Genetics and Genomics Commons^™

Changing Fire Regimes In The Great Basin Usa, Eva K. Strand, Kori Blankenship, Corey Gucker, Mark Brunson, Eugénie Montblanc

Aspen Bibliography

Wildfire is a natural disturbance in landscapes of the Western United States, but the effects and extents of fire are changing. Differences between historical and contemporary fire regimes can help identify reasons for observed changes in landscape composition. People living and working in the Great Basin, USA, are observing altered fire conditions, but spatial information about the degree and direction of change and departure from historical fire regimes is lacking. This study estimates how fire regimes have changed in the major Great Basin vegetation types over the past 60 years with comparisons to historical (pre-1900) fire regimes. We explore potential …

Variation In Thermal Tolerance Plasticity And The Costs Of Heat Exposure In The Estuarine Sea Hare, Phyllaplysia Taylori, Richelle L. Tanner, Rauri C. K. Bowie, Cynthia Y. Wang-Claypool, Jonathan H. Stillman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Climate change is increasing average temperatures and the frequency and intensity of thermal extremes in coastal marine environments. Organisms in coastal marine habitats are accustomed to environmental fluctuations and possess physiological plasticity that may be advantageous in response to increased occurrence of extremes. To examine whether such plasticity is locally adapted to environmental conditions, we investigated the relationship between genetic diversity and thermal tolerance plasticity in 11 populations of the direct-developing intertidal sea hare, Phyllaplysia taylori, on the western coast of the United States. Using whole-organism metrics of muscle function and metabolic rate and a ddRADseq genomic approach, we …

Drought Resilience And Legacy Effects In Two Forest Tree Species On Loess Plateau Of China: Growth And Water-Use Efficiency Under Different Drought Conditions, Lu Han, J. Julio Camarero, Guodong Jia, Zhiqiang Zhang, Lixin Chen

Aspen Bibliography

As droughts become more frequent and severer, understanding tree resilience and its role in mediating drought legacy effects (LEs) is critical for predicting forest ecosystem responses to future droughts and informing forest management. Both Pinus tabuliformis and Populus davidiana are widely distributed in the Loess Plateau region of western China and play important roles in provision of ecosystem services. In this study we quantified the LEs and resilience, including resistance (Rt) and recovery (Rc), of radial growth (BAI, basal area increment) and intrinsic water use efficiency (iWUE) of the two species, determined the external and internal factors influencing Rt and …

Mitochondrial Mrna And The Small Subunit Rrna In Budding Yeasts Undergo 3'-End Processing At Conserved Species-Specific Elements, Michael Anikin, Michael F Henry, Viktoria Hodorova, Hristo B Houbaviy, Jozef Nosek, Dimitri G Pestov, Dmitriy A Markov

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Respiration in eukaryotes depends on mitochondrial protein synthesis, which is performed by organelle-specific ribosomes translating organelle-encoded mRNAs. Although RNA maturation and stability are central events controlling mitochondrial gene expression, many of the molecular details in this pathway remain elusive. These include

Timber Harvesting Was The Most Important Factor Driving Changes In Vegetation Composition, As Compared To Climate And Fire Regime Shifts, In The Mixedwood Temperate Forests Of Temiscamingue Since Ad 1830, Daniela Robles, Yan Boulanger, Jesus Pascual, Victor Danneyrolles, Yves Bergeron, Igor Drobyshev

Aspen Bibliography

Context The vegetation composition of northeastern North American forests has significantly changed since pre-settlement times, with a marked reduction in conifer-dominated stands, taxonomic and functional diversity. These changes have been attributed to fire regime shifts, logging, and climate change.

Methods In this study, we disentangled the individual effects of these drivers on the forest composition in southwestern Quebec from 1830 to 2000 by conducting retrospective modelling using the LANDIS-II forest landscape model. The model was run based on pre-settlement forest composition and fire history reconstructions, historical timber harvest records, and climate reanalysis data. We compared counterfactual scenarios excluding individual factors …

Evaluating Elk Distribution And Conflict Under Proposed Management Alternatives At The National Elk Refuge In Jackson, Wyoming, Gavin G. Cotterill, Paul C. Cross, Eric K. Cole, Jonathan D. Cook, Margaret C. Mceachran, Tabitha A. Graves

Aspen Bibliography

We evaluated measurable attributes describing the current and future distribution of Cervus elaphus canadensis (elk) across a region surrounding Jackson, Wyoming, for five feedground management alternatives proposed by the U.S. Fish and Wildlife Service as a revision to 2007 "Bison and Elk Management Plan" of the National Elk Refuge. A resource selection function evaluated measurable attributes of interest to managers, including elk use of private property and sensitive habitat types at monthly timesteps and varying winter conditions. The study area boundaries were created through an expert elicitation process and consist of the Jackson Elk Herd Unit, Grand Teton National Park, …

Increased Positive Tree Species Mixture Effects On The Abundance And Richness Of Collembola With Stand Development In Canadian Boreal Forests, Yakun Zhang, Sai Peng, Zilong Ma, Chen Chen, Bilei Gao, Xinli Chen, Han Y.H. Chen

Aspen Bibliography

It is well established that species mixtures could enhance ecosystem functioning in diverse ecosystem types, with these benefits increasing over time. However, the impact of tree mixtures on Collembola communities following stand development in natural forests remains unclear, despite the critical roles Collembola plays in litter decomposition and nutrient cycling. We investigated the effects of tree species mixtures on Collembola abundance, diversity, and community structure by sampling pure and mixed jack pine (Pinus banksiana Lamb.) and trembling aspen (Populus tremuloides Michx.) of 15-year-old and 41-year-old stands in natural boreal forest. In total, 6,620 individuals of Collembola were identified …

Gene Model For The Ortholog Of Glys In Drosophila Simulans, Madeline L. Gruys, Madison A. Sharp, Zachary Lill, Caroline Xiong, Amy T. Hark, James J. Youngblom, Chinmay P. Rele, Laura K. Reed

Faculty Journal Articles

Gene model for the ortholog of glycogen synthase ( Glys ) in the Drosophila simulans May 2017 (Princeton ASM75419v2/DsimGB2) Genome Assembly (GenBank Accession: GCA_000754195.3 ). This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

Measuring Spatial And Temporal Variation In Species Composition Of Ephemeral Pond Amphibian Assemblages Using Metabarcoding, Elizabeth Strasko

Masters Theses & Specialist Projects

Amphibian populations worldwide face severe threats, heightening the need for reliable monitoring methods. In this thesis, I explored and tested environmental DNA (eDNA) metabarcoding protocols to survey amphibian assemblages in ephemeral ponds of the the Green River Preserve in central Kentucky, USA. First, I evaluated whether the commonly used mitochondrial cytochrome c oxidase subunit I (COI) gene could effectively capture species-level variation in local amphibians for eDNA metabarcoding. Extensive primer design and testing revealed significant challenges in amplifying fragmented eDNA from water samples. In a second study, I applied a metabarcoding approach using the mitochondrial 12S ribosomal RNA (12S) gene …

Feasibility Of Producing Non-Structural Wood Products Using Trembling Aspen Lumber, Mengyuan Zhang

Aspen Bibliography

Trembling aspen (Populus tremuloides) is abundant in Canada but underutilized in non-structural solid wood products.This study was aimed at evaluating the feasibility of using aspen lumber to produce flooring, moulding, and siding. The shrinkage, surface roughness, and wettability of aspen wood were tested. The surface hardness, screw withdrawal resistance, colour change, and dimensional stability of there products fabricated were examined. The wood yield of each product was analyzed. It was found that aspen showed superior machinability and wettability to silver maple and yellow poplar. Aspen flooring had a Brinell hardness of 13.47 MPa, 60% lower than silver maple. …

Microsatellites Reveal The Population Genetic Structure Of Yellow Perch In Minnesota, Megan Boche

Journal of Earth and Life Science

When analyzing a population’s genetic makeup, looking at variation of individuals and populations is a crucial factor. The management of yellow perch will be aided by this information particularly in regard to stocking or relocation. Microsatellite loci were used to analyze the genetic population structure of yellow perch Perca flavescens within and among 29 sampling areas throughout Minnesota’s basins. Seven microsatellite DNA loci were evaluated, with heterozygosities ranging from 0.41 to 0.78. The Lower Mississippi basin samples showed higher numbers of alleles per locus and greater expected heterozygosities compared to other basins, with Lake Pepin (PEP) exhibiting the highest average …

Marine Heatwave Response Plan For Western Australia’S Wild Capture Fisheries And Aquaculture, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Management Papers

The purpose of the Western Australian wild capture fisheries and aquaculture marine heatwave response plan (the Plan) is to document the Department’s approach for identifying and responding to the hazard of a marine heatwave on wild catch fisheries (commercial, recreational, charter and customary) and aquaculture resources within the geographic boundaries of WA. It provides risk reduction strategies and establishes best-practice processes for each stage of the hazard management and response continuum, ensuring that DPIRD is able to adequately prepare for, respond to, and recover from marine heatwave events. This Plan operates in conjunction with WA’s existing aquatic resource management framework, …

Snake Venoms As Models For Understanding The Origins And Evolution Of Gene Regulatory Networks, Siddharth S. Gopalan

Biology Dissertations - Archive

Understanding the relationship between genotype and phenotype is a fundamental goal of biology. However, the vastly complex nature of eukaryotic gene regulation can make deriving precise relationships between genotype and phenotype challenging. The gene regulatory architecture of snake venom systems provide an opportunity to study this problem in a phenotypic system with immense variation in phenotypes and the underlying genetics. Using a set of integrated functional genomic approaches with snake venoms as a central model, in this dissertation, I provide several examples of the regulatory mechanisms by which diversity in phenotypes arises. Specifically, I identify how gene expression heterogeneity between …

Patterns Of Kinship And Sociality In North American River Otters, Whitney E. Vickers

Cal Poly Humboldt theses and projects

Previous studies of river otters (Lontra canadensis) in coastal Humboldt County, California have documented varying social group compositions over the last four decades. It has been assumed that otters travel between coastal wetland sites, but the extent of movement has been unknown. Socially, river otters have been observed alone, in small family groups that consisted of an otter mom and pup(s), in larger helper groups that consisted of an otter mom, pup(s), and at least one additional adult or juvenile (helpers), and in all-adult social groups. Until now it was unknown whether the composition of social groups was …

History, Annotated Gazetteer, And Bibliography Of Ornithology In Kalimantan, Indonesian Borneo, Frederick H. Sheldon, Mohammad Irham, Daisy G. S. Kho, Erik Meijaard, Subir B. Shakya, Dewi M. Prawiradilaga, Sebastianus (Bas) Van Balen

Occasional Papers of the Museum of Natural Science, Louisiana State University

Kalimantan comprises nearly three quarters of the island of Borneo and is the place where scientific study of Bornean birds began. We describe the history of bird research in Kalimantan from its beginning, highlighting the ornithologists who explored the region and how their interests and methods changed over time, from a concentration on specimen collection, to examinations of community ecology, to conservation in the face of habitat change and species depletion, to the latest investigations using satellite, genetic, and digital technology. We also highlight some future directions for research, especially the need for more work on basic ecology and biogeography. …

Potential Of Using Trembling Aspen To Make Structural Engineered Wood Products, Dawei Wang

Aspen Bibliography

Trembling aspen (Populus tremuloides) is abundant in Canada but is widely considered an underutilized species. This study was aimed at evaluating the potential of using aspen lumber to produce cross-laminated timber (CLT), glued-laminated timber (glulam), and wood I-joists. The key mechanical properties of these engineered wood products, which were fabricated using a modified grading criterion, were examined. It was found that 1) The mean effective bending stiffness and characteristic bending moment resistance of 5-layer CLT specimens in the major-strength direction were 5,069x10⁹ N·mm²/m and 97.65x10⁶ N·mm/m; 2) The mean apparent MOE and characteristic modulus …

Using Rna Sequencing To Examine Encephalic Gene Expression In Cactus Mice, Sarah A. Nicholls

Honors Theses and Capstones

Many of the exact mechanisms by which desert-adapted animals avoid dehydration-induced complications are unknown, though there are likely ties to the general mammalian dehydration response, a multisystem process spearheaded by the brain. Peromyscus eremicus, the cactus mouse, can survive its whole life without intaking water and is commonly used as a model to study desert adaptations. In this study, we have used bulk transcriptomics to characterize the differential gene expression across hydrated and dehydrated P. eremicus in five major regions of the brain: the cerebral cortex (referred to throughout much of this paper as the cortex), hippocampus, thalamus, midbrain, …

Mobula, Bioinspiration, Filter Feeding, Form And Function, J. B. Teeple, S. R. Kahane-Rapport, K. E. Cohen, L. Hamann, J. A. Strother, E. W.M. Paig-Tran

Biological Sciences Faculty Publications

Mobulas (manta and devil rays) are large-scale ram filter feeders that separate planktonic food particles from large volumes of water with minimal clogging. This contrasts with most human-made filters that can suffer from problematic clogging requiring additional mechanisms for clearing blocked surfaces and maintaining performance. Prior studies have shown that mobulas employ a unique mechanism referred to as ricochet separation to filter feed, whereby captive vortices in filter pores cause particles to bounce off the filter surfaces and away from the filter pores. This mechanism enables the filtration of particles smaller than the pore size and reduced clogging. However, few …

‘Who’S Your Daddy?’: Ddradseq Parentage In Broodstock-Offspring Pairs Of Diadema Antillarum In A Population Restoration Initiative, Bianca R. Rosendahl

Undergraduate Scholarship and Creative Works

In the early 1980s Diadema antillarum, or the long-spined urchin, was hit by a catastrophic mass mortality event across the western Atlantic and Gulf of Mexico, inclusive of the Florida Keys. The cause of this die-off event was likely triggered by a pathogen or environmental stressor that decimated native populations by up to 98%. The species has not yet fully recovered and is struggling with recruitment success which is why it may benefit from an ex-situ recovery program. In this study, I used single nucleotide polymorphisms (SNPs) to identify genetic variation and analyze parentage in a captive population of …

Tricolored Bat (Perimyotis Subflavus) Population Genetic Structure In The Southeastern United States, Laura Henderson

Master's Theses

Tricolored bats (Perimyotis subflavus) have experienced substantial population losses from white-nose syndrome (WNS), a disease caused by the pathogenic fungus Pseudogymnoascus destructans (Pd) which infects hibernating bats. Determining population genetic structure helps assess genetic diversity and the impacts of wildlife threats to populations. Pre-WNS data shows weak-to-negligible structure and panmictic P. subflavus populations at core portions of their range. However, current genetic data from their southeastern U.S. range is lacking. I sought to determine whether recent genetic data help resolve genetic structure among southeastern populations and assess genetic differences at two stages of impact: post-WNS and …

Karyotyping As A Method To Verify Phylogenetic Relationships Among The Enneacanthus Species, Ophelia A. Anderson

Theses and Dissertations

The Enneacanthus genus consists of three species of freshwater fish endemic to eastern North America: E. obesus (Banded Sunfish), E. gloriosus (Blue Spotted Sunfish), and E. chaetodon (Black Banded Sunfish). Previous studies using molecular data suggest that E. obesus and E. gloriosus are more closely related, with E. chaetodon as the most distantly related species in the genus. This study investigates the phylogenetic relationship among the Enneacanthus species, using karyotype characteristics - chromosome number, morphology and fundamental number - as comparative metrics. Chromosome spreads were obtained from scale and gill epithelium samples collected between 1993 and 1994. Prepared slides …

Assessing Genetic Diversity And Population Structure In The Imperiled Aconitum Reclinatum (White Monkshood), An Endemic Wildflower Of Central Appalachia, Diamanda A. Zizis

Master’s Theses

Aconitum reclinatum, white monkshood (Ranunculaceae), is a Pennsylvania critically imperiled plant species found in five states of the Appalachian region of the United States: Pennsylvania, West Virginia, Virginia, North Carolina, and Tennessee. This plant is adapted to cool, moist environments but faces threats from increasing habitat loss, deer browse, logging, and changes in rainfall and temperature associated with climate change. Comprehensive knowledge of A. reclinatum genetic population structure remains limited. To address this, we collaborated with Natural Heritage programs within the range of A. reclinatum to sample populations across the species distribution and generate a genotyping-by-sequencing data set of …

Whole Genome Sequencing From Snowshoe Hare Fecal Samples, Jessica J. Powell

Graduate Student Theses, Dissertations, & Professional Papers

Genomic analyses can provide powerful insights into important issues in conservation biology, including rapid estimates of overall genetic diversity and related population genetic parameters. Noninvasive DNA sampling from fecal samples is an affordable, efficient, and broadly applicable sampling method that has been used in many targeted genetic analyses. However, the efficacy of whole genome sequencing from fecal samples remains relatively unexplored in most taxa. Here, we present results from two experiments designed to test the quantity and quality of whole genome resequencing data obtained from snowshoe hare (Lepus americanus) fecal pellets. Extensive previous research has used genetic analyses …

Function Over Form: The Benefits Of Aspen As Surrogate Brood-Rearing Habitat For Greater Sage-Grouse, Michel T. Kohl, Charles P. Sandford, Paul C. Rogers, Renee Chi, Terry A. Messmer, David K. Dahlgren

Aspen Bibliography

Species of conservation concern are often habitat specialists, posing significant risk to those species when specific plant communities are threatened. As a result, practitioners habitually focus conservation efforts on these communities while ignoring ecological mechanisms that explain the wildlife–plant relationships. In doing so, practitioners may overlook alternative vegetation communities that could maintain wildlife populations under alternative conditions (e.g., climate change). Here, we term these areas surrogate habitat, defined as vegetation communities or resource sites that provide similar critical resources as conventional sites, and assess their potential for conservation using a case study of greater sage-grouse (Centrocercus urophasianus) on …

Hidden Markov Model For Identifying Local Variants In Human Genomes Using Simulated Data, Scott Mccallum

Electronic Theses and Dissertations

Identifying adaptive mutations in genetic data is challenging due to the low frequency of occurrence of such events, and because signatures of selection are intertwined with the footprints of various other evolutionary forces that shape our genomes. Even when a larger region appears to be under selection, genomic sites that are linked to adaptive mutations have similar statistical signals, and thus can obfuscate the identification of the actual adaptive mutation. The new method described here uses a Hidden Markov Model that allows for classification of neutral, linked, and sweep (adaptive mutation) genomic sites. This model is general and can be …

Tree Rings Reveal Mixtures Of Aspen And Spruce Exhibit Greater Drought Resilience In A Planted Field Experiment, Jéssica Chaves Cardoso, Linhao Wu, Marcel Schneider, Charles A. Nock

Aspen Bibliography

Boreal forests provide a wealth of ecosystem services, many of which are linked to forest productivity. Climate change is expected to increase the frequency, duration, and severity of drought, and undermine the productivity of western boreal forests. Favouring species mixtures has emerged as a potential strategy to increase forest resilience to drought. To test the hypothesis that mixtures of trembling aspen and white spruce were more productive than pure stands because they were more resistant and resilient to drought, we analyzed community and species responses to drought utilizing measurements of annual growth obtained from stem disc samples from a planted …

Comparing Multivalent Cross-Linked Sodium Alginate/ Montmorillonite Beads Containing Curcumin Or Cayenne Pepper As Drug Carriers And Their Antimicrobial Resistance, Shionainn Traynor, Shubham Sharma

SURE Journal: Science Undergraduate Research Experience Journal

The aim of the following work was to investigate and compare curcumin and cayenne pepper in microbeads composed of sodium alginate (SA) crosslinked with montmorillonite (MMT) to act as drug carriers and their antimicrobial resistance. The microbeads were prepared through ion-exchange in multivalent solutions of CaCl₂, MgCl₂ and AlCl₃. The microbeads were characterized by Scanning Electron Microscopy (SEM), Energy Dispersive X-ray analysis (EDX) and the time required for intercalation of curcumin and cayenne pepper with MMT. Simulated intestinal fluid (pH 7.3) and gastric fluid (pH 1.2) at 37°C were used for comparison in swelling studies. …

Editorial - Sure Journal Vol 6, Anne M. Friel, Eva Campion, Sinead Loughran

SURE Journal: Science Undergraduate Research Experience Journal

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Testing Vivo-Morpholino Mediated Gene Knockdown Of Stat6, Spi1b, And Hnf4Α In Adult Threespine Stickleback, Stella Dipippo

Honors Scholar Theses

The fibrotic immune response to the cestode parasite, Schistocephalus solidus, varies among threespine stickleback populations. Fibrosis suppresses parasite growth but has costly effects on the fish. Previous genomic studies in stickleback have suggested potential roles of Spi1b, STAT6, and HNF4α in modulating fibrosis severity, but there is presently no evidence for this in-vivo. We used antisense vivo-morpholino oligonucleotides (MOs) to attempt to knockdown the expression of each gene in the liver, spleen, and intestine of adult stickleback. Vivo-MOs have been proven effective in other species of teleost fish, as well as in mice and humans, but …

Assessing Spatial Distribution And Quantification Of Native Trees In Saskatchewan's Prairie Landscape Using Remote Sensing Techniques, Elham Shafeian, Bryan J. Mood, Kenneth W. Belcher, Colin P. Laroque

Aspen Bibliography

The importance of trees in non-forest landscapes has been the focus of only a few studies. However, these trees provide many important ecosystem services. In this study, we mapped and quantified these trees using Sentinel-2 (S2) and very high-resolution (VHR) Google satellite imagery without any field campaigns. We performed a Random Forest (RF) classification to map the spatial distribution of native trees in different scenarios. The optimal model showed an overall accuracy and kappa of 0.99 and 0.98, respectively. We mapped 40,500 km² of tree cover, including native tree cover (approximately 29,565 km²≈10.5%), excluding plantations, regional and …