interact With Sars-Cov-2, David Holcomb, Aikaterini Alexaki, Nancy Hernandez, Ryan Hunt, Jacob Kames, Nobuko Hamasaki-Katagiri, Anton A. Komar, Michael Dicuccio, Chava Kimchi-Sarfaty

Biological, Geological, and Environmental Faculty Publications

Increased blood clotting, especially in the lungs, is a common complication of COVID-19. Infectious diseases cause inflammation, which in turn can contribute to increased blood clotting. However, the extent of clot formation that is seen in the lungs of COVID-19 patients suggests that there may be a more direct link. We identified three human proteins that are involved indirectly in the blood clotting cascade and have been shown to interact with proteins of SARS virus, which is closely related to the novel coronavirus. We examined computationally the interaction of these human proteins with the viral proteins. We looked for genetic …

Signaling In Rat Brainstem Via Gpr160 Is Required For The Anorexigenic And Antidipsogenic Actions Of Cocaine- And Amphetamine-Regulated Transcript Peptide, Christopher J. Haddock, Gislaine Almeida-Pereira, Lauren M. Stein, Matthew R. Hayes, Grant R. Kolar, Willis K. Samson, Gina L.C. Yosten

Biological Sciences Faculty Research & Creative Works

Recent work identified Gpr160 as a candidate receptor for cocaine- and amphetamine-regulated transcript peptide (CARTp) and described its role in pain modulation. The aims of the present study were to determine if Gpr160 is required for the CARTp's ability to reduce food intake and water intake and to initially identify the distribution of Gpr160-like immunoreactivity (Gpr160ir) in the rat brain. A passive immunoneutralization approach targeting Gpr160 was used to block the behavioral effects of a pharmacological dose of CARTp in the fourth cerebroventricle (4V) of rats and to determine the importance of endogenously produced CARTp in the control of ingestive …

Ectopic Expression Of Pericentric Hsatii Rna Results In Nuclear Rna Accumulation, Mecp2 Recruitment, And Cell Division Defects, C. C. Landers, Christina Rabeler, E. K. Ferrari, Lia R. D'Alessandro , '21, D. D. Kang, J. Malisa, Safia M. Bashir , '20, Dawn M. Carone

Biology Faculty Works

Within the pericentric regions of human chromosomes reside large arrays of tandemly repeated satellite sequences. Expression of the human pericentric satellite HSATII is prevented by extensive heterochromatin silencing in normal cells, yet in many cancer cells, HSATII RNA is aberrantly expressed and accumulates in large nuclear foci in cis. Expression and aggregation of HSATII RNA in cancer cells is concomitant with recruitment of key chromatin regulatory proteins including methyl-CpG binding protein 2 (MeCP2). While HSATII expression has been observed in a wide variety of cancer cell lines and tissues, the effect of its expression is unknown. We tested the effect …

Utilization Of Recombinant Viruses And In Silico Protein-Protein Interactions To Investigate The Role Of Herpes Simplex Type-1 (Hsv-1) Us9, Gk, And Ul20 Proteins In Virion Assembly And Egress, Anna Reneé Naquin

Honors Capstones

No abstract provided.

Diversity And N2o Production Potential Of Fungi In An Oceanic Oxygen Minimum Zone, Xuefeng Peng, David L. Valentine

Faculty Publications

Fungi in terrestrial environments are known to play a key role in carbon and nitrogen biogeochemistry and exhibit high diversity. In contrast, the diversity and function of fungi in the ocean has remained underexplored and largely neglected. In the eastern tropical North Pacific oxygen minimum zone, we examined the fungal diversity by sequencing the internal transcribed spacer region 2 (ITS2) and mining a metagenome dataset collected from the same region. Additionally, we coupled ¹⁵N-tracer experiments with a selective inhibition method to determine the potential contribution of marine fungi to nitrous oxide (N₂O) production. Fungal communities evaluated by …

Macrophages Expedite Cell Proliferation Of Prostate Intraepithelial Neoplasia Through Their Downstream Target Erk, Mikalah U. Thomas, Justin K. Messex, Tu Dang, Sarki A. Abdulkadir, Cheryl L. Jorcyk, Geou-Yarh Liou

Biology Faculty Publications and Presentations

The risk factors for prostate cancer include a high-fat diet and obesity, both of which are associated with an altered cell environment including increased inflammation. It has been shown that chronic inflammation due to a high-fat diet or bacterial infection has the potential to accelerate prostate cancer as well as its precursor, prostatic intraepithelial neoplasia (PIN), development. However, the underlying mechanism of how chronic inflammation promotes prostate cancer development, especially PIN, remains unclear. In this study, we showed that more macrophages were present in PIN areas as compared to the normal areas of human prostate. When co-culturing PIN cells with …

Life Line March 2021, Otterbein Biology And Earth Science Department

Life Line - The Biology Department Newsletter

In this issue:

A Note from the Chair; The Department Welcomes Dr. Rich; Senior Research Symposium Goes Virtual; Three Department Faculty Members Win Teaching Awards; Svitana Helps NGWA Go Online; Carter '15 Earns Ph.D. in Nuclear Forensics; Revamping a Campus to Return to our Cardinal Community; Professor Uses Novel Teaching Practices During Pandemic; Otterbein Introduces Signature STEM Series to Increase Connection; Young Receives Career Award; Malacogy in a Time of COVID; COVID Conversations; Canine Rabies Vaccination in Ethiopia; The Cardinal Science Scholar Program; Bird Anatomy.

College Of Natural Sciences Newsletter, March 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2. Issue 3

Contents:

Page 1 Dean's Message
Page 2-3 Awards and Recognition
Page 4 Student Club Spotlight: MICROBIOLOGY CLUB
Page 5 Research Spotlight: Dr. Chakravarty
Page 6 Open PRAIRIE Data; Grants Awarded in CNS; Research Collquia
Page 7 A Busy Month in Review; Media Coverage of the College

A Graphical Null Model For Scaling Biodiversity–Ecosystem Functioning Relationships, Kathryn E. Barry, Gabriella A. Pinter, Joseph W. Strini, Karrisa Yang, Istvan G. Lauko, Stefan A. Schnitzer, Adam T. Clark, Jane Cowles, Akira S. Mori, Laura Williams, Peter B. Reich, Alexandra J. Wright

Biological Sciences Faculty Research and Publications

1. Global biodiversity is declining at rates faster than at any other point in human history. Experimental manipulations at small spatial scales have demonstrated that communities with fewer species consistently produce less biomass than higher diversity communities. Understanding the consequences of the global extinction crisis for ecosystem functioning requires understanding how local experimental results are likely to change with increasing spatial and temporal scales and from experiments to naturally assembled systems.
2. Scaling across time and space in a changing world requires baseline predictions. Here, we provide a graphical null model for area scaling of biodiversity–ecosystem functioning relationships using observed macroecological patterns: …

Unifying Ecosystem Responses To Disturbance Into A Single Statistical Framework, Nathan P. Lemoine

Biological Sciences Faculty Research and Publications

Natural ecosystems are currently experiencing unprecedented rates of anthropogenic disturbance. Given the potential ramifications of more frequent disturbances, it is imperative that we accurately quantify ecosystem responses to severe disturbance. Specifically, ecologists and managers need estimates of resistance and recovery from disturbance that are free of observation error, not biased by temporal stochasticity and that standardize disturbance magnitude among many disparate ecosystems relative to normal interannual variability. Here, I propose a statistical framework that estimates all four components of ecosystem responses to disturbance (resistance, recovery, elasticity and return time), while resolving all of the issues described above. Coupling autoregressive time …

General Biology 2 Laboratory Manual, Dmitry Y. Brogun, Azure N. Faucette, Kristin Polizzotto, Farshad Tamari

Open Educational Resources

Currently, many academic institutions are using one or more variations of online modalities due to the Covid-19 pandemic, and science educators face a unique challenge with distance-learning laboratories. Many resources to engage students in virtual, interactive laboratory activities exist, but we found that high costs and/or overlooked content left gaps for several topics typically taught in a general, introductory biology course for undergraduate biology majors (e.g., organismal biology). Additionally, resources for an online lab must be identified and curated from multiple sources, requiring intense demands on the instructors’ time. To meet this need and to overcome the financial burden of …

The Role Of Glutamine In Supporting Gut Health And Neuropsychiatric Factors, Brett J. Deters, Mir Saleem

Biology Faculty Articles

Recent research has shown that the amino acid glutamine can positively affect gut health by supporting the gut microbiome, gut mucosal wall integrity, and by modulating inflammatory responses. As modulated by the vagus nerve, via the enteric nervous system, the gut-brain connection can impact the brain's neurochemical environment. Poor gut health can disrupt the balance of neurotransmitters, which can result in neuropsychiatric based conditions such as depression. Glutamine supplementation may provide significant adjunctive nutritional support in cases of depression by promoting proper gut health and function.

Sirtuin-Dependent Recovery From Aerial Heat Shock: The Effects Of Food Ration, Thermal History, And Sirtuin Inhibition On Clearance Rates And Valve Gape Activity Of The California Mussel, Mytilus Californianus (Conrad), Melissa A. May, Maya K. Feezell, Silvano J. Gonzalez, M. Christina Vasquez, Anne E. Todgham, Lars Tomanek

Biology Faculty Works

Intertidal mussels regularly experience seasonal fluctuations in food availability and heat stress over the course of a tidal cycle, yet little is known about the biochemical mechanisms linking food ration and thermal tolerance, despite evidence that food enhances stress tolerance at the organismal level. We hypothesized that sirtuins (food-dependent protein regulators of cellular homeostasis), which may regulate the cellular stress response of mytilids during heat stress, also affect organismal performance during recovery from heat stress. As part of a broader study, we investigated the effects of acclimation food ration, acclimation emersion (air) temperature, and sirtuin inhibitors on the feeding behavior …

Using Acoustic Telemetry To Analyze The Impacts Of Common Carp On Wild Rice Restoration, Franklin Zomer

All NMU Master's Theses

Wild rice (Zizania palustris) is an important cultural, spiritual, and dietary resource to Lake Superior Ojibwe. Common Carp (Cyprinus carpio) are an introduced species that negatively impact aquatic vegetation through changes in water quality, uprooting of plants, and consumption of seed. Acoustic telemetry was used to document Common Carp movements in Waishkey Bay in the upper St. Marys River, MI where wild rice habitat is present. Exclosures were established to measure the influence of carp presence on wild rice seeding success. Common Carp were observed to spend much of their time in Waishkey Bay but also …

Mitochondrial Opa1 Cleavage Is Reversibly Activated By Differentiation Of H9c2 Cardiomyoblasts, Iraselia Garcia, Fredy Calderon, Patrick De La Torre, Shaynah St. Vallier, Cristobal Rodriguez, Divya Agarwala, Megan Keniry, Wendy Innis-Whitehouse, Robert Gilkerson

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

Optic atrophy-1 (OPA1) is a dynamin-like GTPase localized to the mitochondrial inner membrane, playing key roles in inner membrane fusion and cristae maintenance. OPA1 is regulated by the mitochondrial transmembrane potential (Δψm): when Δψm is intact, long OPA1 isoforms (L-OPA1) carry out inner membrane fusion. Upon loss of Δψm, L-OPA1 isoforms are proteolytically cleaved to short (S-OPA1) isoforms by the stress-inducible OMA1 metalloprotease, causing collapse of the mitochondrial network and promoting apoptosis. Here, we show that L-OPA1 isoforms of H9c2 cardiomyoblasts are retained under loss of Δψm, despite the presence of OMA1. However, when H9c2s are differentiated to a more …

Is This Science? Students' Experiences Of Failure Make A Research-Based Course Feel Authentic, Emma C. Goodwin, Vladimir Anokhin, Mackenzie J. Gray, Daniel E. Zajic, Jason Podrabsky, Erin E. Shortlidge

Biology Faculty Publications and Presentations

Course-based undergraduate research experiences (CUREs) and inquiry-based curricula both expose students to the scientific process. CUREs additionally engage students in novel and scientifically relevant research, with the intention of providing an "authentic" research experience. However, we have little understanding of which course design elements impact students' beliefs that they are experiencing "authentic" research. We designed a study to explore introductory biology students' perceptions of research authenticity in CURE and inquiry classes. Using the Laboratory Course Assessment Survey, we found that students in CURE sections perceived higher levels of authentic research elements than students in inquiry-based sections. To identify specific factors …

Scientism And Secularism: Learning To Respond To A Dangerous Ideology By J. P. Moreland. Wheaton, Il: Crossway, 2018. 224 Pages. Paperback; $16.99. Isbn: 9781433556906., Michael B. Burns, Joseph Vukov

Biology: Faculty Publications and Other Works

No abstract provided.

Conserved And Divergent Aspects Of Robo Receptor Signaling And Regulation Between Drosophila Robo1 And C. Elegans Sax-3, Trant Daiber, Christine J. Vanderzwan-Butler, Greg J. Bashaw, Timonthy A. Evans

Biological Sciences Faculty Publications and Presentations

The evolutionarily conserved Roundabout (Robo) family of axon guidance receptors control midline crossing of axons in response to the midline repellant ligand Slit in bilaterian animals including insects, nematodes, and vertebrates. Despite this strong evolutionary conservation, it is unclear whether the signaling mechanism(s) downstream of Robo receptors are similarly conserved. To directly compare midline repulsive signaling in Robo family members from different species, here we use a transgenic approach to express the Robo family receptor SAX-3 from the nematode Caenorhabditis elegans in neurons of the fruit fly, Drosophila melanogaster. We examine SAX-3’s ability to repel Drosophila axons from the …

Migration Phenology And Patterns Of American Woodcock In Central North America Derived Using Satellite Telemetry, Joseph D. Moore, David E. Andersen, Tom Cooper, Jeffrey P. Duguay, Shaun L. Oldenburger, C. Al Stewart, David G. Krementz

Biological Sciences Faculty Publications and Presentations

American woodcock Scolopax minor (hereafter woodcock) migration ecology is poorly understood, but has implications for population ecology and management, especially related to harvest. To describe woodcock migration patterns and phenology, we captured and equipped 73 woodcock with satellite tracking devices in the Central Management Region (analogous to the Mississippi Flyway) of North America and documented migration paths of 60 individual woodcock and 87 autumn or spring woodcock migrations during 2014-2016. Woodcock migration at the scale of the Central Management Region was more synchronous in spring than in autumn, but unlike most other migratory birds, average duration of autumn migration (31 …

Importation And Preliminary Evaluation Of The Stem Boring Moth Buakea Kaeuae As A Potential Biological Control Agent Of Invasive Guineagrass, Megathyrsus Maximus, Ann T. Vacek, John A. Goolsby, Paul-Andre Calatayud, Bruno Le Ru, Boaz Musyoka, Rupesh R. Kariyat

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

Abstract. Guineagrass, Megathyrsus maximus (Jacq.) B.K.Simon & S.W.L.Jacobs, is an African grass that is invasive in Florida, Hawaii, southern Texas, and northeastern Mexico. Buakea kaeuae Moyal et al., a stem-boring African moth found only on M. maximus, was imported from Kenya and evaluated for its ability to feed and develop on Guineagrass naturalized in southern Texas. Neither larvae nor adults developed or reproduced on Texas Guineagrass.

Resumen. El zacate Guinea (Megathyrsus maximus (Jacq.) B.K.Simon & S.W.L.Jacobs), originario de África, es considerado invasivo en Florida, Hawaii, sur de Texas, y noreste de México. Buakea kaeuae Moyal et al. es una …