Life Sciences Commons^™

Error Rate On The Director’S Task Is Influenced By The Need To Take Another’S Perspective But Not The Type Of Perspective, Edward W. Legg, Laure Olivier, Steven Samuel, Robert Lurz, Nicola S. Clayton

Publications and Research

Adults are prone to responding erroneously to another’s instructions based on what they themselves see and not what the other person sees. Previous studies have indicated that in instruction-following tasks participants make more errors when required to infer another’s perspective than when following a rule. These inference-induced errors may occur because the inference process itself is error-prone or because they are a side effect of the inference process. Crucially, if the inference process is error-prone, then higher error rates should be found when the perspective to be inferred is more complex. Here, we found that participants were no more error …

Review Of The Algal Biology Program Within The National Alliance For Advanced Biofuels And Bioproducts, Clifford J. Unkefer, Richard T. Sayre, Jon K. Magnuson, Daniel B. Anderson, Ivan Baxter, Ian K. Balby, Judith K. Brown, Michael Carleton, Rose Ann Cattolico, Taraka Dale, Timothy P. Devarenne, C. Meghan Downes, Susan K. Dutcher, David T. Fox, Ursula Goodenough, Jan Jaworski, Jonathan E. Holladay, David M. Kramer, Andrew T. Koppisch, Mary S. Lipton, Babetta L. Marrone, Margaret Mccormick, István Molnár, John B. Mott, Kimberly L. Ogden, Ellen A. Panisko, Matteo Pellegrini, Juergen Polle, James W. Richardson, Martin Sabarsky, Shawn R. Starkenburg, Gary D. Stormo, Munehiro Teshima, Scott N. Twary, Pat J. Unkefer, Joshua S. Yuan, José A. Olivares

Publications and Research

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortiumbegan, littlewas known about themolecular basis of algal biomass or oil production. Very fewalgal genome sequenceswere available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played bymetabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome …

The View From Ventress - 2017, University Of Mississippi. College Of Liberal Arts

Liberal Arts Newsletters

Special Section: Higher Levels of Excellence. “Achievements and rankings reinforce our flagship status and are a testament to the value of our degrees, the impact of our research, and the competitiveness of our students, staff, and faculty. While they provide important benchmarks for our university, we remain committed to achieving even higher levels of excellence." -- Chancellor Jeffrey S. Vitter

Fishes Of The Northern Mid-Atlantic Ridge Collected During The Mar-Eco Cruise In June-July 2004: An Annotated Checklist, Filipe M. Porteiro, Tracey Sutton, Ingvar Byrkjedal, Alexy M. Orlov, Mikko Heino, Gui Menezes, Odd Aksel Bergstad

Marine & Environmental Sciences Faculty Reports

Records of the fishes from the northern Mid-Atlantic Ridge (MAR) (41⁰N - 60⁰N) sampled during two research cruises conducted in summer 2004 on the R/V G.O. Sars and M/S Loran are presented. The cruises were major sampling efforts carried out for the MAR-ECO project, i.e. the Census of Marine Life field project entitled “Patterns and Processes of the Ecosystems of the Northern Mid-Atlantic”. The investigation included sampling with several midwater nets, bottom trawl and longlines from surface waters to about 4000 m. The list comprises around 300 species of fishes from 82 families. Many records were new to the northern …

Shining A Light On Fish At Night: An Overview Of Fish And Fisheries In The Dark Of Night, And In Deep And Polar Seas, Neil Hammerschlag, Carl G. Meyer, Michael S. Grace, Steven T. Kessel, Tracey Sutton, Euan S. Harvey, Claire B. Paris-Limouzy, David W. Kerstetter, Steven J. Cooke

Marine & Environmental Sciences Faculty Articles

In aquatic environments, what one observes during the day can differ substantially by night. The species composition and associated ecological processes that occur during the day are often different than night. In polar seas and at great depths, “night” can span, months, years, and beyond. Teleosts and elasmobranchs have evolved unique sensory and behavioral modalities for living in darkness. As a consequence, fishers have adopted unique strategies for exploiting fish at night or in dark systems. We propose that neglecting the night has led to an incomplete understanding of aquatic organismal ecology, population/community dynamics, and ecosystem function with consequences for …

Using Logbook Data To Determine The Immediate Mortality Of Blue Sharks (Prionace Glauca) And Tiger Sharks (Galeocerdo Cuvier) Caught In The Commercial U.S. Pelagic Longline Fishery, Derek R. Dapp, Charlie Huveneers, Terence I. Walker, John Mandelman, David Kerstetter, Richard D. Reina

Marine & Environmental Sciences Faculty Articles

Commercial fisheries are recognized as one of the greatest threats to shark populations worldwide, but factors affecting the likelihood of shark mortality during fishery capture are poorly understood. We used the U.S. pelagic fishery logbook data from 1992 through 2008 to quantify the effects of several variables (fisheries regulatory periods, geographic zone, target catch, and sea surface temperature) on mortality of blue sharks (Prionace glauca) and tiger sharks (Galeocerdo cuvier). Mortality rates and trends in both species closely matched those recorded from other sources, and therefore indicated that the data on sharks discarded dead and discarded …

Evidence Of Morphological And Functional Variation Among Bluegill Lepomis Macrochirus Populations Across Grand Lake St Mary's Watershed Area, Anthony Bell, Stephen J. Jacquemin

Biological Sciences Faculty Publications

A myriad of factors have been shown to influence the morphology offreshwaterfish. However, studies that parse out where variation is comingfrom (e.g. body size, sex, and habitat) as well as what potential thesechanges have to influence function (e.g. swimming performance) areunderstudied. Therefore, the objectives of this study were to describemorphological variation of BluegillLepomis macrochirusacross the GrandLake St Mary’s watershed area (northwest OH, USA) and test forcovariation of morphology with size, sex, and habitat as well as to assessswimming performance to discern whether any differences in habitat (andmorphology) correspond with functional aspects related to criticalswimming velocity. Geometric morphometric methods were used …

The Optical Trapezoid Model: A Novel Approach To Remote Sensing Of Soil Moisture Applied To Sentinel-2 And Landsat-8 Observations, Morteza Sadeghi, Ebrahim Babaeian, Markus Tuller, Scott B. Jones

Plants, Soils, and Climate Faculty Publications

The “trapezoid” or “triangle” model constitutes the most popular approach to remote sensing (RS) of surface soil moisture based on coupled thermal (i.e., land surface temperature) and optical RS observations. The model, hereinafter referred to as Thermal-Optical TRAapezoid Model (TOTRAM), is based on interpretation of the pixel distribution within the land surface temperature - vegetation index (LST-VI) space. TOTRAM suffers from two inherent limitations. It is not applicable to satellites that do not provide thermal data (e.g., Sentinel-2) and it requires parameterization for each individual observation date. To overcome these restrictions we propose a novel OPtical TRApezoid Model (OPTRAM), which …

The Effects Of Work-To-Rest Ratios On Torque, Electromyographic, And Mechanomyographic Responses To Fatiguing Workbouts, Ethan C. Hill, Terry J. Housh, Cory M. Smith, Kristen C. Cochrane, Nathaniel D.M. Jenkins, Richard J. Schmidt, Glen O. Johnson

Department of Nutrition and Health Sciences: Faculty Publications

The purpose of the present study was to examine the effects of 2 different work-to-rest ratios, but the same mean load, cycle time, and total duration of the exercise bout, on maximal voluntary isometric contraction torque and neuromuscular responses to fatiguing, intermittent, submaximal, isometric, forearm flexion muscle actions. Ten men performed 2 fatiguing protocols with different work-to-rest ratios (4 s contraction, 4 s rest vs. 4 s contraction, alternating 6 and 2 s rest) that consisted of 50 intermittent, submaximal (65% of maximal voluntary isometric contraction), isometric, forearm flexion muscle actions. Electromyographic and mechanomyographic signals from the biceps brachii were …

Relationship Between Dietary Total Digestible Nutrients And Digestible Organic Matter In Beef Cattle Finishing And Growing Diets With Or Without Distillers Grains, Hannah C. Hamilton, Jana L. Gramkow, Jim C. Macdonald Donald, Galen E. Erickson, Andrea K. Watson, Terry J. Klopfenstein

Nebraska Beef Cattle Reports

The relationship between organic matter digestibility and total digestible nutrients is unestablished for diets containing distillers grains. Three cattle digestion studies were used to evaluate the relationship between total digestible nutrients and digestible organic matter. Results suggest digestible organic matter is consistent relative to total digestible nutrients content for traditional, corn based diets. In finishing and growing diets containing distillers grains additional digestible energy supplied by distillers grains is not accounted for when evaluating only digestible organic matter. Measuring digestible energy content of diets used in digestion trials is essential.

Lysin Based Antimicrobial Peptides Against Acinetobacter Baumannii, Mya Thandar

Student Theses and Dissertations

Acinetobacter baumannii is a Gram-negative bacterial pathogen responsible for a range of nosocomial infections. The recent rise and spread of multidrug resistant A. baumannii clones has fueled a search for alternative therapies, including bacteriophage endolysins with potent antibacterial activities. A common feature of these lysins is the presence of a highly positively charged C-terminal domain with a likely role in promoting outer membrane penetration. In the current study, we show that the C-terminal amino acids 108-138 of phage lysin PlyF307, named P307, alone was sufficient to kill A. baumannii (>3-logs). Furthermore, P307 could be engineered for improved activity, the …

Transcriptional Governance Of Hair Follicle Stem Cell Quiescence And Niche Maintenance In Long-Term Tissue Regeneration, Kenneth Lay

Student Theses and Dissertations

Adult stem cells are endowed with the remarkable ability to maintain, regenerate and repair tissues throughout the lifetime of the organism. Whether parsimonious utilization of adult stem cells is necessary to preserve their long-term potential has not been fully explored. I investigated this issue using the adult murine hair follicle stem cell (HFSC) as my paradigm. HFSCs reside in their niche called the bulge, and mostly remain in a quiescent state, becoming mobilized only transiently to fuel cyclical bouts of hair follicle regeneration. By ablating a key HFSC transcription factor, Forkhead Box C1 (FOXC1), I discovered that hair follicles underwent …

Ir Laser-Induced Gene Expression For Tracking Development Of Single Embryonic Neurons And Glia In C. Elegans, Anupriya Singhal

Student Theses and Dissertations

The assembly of neural circuits requires a complex choreography of developmental events: neurons must be generated, extend neurites at the correct time and location, and then integrate extracellular information, like long-range guidance cues or cellular contacts, with an internal developmental program to make correct wiring decisions. Visualizing neural-circuit assembly in vivo can provide insight into how these events are coordinated. The C. elegans embryo, which contains only 222 neurons and 56 glia, is an attractive setting to study nervous system development comprehensively in an intact, living organism. However, methods to label and track optically-resolvable neurites or manipulate single neurons through …

Home Sweet Home: Epigenetic Paths Of Stem Cells In And Out Of Their Niche, Rene C. Adam

Student Theses and Dissertations

Adult stem cells reside in niches, which control their long-term ability to selfrenew and produce the differentiated cell lineages necessary to regenerate and repair their tissues. Following injury, culture or transplantation, stem cells outside their niche often acquire broader plasticity in fates. In my graduate work, I showed that super-enhancers underlie the identity, lineage commitment and plasticity of adult stem cells in vivo. My chosen model is the hair follicle, where its stem cells (HFSCs), niche and master regulators are well-characterized. By mapping global chromatin domains of HFSCs in their native niche, and of committed progenitors, I discovered that super-enhancers …

High Throughput Detection Of Pseudouridine: Caveats, Conundrums, And A Case For Open Science, Maryam Zaringhalam

Student Theses and Dissertations

The isomerization of uridine to pseudouridine (Ψ), known as pseudouridylation, is the most abundant post-transcriptional modification of stable RNAs. Due to technical limitations in pseudouridine detection methods, studies on pseudouridylation have historically focused on ribosomal RNAs, transfer RNAs, and spliceosomal small nuclear RNAs, where Ψs play a critical role in RNA biogenesis and function. For decades, Ψ research was confined to this small subset of cellular RNAs, owing to limitations in methods for Ψ detection. Interest in this modification was reinvigorated, however, with reports that Ψ is conditionally induced in different environmental contexts and that pseudouridylation of certain codons recoded …

Structural And Functional Studies Of Mycobacterial General Transcription Factors Rbpa And Card, Elizabeth Hubin

Student Theses and Dissertations

Gene expression in bacteria is highly regulated at the step of transcription initiation. For decades, the vast majority of biochemical and kinetic studies have used Escherichia coli (Eco) RNA polymerase (RNAP) as a model for studying prokaryotic transcription initiation. However, properties of Eco RNAP are not representative of RNAPs from other bacterial species. Transcription in mycobacteria is distinct from Eco by its formation of unstable initiation complexes and its dependence on two transcription factors, RbpA and CarD, which are essential in the pathogen Mycobacteria tuberculosis (Mtb). In this thesis, I report the structural and biochemical characterization of RbpA and describe …

Light Sheet Microscopy And Image Analysis Of Neural Development And Programmed Cell Death In C. Elegans Embryos, Peter Insley

Student Theses and Dissertations

The positioning of neuronal cell bodies and neurites is critical for intact functioning of the nervous system. Mapping the positions of the soma and neurites in the brains of developing embryos as important central nervous system structures are being created may yield novel insight into the role of distinct cell groups in creating these structures. New developments in microscopy have made this an excellent time to study neural development in the C. elegans embryo. In the past decade, implementations of highly light efficient methods such as single plane illumination microscopy have rendered it possible to follow development of embryonic structures …

Investigating Differentiation: A Role For Organelle Inheritance In Epidermal Growth, Amma Asare

Student Theses and Dissertations

Balanced growth and differentiation is essential to tissue morphogenesis and homeostasis. How imbalances arise in disease states such as cancers is poorly understood. Loss of differentiation is associated with poorer prognosis in human patients and increasing malignancy in animal models. Here we explore this intersection between growth and differentiation in the context of epidermal development, where populations of stem cells are maintained in careful equilibrium and induced to proliferate and differentiate in response to stimuli such as injury or cyclical growth signals. During development, a naïve epidermis undergoes rapid proliferation and differentiation to form skin containing hair follicles, neurons, immune …

Pathways Of Nhej At Dysfunctional Telomeres And Their Resolution, Roos Anna Karssemeijer

Student Theses and Dissertations

Shelterin is a multiprotein complex that prevents DNA damage signaling at chromosome ends. In its absence, DNA repair pathways are activated that can promote the fusion of dysfunctional telomeres resulting in chromosomal instability. The work presented here aims to understand how telomeres are protected from these pathogenic repair pathways. The first part of this thesis is focused on the DNA damage response factor 53BP1, a key regulator in double strand break (DSB) repair pathways in mammalian cells. By influencing key regulatory events at and near DNA ends, 53BP1 plays an important role in the decision between non-homologous endjoining (NHEJ) and …

Light Stimulation Of Sensory Hair Cells, Julien Azimzadeh

Student Theses and Dissertations

Hair cells are the mechanosensory detectors that underlie our senses of audition and balance. Their mechanosensitivity arises from direct gating of force-sensitive ion channels by the tension in tip links located at the tops of the stereocilia. The study of hair cells and their mechanically gated channels has heretofore required physical displacement of a hair bundle to open its mechanotransduction channels. The work presented here describes a novel method of hair-bundle stimulation: irradiation with light. The original aim of this study was to elucidate the role of Ca²⁺ in fast adaptation, a process thought to underlie a hair bundle's …

Succession; A Business Strategy, Jan Miller, Department Of Primary Industries And Regional Development, Western Australia

Farm Systems and Economics published reports

Plan, Prepare, Prosper - workshop

This document is part of the Plan, Prepare, Prosper program that was developed under the Pilot of Drought Reform Measures ('the pilot'), a joint initiative between the Australian Government and the Western Australian Government. The program aims to support farmers and rural communities to prepare for drought, climate variability and other challenges.

The Succession planning: A business strategy workshop will help participants to begin and maintain the succession planning process.

This workshop will guide you through the process of exploring, planning and enacting succession planning.

Please use this manual as a checklist to help you …

Specification Of Stem Cells And Niche During Hair Follicle Morphogenesis, Tamara Ouspenskaia

Student Theses and Dissertations

Adult stem cell (SC) behavior is tightly coordinated by the signals received from the "niche" - the microenvironment that the SCs reside in. Little is known about the role of the niche in SC specification during organ morphogenesis. In particular, the question of whether the niche exists prior to SC specification or whether it is recruited after SC establishment in a developing tissue remains largely unanswered. In addition, the signals responsible for the specification and regulation of SCs during morphogenesis remain unexplored. To answer these questions, I focused my analysis on the earliest stages of hair follicle (HF) morphogenesis. Using …

The Apoptotic And Wallerian Degeneration Pathways Regulate Disease Onset And Progression In The Sod-1g93a Transgenic Mouse Model Of Als, Deanna Belsky

Student Theses and Dissertations

Amyotrophic Lateral Sclerosis is a neurodegenerative disorder characterized by progressive muscle denervation, motor axon degeneration and the death of motor neurons. The molecular mechanisms that mediate axon degeneration in ALS remain unknown, but motor neuron cell body death occurs through apoptosis. Genetic deletion of the pro-apoptotic gene Bax delays muscle denervation, prolongs disease onset, prevents motor neuron cell death and improves survival in an ALS mouse model. However, the timing and extent of axon degeneration in these mice is unaffected. Here, we examine the role of Sarm1, a component of the Wallerian degeneration pathway, and its interaction with the classical …

A Comparative Study Of Sensory Neuron Synaptic Activity And The Role Of Presynaptic Diversity, Specificity, And Regulation In Caenorhabitis Elegans, Donovan Ventimiglia

Student Theses and Dissertations

Chemical synapses are complex structures that have a diversity of specific activities that shape nervous system computation. To understand how this diversity contributes to specific circuit functions, we sought to characterize synaptic release in the stereotyped and defined neural circuitry of C. elegans. Here we use pHluorin imaging (Vglut-­pH) to monitor presynaptic glutamate release from single chemosensory neurons in intact animals and characterize the dynamics of endo-­ and exocytosis from two types of glutamatergic neurons, AWC^ON and ASH. In Chapter 1, we describe the optimization of Vglut-­pH, we introduce a reagent for measuring synaptic calcium influx by tethering GCaMP …

Compromising The 20s Proteasome Activates A Quality Control Pathway To Mitigate Proteotoxic Stress, Irit Shachrai

Student Theses and Dissertations

The regulation of the ubiquitin-proteasome system (UPS) has been the subject of a vast body of work because of its implication in normal development and a wide range of diseases. The UPS controls the degradation of a large number of cellular proteins and thereby regulates essential cellular processes critical for cellular adaptation and more. Amongst the main processes are removal of mis-folded and potentially toxic proteins, cell's loss of protein quality control is often associated with muscle atrophy and neurodegenerative diseases. The proteasome is subject to tight regulation, as many different proteins govern its transcription, assembly, stability and activity. Consequently, …

Density-Dependent Foraging In Caenorhabditis Elegans, Joshua Greene

Student Theses and Dissertations

Game theory has long predicted that the density of competitors and their behaviors should affect foraging, and moreover suggests that multiple strategies can evolve and co-exist within a single species. I show that both of these predictions are met by foraging Caenorhabditis elegans. In Chapter 2, I show that animals alter their foraging behavior in response to population density, that certain pheromones induce this behavioral change, and that different wild isolates vary in response to the potent ascaroside icas#9. I use QTL mapping to find a major locus responsible for this variation, and map it to an icas#9 receptor, srx-43. …

Single Molecule Ligand Binding Studies On Ccr5 By Fluorescence Cross-Correlation Spectroscopy, Carlos Rico

Student Theses and Dissertations

The G protein-coupled receptor (GPCR) C-C chemokine receptor 5 (CCR5) is the major co-receptor for HIV-1. CCR5 binds to the viral glycoprotein gp120 allowing HIV particles to infect T cells. Currently, maraviroc is the only Food and Drug Administration (FDA) approved entry inhibitor for HIV-1 but resistance to maraviroc has been reported indicating the need for novel entry inhibitors. Recently, four peptides derived from RANTES (Regulated on Activation, Normal T cell Expressed and Secreted), the endogenous ligand of CCR5, were shown to induce different CCR5 signaling pathways and efficiently block viral entry. The peptide analogues are 5P12, which blocks HIV-1 …

Separate Roles Of Fan1 And Fanconi Anemia Proteins In Dna Interstrand Crosslink Repair And Human Disease, Supawat Thongthip

Student Theses and Dissertations

DNA interstrand crosslink (ICL) repair is vital for cellular proliferation and survival. Defects in the repair of DNA crosslinks have been associated with congenital abnormalities, bone marrow and kidney failure, liver dysfunction, and cancer. DNA nucleases play a significant role during the repair of ICLs and they function at multiple repair steps. Here, we assessed the contributions of FANCD2/FANCI-Associated Nuclease 1 (FAN1) to the repair of ICL lesions and studied the consequences of its deficiency, which results in rare chronic kidney disease - Karyomegalic Interstitial Nephritis (KIN). FAN1 is a highly conserved nuclease from yeast to humans. It was first …

Apobec1-Mediated Rna Editing In Monocytes Contributes To Genetic Heterogeneity And Modulates Monocyte Activity And Development, Violeta Rayón Estrada

Student Theses and Dissertations

Post-transcriptional modifications such as alternative splicing have been shown to add to the complexity needed to compensate for the relatively low number of genes found in higher organisms. Many other modifications recently found in mRNA, which cannot be deduced from what is coded in the genome, such a cytidine to uridine and adenosine to inosine editing, reveal that this complexity is ever expanding. Therefore, the current challenge is to understand what is the function of these modifications. In this thesis, I focus on APOBEC1-mediated RNA editing. In higher eukaryotes RNA editing consists of C to U and A to I …

Regulated Recruitment Of The Chromosomal Passenger Complex To Chromatin And Microtubules Promotes Accurate Cell Division, Michael Wheelock

Student Theses and Dissertations

Aurora B, the kinase subunit of the chromosomal passenger complex (CPC), promotes accurate cell division by destabilizing erroneous kinetochoremicrotubule attachments and activating the spindle assembly checkpoint (SAC). Both functions require Aurora B activation, which is promoted by its binding to the C terminus of the CPC subunit INCENP, and by localization to the inner centromere, which requires the N terminus of INCENP. Inner centromere localization also requires phosphorylation of histone 3 threonine 3 (H3T3ph). While H3T3ph is required for CPC localization and the SAC during early mitosis, it must be dephosphorylated at anaphase to facilitate mitotic exit. However, the H3T3 …