Biology Commons^™

Fisheries Management Paper No.273 - Blue Swimmer Crab Resource Of The Peel-Harvey Estuary Harvest Strategy, 2015-2020. Version 1.0, Department Of Fisheries, Western Australia

Fisheries Management Papers

Harvest strategies for aquatic resources managed by the Western Australian Department of Fisheries (the Department) are formal documents prepared to support the decision-making processes required to ensure the management of these resources are consistent with the principles of Ecologically Sustainable Development (ESD). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA), Section 3, and the draft Aquatic Resources Management Bill 2013 (ARMB), Clause 9, which will replace the FRMA once enacted.

The publication of these strategies is intended to make the decision-making considerations and processes for the management of specified aquatic resources …

The Evolutionary Origination And Diversification Of A Dimorphic Gene Regulatory Network Through Parallel Innovations In Cis And Trans, Eric M. Camino, John C. Butts, Alison J. Ordway, Jordan E. Vellky, Mark Rebeiz, Thomas M. Williams

Biology Faculty Publications

The origination and diversification of morphological characteristics represents a key problem in understanding the evolution of development. Morphological traits result from gene regulatory networks (GRNs) that form a web of transcription factors, which regulate multiple cis-regulatory element (CRE) sequences to control the coordinated expression of differentiation genes. The formation and modification of GRNs must ultimately be understood at the level of individual regulatory linkages (i.e., transcription factor binding sites within CREs) that constitute the network. Here, we investigate how elements within a network originated and diversified to generate a broad range of abdominal pigmentation phenotypes among Sophophora fruit flies. …

Cell Type-Specific Responses To Wingless, Hedgehog And Decapentaplegic Are Essential For Patterning Early Eye-Antenna Disc In Drosophila, Jong-Hoon Won, Orkhon Tsogtbartarr, Wonseok Son, Amit Singh, Kwang-Wook Choi, Kyung-Ok Cho

Biology Faculty Publications

The Drosophila eye-antenna imaginal disc (ead) is a flattened sac of two-layered epithelia, from which most head structures are derived. Secreted morphogens like Wingless (Wg), Hedgehog (Hh), and Decapentaplegic (Dpp) are important for early patterning of ead, but the underlying mechanisms are still largely unknown. To understand how these morphogens function in the ead of early larval stages, we used wg-LacZ and dpp-Gal4 markers for the examination of wild-type and mutant eads. We found that the ead immediately after hatching was crescent-shaped with the Bolwig’s nerve at the ventral edge, suggesting that it consists of dorsal domain. In a subsequent …

Origins Of An Unmarked Georgia Cemetery Using Ancient Dna Analysis, Andrew T. Ozga, Raul Y. Tito, Brian M. Kemp, Hugh Matternes, Alexandra J. Obregon-Tito, Leslie Neal, Cecil M. Lewis Jr.

Biology Faculty Articles

Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and, in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we used ancient DNA extraction methods in well-preserved skeletal fragments from 20 individuals buried in Avondale Burial Place to investigate the origins of the …

Plasma Activated Air Mediates Gene Transfer, Chelsea M. Edelblute

Biological Sciences Theses & Dissertations

Cold plasma is produced when strong applied electric fields accelerate free electrons, which dissociate, excite, or ionize gaseous molecules [1]. The deposition of ions from the plasma source is dependent on power generation, input gas composition, and gas flow rate. In the presence of reactive species, the membrane of eukaryotic cells is compromised allowing for otherwise impermeant molecules, such as DNA, to enter the inner-cell milieu [2].

The efficacy of a novel cold plasma reactor based on shielded sliding discharge for the delivery of plasmid DNA was assessed. The device is entirely non-contact, wherein the plasma never directly touches the …

Functional Screening Of The Cronobacter Sakazakii Baa-894 Genome Reveals A Role For Prop (Esa_02131) In Carnitine Uptake, Audrey Feeney, Roy D. Sleator

Department of Biological Sciences Publications

Cronobacter sakazakii is a neonatal pathogen responsible for up to 80% of fatalities in infected infants. Low birth weight infants and neonates infected with C. sakazakii suffer necrotizing enterocolitis, bacteraemia and meningitis. The mode of transmission most often associated with infection is powdered infant formula (PIF) which, with an aw of ∼0.2, is too low to allow most microorganisms to persist. Survival of C. sakazakii in environments subject to extreme hyperosmotic stress has previously been attributed to the uptake of compatible solutes including proline and betaine. Herein, we report the construction and screening of a C. sakazakii genome bank and …

An Approach For Determining And Measuring Network Hierarchy Applied To Comparing The Phosphorylome And The Regulome, Chao Cheng, Erik Andrews, Koon-Kiu Yan, Matthew Ung, Daifeng Wang, Mark Gerstein

Dartmouth Scholarship

Many biological networks naturally form a hierarchy with a preponderance of downward information flow. In this study, we define a score to quantify the degree of hierarchy in a network and develop a simulated-annealing algorithm to maximize the hierarchical score globally over a network. We apply our algorithm to determine the hierarchical structure of the phosphorylome in detail and investigate the correlation between its hierarchy and kinase properties. We also compare it to the regulatory network, finding that the phosphorylome is more hierarchical than the regulome.

Allelic Polymorphism Of Gigantea Is Responsible For Naturally Occurring Variation In Circadian Period In Brassica Rapa, Qiguang Xie, Ping Lou, Victor Hermand, Rashid Aman

Dartmouth Scholarship

GIGANTEA (GI) was originally identified by a late-flowering mutant in Arabidopsis, but subsequently has been shown to act in circadian period determination, light inhibition of hypocotyl elongation, and responses to multiple abiotic stresses, including tolerance to high salt and cold (freezing) temperature. Genetic mapping and analysis of families of heterogeneous inbred lines showed that natural variation in GI is responsible for a major quantitative trait locus in circadian period in Brassica rapa. We confirmed this conclusion by transgenic rescue of an Arabidopsis gi-201 loss of function mutant. The two B. rapa GI alleles each fully rescued the …

Improved Evidence-Based Genome-Scale Metabolic Models For Maize Leaf, Embryo, And Endosperm, Samuel M. D. Seaver, Louis M. T. Bradbury, Océane Frelin, Raphy Zarecki, Eytan Ruppin, Andrew D. Hanson, Christopher S. Henry

Publications and Research

There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and …

Fighting Microbial Drug Resistance: A Primer On The Role Of Evolutionary Biology In Public Health, Gabriel Perron, R. Inglis, Pleuni Pennings, Sarah Cobey

Biology Department Faculty Works

Although microbes have been evolving resistance to antimicrobials for millennia, the spread of resistance in pathogen populations calls for the development of new drugs and treatment strategies. We propose that successful, long-term resistance management requires a better understanding of how resistance evolves in the first place. This is an opportunity for evolutionary biologists to engage in public health, a collaboration that has substantial precedent. Resistance evolution has been an important tool for developing and testing evolutionary theory, especially theory related to the genetic basis of new traits and constraints on adaptation. The present era is no exception. The articles in …

Increasing Expression Of Hepatitis B Surface Antigen In Maize Through Breeding, Erin Suzanne Miller

Master's Theses

The hepatitis B virus (HBV) is a common virus, with two billion people infected worldwide. It causes approximately 600,000 deaths each year, despite the availability of an effective vaccine since 1982. Maize as a platform for oral vaccination can supply a heat stable vaccine, which does not require syringes or trained personnel to administer. The Hepatitis B Surface antigen was transformed into maize and this seed was used to evaluate expression levels through the breeding process. The transgene was transferred into two elite maize inbreds by backcrossing. Highest expressing ears were selected each generation until approximately 99% commercial parent was …

Temporal Patterns Of Nutrition Dependence In Secondary Sexual Traits And Their Varying Impacts On Male Mating Success, Malcolm F. Rosenthal, Eileen A. Hebets

Eileen Hebets Publications

Variation in the quantity of nutrients ingested over an individual’s lifetime is likely to differentially affect distinct male secondary sexual traits and courtship signals, potentially providing females with information about a male’s past and present foraging history. We hypothesize that female choice is thus influenced by a male’s lifetime foraging history. To test this, we manipulated the quantity of nutrients (i.e. prey items) available to male wolf spiders, Schizocosa stridulans, using a fully crossed 2 × 2 design with low versus high prey quantity across juvenile and adult life stages, and assessed the impact of these diet treatments on male …

Use And Misuse Of Material Transfer Agreements: Lessons In Proportionality From Research, Repositories, And Litigation, Tania M. Bubela, Jenilee Guebert, Amrita Mishra

Office of the Provost

Material transfer agreements exist to facilitate the exchange of materials and associated data between researchers as well as to protect the interests of the researchers and their institutions. But this dual mandate can be a source of frustration for researchers, creating administrative burdens and slowing down collaborations. We argue here that in most cases in pre-competitive research, a simple agreement would suffice; the more complex agreements and mechanisms for their negotiation should be reserved for cases where the risks posed to the institution and the potential commercial value of the research reagents is high.

2015 Oklahoma Research Day Full Program, Northeastern State University

Oklahoma Research Day Abstracts

This document contains all abstracts from the 2015 Oklahoma Research Day held at Northeastern State University.

Developmental Ethanol Exposure Leads To Dysregulation Of Lipid Metabolism And Oxidative Stress In Drosophila, Theresa Logan-Garbisch, Anthony Bortolazzo, Peter Luu, Audrey Ford, David Do, Payam Khodabakhshi, Rachael French

Faculty Publications, Biological Sciences

Ethanol exposure during development causes an array of developmental abnormalities, both physiological and behavioral. In mammals, these abnormalities are collectively known as Fetal Alcohol Effects (FAE) or Fetal Alcohol Spectrum Disorder (FASD). We have established a Drosophila melanogaster model of FASD, and have previously shown that developmental ethanol exposure in flies leads to reduced expression of insulin like peptides (dILPs) and their receptor. In this work, we link that observation to dysregulation of fatty acid metabolism and lipid accumulation. Further, we show that developmental ethanol exposure in Drosophila causes oxidative stress, that this stress is a primary cause of the …

Further Description Of Hybridization In The Sea Stars Asterias Rubens And Asterias Forbesi Through The Application Of Species-Specific Genetic Markers, Callie Bateson

Honors Program Theses

Hybridization occurs when two separate species reproduce to form hybrid offspring. If the hybrid offspring backcross with individuals of their parental species, the subsequent offspring may have varying amounts of the parental genomes, if viable. Following the retreat of the Last Glacial Maxima 20,000 years ago, two sea star species, Asterias forbesi and A. rubens came into secondary contact in the Gulf of Maine where they began to hybridize. Previous research in our lab studied the frequency of hybridization at four locations along the east coast (Quebec, Nova Scotia, New Hampshire, and New York) using morphological identifications as well two …

A Protective Role Of Autophagy In A Drosophila Model Of Friedreich's Ataxia (Frda), Luan Wang

Wayne State University Dissertations

Friedreich’s ataxia (FRDA) is an inherited autosomal recessive neurodegenerative disease. It affects 1 in every 50,000 people in central Europe and North America. FRDA is caused by deficiency of Frataxin, an essential mitochondrial iron chaperone protein, and the associated oxidative stress damages. Autophagy, a housekeeping process responsible for the bulk degradation and turnover of long half-life proteins and organelles, is featured by the formation of double-membrane vacuoles and lysosomal degradation. Previous researches indicate that Danon’s disease, the inherited neural disorder disease that shares similar symptoms with FRDA, is due to the malfunction of autophagy. Based on this, we raise the …

Comparative Proteomics Of Mouse Tears And Saliva: Evidence From Large Protein Families For Functional Adaptation, Robert C. Karn, Christina M. Laukaitis

Scholarship and Professional Work - LAS

We produced a tear proteome of the genome mouse, C57BL/6, that contained 139 different protein identifications: 110 from a two-dimensional (2D) gel with subsequent trypsin digestion, 19 from a one-dimensional (1D) gel with subsequent trypsin digestion and ten from a 1D gel with subsequent Asp-N digestion. We compared this tear proteome with a C57BL/6 mouse saliva proteome produced previously. Sixteen of the 139 tear proteins are shared between the two proteomes, including six proteins that combat microbial growth. Among the 123 other tear proteins, were members of four large protein families that have no counterparts in humans: Androgen-binding proteins (ABPs) …

Genetically Based Low Oxygen Affinities Of Felid Hemoglobins: Lack Of Biochemical Adaptation To High-Altitude Hypoxia In The Snow Leopard, Jan E. Janecka, Simone S. E. Nielsen, Sidsel D. Andersen, Federico G. Hoffmann, Roy E. Weber, Trevor Anderson, Jay F. Storz, Angela Fago

School of Biological Sciences: Faculty Publications

Genetically based modifications of hemoglobin (Hb) function that increase blood–O₂ affinity are hallmarks of hypoxia adaptation in vertebrates. Among mammals, felid Hbs are unusual in that they have low intrinsic O₂ affinities and reduced sensitivities to the allosteric cofactor 2,3-diphosphoglycerate (DPG). This combination of features compromises the acclimatization capacity of blood–O2 affinity and has led to the hypothesis that felids have a restricted physiological niche breadth relative to other mammals. In seeming defiance of this conjecture, the snow leopard (Panthera uncia) has an extraordinarily broad elevational distribution and occurs at elevations above 6000 m in the Himalayas. Here, …

The Complexities Of Female Mate Choice And Male Polymorphisms: Elucidating The Role Of Genetics, Age, And Mate-Choice Copying, Kasey D. Fowler-Finn, Laura Sullivan-Beckers, Amy M. Runck, Eileen A. Hebets

Eileen Hebets Publications

Genetic, life history, and environmental factors dictate patterns of variation in sexual traits within and across populations, and thus the action and outcome of sexual selection. This study explores patterns of inheritance, diet, age, and mate-choice copying on the expression of male sexual signals and associated female mate choice in a phenotypically diverse group of Schizocosa wolf spiders. Focal spiders exhibit one of two male phenotypes: ‘ornamented’ males possess large black brushes on their forelegs, and ‘non-ornamented’ males possess no brushes. Using a quantitative genetics breeding design in a mixed population of ornamented/non-ornamented males, we found a strong genetic basis …

Octopamine Levels Relate To Male Mating Tactic Expression In The Wolf Spider Rabidosa Punctulata, Eileen A. Hebets, Matthew Hansen, Thomas C. Jones, Dustin J. Wilgers

Eileen Hebets Publications

In the wolf spider Rabidosa punctulata, upon encountering a female, males use one of two distinct strategies: (1) they court the female in an attempt to elicit a mating, or (2) they engage in a direct-mount tactic that involves extensive grappling with the female until a mating is achieved. The latter tactic appears more sexually aggressive, and both tactics come with the risk of being cannibalized. We explored the physiological mechanisms underlying this behavioral variation by assessing the relationship between circulating levels of the biogenic amine octopamine (OA), a neuromodulator suggested to play a role in “fight or flight” responses …

Functional Approach To Condition, Dustin J. Wilgers, Eileen A. Hebets

Eileen Hebets Publications

Animal signaling is commonly thought to be costly. Signaling costs can arise via a variety of avenues, including energy expenditure, predator attraction, and so on (reviews in Zuk and Kolluru, 1998; Kotiaho, 2001), and are predicted to increase with signal expression (e.g., size, amplitude, and intensity; Johnstone, 1997). Due to these costs, signaler condition, which is hypothesized to be a reflection of a signaler’s genetic quality, is expected to influence the level of signal expression one can afford (Zahavi, 1975), resulting in a positive correlation between signaler condition and signal expression – that is, condition-dependent signaling (Zahavi, 1977; West-Eberhard, 1979; …

Investigating The Influence Of Chd1 On Gene Expression In Drosophila Melanogaster Using Position Effect Variegation, Phuongngan Thi Bui

Scripps Senior Theses

Position Effect Variegation (PEV) is the mosaic expression of a gene that has been moved out of its optimal environment and into a different area on the chromosome. Changing a gene’s environment may have profound effects on its eligibility for proper expression, which is a complicated process regulated by many factors. The PEV phenomenon is used as an assay to study gene expression as regulated by chromatin structure. In this study, the Drosophila melanogaster white gene was used as a reporter to study the various effects of CHD1, a chromatin regulating factor, on PEV gene expression. Inspired by preliminary data …

High-Throughput Comparison, Functional Annotation, And Metabolic Modeling Of Plant Genomes Using The Plantseed Resource, Samuel M. D. Seaver, Svetlana Gerdes, Océane Frelin, Claudia Lerma-Ortiz, Louis M. T. Bradbury, Rémi Zallot, Ghulam Hasnain, Thomas D. Niehaus, Basma El Yacoubi, Shiran Pasternak, Robert Olson, Gordon Pusch, Ross Overbeek, Valérie De Crécy-Lagarde, Doreen Ware, Andrew D. Hanson, Christopher S. Henry

Publications and Research

There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and …

The Role Of Rnai In Downregulation Of Physcomitrella Patens Defense Genes And The Preliminary Steps Of Peg Mediated Transformation Of Mosses, Adam Beswick

Undergraduate Honors Thesis Collection

When attacked by a pathogen, the moss Physcomitrella patens will undergo both a hypersensitive response (HR) as well as a systematic acquired resistance (SAR) response. The SAR response turns on genes that ready the plant for future pathogen attacks. The hormone jasmonic acid (JA) is one of the products of SAR response in P. patens. In this study interference RNA (RNAi) was used to decrease gene expression of the allene oxide cyclase (ACe) gene, a key gene in the production pathway of JA. Using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), RNAi was found to significantly lower ACC gene levels …

Directed Evolution Of Genetic Regulatory Elements Using Crispr/Cas Genome Engineering, Candice J. Coppola

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Impacts Of Climate, Geography And White-Nose Syndrome Mortality On The Population Genetic Structure And Variation Of Myotis Lucifugus In The Eastern United States, Shannon Marie Dodge Morgan

Legacy Theses & Dissertations (2009 - 2024)

A myriad of biotic and abiotic factors contribute to the fluctuations in geographic range and size of animal populations. In the Nearctic, bat species have experienced drastic historic changes in available habitat due to Pleistocene glaciations, and are recently imperiled by the introduction of a novel fungal pathogen, Pseudogymnoascus destructans within the last decade. Myotis lucifugus in particular has lost 90-95% of the population in the eastern US due to the fungal disease White-Nose Syndrome (WNS). A population decline of this magnitude will likely result in a loss of allelic diversity as a result of a genetic bottleneck. My study …

Genome-Scale Analyses Of Transcription And Transcriptional Regulation In Bacteria, Devon Marie Fitzgerald

Legacy Theses & Dissertations (2009 - 2024)

The textbook model of bacterial transcription regulation posits that promoters occur immediately upstream of genes and that transcription factors (TFs) modulate transcription through promoter-proximal binding. However, the recent application of unbiased genome-wide approaches, such as ChIP-seq and RNA-seq, has revealed a much more complex picture, including TF binding and transcription initiation occurring in unexpected locations. This dissertation describes the use of deep sequencing-based approaches to evaluate the genome-wide binding of transcription-related proteins and identify locations of transcription initiation. I have assessed the genome-wide binding of three Escherichia coli TFs and an alternative σ factor. Additionally, I have analyzed genome-wide patterns …

Foraminiferal Beta 2-Tubulin And Microtubule To Helical Filament Transition In Reticulomyxa Filosa, Ingrid Ann Hahn

Legacy Theses & Dissertations (2009 - 2024)

Foraminifera have unusually fast dynamic movements resulting in the reorganization of the microtubule cytoskeleton (Travis and Bowser, 1988; Travis et al., 1983). We are interested in using Reticulomyxa filosa as a model to investigate the mechanisms and factors that regulate such fast microtubule assembly/disassembly rates (Chen and Schliwa 1990; Travis and Bowser, 1991; Welnhofer and Travis, 1996). Compared to conventional microtubule assembly and disassembly models, foraminifera tubulin can exist in another assembly state termed helical filaments. A novel form of tubulin, β2, in foraminifera is likely critical to these unusual microtubule properties. This thesis investigates Reticulomyxa filosa, a freshwater foraminifera …

Assessing The Contributions Of Two Stocked Strains On A Minnesota-Wisconsin Border Water, Douglas Zentner

Journal of Earth and Life Science

Stocking has long been used as a management tool in the United States even though many of its effects remain cryptic. Past comparisons between stocked strains were generally based on the survival and growth rates of physically marked individuals. More recently the use of genetic markers to assess contributions of stocked individuals has been employed by fisheries managers. Using 13 microsatellite markers we assessed the contributions of two muskellunge (Esox masquinongy) strains (Wisconsin and Leech) stocked into the St. Louis River Estuary. Ancestry in the adult samples remained relatively constant with differences only observed between the 2008 and …