Digital Commons Network^™

Complete Genome Sequence Of Mesorhizobium Australicum Type Strain (Wsm2073t), Wayne Reeve, Kemanthi G. Nandasena, Ronald J. Yates, Ravi P. Tiwari, Graham William O'Hara, Mohamed Ninawi, Wei Gu, Lynne Goodwin, Chris Detter, Roxanne Tapia, Cliff Han, Alex Copeland, Konstantinos Liolios, Amy Chen, Victor Markowitz, Amrita Pati, Konstantinos Mavromatis, Tanja Woyke, Nikos Kyrpides, Natalia Ivanova, John Gregory Howieson

Grain and Other Field Crops Research Articles

Mesorhizobium australicum strain WSM2073T was isolated from root nodules on the pasture legume Biserrula pelecinus growing in Australia in 2000. This aerobic, motile, gram negative, non-spore-forming rod is poorly effective in N2 fixation on B. pelecinus and has gained the ability to nodulate B. pelecinus following in situ lateral transfer of a symbiosis island from the original inoculant strain for this legume, Mesorhizobium ciceri bv. biserrulae WSM1271. We describe that the genome size of M. australicum strain WSM2073T is 6,200,534 bp encoding 6,013 protein-coding genes and 67 RNA-only encoding genes. This genome does not contain any plasmids but has a …

Genome Sequence Of The Lebeckia Ambigua-Nodulating “Burkholderia Sprentiae” Strain Wsm5005ᵀ, Wayne Reeve, Sofie E. De Meyer, Jason Terpolilli, Vanessa Melino, Julie Kaye Ardley, Tian Rui, Ravi P. Tiwari, John Gregory Howieson, Ronald J. Yates, Graham William O'Hara, Megan Lu, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Chia-Lin Wei, Marcel Huntemann, James Han, I-Min Chen, Konstantinos Mavromatis, Victor Markowitz, Ernest Szeto, Natalia Ivanova, Natalia Mikhailova, Galina Ovchinikova, Ioanna Pagani, Amrita Pati, Lynne Goodwin, Lin Peters, Sam Pitluck, Tanja Woyke, Nikos Kyrpides

Grain and Other Field Crops Research Articles

“Burkholderia sprentiae” strain WSM5005T is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated in Australia from an effective N2-fixing root nodule of Lebeckia ambigua collected in Klawer, Western Cape of South Africa, in October 2007. Here we describe the features of “Burkholderia sprentiae” strain WSM5005T, together with the genome sequence and its annotation. The 7,761,063 bp high-quality-draft genome is arranged in 8 scaffolds of 236 contigs, contains 7,147 protein-coding genes and 76 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

Toward Target 2 Of The Global Strategy For Plant Conservation: An Expert Analysis Of The Puerto Rican Flora To Validate New Streamlined Methods For Assessing Conservation Status, James S. Miller, Gary A. Krupnick, Hannah Stevens, Holly Porter-Morgan, Brian Boom, Pedro Acevedo-Rodríguez, James Ackerman, Duane Kolterman, Eugenio Santiago, Christian Torres, Jeanine Velez

Publications and Research

Target 2 of the 2020 Global Strategy for Plant Conservation (GSPC) calls for a comprehensive list of the world's threatened plant species. The lack of such a list is one of the greatest impediments to protecting the full complement of the world's plant species, and work to achieve this has been slow. An efficient system for identifying those species that are at risk of extinction could help to achieve this goal in a time frame sensitive to today's conservation needs. Two systems that efficiently use available data to assess conservation status were tested against a provisional International Union for Conservation …

Census And Mapping Of Chorro Creek Bog Thistle In Reservoir Canyon, San Luis Obispo, Ca, Tyler Michael Lutz

Biological Sciences

Chorro Creek bog thistle (Cirsium fontinale var. obispoense) is a federally endangered variety of Fountain thistle endemic to western San Luis Obispo County. The U.S. Fish and Wildlife Service knows of nineteen populations, many with multiple colonies. A population was discovered in the Reservoir Canyon Natural Reserve in 2001, but has not been monitored or described since the time of its discovery. In fall of 2013, a census of the population was performed, the four colonies were mapped, and a floristic survey was conducted. A field experiment was initiated to determine if reducing the riparian canopy coverage can …

Effects Of Rain And Simulated Rain On Deoxynivalenol Levels In Grain And Chaff Of Winter Wheat With Fusarium Head Blight, Manoj Kumar Pun

Graduate Theses and Dissertations

Wheat grain affected by Fusarium head blight (FHB) contains the mycotoxin deoxynivalenol (DON) that is harmful to humans and animals. Reducing the amount of DON in grain is the goal of management practices for FHB so it is important to understand the factors affecting DON in grain. Some studies on the effects of late-season moisture found increases in DON while others found decreases due to leaching. The objectives of this study were to determine effects of late-season rain and misting on DON concentration in wheat spike tissues and to quantify the amount of DON leached from spikes. Field experiments were …

Forage News [2013-12], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

• Thank You Kentucky Farmers
• Forages at KCA
• Forage Variety Reports Now Available
• Southern Forages Translated Into Spanish
• Small Ruminant Grazing Conference to be held in Lexington on February 1, 2014
• AFGC Annual Conference - Memphis, TN
• 34th Kentucky Alfalfa Conference
• Updated Analysis on Fungicides and Alfalfa

Dual Capture Of A Piñon Deer Mouse And A Silky Pocket Mouse Resulting In Consumption Of The Smaller Animal, Jon C. Pigage, Roger D. Peyton

The Prairie Naturalist

Intraspecific dual captures of rodents are uncommon, but not rare. There are several reports of brown rats (Rattus norvegicus), white-footed deer mice (Peromyscus leucopus), North American deer mice (P. maniculatus), western harvest mice (Reithrodontomys megalotis) and meadow voles (Microtus pennsylvanicus) caught simultaneously in the same trap (i.e. a door-closing live-trap; Davis 1955, Getz 1961, Blaustein and Rothstein 1978, Jenkins and Llewellyn 1981, Novak 1983). Some reports are incidental whereas others are interpreted as social associations or bonding between conspecifics. Interspecific dual captures are rarely reported in the literature. The earliest report of …

Whooping Cranes Consume Plains Leopard Frogs At Migratory Stopover Sites In Nebraska, Keith Geluso, Brad T. Krohn, Mary J. Harner, Michael J. Assenmacher

The Prairie Naturalist

Whooping cranes (Grus americana) currently consist of a single, wild population that migrates annually from breeding grounds at Wood Buffalo National Park, Canada, to wintering grounds on and around the Aransas National Wildlife Refuge along the Texas coast, USA (NRC 2005). This population reached a low of less than 20 individuals in 1941 (Allen 1952) but has rebounded to over 250 individuals (Chavez-Ramirez and Wehtje 2012, Gil-Weir et al. 2012). Whooping cranes migrate approximately 4,000 km each spring and autumn, traversing much of the North American Great Plains (Lewis 1995) and periodically landing along rivers, wetlands, and other …

The Influence Of Hydrogeomorphology, Soil Redox Conditions, And Salinity On The Spatial Zoning Of Saltgrass, Salt Rush, And Cattails In Scotts Creek Marsh, Swanton Pacific Ranch, Ca, Mark D. Gormley

Master's Theses

Scotts Creek Marsh (SCM) is a small coastal wetland ecosystem in Davenport, CA. The vegetation of SCM is dominated by three halophytic zones comprised of saltgrass, salt rush, cattails. The objectives of the study were (i) to investigate the variables that influence the zoning of the three dominant halophyte communities in SCM and (ii) to the test the effectiveness of Indicator of Reduction in Soil (IRIS) tubes to indicate the reduction of S. The study examined the following parameters from April 6 to July 21, 2013: (i) the HGM of Scotts Creek Marsh, (ii) soil oxidation and reduction (redox) conditions, …

Influence Of Poultry-Litter Biochar On Early-Season Growth In Cotton, Taylor Dayne Coomer

Crop, Soil and Environmental Sciences Undergraduate Honors Theses

Cotton (Gossypium hirsutum L.) is known for being sensitive to cool, wet soils, especially in the early stages of growth. Amendments such as soil fertilizers and manures added to soil can aid cotton seedlings in development and nutrient uptake. However, soil fertilizers and manures can be costly and detrimental to the environment, and alternatives such as the addition of biochar have been considered. Biochar is a high-carbon, nutrient-rich charcoal produced from organic matter that has gone through pyrolysis. Biochar has been shown to improve plant yield, soil microbial response, soil structure, soil cation-exchange capacity, and water-use efficiency, however research on …

The Imperative Of Conserving California's Foothill Oak Woodlands, Lauren Phillips

Social Sciences

No abstract provided.

Southeast South Dakota Experiment Farm Annual Progress Report: 2013, Agricultural Experiment Station

Agricultural Experiment Station and Research Farm Annual Reports

The 2013 season brought some welcome relief from the drought of the previous year. Our yields were much improved, averaging 175 bushel per acre for corn and 50 bu/ac for soybeans . Several new developments were undertaken at the farm in the 2013 season. We established an area for research where grazing is integrated with crop production – so we now have some scope to conduct research looking at the effects of how grazing crop residues, cover crops and annual forages impacts crop productivity and soil health. Working with Chris Hay from the Ag. and Biological Systems Engineering Dept. at …

A Seasonal, Density-Dependent Model For The Management Of An Invasive Weed, Esther Shyu, Eleanor A. Pardini, Tiffany M. Knight, Hal Caswell

Biology Faculty Research

The population effects of harvest depend on complex interactions between density dependence, seasonality, stage structure, and management timing. Here we present a periodic nonlinear matrix population model that incorporates seasonal density dependence with stage-selective and seasonally selective harvest. To this model, we apply newly developed perturbation analyses to determine how population densities respond to changes in harvest and demographic parameters. We use the model to examine the effects of popular control strategies and demographic perturbations on the invasive weed garlic mustard (Alliaria petiolata). We find that seasonality is a major factor in harvest outcomes, because population dynamics may …

Molecular And Biochemical Mechanisms Of Pathogenesis In The Maize Foliar Pathogen Cercospora Zeae-Maydis, Winfred-Peck Dorleku

Graduate Theses and Dissertations

GLS is a serious foliar disease of maize, a major staple crop grown commercially in the USA for both human and animal feed production, and increasingly, for ethanol production. The disease is caused by two Cercospora species, C. zeae-maydis and C. zeina, both of which infect maize in the USA and in other parts of the world, with yield losses potentially greater than 50%, depending on local conditions. In culture, C. zeae-maydis produces a phytotoxic, host non-specific perylenequinone, cercosporin, and abscisic acid (ABA), for which there is no known pathological or physiological function in the fungus. Experimental evidence indicates …

A Northward Range Extension Of The Hispid Cotton Rat (Sigmodon Hispidus) In Missouri, Cody W. Thompson, Elmer J. Finck

The Prairie Naturalist

The hispid cotton rat (Sigmodon hispidus) is a widely distributed rodent with a geographic range extending from north-central Mexico to southern Nebraska and central Virginia and from southeastern Arizona east to Florida (Carleton et al. 1999, Peppers and Bradley 2000, Wilson and Reeder 2005) with isolated populations in Arizona (Bradley et al. 2012) and California (Clark 1972). Range expansions for the species have been well documented (Clark 1972, Farney 1975, Benedict et al. 2000, Wright et al. 2010, Wills et al. 2011). The majority of these range expansions have occurred across the Central Plains during the 20th century …

Evaluation Of Three Nest Searching Methods For Ring-Necked Pheasant, Jeffery W. Stackhouse, Kevin K. Sedivec, Benjamin A. Geaumont

The Prairie Naturalist

Ring-necked pheasant (Phasianus colchicus) are a highly sought after game bird and as such, much research has been conducted regarding their ecology (Warner 1981, Trautman 1982, Johnson and Knue 1989). Perhaps the most investigated aspect of pheasant ecology is the species’ reproductive season (e.g. Linder et al. 1960, Dumke and Pils 1979, Leif 1994) with many studies focusing on nesting habitat (Baskett 1947, Clark et al. 1999). Results from previous research have acknowledged the difficulty associated with locating pheasant nests in their preferred cover types (Hanson 1970, Evrard 2000). Studies of pheasant nesting ecology have been based on …

Associations Between Iron Concentration And Productivity In Montane Streams Of The Black Hills, South Dakota, Cari-Ann Hayer, Benjamin M. Holocmb, Steven R. Chipps

The Prairie Naturalist

Iron is an important micronutrient found in aquatic systems that can influence nutrient availability (e.g. phosphorus) and primary productivity. In streams, high iron concentrations often are associated with low pH as a result of acid mine drainage, which is known to affect fish and invertebrate communities. Streams in the Black Hills of South Dakota are generally circumneutral in pH, yet select streams exhibit high iron concentrations associated with natural iron deposits. In this study, we examined relationships among iron concentration, periphyton biomass, macroinvertebrate abundance, and fish assemblages in four Black Hills streams. The stream with the highest iron concentration (~5 …

Positioning An Innovative Flame-Weeding Technology Into Crop Production, Strahinja V. Stepanovic

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

Propane flaming has a potential to be utilized for effective PRE and POST weed control in both organic and conventional farming systems. Field studies were conducted at the Haskell Agricultural Laboratory of the University of Nebraska in 2010, 2011, and 2012 to: (1) describe dose–response curves for propane when flaming selected weed species at different growth stages, (2) determine corn and soybean tolerance to single and repeated flaming by utilizing the equipment designed to selectively flame weeds in row crops with torches positioned parallel to the crop row, and (3) determine the effectiveness of flaming and cultivation for weed control …

Salamander Colonization Of Chase Lake, Stutsman County, North Dakota, David M. Mushet, Kyle I. Mclean, Craig A. Stockwell

The Prairie Naturalist

Salt concentrations in lakes are dynamic. In the western United States, water diversions have caused significant declines in lake levels resulting in increased salinity, placing many aquatic species at risk (Galat and Robinson 1983, Beutel et al. 2001). Severe droughts can have similar effects on salt concentrations and aquatic communities (Swanson et al. 2003). Conversely, large inputs of water can dilute salt concentrations and contribute to community shifts (Euliss et al. 2004).

Chase Lake is a large, shallow, alkaline lake in east-central North Dakota most famously known for supporting one of the largest breeding colonies of the American white pelican …

Relationships Among Walleye Mercury, Selenium, Stable Isotopes, Size And Age, Mark J. Fincel, Robert P. Hanten, Shannon Minerich

The Prairie Naturalist

Bioaccumulation of mercury is well-documented in aquatic ecosystems and occurs as mercury is accumulated and passed up food chains (Kidd et al. 1995, Atwell et al. 1998, Downs et al. 1998). Trophic level correlations have been widely reported for mercury (Snodgrass et al. 2000) and other metals (Barron 1995). Generally, within a system, carnivores have the highest mercury loadings, omnivores intermediate and herbivores the lowest (Phillips et al. 1980). However, little research has focused on the differences in mercury bioaccumulation for a single species that ranges across multiple trophic levels (Burger et al. 2001).

Stable isotope analysis has expanded the …

Mechanisms For Regulation Of Plant Kinesins, Anindya Ganguly, Ram Dixit

Biology Faculty Research

Throughout the eukaryotic world, kinesins serve as molecular motors for the directional transport of cellular cargo along microtubule tracks. Plants contain a large number of kinesins that have conserved as well as specialized functions. These functions depend on mechanisms that regulate when, where and what kinesins transport. In this review, we highlight recent studies that have revealed conserved modes of regulation between plant kinesins and their non-photosynthetic counterparts. These findings lay the groundwork for understanding how plant kinesins are differentially engaged in various cellular processes that underlie plant growth and development.

Long-Term Residue And Water Management Effects On Soil Respiration And Soil Aggregate Stability In A Wheat-Soybean, Double-Crop System In Eastern Arkansas, Sharon Faye Smith

Graduate Theses and Dissertations

Sustainability in agriculture is paramount to assuring continued production from our most naturally fertile soils. Storing carbon (C) in soil as organic matter through sustainable agricultural management practices can both remove atmospheric C and improve soil quality. The objective of this study was to evaluate the long-term effects of water management (irrigation and dryland), residue management [burn and no-burn, conventional (CT) and no-tillage (NT)] and residue/fertility level (high and low) on soil respiration and aggregate stability in a wheat- (Triticum aestivum L.) soybean [Glycine max (L.) Merr.], double-crop system in a silt-loam soil (Aquic Fraglossudalf) in the Mississippi River Delta …

Tracking The Cellulolytic Activity Of Clostridium Thermocellum Biofilms, Alexandru Dumitrache, Gideon M. Wolfaardt, David Allen, Steven N. Liss, Lee R. Lynd

Dartmouth Scholarship

Microbial cellulose conversion by Clostridium thermocellum 27405 occurs predominantly through the activity of substrate-adherent bacteria organized in thin, primarily single cell-layered biofilms. The importance of cellulosic surface exposure to microbial hydrolysis has received little attention despite its implied impact on conversion kinetics.

Response Of Near-Isogenic Sorghum Lines, Differing At The P Locus For Plant Colour, To Grain Mould And Head Smut Fungi, Deanna L. Funnell-Harris, L. K. Prom, Scott E. Sattler, Jeffrey F. Pedersen

Department of Plant Pathology: Faculty Publications

Leaves and stalks of many sorghum genotypes accumulate dark red or purple pigments upon wounding while some plants, called ‘tan,’ do not. Grains with unpigmented ‘white’ pericarps grown on tan plants are more desirable for food. The hypothesis tested was that pigments in plants protected grain against the panicle diseases grain mould and head smut. Near-isogenic tan or purple plant color genotypes with white grain were planted at Lincoln and Ithaca, NE and Corpus Christi, TX. The field grown grain was plated onto semi-selective media to detect the presence of grain colonisation by mould genera Alternaria, Fusarium and Curvularia. …

Early Flowering Mutant Chia And Uses Thereof, David Hildebrand, Watchareewan Jamboonsri, Timothy Phillips

Plant and Soil Sciences Faculty Patents

The invention relates to early flowering Chia (Salvia hispanica L.) strains that are suitable for culturing in a temperate area for seed production. Mutations are introduced to wild type chia seeds. Desired mutant progeny having normal appearance and an altered flora organ development is subsequently identified.

An Intergenic Region Shared By At4g35985 And At4g35987 In Arabidopsis Thaliana Is A Tissue Specific And Stress Inducible Bidirectional Promoter Analyzed In Transgenic Arabidopsis And Tobacco Plants, Joydeep Banerjee, Dipak K. Sahoo, Nrisingha Dey, Robert Houtz, Indu B. Maiti

Kentucky Tobacco Research and Development Center Faculty Publications

On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985) are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS) in both orientations in transient tobacco protoplast and …

Microtubule Severing At Crossover Sites By Katanin Generates Ordered Cortical Microtubule Arrays In Arabidopsis, Quan Zhang, Erica Fishel, Tyler Bertroche, Ram Dixit

Biology Faculty Research

Highlights

• Severing primarily depolymerizes the overlying CMT at crossover sites
• Severing probability increases nonlinearly with crossover time
• Katanin localizes to crossover sites and is required for severing
• Loss of katanin activity prevents the formation of coaligned CMT arrays

Summary
The noncentrosomal cortical microtubules (CMTs) of land plants form highly ordered parallel arrays that mediate cell morphogenesis by orienting cellulose deposition [1, 2 and 3]. Since new CMTs initiate from dispersed cortical sites at random orientations [4], parallel array organization is hypothesized to require selective pruning of CMTs that are not in the dominant orientation. Severing of CMTs at crossover sites …

Forage News [2013-11], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

• Jimmy Ray May, Sr. 1943-2013
• KFGC Awards
• 2013 KFGC Forage Spokesperson Contest
• Small Ruminant Grazing Conference to be held in Lexington on February 1, 2014
• Grass - A Pandrama in Words
• Grass-based Health
• Timing of Grazing Effects on Pasture Productivity
• Hay Bale Fires Still a Threat
• Minnesota Dairy Named Forage Superbowl Grand Champ

The System I And System Iii Holocytochrome C Synthases In Cytochrome C Biogenesis, Brian San Francisco

All Theses and Dissertations (ETDs)

Cytochromes c are proteins that are involved in important redox reactions in organisms from every kingdom of life. C-type cytochromes, uniquely, possess a covalently bound heme. Since cytochromes c are assembled at their site(s) of function: outside of the cytoplasmic membrane in bacteria, in the chloroplast lumen, or in the mitochrondrial intermembrane space), their assembly poses unique challenges to heme trafficking and post translational modification. Three major systems exist in nature for cytochrome c assembly, termed systems I, II, and III. Using recombinant Escherichia coli, aspects of systems I and III were analyzed, with an emphasis on the synthase protein(s) …

Diffuse Migratory Connectivity In Two Species Of Shrubland Birds: Evidence From Stable Isotopes, Steven T. Knick, Matthias Leu, John T. Rotenberry, Steven E. Hanser, Kurt A. Fesenmyer

Articles

Connecting seasonal ranges of migratory birds is important for understanding the annual template of stressors that influence their populations. Brewer’s sparrows (Spizella breweri) and sagebrush sparrows (Artemisiospiza nevadensis) share similar sagebrush (Artemisia spp.) habitats for breeding but have different population trends that might be related to winter location. To link breeding and winter ranges, we created isoscapes of deuterium [stable isotope ratio (δ) of deuterium; δ ²H] and nitrogen (δ ¹⁵N) for each species modeled from isotope ratios measured in feathers of 264 Brewer’s and 82 sagebrush sparrows and environmental …