Biology Commons^™

Sterol Biosynthesis In Four Green Algae: A Bioinformatic Analysis Of The Ergosterol Versus Phytosterol Decision Point, Adam Voshall, Nakeirah T.M. Christie, Suzanne L. Rose, Maya Khasin, James L. Van Etten, Jennifer E. Markham, Wayne R. Riekhof, Kenneth Nickerson

School of Biological Sciences: Faculty Publications

Animals and fungi produce cholesterol and ergosterol, respectively, while plants produce the phytosterols stigmasterol, campesterol, and bsitosterol in various combinations. The recent sequencing of many algal genomes allows the detailed reconstruction of the sterol metabolic pathways. Here, we characterized sterol synthesis in two sequenced Chlorella spp., the free-living C. sorokiniana, and symbiotic C. variabilis NC64A. Chlamydomonas reinhardtii was included as an internal control and Coccomyxa subellipsoidea as a plant-like outlier. We found that ergosterol was the major sterol produced by Chlorella spp. and C. reinhardtii, while C. subellipsoidea produced the three phytosterols found in plants. In silico analysis …

Inaction On Lead Despite The Relevant Knowledge: Predictors, Covariates, And Outreach Implications, Alessandra Rossi, Bernabas Wolde, Pankaj Lal, Melissa Harclerode

Department of Biology Faculty Scholarship and Creative Works

Testing residential soil and paint for lead provides actionable information. By showing where and how much lead exists on the residence, it allows one to quantify risk and determine the best ways to reduce exposure along with the corresponding health and financial costs. For these reasons, several federal and state programs offer outreach to audiences on the benefits of testing residential soil and paint for lead. Not all individuals who know about lead’s adverse health effects, however, test their residence for lead, potentially limiting the actionable information that could have helped to reduce their exposure. Such individuals represent a challenge …

Inheritability Of Ciprofloxacin-Induced Mitochondrial Mutations From Parental To Offspring Generation Using Quantitative Polymerase Chain Reaction, Rose Mccoy

Honors Theses

In all eukaryotes, mitochondria are known as the powerhouse of the cell (Siekevitz, 1957). In plants, however, their mitochondrial genome is especially strange. Plant mitochondrial genomes are extremely large and contain both linear and circular subgenomic DNA fragments. Plant mitochondrial genomes undergo a significant amount of mutations in the form of rearrangements. However, it is not known how often these rearrangements are inherited by the next generation. It is thought that plant cells that are still dividing have higher rates of DNA repair, such as double-strand break repair, to ensure the quality of that plant lineage. As follows, it is …

Mechanistic Insights Into Strigolactone Biosynthesis, Signaling And Regulation During Plant Growth And Development, Kaiser Iqbal Wani, Andleeb Zehra, Sadaf Choudhary, M Naeem, M. Masroor A. Khan, Christian Danve Castroverde, Tariq Aftab

Biology Faculty Publications

Strigolactones (SLs) constitute a group of carotenoid-derived phytohormones with butenolide moieties. These hormones are involved in various functions, including regulation of secondary growth, shoot branching and hypocotyl elongation, and stimulation of seed germination. SLs also control hyphal branching of arbuscular mycorrhizal (AM) fungi, and mediate responses to both abiotic and biotic cues. Most of these functions stem from the interplay of SLs with other hormones, enabling plants to appropriately respond to changing environmental conditions. This dynamic interplay provides opportunities for phytohormones to modulate and augment one another. In this article, we review our current mechanistic understanding of SL biosynthesis, receptors …

Optimal Allocation Of Two Resources In Annual Plants, David Mcmorris

Department of Mathematics: Dissertations, Theses, and Student Research

The fitness of an annual plant can be thought of as how much fruit is produced by the end of its growing season. Under the assumption that annual plants grow to maximize fitness, we can use techniques from optimal control theory to understand this process. We introduce two models for resource allocation in annual plants which extend classical work by Iwasa and Roughgarden to a case where both carbohydrates and mineral nutrients are allocated to shoots, roots, and fruits in annual plants. In each case, we use optimal control theory to determine the optimal resource allocation strategy for the plant …

Genetic Analysis Of Flower Color Differences Between A Hummingbird-Pollinated And A Self-Pollinated Monkeyflower (Mimulus) Species, Caitlin Foster

University Scholar Projects

Flower color plays an important role in pollinator discrimination and speciation. Understanding the genetic contributions to flower color differences between two closely related species, Mimulus cardinalis and Mimulus parishii, can improve understanding of how they developed different pollination syndromes and diverged from a recent common ancestor. M. cardinalis is hummingbird-pollinated and has large, bright red flowers while M. parishii is self-pollinated and has small, pale pink flowers. An F2 hybrid population between these two species was created to establish a platform for analysis of the genetic architecture controlling the differences in anthocyanin pigmentation. Statistical analysis of anthocyanin concentration distribution …

Diversity, Function And Regulation Of Cell Surface And Intracellular Immune Receptors In Solanaceae, Jong Hum Kim, Christian Castroverde

Biology Faculty Publications

The first layer of the plant immune system comprises plasma membrane-localized receptor proteins and intracellular receptors of the nucleotide-binding leucine-rich repeat protein superfamily. Together, these immune receptors act as a network of surveillance machines in recognizing extracellular and intracellular pathogen invasion-derived molecules, ranging from conserved structural epitopes to virulence-promoting effectors. Successful pathogen recognition leads to physiological and molecular changes in the host plants, which are critical for counteracting and defending against biotic attack. A breadth of significant insights and conceptual advances have been derived from decades of research in various model plant species regarding the structural complexity, functional diversity and …

De Novo Sequencing And Analysis Of Salvia Hispanica Tissue-Specific Transcriptome And Identification Of Genes Involved In Terpenoid Biosynthesis, James Wimberley, Joseph Cahill, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Salvia hispanica (commonly known as chia) is gaining popularity worldwide as a healthy food supplement due to its low saturated fatty acid and high polyunsaturated fatty acid content, in addition to being rich in protein, fiber, and antioxidants. Chia leaves contain plethora of secondary metabolites with medicinal properties. In this study, we sequenced chia leaf and root transcriptomes using the Illumina platform. The short reads were assembled into contigs using the Trinity software and annotated against the Uniprot database. The reads were de novo assembled into 103,367 contigs, which represented 92.8% transcriptome completeness and a diverse set of Gene Ontology …

A Rubric For Grading Laboratory Research Paper Writing Assignments In Plant Biology, David Rhoads

Q2S Enhancing Pedagogy

Writing a research paper based on a course laboratory research project is challenging for many students. In addition to providing a 3 page summary on how to write the paper (with details on the type and format of the content to be included for each section), I provide a detailed grading rubric that also contains an outline of the topics to be included in the paper. This rubric was further refined in the Winter 2020 (Q2S) Writing Intensive Faculty Learning Community (WI FLC).

The Development Of Crassulacean Acid Metabolism (Cam) Photosynthesis In Cotyledons Of The C4 Species, Portulaca Grandiflora (Portulacaceae), Lonnie J. Guralnick, Kate E. Gilbert, Diana Denio, Nicholas Antico

Arts & Sciences Faculty Publications

Portulaca grandiflora simultaneously utilizes both the C₄ and Crassulacean acid metabolism (CAM) photosynthetic pathways. Our goal was to determine whether CAM developed and was functional simultaneously with the C₄ pathway in cotyledons of P. grandiflora. We studied during development whether CAM would be induced with water stress by monitoring the enzyme activity, leaf structure, JO₂ (rate of O₂ evolution calculated by fluorescence analysis), and the changes in titratable acidity of 10 and 25 days old cotyledons. In the 10 days old cotyledons, C₄ and CAM anatomy were evident within the leaf tissue. The cotyledons showed …

Seed Source Regions Drive Fitness Differences In Invasive Macrophytes, Morgane B. Gillard, Rebecca E. Drenovsky, Gabrielle Thiébaut, Michèle Tarayre, Caryn J. Futrell, Brenda J. Grewell

2020 Faculty Bibliography

Premise Worldwide, ecosystems are threatened by global changes, including biological invasions. Invasive species arriving in novel environments experience new climatic conditions that can affect their successful establishment. Determining the response of functional traits and fitness components of invasive populations from contrasting environments can provide a useful framework to assess species responses to climate change and the variability of these responses among source populations. Much research on macrophytes has focused on establishment from clonal fragments; however, colonization from sexual propagules has rarely been studied. Our objective was to compare trait responses of plants generated from sexual propagules sourced from three climatic …

Small-Scale Population Connectivity And Genetic Structure In Canada Thistle (Cirsium Arvense), Mahboubeh Hosseinalizadeh Nobarinezhad, Lavanya Challagundla, Lisa E. Wallace

Biological Sciences Faculty Publications

Premise of research. Population connectivity, the exchange of genes among geographically separated subpopulations, is thought to be a key process for the maintenance of genetic diversity and the survival of invasive species in newly colonized areas. Plant populations' degree of genetic connectivity, which occurs via pollen and seed dispersal, leads to different degrees of genetic admixture and genetic structure. Environmental barriers and differential selection pressures that are variable across time and space tend to alter genetic structure within and among populations via restriction or facilitation of gene flow. Canada thistle, an invasive species of the United States and Canada, is …

Allopatric Speciation In Asia Contributed To The Diversity Anomaly Between Eastern Asia And Eastern North America: Evidence From Anchored Phylogenomics Of Stewartia (Theaceae), Jianhua Li, Peter Del Tredici, Alan R. Lemmon, Emily Moriarty Lemmon, Yunpeng Zhao, Chengxin Fu

Faculty Publications

Premise of research. The disjunct distribution of plant genera between eastern Asia (EA) and eastern North America (ENA) has long attracted the attention of biologists and biogeographers. For most genera that have been studied, there are more species in EA than in ENA, and the diversity anomaly may have resulted from the greater physiographical heterogeneity in EA than in ENA in conjunction with climate and sea level changes. However, few empirical studies have explicitly tested the association between species diversity and allopatric speciation events. The genus Stewartia (Theaceae) displays this diversity anomaly, with two species in ENA and 21 …

Effects Of Increased Precipitation On The Life History Of Spring- And Autumn-Germinated Plants Of The Cold Desert Annual Erodium Oxyrhynchum (Geraniaceae), Yanfeng Chen, Xiang Shi, Lingwei Zhang, Jerry M. Baskin, Carol C. Baskin, Huiliang Liu, Daoyuan Zhang

Biology Faculty Publications

Future increased precipitation in cold desert ecosystems may impact annual/ephemeral plant species that germinate in both spring and autumn. Our primary aim was to compare the life history characteristics of plants from spring-germinating (SG) and autumn-germinating (AG) seeds of Erodium oxyrhynchum. Plants in field plots with simulated increases in precipitation of 0, 30 and 50 % in spring and summer were monitored to determine seedling survival, phenology, plant size, seed production and biomass accumulation and allocation. Germination characteristics were determined in the laboratory for seeds produced by plants in all increased precipitation treatments. Increased precipitation in spring significantly improved survival …

Combating Drug Resistance - Comparison Of The Antibiotic Effect Of Hydrastis Canadensis Extract And Pure Berberine Via Minimum Inhibitory Concentration Assay, William Luke Scott, Timothy D. Trott

Research in Biology

Herbal medicines are a melee of complex organic chemicals, making it difficult to ascertain their direct mechanism of action. In contrast to mainstream pharmaceuticals, it is argued that herbal medicines are effective because of multiple constituents working synergistically. The complexity of herbal medicines may give them advantages over simpler pharmaceuticals in combating antibiotic resistant microbes, but these advantages can be difficult to quantitate. Popular literature frequently espouses the healing properties of herbal medicines, but many of these claims are not scientifically supported. Many gains could be realized in public health and medicine if more research was aimed at validating / …

A Stimulatory Role For Cytokinin In The Arbuscular Mycorrhizal Symbiosis Of Pea, Dane M. Goh, Marco Cosme, Anna B. Kislala, Samantha Mulholland, Zakaria M.F. Said, Lukáš Spíchal, R.J. Neil Emery, Stéphane Declerck, Frédérique C. Guinel

Biology Faculty Publications

The arbuscular mycorrhizal (AM) symbiosis between terrestrial plants and AM fungi is regulated by plant hormones. For most of these, a role has been clearly assigned in this mutualistic interaction; however, there are still contradictory reports for cytokinin (CK). Here, pea plants, the wild type (WT) cv. Sparkle and its mutant E151 (Pssym15), were inoculated with the AM fungus Rhizophagus irregularis. E151 has previously been characterized as possessing high CK levels in non-mycorrhizal (myc^-) roots and exhibiting high number of fungal structures in mycorrhizal (myc⁺) roots. Myc^- and myc⁺ plants were …

Seasonal Origins Of Soil Water Used By Trees, Scott T. Allen, James W. Kirchner, Sabine Braun, Rolf T. W. Siegwolf, Gregory R. Goldsmith

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Rain recharges soil water storages and either percolates downward into aquifers and streams or is returned to the atmosphere through evapotranspiration. Although it is commonly assumed that summer rainfall recharges plant-available water during the growing season, the seasonal origins of water used by plants have not been systematically explored. We characterize the seasonal origins of waters in soils and trees by comparing their midsummer isotopic signatures (δ2H) to seasonal isotopic cycles in precipitation, using a new seasonal origin index. Across 182 Swiss forest sites, xylem water isotopic signatures show that summer rain was not the predominant water source …

Extending The Osmometer Method For Assessing Drought Tolerance In Herbaceous Species, Robert J. Griffin-Nolan, Troy W. Ocheltree, Kevin E. Mueller, Dana M. Blumenthal, Julie A. Kray, Alan K. Knapp

Biological, Geological, and Environmental Faculty Publications

Community-scale surveys of plant drought tolerance are essential for understanding semi-arid ecosystems and community responses to climate change. Thus, there is a need for an accurate and rapid methodology for assessing drought tolerance strategies across plant functional types. The osmometer method for predicting leaf osmotic potential at full turgor ((o)), a key metric of leaf-level drought tolerance, has resulted in a 50-fold increase in the measurement speed of this trait; however, the applicability of this method has only been tested in woody species and crops. Here, we assess the osmometer method for use in herbaceous grassland species and test whether …

Refernment: An R Package For Annotating Rna Editing In Plastid Genomes, Tanner A. Robison, Paul G. Wolf

Biology Faculty Publications

PREMISE OF THE STUDY: In the absence of cDNA, the annotation of RNA editing in plastomes must be done manually, representing a significant time cost to those studying the organellar genomes of ferns and hornworts.

METHODS AND RESULTS: We developed an R package to automatically annotate apparent nonsense mutations in plastid genomes. The software successfully annotates such sites and results in no false positives for data with no sequencing or assembly errors.

CONCLUSIONS: Compared to manual annotation, ReFernment offers greater speed and accuracy for annotating RNA editing sites. This software should be especially useful for researchers generating large numbers of …

Structural Basis For Light Control Of Cell Development Revealed By Crystal Structures Of A Myxobacterial Phytochrome, Nicole C. Woitowich, Andrei S. Halavaty, Patricia Waltz, Christopher Kupitz, Joseph Valera, Gregory Tracy, Kevin D. Gallagher, Elin Claesson, Takanori Nakane, Suraj Pandey, Garrett Nelson, Rie Tanaka, Eriko Nango, Eiichi Mizohata, Shigeki Owada, Kensure Tono, Yasumasa Joti, Angela C. Nugent, Hardik Patel, Ayesha Mapara, James Hopkins, Phu Duong, Dorina Bizhga, Svetlana E. Kovaleva, Rachel St. Peter, Cynthia N. Hernandez, Wesley B. Ozarowski, Shatabdi Roy-Chowdhuri, Jay-How Yang, Petra Edlund, Heikki Takala, Janne Ihalainen, Jennifer Brayshaw, Tyler Norwood, Ishwor Poudyal, Petra Fromme, John C.H. Spence, Keith Moffat, Sebastian Westenhoff, Marius Schmidt, Emina A. Stojkovic

Biology Faculty Publications

Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxobacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruitingbody formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding …

Mobile Elements Shape Plastome Evolution In Ferns, Tanner A. Robison, Amanda L. Grusz, Paul G. Wolf, Jeffrey P. Mower, Blake D. Fauskee, Karla Sosa, Eric Schuettpelz

Biology Faculty Publications

Plastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even …

Apiaceae Of Northcentral New Mexico, Asha Hamaker

Northcentral New Mexico Plants Specimen Collection, 2018

No abstract provided.

Nonpolar Residues In The Presumptive Pore‐Lining Helix Of Mechanosensitive Channel Msl10 Influence Channel Behavior And Establish A Nonconducting Function, Grigory Maksaev, Jennette K. Shoots, Simran Ohri, Elizabeth S. Haswell

Biology Faculty Publications & Presentations

Mechanosensitive (MS) ion channels provide a universal mechanism for sensing and responding to increased membrane tension. MscS‐like (MSL) 10 is a relatively well‐studied MS ion channel from Arabidopsis thaliana that is implicated in cell death signaling. The relationship between the amino acid sequence of MSL10 and its conductance, gating tension, and opening and closing kinetics remains unstudied. Here, we identify several nonpolar residues in the presumptive pore‐lining transmembrane helix of MSL10 (TM6) that contribute to these basic channel properties. F553 and I554 are essential for wild type channel conductance and the stability of the open state. G556, a glycine residue …

Cuban Land Use And Conservation, From Rainforests To Coral Reefs, Gillian L. Galford, Margarita Fernandez, Joe Roman, Irene Monasterolo, Sonya Ahamed, Greg Fiske, Patricia Gonzalez-Diaz, Les Kaufman

Rubenstein School of Environment and Natural Resources Faculty Publications

Cuba is an ecological rarity in Latin America and the Caribbean. Its complex political and economic history shows limited disturbances, extinctions, pollution, and resource depletion by legal or de facto measures. Vast mangroves, wetlands, and forests play key roles in protecting biodiversity and reducing risks of hazards caused or aggravated by climate change. Cuba boasts coral reefs with some of the region’s greatest fish biomass and coral cover. Although Cuba has set aside major protected areas that safeguard a host of endemic species, its environment is by no means pristine. Its early history is one of deforestation and agricultural production …

Kelch F-Box Protein Positively Influences Arabidopsis Seed Germination By Targeting Phytochrome-Interacting Factor1, Manoj Majee, Santosh Kumar, Praveen Kumar Kathare, Shuiqin Wu, Derek Gingerich, Nihar R. Nayak, Louai Salaita, Randy Dinkins, Kathleen Martin, Michael Goodin, Lynnette M A Dirk, Taylor D. Lloyd, Ling Zhu, Joseph Chappell, Arthur G. Hunt, Richard D. Vierstra, Enamul Huq, A Bruce Downie

Biology Faculty Publications & Presentations

Seeds employ sensory systems that assess various environmental cues over time to maximize the successful transition from embryo to seedling. Here we show that the Arabidopsis F-BOX protein COLD TEMPERATURE-GERMINATING (CTG)-10, identified by activation tagging, is a positive regulator of this process. When overexpressed (OE), CTG10 hastens aspects of seed germination. CTG10 is expressed predominantly in the hypocotyl, and the protein is localized to the nucleus. CTG10 interacts with PHYTOCHROME-INTERACTING FACTOR 1 (PIF1) and helps regulate its abundance in planta. CTG10-OE accelerates the loss of PIF1 in light, increasing germination efficiency, while PIF1-OE lines fail to complete germination in …

Drivers And Mechanisms Of Peat Collapse In Coastal Wetlands, Benjamin J. Wilson

FIU Electronic Theses and Dissertations

Coastal wetlands store immense amounts of carbon (C) in vegetation and sediments, but this store of C is under threat from climate change. Accelerated sea level rise (SLR), which leads to saltwater intrusion, and more frequent periods of droughts will both impact biogeochemical cycling in wetlands. Coastal peat marshes are especially susceptible to saltwater intrusion and changes in water depth, but little is known about how exposure to salinity affects organic matter accumulation and peat stability. I investigated freshwater and brackish marsh responses to elevated salinity, greater inundation, drought, and increased nutrient loading. Elevated salinity pulses in a brackish marsh …

Genetic Diversity And Distinctness Of Wild Nebraska Hops And Hop Cultivars (Humulus Lupulus L.), Megan Franklin

Honors Theses

Background Commercial hop (Humulus lupulus) cultivars that are being grown in the Midwest are not performing as successfully as when they are grown in the Pacific Northwest, the region to which they are adapted. To increase adaptation to the Midwest environment, one strategy is to draw from the genetic pool of wild native Midwest hops, which have developed genes that allow them to grow successfully in this environment. Wild hop plants that are genetically distinct from commercial cultivars are likely to have more adaptations, such as pest/disease resistance and drought tolerance, which can be bred into commercial lines. The …

Lethal Effects Of Leaf Leachate From The Non-Native Invasive Shrub Amur Honeysuckle (Lonicera Maackii) On A Model Aquatic Organism (Hyalella Azteca), Eric B. Borth, Kevin W. Custer, Ryan W. Mcewan

Biology Faculty Publications

The invasive shrub Lonicera maackii (Amur honeysuckle) is a problematic species in the eastern United States and there is growing evidence that materials from this species have toxic effects on some organisms. We used a sequence of microcosm bioassays to assess the influence of L. maackii leaf leachate on the macroinvertebrate Hyalella azteca, which is a standard aquatic organism for toxicity assessment. In a laboratory setting, H. azteca were exposed to a leaf leachate dilution series (6.25%, 12.5%, 25%, 50%, 100%) in 48-h toxicity tests. This was repeated throughout the growing season to assess the potential for changes in …

Bulked-Segregant Analysis Coupled To Whole Genome Sequencing (Bsa-Seq) For Rapid Gene Cloning In Maize, Harry Klein, Yuguo Xiao, Phillip A. Conklin, Rajanikanth Govindarajulu, Jacob A. Kelly, Michael J. Scanlon, Clinton J. Whipple, Madelaine Bartlett

Faculty & Staff Scholarship

Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can …

The Role Of Environmental Filtering In Structuring Appalachian Tree Communities: Topographic Influences On Functional Diversity Are Mediated Through Soil Characteristics, Julia I. Chapman, Ryan W. Mcewan

Biology Faculty Publications

Identifying the drivers of community assembly has long been a central goal in ecology, and the development of functional diversity indices has provided a new way of detecting the influence of environmental gradients on biotic communities. For an old-growth Appalachian forest, we used path analysis to understand how patterns of tree functional diversity relate to topography and soil gradients and to determine whether topographic effects are mediated through soil chemistry. All of our path models supported the idea of environmental filtering: stressful areas (high elevation, low soil moisture, low soil nutrients) were occupied by communities of low functional diversity, which …