Biology Commons^™

Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

The past two decades have witnessed significant advances in high-throughput ``omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive ``omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential …

Sustainable Agriculture Lesson For Middle School Classrooms, Sara Colombe, Madhav P. Nepal, Jennifer Mclaughlin, Matthew L. Miller, Larry B. Browning, P. Troy White

iLEARN Teaching Resources

In this lesson, students will learn about sustainability, where farmers/agriculturists can meet the needs of food, fiber, and fuel for the growing population. Students learn about growing population, its growth rate, major food source, sustainability barrel, potential ripple effects of positive impacts as well as the food waste and its effects.

Survey Of Bird/Window Collisions At Utah State University-Brigham City, Spencer Smith

Research on Capitol Hill

When birds fly at full speed into the highly reflective glass windows of human structures, death is often the outcome. This research investigates the impact of architecture on bird population through a specific case study. Bird/window collisions claim from around 350 million to over 1 billion birds per year (Kahle, Flannery, & Dumbacher, 2016). Studies have shown that window surface area (Borden, Lockhart, Jones, & Lyons, 2011) can increase incidents of bird-window collisions. In 2015, Utah State University –Brigham City campus finished their new Classroom and Student Services building which features large windows and an interior tree that can be …

White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated With Wound Healing And The Maintenance Of Genome Stability, Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Minghui Wang, Qi Sun, Paulina D. Pavinski Bitar, Vincent P. Richards, Aleksey S. Komissarov, Mike Rayko, Sergey Kliver, Bryce J. Stanhope, Chuck Winkler, Stephen James O'Brien, Agostinho Antunes, Salvador Jorgensen, Mahmood S. Shivji

Biology Faculty Articles

The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability …

Silkworms With Spider Silklike Fibers Using Synthetic Silkworm Chow Containing Calcium Lignosulfonate, Carbon Nanotubes, And Graphene, Xiaoli Zhang, Ana Laura Licon, Thomas I. Harris, Paula F. Oliveira, Bailey J. Mcfarland, Blake E. Taurone, Brittney J. Walsh, Brianne E. Bell, Caleb T. Walker, Randolph V. Lewis, Justin A. Jones

Biology Faculty Publications

Silkworm silk has become increasingly relevant for material applications. However, the industry as a whole is retracting because of problems with mass production. One of the key problems is the inconsistent properties of the silk. A means by which to improve the silk material properties is through enhanced sericulture techniques. One possible technique is altering the feed of the silkworms to include single-wall carbon nanotubes (SWNTs) or graphene (GR). Recently published results have demonstrated substantial improvement in fiber mechanical properties. However, the effect of the surfactant used to incorporate those materials into the feed on the fiber mechanical properties in …

Genetic And Physical Interactions Between The Organellar Mechanosensitive Ion Channel Homologs Msl1, Msl2, And Msl3 Reveal A Role For Inter-Organellar Communication In Plant Development, Josephine S. Lee, Margaret E. Wilson, Ryan A. Richardson, Elizabeth S. Haswell

Biology Faculty Research

Plant development requires communication on many levels, including between cells and between organelles within a cell. For example, mitochondria and plastids have been proposed to be sensors of environmental stress and to coordinate their re- sponses. Here we present evidence for communication between mitochondria and chloroplasts during leaf and root development, based on genetic and physical inter- actions between three Mechanosensitive channel of Small conductance-Like (MSL) proteins from Arabidopsis thaliana. MSL proteins are Arabidopsis homologs of the bac- terial Mechanosensitive channel of Small conductance (MscS), which relieves cellular osmotic pressure to protect against lysis during hypoosmotic shock. MSL1 localizes to …

Agro And Water Saving Technologies And Approaches Of Assessing Their Effectiveness, B Mambetnazarov

Karakalpak Scientific Journal

The article presents aggro-ecological peculiarities of the Aral Sea region and opportunities of specialization on creating territories, also, recommendations on wisely and effective use of existing land and water resources

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

Chemical Alternatives For Managing Key Stored Product Insects, Rizana M. Mahroof

Journal of the South Carolina Academy of Science

In this short review paper, possible alternatives to manage some key stored product insects pests are discussed. With the phase out of methyl bromide and insects developing resistance to phosphine, fumigants available to manage stored product insects are becoming limited. Potential non-chemical alternatives, those are environmentally benign and do not leave harmful residues on treated products are most favoured. Two techniques; sex pheromone based mating disruption and ozone gas, are explored as safer insect management tools in this paper.

Pregnancy In Zoo-Managed African Elephants (Loxodonta Africana): Investigating Possible Hormonal And Metabolic Indicators Of Successful And Unsuccessful Pregnancies., Chelsi Marolf

UNO Student Research and Creative Activity Fair

Female African elephants (Loxodanta africana) in zoos in the United States currently have high rates of ovarian acyclicity and if they do become pregnant, the calf is often lost before or during birth. This issue likely stems from various metabolic and reproductive factors, including obesity, advanced age, and stress. While this is a complicated problem, analyzing certain hormones related to reproduction and nutrition in elephants might reveal biological indicators for successful and unsuccessful pregnancies in African elephants. The goal of this study is to create a range of hormone levels throughout a typical successful pregnancy, and to compare …

Isolating And Characterizing Novel Bacteriophages From Freshwater Samples, Mackenzie Conrin, Avery Misfeldt

UNO Student Research and Creative Activity Fair

Bacteria are responsible for many Healthcare-Associated infections each year and are evolving to become multidrug resistant (MDR). Bacteriophages, also called phages, are naturally occurring bacterial viruses. These phages infect and kill their bacterial hosts. It is estimated that there are 10 different phages, per bacterium. This makes phages the most abundant entity in the biosphere. Isolating and characterizing these naturally occurring bacterial killers offers the potential for strain specific treatment of MDR infections. Such treatments, coined Phage Therapy, can be used in the fight against evolving bacterial infections. Pseudomonads are a classification of bacteria that infect a variety of plants …

Taxonomic Classification Of Diplazium Molokaiense, A Fern Endemic To Hawaii, Using Molecular And Morphological Characters, Sarah Jaksich

UNO Student Research and Creative Activity Fair

Diplazium molokaiense is an endangered fern species endemic to Hawaii. There are only an estimated 61 individuals left in the wild. Taxonomic classification of this species is an important element to its conservation. Using the following morphological characters: sori size and shape, scale size and shape, and frond shape, D. molokaiense was preliminarily placed into the Diplazium genus. Six regions (rbcL, matK, atpA, atpB, trnLF, and rps4-trnS) of the chloroplast genome were amplified and sequenced using Sanger-sequencing. Sequences for outgroup taxa and 20 Diplazium species were downloaded from GenBank and used to infer a phylogeny. Our data provide …

Skeletal Muscle Mitochondrial Biogenesis In Response To Exercise And Cold Exposure, Camille Larson

UNO Student Research and Creative Activity Fair

BACKGROUND: Aerobic exercise triggers mitochondrial biogenesis, the generation of new mitochondria, by ATP depletion and subsequent activation of the AMPK signaling pathway. This leads to enhanced expression of PGC-1α, a positive regulator of respiration, mitochondrial biogenesis, and adaptive thermogenesis. Previous research from our lab has shown that exercise followed by cold recovery enhances the transcription of genes associated with mitochondrial growth and division, however the recovery period was necessary for this response. Perhaps exercising in a colder external environment would induce a greater thermoregulatory response and gradient between ambient skin and core temperature that may lead to altered mitochondrial …

Impacts Of Exercise And Environmental Temperature On Mitochondrial Quantity And Quality, Halee Keller

UNO Student Research and Creative Activity Fair

Halee Keller, Robert Shute, Dustin Slivka

University of Nebraska at Omaha, School of Health and Kinesiology, Omaha, NE

BACKGROUND: Mitochondria are highly concentrated in skeletal muscle tissue, and undergo damage from ROS during metabolic processes. This damage is often left unrepaired and leads to mitochondrial dysfunction, which has been linked to many common diseases. Exercise training increases mitochondrial development within skeletal muscle tissue and thus may be protective. Environmental temperature, when paired with exercise may provide an even greater effect than exercise alone. PURPOSE: The purpose of this study is to analyze the effects of three weeks of exercise …

Effects Of Rangeland Management On Milkweed Grazing And Monarch Conservation, Brittany Poynor

UNO Student Research and Creative Activity Fair

Cattle typically avoid consuming milkweed plants that contain high levels of toxic defense compounds, and therefore many people assume cattle avoid all milkweeds. However, common milkweed (Asclepias syriaca) contains only moderate levels of toxic compounds, and observations suggest that cattle regularly consume common milkweed and may even preferentially graze flowers and leaves of this species. These observations directly relate to efforts to add over one billion stems of milkweed to the central USA for monarch butterfly (Danaus plexippus) conservation. If cattle intentionally consume common milkweed and other milkweed species, and if certain management practices can reduce …

Alternative Nad(P)H Dehydrogenase And Alternative Oxidase: Proposed Physiological Roles In Animals, Allison Mcdonald, Dmytro V. Gospodaryov

Biology Faculty Publications

The electron transport systems in mitochondria of many organisms contain alternative respiratory enzymes distinct from those of the canonical respiratory system depicted in textbooks. Two of these enzymes, the alternative NADH dehydrogenase and the alternative oxidase, were of interest to a limited circle of researchers until they were envisioned as gene therapy tools for mitochondrial disease treatment. Recently, these enzymes were discovered in several animals. Here, we analyse the functioning of alternative NADH dehydrogenases and oxidases in different organisms. We propose that both enzymes ensure bioenergetic and metabolic flexibility during environmental transitions or other conditions which may compromise the operation …

Cognition And The Brain Of Brood Parasitic Cowbirds., David F Sherry, Mélanie F Guigueno

Psychology Publications

Cowbirds are brood parasites. Females lay their eggs in the nests of other species, which then incubate the cowbird eggs and raise the young cowbirds. Finding and returning to heterospecific nests presents cowbirds with several cognitive challenges. In some species, such as brown-headed cowbirds (Molothrus ater), females but not males search for and remember the locations of potential host nests. We describe recent research on sex differences in cognition and the hippocampus associated with this sex difference in search for host nests. Female brown-headed cowbirds perform better than males on some, but not all, tests of spatial memory and females …

Loss Of Ion Homeostasis Is Not The Cause Of Chill Coma Or Impaired Dispersal In False Codling Moth Thaumatotibia Leucotreta (Lepidoptera: Tortricidae), Minette Karsten, Jacqueline E. Lebenzon, Brent J. Sinclair, John S. Terblanche

Biology Publications

Dispersal is a central requirement of a successful sterile insect release programme, but field-released false codling moth (FCM) typically suffer from poor dispersal ability, especially at low ambient temperatures. Here we test the hypothesis that poor activity and dispersal in FCM is caused by delayed or perturbed recovery of ion and/or water homeostasis after chilling for handling and transport prior to field release. Hemolymph and flight muscle were collected from two treatment groups at three time points that targeted thermal conditions above and below the chill coma induction threshold of ~ 6 °C: 1) control moths kept at 25 °C, …

How Crickets Become Freeze Tolerant: The Transcriptomic Underpinnings Of Acclimation In Gryllus Veletis, Jantina Toxopeus, Lauren E. Des Marteaux, Brent J. Sinclair

Biology Publications

Some ectotherms can survive internal ice formation. In temperate regions, freeze tolerance is often induced by decreasing temperature and/or photoperiod during autumn. However, we have limited understanding of how seasonal changes in physiology contribute to freeze tolerance, and how these changes are regulated. During a six week autumn-like acclimation, late-instar juveniles of the spring field cricket Gryllus veletis (Orthoptera: Gryllidae) become freeze tolerant, which is correlated with accumulation of low molecular weight cryoprotectants, elevation of the temperature at which freezing begins, and metabolic rate suppression. We used RNA-Seq to assemble a de novo transcriptome of this emerging laboratory model for …

The Aqueous Environment As An Active Participant In The Protein Folding Process, Michal Brylinski

Faculty Publications

Existing computational models applied in the protein structure prediction process do not sufficiently account for the presence of the aqueous solvent. The solvent is usually represented by a predetermined number of H2O molecules in the bounding box which contains the target chain. The fuzzy oil drop (FOD) model, presented in this paper, follows an alternative approach, with the solvent assuming the form of a continuous external hydrophobic force field, with a Gaussian distribution. The effect of this force field is to guide hydrophobic residues towards the center of the protein body, while promoting exposure of hydrophilic residues on its surface. …

Escaping Death: Naloxone's Chemical Nature And Potential To Combat The Opioid Epidemic, Abigale Miller

Honors Program: Senior Projects (Public)

Naloxone is a life-saving drug with the ability to reverse an opioid overdose. As the opioid epidemic’s death toll rises, we can turn to Naloxone as a tool to combat the crisis. The epidemic, born of corruption, has a wide reach among the people of the United States, with especially firm grasps on middle-aged people, sufferers of chronic pain, white Americans and those living in the eastern portion of the country. Naloxone’s elegant design saves lives by effectively competing for a position on an opioid biding receptor in the brain to almost instantly end an overdose and restore normal breathing. …

Student Perceptions Of Reasons For Lecture And Active Learning, Calan Koch

Honors Program: Senior Projects (Public)

With perceived student resistance to active learning in the classroom, instructors are hesitant to implement such methods into their classroom structure despite how effective they may be. This research seeks to understand student perceptions related to the transition to higher prevalence of active learning techniques. We aimed to find answers to how students perceive the ideal classroom to be structured, what reasons they perceive for lecture and active learning components, and possible explanations to concerns of groupwork during class time. We analyzed 64 interviews with undergraduate biology students at the University of Nebraska- Lincoln, developed coding rubrics from commonly found …

Diversity Of Resistance Mechanisms In Carbapenem-Resistant Enterobacteriaceae At A Health Care System In Northern California, From 2013 To 2016, Fiona Senchyna, Rajiv L. Gaur, Johanna Sandlund, Cynthia Truong, Guillaume Tremintin, Dietmar Kültz, Carlos A. Gomez, Fiona B. Tamburini, Tessa Andermann, Ami Bhatt, Isabella A. Tickler, Nancy Watz, Indre Budvytiene, Gongyi Shi, Fred C. Tenover, Niaz Banaei

Biology Faculty Publications

The mechanism of resistance in carbapenem-resistant Enterobacteriaceae (CRE) has therapeutic implications. We comprehensively characterized emerging mechanisms of resistance in CRE between 2013 and 2016 at a health system in Northern California. A total of 38.7% (24/62) of CRE isolates were carbapenemase gene-positive, comprising 25.0% (6/24) blaOXA-48 like, 20.8% (5/24) bla_KPC, 20.8% (5/24) bla_NDM, 20.8% (5/24) bla_SME, 8.3% (2/24) bla_IMP, and 4.2% (1/24) bla_VIM. Between carbapenemases and porin loss, the resistance mechanism was identified in 95.2% (59/62) of CRE isolates. Isolates expressing bla_KPC were 100% susceptible to ceftazidime–avibactam, meropenem–vaborbactam, …

The Yeast Mitochondrial Proteins Rcf1 And Rcf2 Support The Enzymology Of The Cytochrome C Oxidase Complex And Generation Of The Proton Motive Force, Vera Strogolova, Ngoc H. Hoang, Jonathan Hosler, Rosemary A. Stuart

Biological Sciences Faculty Research and Publications

The yeast mitochondrial proteins Rcf1 and Rcf2 are associated with a subpopulation of the cytochrome bc₁–cytochrome c oxidase supercomplex and have been proposed to play a role in the assembly and/or modulation of the activity of the cytochrome c oxidase (complex IV, CIV). Yeast mutants deficient in either Rcf1 or Rcf2 proteins can use aerobic respiration–based metabolism for growth, but the absence of both proteins results in a strong growth defect. In this study, using assorted biochemical and biophysical analyses of Rcf1/Rcf2 single and double null-mutant yeast cells and mitochondria, we further explored how Rcf1 and Rcf2 support …

Phylogenetic Relationships Within The Primitive Acanthomorph Fish Genus Polymixia, With Changes To Species Composition And Geographic Distributions, W. Calvin Borden, Terry C. Grande, Mark Vh Wilson

Biology: Faculty Publications and Other Works

The genus Polymixia is the only survivor of a Late Cretaceous marine fish radiation and is often said to be the most primitive living acanthomorph (i.e., Polymixia possesses the greatest number of primitive character states for Acanthomorpha). Recent studies, including this one, place Polymixia as the sister to all other Paracanthopterygii. Despite its importance, most species of Polymixia are extremely difficult to discriminate on the basis of morphology. As a result, the number of valid species is uncertain. Moreover, there has never been a phylogenetic analysis of the genus. Thus, a molecular phylogenetic study was needed to clarify species boundaries …

Connectivity Explains Local Ant Community Structure In A Neotropical Forest Canopy: A Large‐Scale Experimental Approach, Benjamin J. Adams, Stefan A. Schnitzer, Stephen P. Yanoviak

Biological Sciences Faculty Research and Publications

Understanding how habitat structure and resource availability affect local species distributions is a key goal of community ecology. Where habitats occur as a mosaic, variation in connectivity among patches influences both local species richness and composition, and connectivity is a key conservation concern in fragmented landscapes. Similarly, availability of limiting resources frequently determines species coexistence or exclusion. For primarily cursorial arthropods like ants, gaps between neighboring trees are a significant barrier to movement through the forest canopy. Competition for limited resources such as nest sites also promotes antagonistic interactions. Lianas (woody vines) connect normally isolated neighboring tree crowns and often …

Host-Parasite Associations Of The Cratogeomys Fumosus Species Group And Their Chewing Lice, Geomydoecus, Alex Popinga, James W. Demastes, Theresa A. Spradling, David J. Hafner, Mark S. Hafner

Faculty Work

Chewing lice (Phthiraptera: Trichodectidae) and the pocket gophers (Rodentia: Geomyidae) that they inhabit have shared an intimate historical association that has made them a textbook study for cophylogeny. Herein, we examine the chewing lice found on pocket gophers of the Cratogeomys fumosus species group using DNA sequence data from the mitochondrial cytochrome c oxidase subunit I gene to determine relationships among lice for comparison to published host phylogeny. Although matrix approaches indicate a correlation between host and parasite genetic distances, cophylogenetic reconstruction methods fail to detect a pattern of widespread cophylogeny. In conclusion, this study provides an exception to the …

The Demographic And Life-History Costs Of Fear: Trait-Mediated Effects Of Threat Of Predation On Aedes Triseriatus, Geoffrey D. Ower, Steven A. Juliano

Faculty Publications – Biological Sciences

1. Predators alter prey populations via direct lethality (density-mediated effects), but in many taxa, the indirect nonlethal threat of predation may be almost as strong an effect, altering phenotypically plastic traits such as prey morphology, behavior, and life history (trait-mediated effects). There are costs to antipredator defenses and the strength of prey responses to cues of predation likely depends on both the perceived level of risk and food availability.
2. The goal of this study was to test the hypothesis that the costs of nonlethal trait-mediated interactions impacting larvae can have carryover effects that alter life-history traits, adult characteristics, and ultimately population …

Humans, Vegetation, And Drought In Late Holocene Amazonia, Christine Michelle Åkesson

Theses and Dissertations

The resilience and adaptation of past societies to climate change remain unclear, especially in the tropical cloud-forests of the Andes and the aseasonal forests of lowland western Amazonia. Long thought to have been too humid for significant human settlement, a new image of cloud-forests is emerging in which they supported human settlements for millennia. Anthropogenic disturbance, such as forest clearance, fire activity, and land-use has been suggested to have intensified during times of drier climates. Even so, the mid-elevational Andes and western Amazonia probably supported smaller pre-Columbian populations than settings with a distinct dry season. Uncertainties persist, however, regarding the …

Draft Genome Assembly And Population Genetics Of An Agricultural Pollinator, The Solitary Alkali Bee (Halictidae: Nomia Melanderi), Karen M. Kapheim, Hailin Pan, Cai Li, Charles Blatti Ill, Brock A. Harpur, Panagiotis Ioannidis, Beryl M. Jones, Clement F. Kent, Livio Ruzzante, Laura Sloofman, Eckart Stolle, Robert M. Waterhouse, Amro Zayed, Guojie Zhang, William T. Wcislo

Biology Faculty Publications

Alkali bees (Nomia melanderi) are solitary relatives of the halictine bees, which have become an important model for the evolution of social behavior, but for which few solitary comparisons exist. These ground-nesting bees defend their developing offspring against pathogens and predators, and thus exhibit some of the key traits that preceded insect sociality. Alkali bees are also efficient native pollinators of alfalfa seed, which is a crop of major economic value in the United States. We sequenced, assembled, and annotated a high-quality draft genome of 299.6 Mbp for this species. Repetitive content makes up more than one-third of …