Genetics and Genomics Commons^™

Sheep Updates 2015 - Katanning, Bruce Mullan, Kate Pritchett, Kimbal Curtis, Chris Wilcox, Mike Hyder, Leigh Sonnerman, Lynne Bradshaw, Geoff Lindon, Katherine Davies, Joe Young, Stephen Lee, Ian Robertson, Lucy Anderton, Hayley Norman, Ed Barrett-Lennard, Jackie Jarvis, Ben Patrick

Sheep Updates

This session covers fourteen papers from different authors:

1. The Sheep Industry Business Innovation project, Bruce Mullan, Sheep Industry Development Director, Department of Agriculture and Food, Western Australia

2. Western Australian sheep stocktake, Kate Pritchett and Kimbal Curtis, Research Officers, Department of Agriculture and Food, Western Australia

3. Wool demand and supply - short term volatility, long term opportunities, Chris Wilcox, Principal of Poimena Analysis

4. Lifetime management for maternal ewes, Mike Hyder, Research Officer, Department of Agriculture and Food, Western Australia

5. National Livestock Identification System (NLIS) for sheep and goats - what is the NLIS database? Leigh Sonnermann, …

Large Dsdna Chloroviruses Encode Diverse Membrane Transport Proteins, Gerhard Thiel, Timo Greiner, David Dunigan, Anna Moroni

James Van Etten Publications

Many large DNA viruses that infect certain isolates of chlorella-like green algae (chloroviruses) are unusual because they often encode a diverse set of membrane transport proteins, including functional K+ channels and aquaglyceroporins as well as K+ transporters and calcium transporting ATPases. Some chloroviruses also encode putative ligand-gated-like channel proteins. No one protein is present in all of the chloroviruses that have been sequenced, but the K+ channel is the most common as only two chloroviruses have been isolated that lack this complete protein. This review describes the properties of these membrane-transporting proteins and suggests possible physiological functions and evolutionary histories …

Quaking Aspen At The Residential-Wildland Interface: Elk Herbivory Hinders Forest Conservation., Paul C. Rogers, Allison Jones, James Catlin, James Shuler, Arthur Morris, Michael R. Kuhns

Aspen Bibliography

T: Quaking aspen (Populus tremuloides) forests are experiencing numerous impediments across North America. In the West, recent drought, fire suppression, insects, diseases, climate trends, inappropriate management, and ungulate herbivory are impacting these high biodiversity forests. Additionally, ecological tension zones are sometimes created at residential-wildland interfaces with divergent management directives. For example, private conservation reserves bordering public land may be degraded from browsing where game species find refuge from hunting and plentiful forage. We examined putative herbivore impacts to nearly pure aspen forests at Wolf Creek Ranch (WCR), a sparsely developed residential landscape in northern Utah. Forty-three one-hectare monitoring …

Altered Fire Regimes And The Persistence Of Quaking Aspen In The Rocky Mountains: A Literature Review, Aaron Rosenblum

Aspen Bibliography

The persistence of quaking aspen (Populus tremuloides Michx.) is of significant importance to land managers in the Rocky Mountain region. Fire suppression in the past century has been implicated as a mechanism influencing aspen population dynamics, as aspen are generally considered an early seral disturbance adapted species. The heterogeneity of aspen community assemblages and fire regimes makes it difficult to discern what the result of fire suppression has been at large spatial and temporal scales. Decision makers should investigate the questions at hand at the stand level in their study location to best determine the mechanisms at play, as well …

Long-Term Vegetation Change In Utah's Henry Mountains: A Study In Repeat Photography, Charles E. Kay

Aspen Bibliography

An extensive search was conducted of archival and other sources to locate as many historical photographs as possible for the Henry Mountains in south-central Utah. Those images were then taken into the field, the original camera stations relocated, and modern pictures made of the historical scenes to evaluate long-term vegetation change and land management activities. In all, 626 repeat photo sets were compiled—608 by the author and 18 by Earl Hindley. This book includes 126 photo sets that were representative of the areas studied.

Regeneration Dynamics Of White Spruce, Trembling Aspen, And Balsam Poplar In Response To Disturbance, Climatic, And Edaphic Factors In The Cold, Dry Boreal Forests Of The Southwest Yukon, Canada, Shyam K. Paudel, Craig R. Nitschke, Suzanne W. Simard, John L. Innes

Aspen Bibliography

The southwestern region of the Yukon Territory of Canada has experienced an unprecedented spruce bark beetle outbreak (Dendroctonus rufipennis) and an increase in the frequency of forest fires that extend beyond historical trends and that have caused significant impacts on forest structure and composition. A Strategic Forest Management Plan (SFMP) for the Champagne and Aishihik Traditional Territory located in the southwest Yukon was implemented in 2004 in response to the spruce bark beetle (D. rufipennis) infestation and increased fire risk. The plan has recommended salvage harvesting of beetle-killed stands as a strategy to facilitate the development …

Draft Genome Sequence Of Cercospora Arachidicola, Causal Agent Of Early Leaf Spot In Peanuts, Valerie A. Orner, Emily G. Cantowine, Xinye Monica Wang, Amr Abouelleil, James Bochicchio, Chad Nusbaum, Albert C. Culbreath, Zaid Abdo, Renee S. Arias

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Cercospora arachidicola, causal agent of early leaf spot, is an economically important peanut pathogen. Lack of genetic information about this fungus prevents understanding the role that potentially diverse genotypes may have in peanut breeding programs. Here, we report for the first time a draft genome sequence of C. arachidicola.

Up Regulation Of Heat Shock Protein 70b (Hsp70b) And Ssa1 In Chlamydomonas Reinhardtii Via Hsp70a-Rbcs2 And Psad Promoter, B. Kirtley Amos

Theses and Dissertations--Biosystems and Agricultural Engineering

Fabrication of effective algae cultivation systems adjacent to coal-fired power plants to fixate waste CO₂ would represent a sizable step towards achieving a carbon neutral energy cycle. However, emission gas would elevate the algal cultivation system temperature and decreases its pH without expensive preprocessing. Increased temperature and acidity constitutes a profound stress on the algae. Although stressed algae produce heat shock proteins (HSPs) that promote protein folding and protect against stress, the ordinary biological response is insufficient to protect against coal flue gas. Experimental upregulation of HSPs could make algae respond to the stress caused by high temperatures and …

Target-Directed Biosynthetic Evolution: Redirecting Plant Evolution To Genomically Optimize A Plant’S Pharmacological Profile, Dustin Paul Brown

Theses and Dissertations--Neuroscience

The dissertation describes a novel method for plant drug discovery based on mutation and selection of plant cells. Despite the industry focus on chemical synthesis, plants remain a source of potent and complex bioactive metabolites. Many of these have evolved as defensive compounds targeted on key proteins in the CNS of herbivorous insects, for example the insect dopamine transporter (DAT). Because of homology with the human DAT protein some of these metabolites have high abuse potential, but others may be valuable in treating drug dependence. This dissertation redirects the evolution of a native Lobelia species toward metabolites with greater activity …

Sheep Updates 2015 - Ravensthorpe, Bruce Mullan, Kate Pritchett, Kimbal Curtis, Chris Wilcox, Mike Hyder, Leigh Sonnerman, Lynne Bradshaw, Geoff Lindon, Katherine Davies, Joe Young, Stephen Lee, Ian Robertson, Lucy Anderton, Hayley Norman, Ed Barrett-Lenard, Jackie Jarvis, Ben Patrick

Sheep Updates

This session covers fourteen papers from different authors:

1. The Sheep Industry Business Innovation project, Bruce Mullan, Sheep Industry Development Director, Department of Agriculture and Food, Western Australia

2. Western Australian sheep stocktake, Kate Pritchett and Kimbal Curtis, Research Officers, Department of Agriculture and Food, Western Australia

3. Wool demand and supply - short term volatility, long term opportunities, Chris Wilcox, Principal of Poimena Analysis

4. Lifetime management for maternal ewes, Mike Hyder, Research Officer, Department of Agriculture and Food, Western Australia

5. National Livestock Identification System (NLIS) for sheep and goats - what is the NLIS database? Leigh Sonnermann, …

Generation Of An Attenuated, Cross-Protective Pepino Mosaic Virus Variant Through Alignment-Guided Mutagenesis Of The Viral Capsid Protein, Godwill M. Chewachong, Sally A. Miller, Joshua J. Blakeslee, David M. Francis, Thomas Jack Morris, Feng Qu

School of Biological Sciences: Faculty Publications

Mild variants of many viruses are able to protect infected plants from subsequent invasion by more severe variants of the same viruses through a process known as cross-protection. In the past, the cross-protective viral variants were commonly derived from mild field isolates that were sometimes genetically heterogeneous, providing variable levels of crossprotection. Here, we report a novel approach to rapidly generate crossprotective variants of the tomato-infecting Pepino mosaic virus (PepMV) independently of the availability of mild field isolates. Our approach sought to attenuate PepMV by mutating less conserved amino acid residues of the abundantly produced capsid protein (CP). These less-conserved …

Ploidy Number For Panicum Virgatum (Switchgrass) From The Long Island Sound Coastal Lowland Compared To Upland And Lowland Cultivars., Tanisha Williams, Carol Auer

Plant Science Articles

Panicum virgatum L. (switchgrass) is a native, perennial grass in North America with important ecological function in ecoregions including the Long Island Sound Coastal Lowland in the Northeastern United States. In recent decades, switchgrass has become a model lignocellulosic bioenergy crop with a large research portfolio describing its distribution, genetics, genomics, phenology, traits, gene flow, and cultivation. Switchgrass has been divided into two ecotypes, the Lowland ecotype which is tetraploid (2n= 4x= 36 chromosomes) and the Upland ecotype which is tetraploid or octaploid (2n= 8x= 72). While most switchgrass research has focused on genotypes from the Midwest or Southeastern regions, …

Chlorovirus Atcv-1 Is Part Of The Human Oropharyngeal Virome And Is Associated With Changes In Cognitive Functions In Humans And Mice, Robert H. Yolken, Lorraine Jones-Brando, David D. Dunigan, Geetha Kannan, Faith Dickerson, Emily Severance, Sarven Sabunciyan, C. Conover Talbot Jr., Emese Prandovszky, James R. Gurnon, Irina V. Agarkova, Flora Leister, Kristin L. Gressitt, Ou Chen, Bryan Deuber, Fangrui Ma, Mikhail V. Pletnikov, James L. Van Etten

James Van Etten Publications

Chloroviruses (family Phycodnaviridae) are large DNA viruses known to infect certain eukaryotic green algae and have not been previously shown to infect humans or to be part of the human virome. We unexpectedly found sequences homologous to the chlorovirus Acanthocystis turfacea chlorella virus 1 (ATCV-1) in a metagenomic analysis of DNA extracted from human oropharyngeal samples. These samples were obtained by throat swabs of adults without a psychiatric disorder or serious physical illness who were participating in a study that included measures of cognitive functioning. The presence of ATCV-1 DNA was confirmed by quantitative PCR with ATCV-1 DNA being …

Legume Crops Phylogeny And Genetic Diversity For Science And Breeding, Petr Smýkal, Clarice J. Coyne, Mike J. Ambrose, Nigel Maxted, Hanno Schaefer, Matthew W. Blair

Agricultural and Environmental Sciences Faculty Research

Economically, legumes (Fabaceae) represent the second most important family of crop plants after the grass family, Poaceae. Grain legumes account for 27% of world crop production and provide 33% of the dietary protein consumed by humans, while pasture and forage legumes provide vital part of animal feed. Fabaceae, the third largest family of flowering plants, has traditionally been divided into the following three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae, all together with 800 genera and 20,000 species. The latter subfamily contains most of the major cultivated food and feed crops. Among the grain legumes are some of mankind's earliest crop plants, …

Identification And Characterization Of Factors Involved In Dna Demethylation And Anti-Silencing In Arabidopsis, Zhaobo Lang

Open Access Dissertations

DNA methylation is a key epigenetic mark for transcriptional gene silencing in many eukaryotes. DNA methylation status can be dynamically controlled by methylation and active demethylation processes. Compared to the well-known mechanisms of DNA methylation, the mechanisms of DNA demethylation and its regulation are poorly understood. In order to better understand the DNA demethylation pathway, we developed two genetic screening systems in Arabidopsis to identify new components involved in the DNA demethylation. In the first system, which is based on 35S promoter driven SUC2 (sucrose transporter 2) transgene, a mutant (91-1) was isolated and map-based cloning identified the …

Chlorovirus Skp1-Binding Ankyrin Repeat Protein Interplay And Mimicry Of Cellular Ubiquitin Ligase Machinery, Eric A. Noel, Ming Kang, Jiri Adamec, James L. Van Etten, George A. Oyler

James Van Etten Publications

The ubiquitin-proteasome system is targeted by many viruses that have evolved strategies to redirect host ubiquitination machinery. Members of the genus Chlorovirus are proposed to share an ancestral lineage with a broader group of related viruses, nucleo-cytoplasmic large DNA viruses (NCLDV). Chloroviruses encode an Skp1 homolog and ankyrin repeat (ANK) proteins. Several chlorovirus-encoded ANK repeats contain C-terminal domains characteristic of cellular F-boxes or related NCLDV chordopox PRANC (pox protein repeats of ankyrin at C-terminal) domains. These observations suggested that this unique combination of Skp1 and ANK repeat proteins might form complexes analogous to the cellular Skp1-Cul1-F-box (SCF) ubiquitin ligase complex. …

The Trehalose Pathway In Maize: Conservation And Gene Regulation In Response To The Diurnal Cycle And Extended Darkness, Clémence Henry, Samuel W. Bledsoe, Allison Siekman, Alec Kollman, Brian M. Waters, Regina Feil, Mark Stitt, L. Mark Lagrimini

Department of Agronomy and Horticulture: Faculty Publications

Energy resources in plants are managed in continuously changing environments, such as changes occurring during the day/night cycle. Shading is an environmental disruption that decreases photosynthesis, compromises energy status, and impacts on crop productivity. The trehalose pathway plays a central but not well-defined role in maintaining energy balance. Here, we characterized the maize trehalose pathway genes and deciphered the impacts of the diurnal cycle and disruption of the day/night cycle on trehalose pathway gene expression and sugar metabolism. The maize genome encodes 14 trehalose-6-phosphate synthase (TPS) genes, 11 trehalose-6-phosphate phosphatase (TPP) genes, and one trehalase gene. Transcript abundance of most …

Regulation Of Mor By Different Abiotic Stresses In Arabidopsis Thaliana, Luke Stepan, Rucha Karve, Anjali Iyer-Pascuzzi

The Summer Undergraduate Research Fellowship (SURF) Symposium

The climate is changing and as a consequence the environment is becoming hotter and drier. How different plants will react to these changes is unknown. Identification of genes involved in stress tolerance can help predict plant-environment interactions and lead to stress tolerant plants. The MOR gene (Modulator Of Root ROS, ROS = Reactive Oxygen Species) in the model plant Arabidopsis thaliana encodes a transcription factor that may regulate stress responses, as mor mutants are drought tolerant. We hypothesized that MOR expression changes in response to different abiotic stress stimuli. We tested MOR expression in response to salt (NaCl), abscisic acid …

Chlorovirus Pbcv-1 Encodes An Active Copper-Zinc Superoxide Dismutase, Ming Kang, Garry A. Duncan, Charles Kuszynski, George Oyler, Jiayin Zheng, Donald F. Becker, James L. Van Etten

James Van Etten Publications

Superoxide dismutases (SODs) are metalloproteins that protect organisms from toxic reactive oxygen species by catalyzing the conversion of superoxide anion to hydrogen peroxide and molecular oxygen. Chlorovirus PBCV-1 encodes a 187-amino-acid protein that resembles a Cu-Zn SOD with all of the conserved amino acid residues for binding copper and zinc (named cvSOD). cvSOD has an internal Met that results in a 165-amino-acid protein (named tcvSOD). Both cvSOD and tcvSOD recombinant proteins inhibited nitroblue tetrazolium reduction of superoxide anion generated in a xanthine-xanthine oxidase system in solution. tcvSOD was chosen for further characterization because it was easier to produce. Recombinant tcvSOD …

An Exploration Of Fern Genome Space, Paul G. Wolf, Emily B. Sessa, D. Blaine Marchant, Fay-Wei Li, Carl J. Rothfels, Erin M. Sigel, Mathew A. Gitzendanner, Clayton J. Visger, Jo Ann Banks, Douglas E. Soltis, Pamela S. Soltis, Kathleen M. Pryer, Joshua P. Der

An Exploration of Fern Genome Space

Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (1X to 2X) for six fern species from the Polypodiales (Ceratopteris …

Expression Of Chlorovirus Mt325 Aquaglyceroporin (Aqpv1) In Tobacco And Its Role In Mitigating Drought Stress, Saadia Bihmidine, Mingxia Cao, Ming Kang, Tala Awada, James L. Van Etten, David Dunigan, Thomas E. Clemente

James Van Etten Publications

Main conclusions A Chlorovirus aquaglyceroporin expressed in tobacco is localized to the plastid and plasma membranes. Transgenic events display improved response to water deficit. Necrosis in adult stage plants is observed.

Aquaglyceroporins are a subclass of the water channel aquaporin proteins (AQPs) that transport glycerol along with other small molecules transcellular in addition to water. In the studies communicated herein, we analyzed the expression of the aquaglyceroporin gene designated, aqpv1, from Chlorovirus MT325, in tobacco (Nicotiana tabacum), along with phenotypic changes induced by aqpv1 expression in planta. Interestingly, aqpv1 expression under control of either a constitutive or …

Functional Genomics Of Maize Endosperm Maturation And Protein Quality, Lingling Yuan

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Maize is one of the most important cereal crops and widely cultivated throughout the world. The study on maize kernel development including protein quality improvement is essential for removing dietary protein deficiency because of the lack of essential amino acids, especially lysine and tryptophan, in maize kernel. Quality Protein Maize (QPM) is a hard kernel variant of the high-lysine mutant, opaque-2. We created opaque QPM variants to identify opaque-2 modifier genes and to investigate deletion mutagenesis combined with Illumina sequencing as a maize functional genomics tool. A K0326Y-QPM deletion mutant, line 107, was null for the 27- and 50-kD …

Mapping Quantitative Trait Loci Associated With Alternaria Leaf Blight Resistance And Elemental Sulfur Tolerance In Melon, James Daley

All Theses

Melon (Cucumis melo L.) production is significantly affected by Alternaria leaf blight, caused by Alternaria cucumerina. Fungicide application is the primary control method; however, this could be mitigated through the increased use of resistant varieties. USDA-ARS breeding line MR-1 has been shown to have a high level of resistance to Alternaria cucumerina. However, molecular markers linked MR-1 Alternaria resistance have yet to be identified. In order in identify QTL associated with Alternaria resistance MR-1 x Ananas Yokneum (AY) derived recombinant inbred lines (RILs) were phenotyped using a modified wounded-leaf assay. Elemental sulfur is an effective fungicide for several foliar pathogens …

Development Of A Quantitative Real-Time Polymerase Chain Reaction (Rt-Pcr) Assay For Plant Species, Kayla Curtis, Heather Miller Coyle

Forensic Science Publications

In order to facilitate optimal plant DNA quantitation and identification, an assay has been developed that uses generic plant PCR primers that amplify a region in the chloroplast genome of plant samples. The assay uses the SYBR green detection dye to detect the PCR product with a universal PCR primer set to the large subunit of ribulose bisphosphate carboxylase, rbcL, but can be used with any of the universal barcode primers for land plants (rbcL, matK, trnH, psbA). Standard dilutions of control wheat DNA of varying concentrations were tested to create a standard curve. Several plant DNA extractions of different …

Phylogeny And Population Genetics Of The Endangered Dwarf Bear-Poppy, Arctomecon Humilis Coville (Papaveraceae) Using Microsatellite Markers, Joshua Simpson

Dissertations, Theses, and Capstone Projects

The genus Arctomecon (Papaveraceae) is comprised of three narrowly endemic rare species that are largely restricted to gypsum soils of the eastern Mojave Desert. The small, remaining populations of these species have become increasingly isolated by urban development and habitat fragmentation. Arctomecon humilis is federally listed as endangered due to its limited distribution within a ~15 km radius of an actively expanding city. Organizations involved with land management and conservation have called for greater insight into the genetic variation and population structure of the remaining subpopulations as they make important decisions regarding where to focus their efforts and resources.

The …

Ether Bridge Formation And Chemical Diversification In Loline Alkaloid Biosynthesis, Juan Pan

Theses and Dissertations--Plant Pathology

Loline alkaloids, found in many grass-Epichloë symbiota, are toxic or feeding deterrent to invertebrates. The loline alkaloids all share a saturated pyrrolizidine ring with a 1-amine group and an ether bridge linking C2 and C7. The steps in biosynthesis of loline alkaloids are catalyzed by enzymes encoded by a gene cluster, designated LOL, in the Epichloë genome. This dissertation addresses the enzymatic, genetic and evolutionary basis for diversification of these alkaloids, focusing on ether bridge formation and the subsequent modifications of the 1-amine to form different loline alkaloids.

Through gene complementation of a natural lolO mutant and comparison …

The Complete Plastid Genome Sequence Of Iris Gatesii (Section Oncocyclus), A Bearded Species From Southeastern Turkey, Carol A. Wilson

Aliso: A Journal of Systematic and Floristic Botany

Iris gatesii is a rare bearded species in subgenus Iris section Oncocyclus that occurs in steppe communities of southeastern Turkey. This species is not commonly cultivated, but related species in section Iris are economically important horticultural plants. The complete plastid genome is reported for I. gatesii based on data generated using the Illumina HiSeq platform and is compared to genomes of 16 species selected from across the monocotyledons. This Iris genome is the only known plastid genome available for order Asparagales that is not from Orchidaceae. The I. gatesii plastid genome, unlike orchid genomes, has little gene loss and rearrangement …

Sudden Aspen Decline Report For Spruce Beetle Epidemic And Aspen Decline Management Response Eis, Jim Worrall, Suzanne Marchetti, Gerald E. Rehfeldt

Aspen Bibliography

Aspen is an important component of GMUG’s forests. Over 288,000 ha (712,000 acres) of aspendominated forest type (TAA) occur across the GMUG (Table 1). Just over half (55%) of the aspen forest type is outside wilderness and roadless areas.

Ficotylus Laselvae N. Sp. (Tylenchomorpha: Anguinidae) Associated With Ficus Colubrinae In Costa Rica, Robin M. Giblin-Davis, Natsumi Kanzaki, Kerrie A. Davies, Weimin Ye, Yongsan Zeng, Barbara J. Center, Alejandro Esquivel, Thomas O. Powers

Department of Plant Pathology: Faculty Publications

Ficotylus laselvae n. sp. was recovered from under the bracts of figs (syconia) of Ficus colubrinae from La Selva, Costa Rica, during a survey of nematode rainforest biodiversity and is described herein. This is only the second report of an association between the nematode suborder Tylenchina and the sycones of figs. Previous reports of most nematode associates of the sycones of figs have been from the lumen and involved transmission by female fig wasp pollinators (Agaonidae) during pollination/oviposition (e.g., Schistonchus and Parasitodiplogaster spp.). The association between F. laselvae n. sp. and Ficus colubrinae may involve an invertebrate host, …

Viruses As Nanoparticles: Structure Versus Collective Dynamics, S. Sirotkin, A. Mermet, M. Bergoin, V. Ward, James L. Van Etten

James Van Etten Publications

In order to test the application of the “nanoparticle” concept to viruses in terms of low-frequency dynamics, large viruses (140–190 nm) were compared to similar-sized polymer colloids using ultra-small-angle x-ray scattering and very-low-frequency Raman or Brillouin scattering. While both viruses and polymer colloids show comparable highly defined morphologies, with comparable abilities of forming self-assembled structures, their respective abilities to confine detectable acoustic vibrations, as expected for such monodisperse systems, differed. Possible reasons for these different behaviors are discussed.