Biology Commons^™

An Empirical And Theoretical Comparison Of The Socio-Ecological Behaviors Of Captive Chimpanzees (Pan Troglodytes), Bonobos (Pan Paniscus), And Western Lowland Gorillas (Gorilla Gorilla): Social Tolerance And Behavioral Responses To Changes In Food Quality And Distribution, Scott C. Milne

Master of Science in Integrative Biology Theses

Chimpanzees and gorillas are sympatric in most of their range in Central Africa, however, bonobos do not overlap with either of the other two species. This difference has been hypothesized to be the main factor leading to the socio-ecological traits of each species. Access to, and competition for, terrestrial herbaceous vegetation (THV) in each of the three species in thought to be linked to the social relationships and female-female bonds of each species. This study sought to provide a direct comparison of the social relationships of each of the three African Great Apes in captivity in order to elucidate similarities …

Biofilm Formation By Borrelia Burgdorferi Sensu Lato, Venkata Arun Timmaraju, Priyanka A.S. Theophilus, Kunthavai Balasubramanian, Shafiq Shakih, David F. Luecke, Eva Sapi

Biology and Environmental Science Faculty Publications

Bacterial biofilms are microbial communities held together by an extracellular polymeric substance matrix predominantly composed of polysaccharides, proteins and nucleic acids. We had previously shown that Borrelia burgdorferi sensu stricto, the causative organism of Lyme disease in the United States is capable of forming biofilms in vitro. Here, we investigated biofilm formation by B. afzelii and B. garinii, which cause Lyme disease in Europe. Using various histochemistry and microscopy techniques, we show that B. afzelii and B. garinii form biofilms, which resemble biofilms formed by B. burgdorferisensu stricto. High-resolution atomic force microscopy revealed similarities in the …

The Fkbp52 Cochaperone Acts In Synergy With Β-Catenin To Potentiate Androgen Receptor Signaling, Cheryl Samaniego, Ji Ho Suh, Arundhati Chattopadhyay, Karen Olivares, Naihsuan Guy, Jeffrey C. Sivils, Prasenjit Dey, Fumiak Yumoto, Robert J. Fletterick, Anders M. Strom, Jan-Åke Gustafsson, Paul Webb, Marc B. Cox

Biology Publications

FKBP52 and β-catenin have emerged in recent years as attractive targets for prostate cancer treatment. β-catenin interacts directly with the androgen receptor (AR) and has been characterized as a co-activator of AR-mediated transcription. FKBP52 is a positive regulator of AR in cellular and whole animal models and is required for the development of androgendependent tissues. We previously characterized an AR inhibitor termed MJC13 that putatively targets the AR BF3 surface to specifically inhibit FKBP52-regulated AR signaling. Predictive modeling suggests that β-catenin interacts with the AR hormone binding domain on a surface that overlaps with BF3. Here we demonstrate that FKBP52 …

Alternative Preprocessing Of Rna-Sequencing Data In The Cancer Genome Atlas Leads To Improved Analysis Results, Mumtahena Rahman, Laurie K. Jackson, W. Evan Johnson, Dean Y. Li, Andrea H. Bild, Stephen R. Piccolo

Faculty Publications

Motivation: The Cancer Genome Atlas (TCGA) RNA-Sequencing data are used widely for research. TCGA provides ‘Level 3’ data, which have been processed using a pipeline specific to that resource. However, we have found using experimentally derived data that this pipeline produces gene-expression values that vary considerably across biological replicates. In addition, some RNA-Sequencing analysis tools require integer-based read counts, which are not provided with the Level 3 data. As an alternative, we have reprocessed the data for 9264 tumor and 741 normal samples across 24 cancer types using the Rsubread package. We have also collated corresponding clinical data for these …

Assessing Feeding Preferences And Spatial Patterns Of Lagodon Rhomboides Linnaeus, Alexandria V. Lamle

Master of Science in Integrative Biology Theses

Mesograzers have the ability to greatly mitigate the effects of eutrophication in seagrass systems. In this study we look at pinfish (Lagodon rhomboides Linnaeus) as a potential epiphytic grazer and assess feeding preferences during a transitional stage in the ontogenetic diet shift exhibited by these fish. Since pinfish are abundant in seagrass meadows in the northern Gulf of Mexico, their dietary preferences have the potential to greatly impact seagrasses in this system. Twenty-four hour feeding trials were conducted to determine pinfish preference between seagrass (Thalassia testudinum) and algal epiphytes. St. Joseph Bay, FL was also surveyed to …

Polyq-Dependent Rna–Protein Assemblies Control Symmetry Breaking, Changhwan Lee, Patricia Occhipinti, Amy S. Gladfelter

Dartmouth Scholarship

Dendritic growth in fungi and neurons requires that multiple axes of polarity are established and maintained within the same cytoplasm. We have discovered that transcripts encoding key polarity factors including a formin, Bni1, and a polarisome scaffold, Spa2, are nonrandomly clustered in the cytosol to initiate and maintain sites of polarized growth in the fungus Ashbya gossypii. This asymmetric distribution requires the mRNAs to interact with a polyQ-containing protein, Whi3, and a Pumilio protein with a low-complexity sequence, Puf2. Cells lacking Whi3 or Puf2 had severe defects in establishing new sites of polarity and failed to localize Bni1 protein. Interaction …

Influence Of Native And Processed Cereal Grain Fibers On Gut Health, Junyi Yang

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Cereal fibers that can be metabolized by gut microbiota have been shown to promote the growth of beneficial bacteria in the gut. Increased consumption of cereal fibers may improve host / gut microbiota interactions in obesity and other metabolic diseases by normalizing gut dysbiosis. The present dissertation describes four research projects to assess the impact of cereal dietary fibers on gut microbiota and host metabolism. In the first study, we determined the treatment temperatures for production of soluble, non-digestible, feruloylated oligo- and polysaccharides (FOPS) from maize bran and wheat bran, and determined the fermentation properties of partially purified FOPS from …

Akirin-Mediated Gene Regulation During Cardiac Development, Austin M. Howard

Master of Science in Integrative Biology Theses

The highly conserved nuclear protein Akirin was previously identified as a cofactor that modulates Twist transcription factor activity during muscle development in Drosophila melanogaster. Akirin mediates an interaction between the Twist transcription factor and the multisubunit Brahma SWI/SNF-class chromatin remodeling complex at control elements of the Dmef2 locus to maintain optimal myogenic gene expression levels. Therefore, Akirin represents a class of novel secondary cofactors that work with transcription machinery to link transcription factor output with chromatin remodeling machinery to facilitate gene expression. Previous work establishes that Twist and Akirin also interact at Twist-responsive control elements of the tinman gene, …

Creation As Art, Jeff Ploegstra

Faculty Work Comprehensive List

"If we consider God an artist, we should study His technique, the elements of balance, proportion, repetition, and variation in what He has made."

Posting about experiencing God through interacting with nature from In All Things - an online hub committed to the claim that the life, death, and resurrection of Jesus Christ has implications for the entire world.

Delineation Of Aeromonas Hydrophila Pathotypes By Dectection Of Putative Virulence Factors Using Polymerase Chain Reaction And Nematode Challenge Assay, John Metz

Master of Science in Integrative Biology Theses

Aeromonas hydrophila is a Gram-negative, bacterial pathogen of humans and other vertebrates. To delineate pathotypes, the genomes of twenty-eight Aeromonas isolates were screened by PCR to determine the presence of virulence factors including: aerolysin (aerA), cytotoxic enterotoxin (act), hemolysin (ahh1), elastase (ahyB), enolase (eno), S-layer protein (ahsA), serine protease (ser), Type IV Aeromonas pilus (tapA), lipase (lip), and Type Three Secretion System (T3SS) components (aopB, ascV). Genes for ahh1, lip, ser, and ahyB …

Biodiversity Assessment Among Two Nebraska Prairies: A Comparison Between Traditional And Phylogenetic Diversity Indices, Shelly K. Aust, Dakota L. Ahrendsen, P. Roxanne Kellar

Biology Faculty Publications

Conservation of the evolutionary diversity among organisms should be included in the selection of priority regions for preservation of Earth’s biodiversity. Traditionally, biodiversity has been determined from an assessment of species richness (S), abundance, evenness, rarity, etc. of organisms but not from variation in species’ evolutionary histories. Phylogenetic diversity (PD) measures evolutionary differences between taxa in a community and is gaining acceptance as a biodiversity assessment tool. However, with the increase in the number of ways to calculate PD, end-users and decision-makers are left wondering how metrics compare and what data are needed to calculate various metrics.

Nervous System Development In Lecithotrophic Larval And Juvenile Stages Of The Annelid Capitella Teleta, Néva P. Meyer, Allan Carrillo-Baltodano, Richard E. Moore, Elaine C. Seaver

Biology

Background: Reconstructing the evolutionary history of nervous systems requires an understanding of their architecture and development across diverse taxa. The spiralians encompass diverse body plans and organ systems, and within the spiralians, annelids exhibit a variety of morphologies, life histories, feeding modes and associated nervous systems, making them an ideal group for studying evolution of nervous systems. Results: We describe nervous system development in the annelid Capitella teleta (Blake JA, Grassle JP, Eckelbarger KJ. Capitella teleta, a new species designation for the opportunistic and experimental Capitella sp. I, with a review of the literature for confirmed records. Zoosymposia. 2009;2:25-53) using …

Caspase-Cleaved Tau Co-Localizes With Early Tangle Markers In The Human Vascular Dementia Brain, Ryan J. Day, Maria J. Mason, Chloe Thomas, Wayne W. Poon, Troy T. Rohn

Biology Faculty Publications and Presentations

Vascular dementia (VaD) is the second most common form of dementia in the United States and is characterized as a cerebral vessel vascular disease that leads to ischemic episodes. Whereas the relationship between caspase-cleaved tau and neurofibrillary tangles (NFTs) in Alzheimer’s disease (AD) has been previously described, whether caspase activation and cleavage of tau occurs in VaD is presently unknown. To investigate a potential role for caspase-cleaved tau in VaD, we analyzed seven confirmed cases of VaD by immunohistochemistry utilizing a well-characterized antibody that specifically detects caspase-cleaved tau truncated at Asp⁴²¹. Application of this antibody (TauC3) revealed consistent …

The Complexity Of Background Clutter Affects Nectar Bat Use Of Flower Odor And Shape Cues, Nathan Muchhala, Diana Serrano

Biology Department Faculty Works

Given their small size and high metabolism, nectar bats need to be able to quickly locate flowers during foraging bouts. Chiropterophilous plants depend on these bats for their reproduction, thus they also benefit if their flowers can be easily located, and we would expect that floral traits such as odor and shape have evolved to maximize detection by bats. However, relatively little is known about the importance of different floral cues during foraging bouts. In the present study, we undertook a set of flight cage experiments with two species of nectar bats (Anoura caudifer and A. geoffroyi) and artificial flowers …

The Role Of The Pleckstrin Homology Domain-Containing Protein Ckip-1 In Activation Of P21-Activated Kinase 1 (Pak1), Yong-Bae Kim, Yong Jae Shin, Adhiraj Roy, Jeong-Ho Kim

Biochemistry and Molecular Medicine Faculty Publications

Upon growth factor stimulation, PAK1 is recruited to the plasma membrane and activated by a mechanism that requires its phosphorylation at S223 by the protein kinase CK2. However, the upstream signaling molecules that regulate this phosphorylation event are not clearly defined. Here, we demonstrate a major role of the CK2α-interacting protein CKIP-1 in activation of PAK1. CK2α, CKIP-1 and PAK1 are translocated to membrane ruffles in response to the epidermal growth factor (EGF), where CKIP-1 mediates the interaction between CK2α, and PAK1 in a PI3K-dependent manner. Consistently, we observe that PAK1 mediates phosphorylation and modulation of the activity of p41-Arc, …

Century-Long Warming Trends In The Upper Water Column Of Lake Tanganyika, Benjamin Kraemer, Simon Hook, Timo Huttula, Pekka Kotilainen, Catherine M. O'Reilly, Anu Peltonen, Pierre-Denis Plisnier, Jouko Sarvala, Rashid Tamatamah, Yvonne Vadeboncoeur, Bernhard Wehrli, Peter B. Mcintyre

Biological Sciences Faculty Publications

Lake Tanganyika, the deepest and most voluminous lake in Africa, has warmed over the last century in response to climate change. Separate analyses of surface warming rates estimated from in situ instruments, satellites, and a paleolimnological temperature proxy (TEX86) disagree, leaving uncertainty about the thermal sensitivity of Lake Tanganyika to climate change. Here, we use a comprehensive database of in situ temperature data from the top 100 meters of the water column that span the lake’s seasonal range and lateral extent to demonstrate that long-term temperature trends in Lake Tanganyika depend strongly on depth, season, and latitude. The observed spatiotemporal …

Bacterially-Based Immune Challenges And Trauma Elicit Terminal Investment In Male Aedes Aegypti, Molly K. Schumacher

Theses and Dissertations

Investment in life history traits such as immune function and reproduction is constrained by finite available resources. A cost-of-immunity trade-off may occur in response to infection when resources are diverted away from reproductive effort and into an immune response. Alternatively, an infected individual may enhance reproductive effort to maximize terminal reproductive success in response to the survival threat inherent to infection (terminal investment). We measured male Aedes aegypti reproductive behavior following inoculations with: living bacteria; killed bacteria as an immune elicitor; and a sham control. Mating competitiveness relative to naïve males was also determined through a binary mate choice experiment …

The Role Of The Pericardium In The Valveless, Tubular Heart Of The Tunicate, Ciona Savignyi, Lindsay D. Waldrop, Laura A. Miller

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Tunicates, small invertebrates within the phylum Chordata, possess a robust tubular heart which pumps blood through their open circulatory systems without the use of valves. This heart consists of two major components: the tubular myocardium, a flexible layer of myocardial cells that actively contracts to drive fluid down the length of the tube; and the pericardium, a stiff, outer layer of cells that surrounds the myocardium and creates a fluid-filled space between the myocardium and the pericardium. We investigated the role of the pericardium through in vivo manipulations on tunicate hearts and computational simulations of the myocardium and pericardium using …

Lesion-Specific Immune Response In Granulomas Of Patients With Pulmonary Tuberculosis: A Pilot Study, Selvakumar Subbian, Liana Tsenova, Mi-Jeong Kim, Helen C. Wainwright, Annalie Visser, Nirmalya Bandyopadhyay, Joel S. Bader, Petros C. Karakousis, Gabriele B. Murrmann, Linda-Gail Bekker, David G. Russell, Gilla Kaplan

Publications and Research

The formation and maintenance of granulomas is central to the host response to Mycobacterium tuberculosis (Mtb) infection. It is widely accepted that the lungs of patients with tuberculosis (TB) usually contain multiple infection foci, and that the granulomas evolve and differentiate independently, resulting in considerable heterogeneity. Although gene expression profiles of human blood cells have been proposed as biomarkers of Mtb infection and/or active disease, the immune profiles of discrete lesion types has not been studied extensively. Using histology, immunopathology and genome-wide transcriptome analysis, we explored the immunological profile of human lung TB granulomas. We show that although the different …

Distribution Of Three Congeneric Shrub Species Along An Aridity Gradient Is Related To Seed Germination And Seedling Emergence, Liming Lai, Yuan Tian, Yongji Wang, Xuechun Zhao, Lianhe Jiang, Jerry M. Baskin, Carol C. Baskin, Yuanrun Zheng

Biology Faculty Publications

Environmental tolerance of a species has been shown to correlate positively with its geographical range. On the Ordos Plateau, three Caragana species are distributed sequentially along the precipitation gradient. We hypothesized that this geographical distribution pattern is related to environmental tolerances of the three Caragana species during seed germination and seedling emergence stages. To test this hypothesis, we examined seed germination under different temperature, light and water potentials, and monitored seedling emergence for seeds buried at eight sand depths and given different amounts of water. Seeds of C. korshinskii germinated to high percentages at 5 : 15 to 25 : …

The Production Of Alpha/Beta And Gamma/Delta Double Negative (Dn) T-Cells And Their Role In The Maintenance Of Pregnancy, John C. Chapman, Fae M. Chapman, Sandra D. Michael

Biological Sciences Faculty Scholarship

The ability of the thymus gland to convert bone marrow-derived progenitor cells into single positive (SP) T-cells is well known. In this review we present evidence that the thymus, in addition to producing SP T-cells, also has a pathway for the production of double negative (DN) T-cells. The existence of this pathway was noted during our examination of relevant literature to determine the cause of sex steroid-induced thymocyte loss. In conducting this search our objective was to answer the question of whether thymocyte loss is the end product of a typical interaction between the reproductive and immune systems, or evidence …

Telonicher Marine Laboratory, Hsu Telonicher Marine Laboratory

Newsletters

No abstract provided.

Great Lake Island Biogeography Of Plethodon Cinereus: Effect Of Island Elevation On Color Polymorphism, Cameron N. Eddy

Masters Theses

Islands have long fascinated ecologists and evolutionary biologists because they provide replicated systems with which to test hypotheses regarding evolutionary and ecological theory. Because islands are relatively simple systems, they enable researchers to isolate specific factors responsible for observed phenomena. Many current questions in ecology and evolutionary biology have been addressed in island systems. For example, factors involved in the genetic divergence of populations are easier to discern in island populations because confounding effects of gene flow from adjacent populations are limited. This study focuses on isolated island populations of the color polymorphic Eastern Red-backed Salamander (Plethodon cinereus) …

The Physiology Of Proinsulin C-Peptide: Unanswered Questions And A Proposed Model, Gina L.C. Yosten, Grant R. Kolar

Biological Sciences Faculty Research & Creative Works

C-peptide is produced, processed, and secreted with insulin, and appears to exert separate but intimately related effects. In this review, we address the existence of the C-peptide receptor, the interaction between C-peptide and insulin, and the potential physiological significance of proinsulin C-peptide. C-peptide is produced, processed, and secreted with insulin, and appears to exert separate but intimately related effects. In this review, we address the existence of the C-peptide receptor, the interaction between C-peptide and insulin, and the potential physiological significance of proinsulin C-peptide.

Functional Characterization Of A Cathepsin L In Drosophila Melanogaster, Qian Dong

Masters Theses & Specialist Projects

The Drosophila dorsal Air Sac Primordium (ASP) is a tracheal tube that invasively grows toward and into the wing imaginal disc. The unfolding of Drosophila wing is a process following eclosion with a cuticular bilayer replacing epithelial cells originally packing the wing. We reasoned that protease functions might be needed for the invasion of ASP into the wing imaginal disc as well as the rearrangement of epithelia cells during wing unfolding. Our study is particularly focused on understanding the role of a Cathepsin L like cysteine protease (CP1) in the development of dorsal ASP and wing development of Drosophila melanogaster. …

Welcome To The Brave New World: Crispr Mediated Genome Editing‐Pathway To Designer Babies?, Hemayet Ullah

Department of Biology Faculty Publications

The world literature circle was abuzz in 1932 when Aldous Huxley published his seminal book “Brave New World”. He painted the efforts of a totalitarian state to lab manufacture “sub‐human” people who would be capable of work but not of independent thought. Though the plot was set almost 500 years in the future, the author may not have envisioned that within a century of his writing scientists would embark on developing technologies that could potentially set the road for ʺdesigner babiesʺ in the future. The recent availability of the simple, yet highlyeffective, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology …

Extinction In A Hyperdiverse Endemic Hawaiian Land Snail Family And Implications For The Underestimation Of Invertebrate Extinction, Claire Régnier, Philippe Bouchet, Kenneth Hayes, Norine Yeung, Carl Christensen, Daniel Chung, Benoit Fontaine, Robert Cowie

Department of Biology Faculty Publications

The International Union for Conservation of Nature (IUCN) Red List includes 832 species listed as extinct since 1600, a minuscule fraction of total biodiversity. This extinction rate is of the same order of magnitude as the background rate and has been used to downplay the biodiversity crisis. Invertebrates comprise 99% of biodiversity, yet the status of a negligible number has been assessed. We assessed extinction in the Hawaiian land snail family Amastridae (325 species, IUCN lists 33 as extinct). We did not use the stringent IUCN criteria, by which most invertebrates would be considered data deficient, but a more realistic …

Bactericera Cockerelli (Sulc) (Hemiptera: Triozidae): Nearly Complete Mitochondrial Genome, Single Mitochondrial Genes And Complete Mitochondrial Genome Comparison, And Insecticide Resistance Genes Of Potato Psyllid Populations From North America, Amalia Rosa Lopez Montiel

Biology Theses

The potato psyllid, Bactericera cockerelli (Sulc.), is an economic pest of potatoes and other solanaceous crops, and the vector of the causal agent of zebra chip disease. The expanded distribution of the potato psyllid has resulted in the differentiation of biotypes (central and western), and haplotypes (southwestern and northwestern), according to analysis of the mitochondrial gene cytochrome oxidase I (COI). In this study, the nearly complete (part of the control region unsequenced) mitochondrial genome from potato psyllid populations occurring in North America: Texas, Nebraska, California, Washington, northwest (Washington) and southwest (Arizona), were sequenced using next generation sequencing technology. The raw …

The Mouse That Trolled: The Long And Tortuous History Of A Gene Mutation Patent That Became An Expensive Impediment To Alzheimer's Research, Tania M. Bubela, Saurabh Vishnubhakat, Robert Cook-Deegan

Office of the Provost

This case study presents the tale of the academic discovery of a rare mutation for early-onset Alzheimer's disease that was patented by a sole inventor and licensed to a non-practicing entity (NPE), the Alzheimer's Institute of America (AIA). Our aims are (1) to relate this story about patents, research tools, and impediments to medical progress, and (2) to inform ongoing debates about how patents affect research, disposition of university inventions, and the distribution of benefits from publicly funded research. We present an account of the hunt for Alzheimer's genes, their patenting, assignment, and enforcement based on literature, litigation records and …

Origin And Evolution Of Petrocosmea (Gesneriaceae) Inferred From Both Dna Sequence And Novel Findings In Morphology With A Test Of Morphology-Based Hypotheses, Zhi-Jing Qiu, Yuan-Xue Lu, Chao-Qun Li, Yang Dong, James F. Smith, Yin-Zheng Wang

Biology Faculty Publications and Presentations

Background: Petrocosmea Oliver (Gesneriaceae) currently comprises 38 species with four non-nominate varieties, nearly all of which have been described solely from herbarium specimens. However, the dried specimens have obscured the full range of extremely diverse morphological variation that exists in the genus and has resulted in a poor subgeneric classification system that does not reflect the evolutionary history of this group. It is important to develop innovative methods to find new morphological traits and reexamine and reevaluate the traditionally used morphological data based on new hypothesis. In addition, Petrocosmea is a mid-sized genus but exhibits extreme diverse floral variants. This …