Life Sciences Commons^™

Applications Of Crispr/Cas9-Based Genome Editing In The Plant Biology, Yingzhuan Zheng, Qianqian Li, Mingwang Ye, Aie Cehn, Hongyang Wang

Turkish Journal of Botany

Clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR/Cas) is an acquired immune system found in bacteria and archaea that can specifically silence or degrade a foreign single or double strand nucleic acid to protect it from infection. In recent years, the CRISPR/Cas9 system has rapidly been evolved into a genome editing technology, in which the Cas9 endonuclease can be targeted to specific DNA sequences by guide RNAs (gRNAs) that are easily programmable. Due to simplicity, specificity and high efficiency, CRISPR/Cas9 is gradually replacing other gene editing technologies and has been implemented in basic and applied plant sciences to boost yield, …

Exploration Of Antiviral Effects Of Rna-Dependent Rna Polymerases 3, 4 And 5 In Arabidopsis., Eli R. Kallison, Aleksandra Beric, Blake Meyers

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Small RNAs play a number of vital roles in plants, including viral resistance. A particular class of small RNA that regulates plant defense from pathogens, among other functions, is known as small interfering RNAs (siRNAs). A key player in the biogenesis pathway of siRNAs are RNA-Dependent RNA Polymerases (RDRs). There are six RDR proteins in Arabidopsis thaliana, three of which have well documented roles (RDRs 1, 2 and 6), and three of which have no documented role. Here, we look at the functions of the unstudied RDRs, RDRs 3, 4 and 5, to see whether they affect antiviral resistance.

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 …

Taking Temperature With Leaves: A Semester-Long Structured- Inquiry Research Investigation For Undergraduate Plant Biology, Paige E. Copenhaver-Parry

Faculty Publications - Department of Biological & Molecular Science

Inquiry- and course-based research pedagogies have demonstrated effectiveness for preparing undergraduate biology students with authentic scientific skills and competencies, yet many students lack the experience to engage successfully in open-ended research activities without sufficient scaffolding and structure. Further, curricula for student-centered laboratory activities are lacking for several biological disciplines, including plant biology and botany. In this article, I describe a semester-long structured-inquiry research curriculum developed for a plant biology course taught to second-year biology students that integrates key elements of inquiry and discovery while providing a structured approach to gaining research skills. In the research project, students collect leaves from …

Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel

Dan Nettleton

Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the …

Examining Genetic And Ecological Differentiation Of An Endemic Plant Species Found Across The Hawaiian Archipelago, Psychotria Mariniana, Tiffany L. Kho

Master's Theses

Speciation is a fundamental evolutionary process that remains poorly understood. Speciation ultimately begins with population divergence, so we can elucidate the complexities of speciation by first understanding the process and drivers of population divergence. To conduct population-level analyses, ecologists and evolutionary biologists have turned to island systems, primarily for their geographic orientation and high endemism. The Hawaiian archipelago is home to over 8,700 endemic species making it a great natural laboratory to study species diversification at the population level. The Hawaiian Psychotria (kōpiko, or wild coffee) make up 11 of these species and have been used to understand colonization and …

Genome-Wide Characterization, Molecular Evolution And Mexpression Profiling Of The Metacaspases In Potato (Solanum Tuberosum L.), Nehal Dubey, Maitri Trivedi, Suresh Varsani, Vishal Vyas, Manisha Farsodia, Sunil Kumar Singh

Department of Entomology: Faculty Publications

Metacaspases are distant relatives of animal caspases found in plants, protozoa and fungi. Some recent studies have demonstrated that metacaspases are involved in regulating the developmental and environmentally induced programmed cell death in plants. In this study, we identified metacaspase gene family in potato (Solanum tuberosum L.) and analyzed their expression pattern in various developmental tissues and stress responses of plants. There were eight metacaspase genes identified in the Peptidase (Cysteine protease) C14 family and based upon sequence alignment and phylogenetic analysis, a systematic nomenclature of potato metacaspases (SotubMCs) has been proposed. Three of the eight candidate genes showing homology …

Elucidating The Surface Geometric Design Of Hydrophobic Australian Eucalyptus Leaves: Experimental And Modeling Studies, Hua Guo, Zonghan Xie, Jeremy Shaw, Kingsley Dixon, Zhong-Tao Jiang, Chun-Yang Yin, Xuemei Liu

Research outputs 2014 to 2021

Three Australian native Eucalyptus species, i.e., Eucalyptus woodwardii, Eucalyptus pachyphylla and Eucalyptus dolorosa, were investigated, for the first time, with respect to the hydrophobicity of their leaves. It is well established that these leaves exhibit exceptionally high water repellency, in addition to an extraordinary ability to retain water, albeit their specific wetting mechanisms are still poorly understood. To identify the critical factors underlying this phenomenon, the surface topography of these leaves was subjected to micro-examination (SEM). Micro- and nanometer scale surface roughness was revealed, resembling that of the quintessential “lotus effect”. Surface free energy analysis was performed on two models …

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 …

Evaluation Of Receptor Protein Too Many Mouths (Tmm) As A Glycosylphosphatidylinositol-Anchored Protein, Emily J. Miller

Chancellor’s Honors Program Projects

No abstract provided.

Crassulacean Acid Metabolism As A Continuous Trait: Variability In The Contribution Of Crassulacean Acid Metabolism (Cam) In Populations Of Portulacaria Afra, Lonnie J. Guralnick, Kate Gladsky

Arts & Sciences Faculty Publications

Portulacaria afra L. is a dominant facultative CAM species growing in the Southeastern Cape of South Africa. P. afra is well adapted to regions of the Spekboom thicket in areas of limited and sporadic rainfall. P. afra populations occur in isolated drainages. We hypothesized the utilization of CAM would vary in the different populations in response to rainfall and temperature gradients. Carbon isotope composition can be used to determine the contribution of CAM in leaf tissue. P. afra leaves of populations were analyzed in transects running south to north and east to west in locations from the coast to elevations …

There's Much Left To Learn: Clethra's Chromosomes, W. John Hayden

Biology Faculty Publications

Many would argue that chromosomes, genes, and DNA form the ineluctable essence of modern biology. Not only do these fundamental components of living cells provide moment-to-moment instructions by which cells carry out basic life processes, they also control inheritance of characteristics from one generation to the next. These essential functions of DNA stem from its repetitive structure. Hugely long DNA molecules are built from just four components, referenced by their singleletter abbreviations, A, C, G, and T. It is the specific sequence of these As, Cs, Gs, and Ts that constitutes the coded information of DNA. Moreover, molecular biologists have …

Morphologic And Taxonomic Analysis Of The Weedy And Cultivated Amaranthus Hybridus Species Complex, Dinesh Adhikary, Donald B. Pratt

Faculty Publications

The hybridus species complex of the genus Amaranthus is a group of weedy and cultivated plants from the New World that are considered difficult to identify. Classification schemes have varied between a single species approach, Amaranthus hybridus s.l., and a five species approach that recognizes the widespread weedy A. hybridus s.s., the South American endemic A. quitensis, and the three cultivated taxa (A. hypochondriacus, A. cruentus, and A. caudatus) as distinct species. The goals of this study were to analyze patterns of floral variation within the species complex and to determine distinguishing morphological features of …

Development And Application Of Mass Spectrometry-Based Proteomics To Generate And Navigate The Proteomes Of The Genus Populus, Paul Edward Abraham

Doctoral Dissertations

Historically, there has been tremendous synergy between biology and analytical technology, such that one drives the development of the other. Over the past two decades, their interrelatedness has catalyzed entirely new experimental approaches and unlocked new types of biological questions, as exemplified by the advancements of the field of mass spectrometry (MS)-based proteomics. MS-based proteomics, which provides a more complete measurement of all the proteins in a cell, has revolutionized a variety of scientific fields, ranging from characterizing proteins expressed by a microorganism to tracking cancer-related biomarkers. Though MS technology has advanced significantly, the analysis of complicated proteomes, such as …

Using Student-Produced Time-Lapse Plant Movies To Communicate Concepts In Plant Biology, Marcia Harrison-Pitaniello Phd

Biological Sciences Faculty Research

Why do students think plants are “boring”? One factor may be that they do not see plant movement in real (i.e., their) time. This attitude may negatively impact their understanding of plant biology. Time-lapse movies of plants allow students to see the sophistication of movements involved in both organ development and orientation.

The objective of this project was to develop simple methods to capture image sequences for lab analysis and for converting to movies. The technology for making time-lapse movies is now easily attainable and fairly inexpensive, allowing its use for skill levels from grade school through college undergraduates. In …

Partridge Berry: Simple Beauty Belies Complexity, W. John Hayden

Biology Faculty Publications

Superficially, plants seem so simple. Rooted in place, they do not move around. And while plant growth is a dynamic process, without time-lapse photography, growth events are so imperceptibly slow that, to us impatient humans, plants seem both immobile and static. Nevertheless, there is a lot going on inside the plant body, and this is especially true for the events of reproduction that play out inside flowers and fruits. As one of my students recently commented, “I used to think it was just a matter of pollen plus stigma and, presto-change-o, seeds happen.” That student, I hope, learned otherwise, as …

Occurrence Of Anisophylly And Anisoclady Within The Amaranthaceae [Abstract], Donald B. Pratt, Lynn G. Clark

Faculty Publications

No abstract provided.

2c Dna Content Values In Amaranthus (Amaranthaceae) [Abstract], Donald B. Pratt, Shalini N. Jhangiani, Robert J. Wiggers

Faculty Publications

No abstract provided.

Development And Characterization Of Microsatellite Markers For The Grain Amaranths [Abstract], Melanie A. Mallory, Rozaura V. Hall, Andrea R. Mcnabb, Donald B. Pratt, Eric N. Jellen, Peter J. Maughan

Faculty Publications

No abstract provided.

Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua Udall, Lex E. Flagel, Foo Chung, Andrew W. Woodward, Ran Hovav, Ryan A. Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel

Faculty Publications

Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Results: Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from <50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome and previously studied cotton genes, transcription factors, and genes with homology to Arabidopsis. A small portion of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from fiber-specific cDNA libraries, the microarray has direct application for analysis of the fiber transcriptome. To illustrate the utility of the microarray, we hybridized labeled bud and leaf cDNAs from G. hirsutum and demonstrate technical consistency of results. Conclusion: The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info.

Assessment Of Genetic Diversity In The Usda And Cip-Fao International Nursery Collections Of Quinoa (Chenopodium Quinoa Willd.) Using Microsatellite Markers [Abstract], S. A. Christensen, Donald B. Pratt, C. Pratt, P. T. Nelson, M. R. Stevens, Eric N. Jellen, C. E. Coleman, D. J. Fairbanks, A. Bonifacio, Peter J. Maughan

Faculty Publications

No abstract provided.

Emerging Research Techniques & New Instrumentation For Plant Biology, Bruce Bugbee

Techniques and Instruments

We have not achieved an efficient food production system in US Agriculture by manipulating only the environment.

Genetic engineering techniques now allow us to quickly develop new crop cultivars.

The Malagasy Endemic Dendroportulaca (Portulacaceae) Is Referable To Deeringia (Amaranthaceae): Molecular And Morphological Evidence [Abstract], Wendy L. Applequist, Donald B. Pratt

Faculty Publications

No abstract provided.

Blackspot Disease Of Roses [Abstract], Robert J. Wiggers, Josephine Taylor, J. A. Margoitta, S. G. Pandalai

Faculty Publications

No abstract provided.

Amaranthus Rudis And A. Tuberculatus, One Species Or Two? [Abstract], Donald B. Pratt, Lynn G. Clark

Faculty Publications

No abstract provided.

Pycnothyrium Ultrastructure In Tubakia Dryina [Abstract], Josephine Taylor

Faculty Publications

No abstract provided.

Amanoa, W. John Hayden

Biology Faculty Publications

Monoecious or dioecious trees or shrubs, latex absent. Leaves alternate, distichous, evergreen, simple, coriaceous, glabrous; stipules intrapetiolar, paired, or confluent across the leaf axil; margins entire; venation pinnate. Inflorescence axillary and/or terminal, of densely bracteate clusters (reduced cymules), in the axils of ordinary foliage leaves, in nonleafy pseudoterminal aggregates that revert to vegetative growth, or (in neotropical species) in the axils of alternate, reduced, crescentiform stipular bracts of determinate deciduous spiciform axes borne in groups of 1-several per branch apex; axes straight or sinuous; floral bracts minute, deltate, with abaxially pubescent midribs. Staminate flowers sessile or pedicellate, regular; perianth biseriate; …

Seedling Development In Species Of Chamaesyce (Euphorbiaceae) With Erect Growth Habits, W. John Hayden, Olga Troyanskaya

Biology Faculty Publications

Seedling development is described for Chamaesyce hirta, C. hypericifolia, and C. mesembrianthemifolia as discerned by light microscopy and scanning electron microscopy. Although these species ultimately develop erect to ascending growth habits, epicotyl development is limited to the production of a single pair ofleaves located immediately superjacent to and decussate with the cotyledons. The shoot system develops from one or more buds located in the axils of the cotyledons. In all respects, seedling ontogeny is very similar to that of previously studied prostrate species of Chamaesyce. Evidence from seedling ontogeny thus contradicts a hypothesis concerning homologies of plant …

Revision Of The Cerrado Hemicryptophytic Chamaesyce Of Boissier's "Pleiadeniae" (Euphorbiaceae), Mark P. Simmons, W. John Hayden

Biology Faculty Publications

The species of Chamaesyce classified by Boissier as the "Pleiadeniae'" are revised in light of presently available collections. Six species are accepted and new combinations are proposed for C. nana, C. setosa, C. tamanduana, and C. viscoides. Although these herbaceous perennials of cerrado vegetation of Brazil, northern Argentina, and adjacent countries are distinctive ecologically and geographically, cladistic analysis does not support their recognition as a monophyletic group.

Conidial Germination And Infection By Diplocarpon Rosae On Susceptible And Resistant Rose Species, Robert J. Wiggers, J. G. West, Josephine Taylor

Faculty Publications

Conidial germination and infection by Dipplocarpon rosae, the causal organism of rose blackspot, were examined on two resistant species of roses, Rosa roxburghii and R. wichuraiana and two susceptible hybrid tea roses (R. hybrid cv. Chicago Peace and Garden Party). Fungal conidia germinated and gave rise to subcuticular mycelium that formed haustoria within epidermal cells of all four roses tested. On the resistant rose species, epidermal cells associated with the infection site became necrotic, indicating that a hypersensitive response is involved in conferring their resistance D. rosae.