Botany Commons^™

List Of The Federal And State-Listed Rare, Endangered, & Threatened Plants Of California, James P. Smith Jr

Botanical Studies

No abstract provided.

Long-Term Ecological Research In Southern Brazil Grasslands: Effects Of Grazing Exclusion And Deferred Grazing On Plant And Arthropod Communities, Pedro M.A. Ferreira, Bianca O. Andrade, Luciana R. Podgaiski, Amanda C. Dias, Valerio D. Pillar, Gerhard E. Overbeck, Milton De S. Mendonca Jr., Ilsi I. Boldrini

Department of Agronomy and Horticulture: Faculty Publications

Grazing exclusion may lead to biodiversity loss and homogenization of naturally heterogeneous and species-rich grassland ecosystems, and these effects may cascade to higher trophic levels and ecosystem properties. Although grazing exclusion has been studied elsewhere, the consequences of alleviating the disturbance regime in grassland ecosystems remain unclear. In this paper, we present results of the first five years of an experiment in native grasslands of southern Brazil. Using a randomized block experimental design, we examined the effects of three grazing treatments on plant and arthropod communities: (i) deferred grazing (i.e., intermittent grazing), (ii) grazing exclusion and (iii) a control under …

Editorial: New Insights Into Mechanisms Of Epigenetic Modifiers In Plant Growth And Development, Ming Luo, Gabino Ríos, Tomasz Jacek Sarnowski, Shoudong Zhang, Nitin Mantri, Jean-Benoit Charron, Marc Libault

Department of Agronomy and Horticulture: Faculty Publications

In eukaryotic cells, chromatin, a highly dynamic nucleoprotein complex, plays a critical role in controlling gene expression notably by regulating the interaction between transcription factors and regulatory elements. The structure of the chromatin is determined by epigenetic mechanisms, including DNA methylation, histone modifications, and chromatin remodeling. A growing body of evidence indicates that epigenetic regulations are involved in plant adaptation to environmental stresses, and in plant development, including flowering control, fruit and root development, as well as seed maturation and germination. Furthermore, epigenetic mechanisms have the potential to stabilize cell identity and maintain tissue organization. Hence, epigenetic diversity is now …

Yield And Quality In Purple-Grained Wheat Isogenic Lines, Alexey Morgounov, Yasar Karaduman, Beyhan Akin, Sinan Aydogan, Peter Stephen Baenziger, Madhav Bhatta, Vladimir Chudinov, Susanne Dreisigacker, Velu Govindan, Safure Güler, Carlos Guzman, Ajit Nehe, Rachana Poudel, Devin J. Rose, Elena Gordeeva, Vladimir Shamanin, Kemal Subasi, Yuriy Zelenskiy, Elena Khlestkina

Department of Agronomy and Horticulture: Faculty Publications

Breeding programs for purple wheat are underway in many countries but there is a lack of information on the effects of Pp (purple pericarp) genes on agronomic and quality traits in variable environments and along the product chain (grain-flour-bread). This study was based on unique material: two pairs of isogenic lines in a spring wheat cv. Saratovskaya-29 (S29) background differing only in Pp genes and grain color. In 2017, seven experiments were conducted in Kazakhstan, Russia, and Turkey with a focus on genotype and environment interaction and, in 2018, one experiment in Turkey with a focus on grain, flour, and …

The Land Variational Ensemble Data Assimilation Framework: Lavendar V1.0.0, Ewan Pinnington, Tristan Quaife, Amos Lawless, Karina Williams, Tim Arkebauer, David Scoby

Department of Agronomy and Horticulture: Faculty Publications

The Land Variational Ensemble Data Assimilation Framework (LAVENDAR) implements the method of fourdimensional ensemble variational (4D-En-Var) data assimilation (DA) for land surface models. Four-dimensional ensemble variational data assimilation negates the often costly calculation of a model adjoint required by traditional variational techniques (such as 4D-Var) for optimizing parameters or state variables over a time window of observations. In this paper we present the first application of LAVENDAR, implementing the framework with the Joint UK Land Environment Simulator (JULES) land surface model. We show that the system can recover seven parameters controlling crop behaviour in a set of twin experiments. We …

Adaptive Capacity In Ecosystems, David G. Angeler, Hannah Fried-Petersen, Craig R. Allen, Ahjond Garmestani, Dirac L. Twidwell Jr, H.E. Birgé, W. Chuang, V. M. Donovan, T. Eason, C.P. Roberts, S.M. Sundstrom, C.L. Wonkka

Department of Agronomy and Horticulture: Faculty Publications

Understanding the adaptive capacity of ecosystems to cope with change is crucial to management. However, unclear and often confusing definitions of adaptive capacity make application of this concept difficult. In this paper, we revisit definitions of adaptive capacity and operationalize the concept. We define adaptive capacity as the latent potential of an ecosystem to alter resilience in response to change. We present testable hypotheses to evaluate complementary attributes of adaptive capacity that may help further clarify the components and relevance of the concept. Adaptive sampling, inference and modeling can reduce key uncertainties incrementally over time and increase learning about adaptive …

Characterization Of The Transcriptional Divergence Between The Subspecies Of Cultivated Rice (Oryza Sativa), Malachy T. Campbell, Qian Du, Kan Li, Sandeep Sharma, Chi Zhang, Harkamal Walia

Agronomy & Horticulture -- Faculty Publications

Background: Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1).

Results: The transcriptomes of the two subspecies of rice are highly divergent. Japonica have significantly lower expression and genetic diversity relative to Indica, which is likely a consequence of a population bottleneck during Japonica domestication. We leveraged high-density genotypic data and …

Spatial Distribution And Risk Area Assessment Of Aphelenchoides Besseyi Using Geostatistical Approaches In Giridih District Of Jharkhand, India, Sandip Mondal, Matiyar Rahaman Khan, Abhishek Mukherjee

ISI Best Publications

Distributed widely across the rice growing regions of India, the rice leaf and bud nematode (Aphelenchoides besseyi Christie 1942) can cause substantial yield loss in rice. Whitening of leaf tips is the characteristics damage symptom of this nematode and therefore it is popularly referred to as the rice white tip nematode (RWTN). While information on the damage severity of RWTN is available from others parts of the country, to date, no information is available from the state of Jharkhand. In order to generate a detailed information on spatial distribution of this nematode and to identify infestation hotspots, extensive field sampling …

A Preliminary Checklist Of Lichens From Kamiak Butte County Park, Washington State, Emma Sell, Amanda Chandler

2020 Symposium Posters

The semiarid Palouse ecoregion of North America was once dominated by temperate prairies and connects areas of southeast Washington, north-central Idaho, and northeast Oregon. Transformation of nearly all habitats comprising this ecosystem into agricultural lands has drastically reduced extant native grasslands to small, highly fragmented pieces. These land conversion practices, coupled with the subsequent takeover of invasive plant species, have placed the Palouse ecoregion among the most critically endangered ecosystems in the United States, with < 1% of land remaining that is suitable to host native species. The enormous loss of biodiversity across the Palouse has prompted a need for further study regarding a wide variety of organisms. In particular, lichen diversity of the Palouse ecoregion has never been formally characterized, and there are overall very few detailed studies of lichens throughout eastern Washington. To improve knowledge of Palouse lichen diversity, we first reviewed collection data from historical herbarium specimens via the Consortium of North American Lichen Herbaria (CNALH) database. We then collected lichen voucher specimens from Kamiak Butte County Park (KBCP), one of the largest contiguous natural areas within the Palouse ecoregion as its relatively steep, rocky slopes make it ill-suited for agricultural conversion. KBCP consists of 298 acres of mixed Pinus ponderosa (ponderosa pine) and Pseudotsuga menziesii (Douglas fir) forest and native grassland that rises above the surrounding farmland, as well as an east-west ridgeline …

Annonex2embl: Automatic Preparation Of Annotated Dna Sequences For Bulk Submissions To Ena, Michael Gruenstaeudl

Biological Sciences Faculty Publications

The submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research. The surge of novel DNA sequences awaiting database submission due to the application of next-generation sequencing has increased the need for software tools that facilitate bulk submissions. This need has yet to be met with the concurrent development of tools to automate the preparatory work preceding such submissions.The author introduce annonex2embl, a Python package that automates the preparation of complete sequence flatfiles for large-scale sequence submissions to the European Nucleotide Archive. The tool enables the conversion of DNA sequence alignments that are co-supplied …

Vascular Plants Of The Klamath-Siskiyou Region Of California And Oregon: A Numerical Conspectus, James P. Smith Jr

Botanical Studies

No abstract provided.

Vascular Plants Endemic To The Klamath-Siskiyou Region, James P. Smith Jr

Botanical Studies

No abstract provided.

Wood Anatomy Of Argophyllaceae (Asterales): Adaptation In A Small Clade, Sherwin Carlquist, Mark E. Olson

Aliso: A Journal of Systematic and Floristic Botany

Argophyllaceae (Argophyllum, 14 spp.; Corokia, 6 spp.; Lautea, 1 sp.), are shrubs that occur in the southwestern Pacific and eastern Australia. They occur in habitats where moisture is relatively common but dry days and mild frost may occur. The woods of these genera show enough distinctive features to justify their grouping in a single family: perforation plates with 10–20 bars, vessel elements narrow and numerous per mm², imperforate tracheary elements about 50% longer than the vessel elements, axial parenchyma scarce, diffuse, multiseriate rays narrow and heterocellular (upright cells common in uniseriate rays), crystals absent, …

Justicieae Ii: Resolved Placement Of Many Genera And Recognition Of A New Lineage Sister To Isoglossinae, Lucinda A. Mcdade, Carrie A. Kiel, Thomas F. Daniel, Iain Darbyshire

Aliso: A Journal of Systematic and Floristic Botany

We present phylogenetic results for Justicieae, the largest of the major lineages of Acanthaceae. With 300% more sequence data and a similarly increased but also more geographically representative taxon sample compared to the only previous study of the lineage as a whole, we confirm the existence of the Pseuderanthemum Lineage, Isoglossinae, the Tetramerium Lineage and the Justicioid Lineage. To the last three lineages, we add a number of taxa with the goal of advancing our knowledge of genera (e.g., Isoglossa, Rhinacanthus) and of geographic areas (e.g., Malagasy and Asian Acanthaceae). These added taxa are accommodated within the phylogenetic …

The Influences Of Green Infrastructure On Levels Of Somatic And Male-Specific Coliphages At Shadyside Park, Oula Salih

Student Papers and Reports

Microbial contamination is still considered one of the major causes of diminished function and quality of urban rivers and streams in Michigan. Floodplains, a type of green infrastructure used to reduce flooding after large amounts of rainfall, were reported to have variable effects of reducing levels of stormwater runoff within these bodies of water ( Hubbart et al., 2011 ). Viral indicators of fecal contamination in bodies of water include male-specific and somatic coliphages. Water samples from Plaster Creek were collected before and after the floodplain in order to identify the levels of somatic and male-specific coliphages during dry and …

Ms Environmental Biology Capstone Project, Alexandra Sorenson

Regis University Student Publications (comprehensive collection)

• Chapter 1. Literature Review: Invasive Plant Considerations in Alpine Restoration Project Planning
• Chapter 2. Grant Proposal: Success Rates of Native See Germination on Esplanade-Treated Plots
• Chapter 3. Journal Manuscript: Meta-Analysis of Cheatgrass (Bromus Tectorum) Control with Three Commonly Used Herbicides
• Chapter 4. Stakeholder Analysis: Stakeholder Analysis: Recommendation for Herbicide Use at Lippincott Ranch

Biology 4920g: Companion Planting In The Community, Jacquline A. Nathaniel

Community Engaged Learning Final Projects

LIFE*SPIN is a local organization in London, Ontario that provides resources to individuals and families dependent on low income to ultimately break the poverty cycle by encouraging sustainable living and self-sufficiency. For this Seminar in Biology course, Maria Bata and I partnered with LIFE*SPIN to plan and execute a "Seeding Planting Party" to teach children about basic botany, nutrition, and leadership. The following final paper for this seminar discusses the project deliverables and efforts, biological research concerning companion planting, and personal reflection on this experience.

Discovery: The Student Journal Of Dale Bumpers College Of Agricultural, Food And Life Sciences - Volume 21 2020, Several Authors

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Pacvr: Plastome Assembly Coverage Visualization In R, Michael Gruenstaeudl, Nils Jenke

Biological Sciences Faculty Publications

Plastid genomes typically display a circular, quadripartite structure with two inverted repeat regions, which challenges automatic assembly procedures. The correct assembly of plastid genomes is a prerequisite for the validity of subsequent analyses on genome structure and evolution. The average coverage depth of a genome assembly is often used as an indicator of assembly quality. Visualizing coverage depth across a draft genome is a critical step, which allows users to inspect the quality of the assembly and, where applicable, identify regions of reduced assembly confidence. Despite the interplay between genome structure and assembly quality, no contemporary, user-friendly software tool can …

Trichome Micromorphology And Its Significance In The Systematics Of Convolvulus L. (Convolvulaceae), Elham Roudi, Hamed Khodayari, Valiollah Mozaffarian, Shahin Zarre

Turkish Journal of Botany

Trichomes of 35 species of the genus Convolovulus and one species of the genus Calystegia (C. sepium) were investigated using light and scanning electron microscopy. The trichomes show a great variation, which provides valuable data for sections and species delimitation in Convolvulus. Trichomes of Convolvulus are nonglandular, simple, and basifixed or rarely asymmetrically medifixed. Characters of taxonomic interest were the degree of curviness (straight to spiral), orientation relative to the epidermal surface (appressed to erect), and presence of papillae on trichome surface. The trichomes are divided into two basic types: cylindrical and flattened ribbon-like. Our data provide the additional evidence …

Defensive Manoeuvres Of Nhx1 And Sos1 Co/Overexpression In Plant Salt Tolerance, Necla Pehli̇van Gedi̇k, Li Sun, Neelam Mishra

Turkish Journal of Botany

Excessive accumulation of salts is one of the most important factors affecting the production quality of plants. The difficulty to develop salt stress tolerant crops has prevented the security of the global food system. The classical crop breeding approach that uses random mutagenesis/recombination is time-consuming in the face of an ever-increasing human population and extreme weather pattern shifts. Today, technologies introducing foreign genetic material into plants have the best potential to assist in crop breeding improvement due to its high efficiency, accuracy, low risk of off-target effects, and minimal labour compared to classical methods. The notion of Na+/H+ antiporters in …

Molecular Cloning And Enzymatic Characteristics Of Chalcone Isomerase From Rheum Palmatum, Xiaowei Huo, Gang Zhang, Mengmeng Liu

Turkish Journal of Botany

Rheum palmatum has been widely developed in traditional Chinese medicine. One of the major active compounds in R. palmatum is flavonoids. Until now, few genes involved in flavonoid biosynthesis have been isolated from this medicinal plant. In this study, a new chalcone isomerase gene (RpCHI) was cloned from an RNA-seq library of R. palmatum. The 714bp RpCHI cDNA was cloned and sequenced. The RpCHI recombinant protein was successfully overexpressed in a prokaryotic expression system and purified to homogeneity by a nickel-nitrilotriacetic acid (Ni-NTA) prepacked column, and the enzymatic activity was investigated. The results have clarified that RpCHI was assembled into …

Relation Between Soil Salinity And Species Composition Of Halophytic Plant Communities: A Baseline Data Inventory For Wetland Monitoring, Kemal Tulühan Yilmaz, Erhan Akça, Hali̇l Çakan, Yüksel Ünlükaplan, Seli̇m Kapur

Turkish Journal of Botany

Our study sets forth the outcomes of an interdisciplinary project conducted in order to fill the information gap on the management of a wetland ecosystem, in the case of a protected area on the south-eastern coast of Turkey. The hypothesis of the study is that the pattern of species composition reflects soil salinity level and some species can act as relevant indicators. The study aimed to discover a relationship between soil salinity and vegetation composition and establish some indicators useful for monitoring. For this aim, the temporal and spatial changes of soil salinity were monitored and the distribution of coastal …

Effect Of Fungicide Pretreatment On Lipid Peroxidation, Antioxidant Enzyme Systems And Proline Accumulation In Tomato (Lycopersicon Esculentum Mill.) Leaves Under High Temperature Stress, Eli̇f Yüzbaşioğlu

Turkish Journal of Botany

The aim of the present study was to determine the effect of high temperature stress (HT) and to evaluate the protective role of fungicide pretreatment against HT stress in tomato leaves. The oxidative stress was triggered under HT stress through an increase in the content of malondialdehyde (MDA) and hydrogen peroxide (H2O2). Also, it caused a decline in photosynthetic pigments and enhanced the proline in tomato. However, the activities of catalase (CAT; EC 1.11.1.6), peroxidase (POX; EC 1.11.1.7), and glutathione S-transferase (GST; EC.2.5.1.18), as well as ascorbate-glutathione cycle enzymes (APX, EC 1.11.1.11, DHAR, EC 1.8.5.1, MDHAR EC 1.6.5.4, GR; EC …

Factors Associated With Larval Freshwater Drum Annual Peak Density In A Nebraska Irrigation Reservoir, Brett T. Miller, Brian C. Peterson, Keith D. Koupal, Casey W. Schoenebeck

The Prairie Naturalist

Freshwater drum (Aplodinotus grunniens) represent one of the most widely distributed fish species in North America. Identifying biotic and abiotic factors that influence larval freshwater drum densities can improve understanding of early life history. Our objective was to investigate correlations between annual peak density of larval freshwater drum and combinations of five variables (chlorophyll a, growing degree days [GDD], reservoir discharge, turbidity, and cladoceran density) from a longterm (2003–2017) monitoring program in a Nebraska irrigation reservoir. Twenty-eight a priori candidate models were assessed to determine the relative support of explanatory variables associated with annual peak density of larval freshwater drum …

Captive Ring-Necked Pheasant Response To Very High Experimental Doses Of Lead, Travis J. Runia, Alex J. Solem

The Prairie Naturalist

Ingestion of spent lead pellets is a well-documented source of lead exposure in free-ranging birds, although the consequence of lead ingestion varies widely among avian guilds. Ring-necked pheasants (Phasianus colchicus) appear to be less susceptible to lead poisoning than other game birds. Our objectives were to determine survival, liver lead accumulation, and body mass change of 129 captive-raised pheasants in response to being gavage-fed 5, 10, 20, or 40 lead pellets. All pheasants survived the 21-day experiment. Liver-lead levels were positively correlated with the number of lead pellets retained and negatively correlated with beginning body mass. Change in percent body …

Evaluation Of Four Larval Fish Sampling Methods In A Large Midwestern River, Nathan J. Lederman, Anthony R. Sindt, Douglas J. Dieterman, John D. Krenz, Shannon J. Fisher

The Prairie Naturalist

Understanding limitations of larval fish capture gears is critical for developing appropriate sampling protocols and interpreting catch data. We evaluated genera richness, genera diversity, assemblage similarities, abundance indices (i.e., density or catch per unit effort [CPUE]), and sample size requirements between a surface slednet and glow-stick light traps used in 2014 and 2015 and a benthic slednet and light-emitting diode light (LED) traps used in 2015 in the Minnesota River. The surface slednet captured the greatest number of larval fish genera (15) while the LED light trap captured the fewest (1). Similarities of assemblages sampled was highest between surface and …

Comparing Native Bee Communities On Reconstructed And Remnant Prairie In Missouri, Joseph Larose, Elisabeth B. Webb, Deborah Finke

The Prairie Naturalist

The tallgrass prairie of North America is an imperiled ecosystem that has been the subject of considerable restoration effort and research in the past two decades. While native prairie plant species are purposely introduced during restoration, prairie invertebrates, including native bees (Anthophila), are not and must colonize from surrounding remnants. Prairie restorations may not support the same bee communities as remnant prairies because of habitat differences and dispersal limitations. We sampled native bees on reconstructed and remnant prairies in Missouri in the summers of 2016 and 2017 and compared the communities by evaluating species richness, diversity, and community composition. We …

Greater Prairie-Chickens And Sharp-Tailed Grouse Have Similarly High Nest Survival In The Nebraska Sandhills, Larkin Powell, Walter Schacht, Julia P. Ewald, Kathryn R. Mccollum

The Prairie Naturalist

The ranges of two native galliform species overlap in the Nebraska Sandhills, the largest contiguous grassland in North America. We monitored nests of greater prairie-chickens (Tympanuchus cupido) and sharp-tailed grouse (Tympanuchus phasianellus) in Cherry County, Nebraska, in 2015 and 2016. Our objectives were to 1) compare daily probability of nest survival between species, 2) evaluate vegetation structure at nests for potential effects on nest survival, 3) compare nest site topography between species, and 4) use a simple model of breeding season success to evaluate the potential for stable populations at our study sites. We captured and …

Leaf-Tip Morphology Does Not Support Species Status For The Seagrass Halodule Beaudettei In Florida, Usa, Michael E. Wheeler, Bradley T. Furman, Margaret O. Hall

Gulf and Caribbean Research

No abstract provided.