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Iowa State University

Cell and Developmental Biology

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The Mir319-Targeted Ghtcp4 Promotes The Transition From Cell Elongation To Wall Thickening In Cotton Fiber, Jun-Feng Cao, Bo Zhao, Chao-Chen Huang, Zhi-Wen Chen, Ting Zhao, Hong-Ru Liu, Guan-Jing Hu, Xiao-Xia Shangguan, Chun-Min Shan, Ling-Jian Wang, Tian-Zhen Zhang, Jonathan F. Wendel, Xue-Ying Guan, Xiao-Ya Chen Jul 2020

The Mir319-Targeted Ghtcp4 Promotes The Transition From Cell Elongation To Wall Thickening In Cotton Fiber, Jun-Feng Cao, Bo Zhao, Chao-Chen Huang, Zhi-Wen Chen, Ting Zhao, Hong-Ru Liu, Guan-Jing Hu, Xiao-Xia Shangguan, Chun-Min Shan, Ling-Jian Wang, Tian-Zhen Zhang, Jonathan F. Wendel, Xue-Ying Guan, Xiao-Ya Chen

Ecology, Evolution and Organismal Biology Publications

Plant cell growth involves a complex interplay among cell-wall expansion, biosynthesis, and, in specific tissues, secondary cell wall (SCW) deposition, yet the coordination of these processes remains elusive. Cotton fiber cells are developmentally synchronous, highly elongated, and contain nearly pure cellulose when mature. Here, we report that the transcription factor GhTCP4 plays an important role in balancing cotton fiber cell elongation and wall synthesis. During fiber development the expression of miR319 declines while GhTCP4 transcript levels increase, with high levels of the latter promoting SCW deposition. GhTCP4 interacts with a homeobox-containing factor, GhHOX3, and repressing its transcriptional activity. GhTCP4 and ...


Control Of Translation During The Unfolded Protein Response In Maize Seedlings: Life Without Perks, Pulkit Kanodia, Paramasivan Vijayapalani, Renu Srivastava, Ran Bi, Peng Liu, W. Allen Miller, Stephen H. Howell Jul 2020

Control Of Translation During The Unfolded Protein Response In Maize Seedlings: Life Without Perks, Pulkit Kanodia, Paramasivan Vijayapalani, Renu Srivastava, Ran Bi, Peng Liu, W. Allen Miller, Stephen H. Howell

Plant Pathology and Microbiology Publications

The accumulation of misfolded proteins in the endoplasmic reticulum (ER) defines a condition called ER stress that induces the unfolded protein response (UPR). The UPR in mammalian cells attenuates protein synthesis initiation, which prevents the piling up of misfolded proteins in the ER. Mammalian cells rely on Protein Kinase RNA‐Like Endoplasmic Reticulum Kinase (PERK) phosphorylation of eIF2α to arrest protein synthesis, however, plants do not have a PERK homolog, so the question is whether plants control translation in response to ER stress. We compared changes in RNA levels in the transcriptome to the RNA levels protected by ribosomes and ...


Crispr-Cas12a Has Widespread Off-Target And Dsdna-Nicking Effects, Karthik Murugan, Arun S. Seetharam, Andrew J. Severin, Dipali G. Sashital Mar 2020

Crispr-Cas12a Has Widespread Off-Target And Dsdna-Nicking Effects, Karthik Murugan, Arun S. Seetharam, Andrew J. Severin, Dipali G. Sashital

Office of Biotechnology Publications

Cas12a (Cpf1) is an RNA-guided endonuclease in the bacterial type V-A CRISPR-Cas anti-phage immune system that can be repurposed for genome editing. Cas12a can bind and cut dsDNA targets with high specificity in vivo, making it an ideal candidate for expanding the arsenal of enzymes used in precise genome editing. However, this reported high specificity contradicts Cas12a’s natural role as an immune effector against rapidly evolving phages. Here, we employed high-throughput in vitro cleavage assays to determine and compare the native cleavage specificities and activities of three different natural Cas12a orthologs (FnCas12a, LbCas12a, and AsCas12a). Surprisingly, we observed pervasive ...


Pyrpipe: A Python Package For Rna-Seq Workflows, Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele Mar 2020

Pyrpipe: A Python Package For Rna-Seq Workflows, Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele

Genetics, Development and Cell Biology Publications

Implementing RNA-Seq analysis pipelines is challenging as data gets bigger and more complex. With the availability of terabytes of RNA-Seq data and continuous development of analysis tools, there is a pressing requirement for frameworks that allow for fast and efficient development, modification, sharing and reuse of workflows. Scripting is often used, but it has many challenges and drawbacks. We have developed a python package, python RNA-Seq Pipeliner (pyrpipe) that enables straightforward development of flexible, reproducible and easy-to-debug computational pipelines purely in python, in an object-oriented manner. pyrpipe provides high level APIs to popular RNA-Seq tools. Pipelines can be customized by ...


Evaluation Of The Functional Role Of The Maize Glossy2 And Glossy2-Like Genes In Cuticular Lipid Deposition, Liza Esther Alexander, Yozo Okazaki, Michael A. Schelling, Aeriel Davis, Xiaobin Zheng, Ludmila Rizhsky, Marna D. Yandeau-Nelson, Kazuki Saito, Basil J. Nikolau Feb 2020

Evaluation Of The Functional Role Of The Maize Glossy2 And Glossy2-Like Genes In Cuticular Lipid Deposition, Liza Esther Alexander, Yozo Okazaki, Michael A. Schelling, Aeriel Davis, Xiaobin Zheng, Ludmila Rizhsky, Marna D. Yandeau-Nelson, Kazuki Saito, Basil J. Nikolau

Genetics, Development and Cell Biology Publications

Plant epidermal cells express unique molecular machinery that juxtapose the assembly of intracellular lipid components and the unique extracellular cuticular lipids that are unidirectionally secreted to plant surfaces. In maize (Zea mays L.), mutations at the glossy2 (gl2) locus affect the deposition of extracellular cuticular lipids. Sequence-based genome scanning identified a novel gl2 homolog in the maize genome, Gl2-like. Sequence homology identifies that both the Gl2-like and Gl2 genes are members of the BAHD superfamily of acyltransferases, with close sequence homology to the Arabidopsis CER2 gene. Transgenic experiments demonstrate that Gl2-like and Gl2 functionally complement the Arabidopsis cer2 mutation, with ...


Population Modeling Of Tumor Growth Curves And The Reduced Gompertz Model Improve Prediction Of The Age Of Experimental Tumors, Cristina Vaghi, Anne Rodallec, Raphaelle Fanciullin, Joseph Ciccolini, Jonathan P. Mochel, Michalis Mastri, Clair Poignard, John M. L. Ebos, Sebastien Benzekry Feb 2020

Population Modeling Of Tumor Growth Curves And The Reduced Gompertz Model Improve Prediction Of The Age Of Experimental Tumors, Cristina Vaghi, Anne Rodallec, Raphaelle Fanciullin, Joseph Ciccolini, Jonathan P. Mochel, Michalis Mastri, Clair Poignard, John M. L. Ebos, Sebastien Benzekry

Biomedical Sciences Publications

Tumor growth curves are classically modeled by means of ordinary differential equations. In analyzing the Gompertz model several studies have reported a striking correlation between the two parameters of the model, which could be used to reduce the dimensionality and improve predictive power. We analyzed tumor growth kinetics within the statistical framework of nonlinear mixed-effects (population approach). This allowed the simultaneous modeling of tumor dynamics and inter-animal variability. Experimental data comprised three animal models of breast and lung cancers, with 833 measurements in 94 animals. Candidate models of tumor growth included the exponential, logistic and Gompertz models. The exponential and ...


Recovery Of Encapsulated Adult Neural Progenitor Cells From Microfluidic-Spun Hydrogel Fibers Enhances Proliferation And Neuronal Differentiation, Bhavika B. Patel, Marilyn C. Mcnamara, Laura S. Pesquera-Colom, Emily M. Kozik, Jasmin Okuzonu, Nicole N. Hashemi, Donald S. Sakaguchi Jan 2020

Recovery Of Encapsulated Adult Neural Progenitor Cells From Microfluidic-Spun Hydrogel Fibers Enhances Proliferation And Neuronal Differentiation, Bhavika B. Patel, Marilyn C. Mcnamara, Laura S. Pesquera-Colom, Emily M. Kozik, Jasmin Okuzonu, Nicole N. Hashemi, Donald S. Sakaguchi

Genetics, Development and Cell Biology Publications

Because of the limitations imposed by traditional two-dimensional (2D) cultures, biomaterials have become a major focus in neural and tissue engineering to study cell behavior in vitro. 2D systems fail to account for interactions between cells and the surrounding environment; these cell–matrix interactions are important to guide cell differentiation and influence cell behavior such as adhesion and migration. Biomaterials provide a unique approach to help mimic the native microenvironment in vivo. In this study, a novel microfluidic technique is used to encapsulate adult rat hippocampal stem/progenitor cells (AHPCs) within alginate-based fibrous hydrogels. To our knowledge, this is the ...


Experimental Study Using Multiple Strains Of Prion Disease In Cattle Reveals An Inverse Relationship Between Incubation Time And Misfolded Prion Accumulation, Neuroinflammation And Autophagy, Najiba Mammadova, M. Heather West Greenlee, S. Jo Moore, Donald S. Sakaguchi, Justin J. Greenlee Jan 2020

Experimental Study Using Multiple Strains Of Prion Disease In Cattle Reveals An Inverse Relationship Between Incubation Time And Misfolded Prion Accumulation, Neuroinflammation And Autophagy, Najiba Mammadova, M. Heather West Greenlee, S. Jo Moore, Donald S. Sakaguchi, Justin J. Greenlee

Genetics, Development and Cell Biology Publications

Proteinopathies result from aberrant folding and accumulation of specific proteins. Currently, there is a lack of knowledge about the factors that influence disease progression making this a key challenge for the development of therapies for proteinopathies. Due to the similarities between transmissible spongiform encephalopathies (TSEs) and other protein misfolding diseases, TSEs can be used to understand other proteinopathies. Bovine spongiform encephalopathy (BSE) is a TSE that occurs in cattle and can be subdivided into three strains: classical BSE, and atypical BSEs (H-type and L-type) that have shorter incubation periods. The NLRP3 inflammasome is a critical component of the innate immune ...


Cholinergic Receptors On Intestine Cells Of Ascaris Suum And Activation Of Nachrs By Levamisole, Mark Mchugh, Paul Williams, Saurabh Verma, Jo Anne Powell-Coffman, Alan P. Robertson, Richard J. Martin Jan 2020

Cholinergic Receptors On Intestine Cells Of Ascaris Suum And Activation Of Nachrs By Levamisole, Mark Mchugh, Paul Williams, Saurabh Verma, Jo Anne Powell-Coffman, Alan P. Robertson, Richard J. Martin

Genetics, Development and Cell Biology Publications

Cholinergic agonists, like levamisole, are a major class of anthelmintic drug that are known to act selectively on nicotinic acetylcholine receptors (nAChRs) on the somatic muscle and nerves of nematode parasites to produce their contraction and spastic paralysis. Previous studies have suggested that in addition to the nAChRs found on muscle and nerves, there are nAChRs on non-excitable tissues of nematode parasites. We looked for evidence of nAChRs expression in the cells of the intestine of the large pig nematode, Ascaris suum, using RT-PCR and RNAscope in situ hybridization and detected mRNA of nAChR subunits in the cells. These subunits ...


Efficient Targeted Integration Directed By Short Homology In Zebrafish And Mammalian Cells, Wesley A. Wierson, Jordan M. Welker, Maira P. Almeida, Carla M. Mann, Melanie E. Torrie, Trevor J. Weiss, Sekhar Kambakam, Merrina Lan, Kenna C. Mckeighan, Jacklyn Levey, Zhitao Ming, Alec Wehmeier, Christopher S. Mikelson, Jeffrey A. Haltom, Drena L. Dobbs, Maura Mcgrail, Jeffrey Essner, Et Al. Jan 2020

Efficient Targeted Integration Directed By Short Homology In Zebrafish And Mammalian Cells, Wesley A. Wierson, Jordan M. Welker, Maira P. Almeida, Carla M. Mann, Melanie E. Torrie, Trevor J. Weiss, Sekhar Kambakam, Merrina Lan, Kenna C. Mckeighan, Jacklyn Levey, Zhitao Ming, Alec Wehmeier, Christopher S. Mikelson, Jeffrey A. Haltom, Drena L. Dobbs, Maura Mcgrail, Jeffrey Essner, Et Al.

Genetics, Development and Cell Biology Publications

Efficient precision genome engineering requires high frequency and specificity of integration at the genomic target site. Here, we describe a set of resources to streamline reporter gene knock-ins in zebrafish and demonstrate the broader utility of the method in mammalian cells. Our approach uses short homology of 24–48 bp to drive targeted integration of DNA reporter cassettes by homology-mediated end joining (HMEJ) at high frequency at a double strand break in the targeted gene. Our vector series, pGTag (plasmids for Gene Tagging), contains reporters flanked by a universal CRISPR sgRNA sequence which enables in vivo liberation of the homology ...


A Role For Arabidopsis Myosins In Sugar-Induced Hypocotyl Elongation, Damilola Olatunji, Dior R. Kelley Jan 2020

A Role For Arabidopsis Myosins In Sugar-Induced Hypocotyl Elongation, Damilola Olatunji, Dior R. Kelley

Genetics, Development and Cell Biology Publications

The ability of developing seedlings to respond and adapt to diverse environmental conditions including light is critical for their emergence and establishment (Benvenuti et al., 2001; Forcella et al., 2000; Salter et al., 2003; Yu and Huang, 2017). Cell expansion within the hypocotyl optimizes light and energy capture by the cotyledons, and enables the transition to autotrophic status (Botterweg-Paredes et al., 2020; Dowson‐Day and Millar, 1999; Oh et al., 2013). Hypocotyl elongation is regulated by multiple factors including temperature, phytohormones, circadian clock and light (Dowson‐Day and Millar, 1999; Ma et al., 2016; Procko et al., 2014; Reed et ...


A Rapid And Simple Quantitative Method For Specific Detection Of Smaller Co-Terminal Rna By Pcr (Desco-Pcr): Application To The Detection Of Viral Subgenomic Rnas, Pulkit Kanodia, K. Reddisiva Prasanth, Vicky C. Roa-Linares, Shelton S. Bradrick, Mariano A. Garcia-Blanco, W. Allen Miller Jan 2020

A Rapid And Simple Quantitative Method For Specific Detection Of Smaller Co-Terminal Rna By Pcr (Desco-Pcr): Application To The Detection Of Viral Subgenomic Rnas, Pulkit Kanodia, K. Reddisiva Prasanth, Vicky C. Roa-Linares, Shelton S. Bradrick, Mariano A. Garcia-Blanco, W. Allen Miller

Plant Pathology and Microbiology Publications

RNAs that are 5’-truncated versions of a longer RNA, but share the same 3’ terminus can be generated by alternative promoters in transcription of cellular mRNAs or by replicating RNA viruses. These truncated RNAs cannot be distinguished from the longer RNA by a simple two-primer RT-PCR because primers that anneal to the cDNA from the smaller RNA also anneal to - and amplify - the longer RNA-derived cDNA. Thus, laborious methods, such as northern blot hybridization, are used to distinguish shorter from longer RNAs. For rapid, low-cost and specific detection of these truncated RNAs, we report Detection of Smaller Co-terminal RNA ...


Expanding The Crispr Toolbox With Ercas12a In Zebrafish And Human Cells, Wesley A. Wierson, Brandon W. Simone, Zachary Warejoncas, Carla Mann, Jordan M. Welker, Bibekananda Kar, Michael J. Emch, Iddo Friedberg, William A. C. Gendron, Michael A. Barry, Karl J. Clark, Drena L. Dobbs, Maura A. Mcgrail, Stephen C. Ekker, Jeffrey J. Essner Dec 2019

Expanding The Crispr Toolbox With Ercas12a In Zebrafish And Human Cells, Wesley A. Wierson, Brandon W. Simone, Zachary Warejoncas, Carla Mann, Jordan M. Welker, Bibekananda Kar, Michael J. Emch, Iddo Friedberg, William A. C. Gendron, Michael A. Barry, Karl J. Clark, Drena L. Dobbs, Maura A. Mcgrail, Stephen C. Ekker, Jeffrey J. Essner

Genetics, Development and Cell Biology Publications

CRISPR and CRISPR-Cas effector proteins enable the targeting of DNA double-strand breaks to defined loci based on a variable length RNA guide specific to each effector. The guide RNAs are generally similar in size and form, consisting of a ∼20 nucleotide sequence complementary to the DNA target and an RNA secondary structure recognized by the effector. However, the effector proteins vary in protospacer adjacent motif requirements, nuclease activities, and DNA binding kinetics. Recently, ErCas12a, a new member of the Cas12a family, was identified in Eubacterium rectale. Here, we report the first characterization of ErCas12a activity in zebrafish and expand on ...


Systems Analyses Of Key Metabolic Modules Of Floral And Extrafloral Nectaries Of Cotton, Elizabeth C. Chatt, Siti-Nabilla Mahalim, Nur-Aziatull Mohd-Fadzil, Rahul Roy, Peter M. Klinkenberg, Harry T. Horner, Marshall Hampton, Clay J. Carter, Basil J. Nikolau Nov 2019

Systems Analyses Of Key Metabolic Modules Of Floral And Extrafloral Nectaries Of Cotton, Elizabeth C. Chatt, Siti-Nabilla Mahalim, Nur-Aziatull Mohd-Fadzil, Rahul Roy, Peter M. Klinkenberg, Harry T. Horner, Marshall Hampton, Clay J. Carter, Basil J. Nikolau

Genetics, Development and Cell Biology Publications

Nectar is a primary reward mediating plant-animal mutualisms to improve plant fitness and reproductive success. In Gossypium hirsutum (cotton), four distinct trichomatic nectaries develop, one floral and three extrafloral. The secreted floral and extrafloral nectars serve different purposes, with the floral nectar attracting bees to promote pollination and the extrafloral nectar attracting predatory insects as a means of indirect resistance from herbivores. Cotton therefore provides an ideal system to contrast mechanisms of nectar production and nectar composition between floral and extrafloral nectaries. Here, we report the transcriptome, ultrastructure, and metabolite spatial distribution using mass spectrometric imaging of the four cotton ...


Scan Parameter Optimization For Histotripsy Treatment Of S. Aureus Biofilms On Surgical Mesh, Timothy Bigelow, Clayton L. Thomas, Huaiqing Wu Oct 2019

Scan Parameter Optimization For Histotripsy Treatment Of S. Aureus Biofilms On Surgical Mesh, Timothy Bigelow, Clayton L. Thomas, Huaiqing Wu

Electrical and Computer Engineering Publications

There is a critical need to develop new noninvasive therapies to treat bacteria biofilms. Previous studies have demonstrated the effectiveness of cavitation-based ultrasound histotripsy to destroy these biofilms. In this study, the dependence of biofilm destruction on multiple scan parameters was assessed by conducting exposures at different scan speeds (0.3-1.4 beam widths/sec), step sizes (0.25-0.5 beam widths), and number of passes of the focus across the mesh (2-6). For each of the exposure conditions, the number of colony forming units (CFUs) remaining on the mesh was quantified. A regression analysis was then conducted revealing that ...


Auxin Induces Widespread Proteome Remodeling In Arabidopsis Seedlings, Natalie M. Clark, Zhouxin Shen, Steven P. Briggs, Justin W. Walley, Dior R. Kelley Aug 2019

Auxin Induces Widespread Proteome Remodeling In Arabidopsis Seedlings, Natalie M. Clark, Zhouxin Shen, Steven P. Briggs, Justin W. Walley, Dior R. Kelley

Genetics, Development and Cell Biology Publications

It is known that auxin induces rapid gene expression changes throughout plant development, but how these transcriptional responses relate to changes in protein abundance is not well characterized. This report identifies early auxin responsive proteins in whole Arabidopsis seedlings using an iTRAQ (isobaric Tags for Relative and Absolute Quantification)-based quantitative proteomics approach. Approximately 25% of the detected proteins (1045 out of 4257 proteins) were auxin responsive, which is in line with the central role of auxin in the regulation of plant growth and development. Several well-known auxin pathway proteins were identified as differentially expressed, validating this quantitative proteomics approach ...


The Gene Sculpt Suite: A Set Of Tools For Genome Editing, Carla M. Mann, Gabriel Martínez-Gálvez, Jordan M. Welker, Wesley A. Wierson, Hirotaka Ata, Maira P. Almeida, Karl J. Clark, Jeffrey J. Essner, Maura Mcgrail, Stephen C. Ekker, Drena Dobbs Jul 2019

The Gene Sculpt Suite: A Set Of Tools For Genome Editing, Carla M. Mann, Gabriel Martínez-Gálvez, Jordan M. Welker, Wesley A. Wierson, Hirotaka Ata, Maira P. Almeida, Karl J. Clark, Jeffrey J. Essner, Maura Mcgrail, Stephen C. Ekker, Drena Dobbs

Genetics, Development and Cell Biology Publications

The discovery and development of DNA-editing nucleases (Zinc Finger Nucleases, TALENs, CRISPR/Cas systems) has given scientists the ability to precisely engineer or edit genomes as never before. Several different platforms, protocols and vectors for precision genome editing are now available, leading to the development of supporting web-based software. Here we present the Gene Sculpt Suite (GSS), which comprises three tools: (i) GTagHD, which automatically designs and generates oligonucleotides for use with the GeneWeld knock-in protocol; (ii) MEDJED, a machine learning method, which predicts the extent to which a double-stranded DNA break site will utilize the microhomology-mediated repair pathway; and ...


A Critical Analysis Of Powell’S Results On The Interdivision Time Distribution, Vincent Quedeville, Jérôme Morchain, Philippe Villedieu, Rodney O. Fox Jun 2019

A Critical Analysis Of Powell’S Results On The Interdivision Time Distribution, Vincent Quedeville, Jérôme Morchain, Philippe Villedieu, Rodney O. Fox

Chemical and Biological Engineering Publications

The cell-age and interdivision-time probability density functions (PDFs) have been extensively investigated since the 1940s due to their fundamental role in cell growth. The pioneering work of Powell established the first relationship between the interdivision-time and cell-age PDFs. In the literature, two definitions for the interdivision-time PDF have been proposed. One stands for the age-at-rupture PDF and is experimentally observable, whereas the other is the probability density that a cell divides at a certain age and is unobservable. From Powell’s results pertaining to the unobservable interdivision-time PDF, Painter and Marr derived an inequality that is true but is incorrectly ...


The Vertebrate Codex Gene Breaking Protein Trap Library For Genomic Discovery And Disease Modeling Applications, Noriko Ichino, Ying Wang, Hsin-Kai Liao, Maura Mcgrail, Jeffrey J. Essner, Shawn Burgess, Et Al. May 2019

The Vertebrate Codex Gene Breaking Protein Trap Library For Genomic Discovery And Disease Modeling Applications, Noriko Ichino, Ying Wang, Hsin-Kai Liao, Maura Mcgrail, Jeffrey J. Essner, Shawn Burgess, Et Al.

Genetics, Development and Cell Biology Publications

The zebrafish is a powerful model to explore the molecular genetics and expression of the vertebrate genome. The gene break transposon (GBT) is a unique insertional mutagen that reports the expression of the tagged member of the proteome while generating Cre-revertible genetic alleles. This 1000+ locus collection represents novel codex expression data from the illuminated mRFP protein trap, with 36% and 87% of the cloned lines showcasing to our knowledge the first described expression of these genes at day 2 and day 4 of development, respectively. Analyses of 183 molecularly characterized loci indicate a rich mix of genes involved in ...


Age-Dependent Changes In Transcription Factor Foxo Targeting In Female Drosophila, Allison Birnbaum, Xiaofen Wu, Marc Tatar, Nan Liu, Hua Bai May 2019

Age-Dependent Changes In Transcription Factor Foxo Targeting In Female Drosophila, Allison Birnbaum, Xiaofen Wu, Marc Tatar, Nan Liu, Hua Bai

Genetics, Development and Cell Biology Publications

FOXO transcription factors have long been associated with longevity control and tissue homeostasis. Although the transcriptional regulation of FOXO have been previously characterized (especially in long-lived insulin mutants and under stress conditions), how normal aging impacts the transcriptional activity of FOXO is poorly understood. Here, we conducted a chromatin immunoprecipitation sequencing (ChIP-Seq) analysis in both young (2-week-old) and aged (5-week-old) wild-type female fruit flies, Drosophila melanogaster, to evaluate the dynamics of FOXO gene targeting during aging. Intriguingly, the number of FOXO-bound genes dramatically decreases with age (from 2617 to 224). Consistent to the reduction of FOXO binding activity, many genes ...


Organelle Aging: Lessons From Model Organisms, Mark Bouska, Kerui Huang, Ping Kang, Hua Bai Apr 2019

Organelle Aging: Lessons From Model Organisms, Mark Bouska, Kerui Huang, Ping Kang, Hua Bai

Genetics, Development and Cell Biology Publications

Most cellular processes descend into failure during aging. While a large collection of longevity pathways has been identified in the past decades, the mechanism for age-related decline of cellular homeostasis and organelle function remains largely unsolved. It is known that many organelles undergo structural and functional changes during normal aging, which significantly contributes to the decline of tissue function at old ages. Since recent studies have revealed an emerging role of organelles as regulatory hubs in maintaining cellular homeostasis, understanding of organelle aging will provide important insights into the cellular basis of organismal aging. Here we review current progress on ...


Development And Application Of A Quantitative Bioassay To Evaluate Maize Silk Resistance To Corn Earworm Herbivory Among Progenies Derived From Peruvian Landrace Piura, Miriam D. Lopez, Tesia S. Dennison, Tina M. Paque, Marna D. Yandeau-Nelson, Craig A. Abel, Nick Lauter Apr 2019

Development And Application Of A Quantitative Bioassay To Evaluate Maize Silk Resistance To Corn Earworm Herbivory Among Progenies Derived From Peruvian Landrace Piura, Miriam D. Lopez, Tesia S. Dennison, Tina M. Paque, Marna D. Yandeau-Nelson, Craig A. Abel, Nick Lauter

Genetics, Development and Cell Biology Publications

Corn earworm (CEW), Helicoverpa zea (Boddie), (Lepidoptera: Noctuidae), is a major insect pest of corn (Zea mays spp. mays L.). CEW larvae feed on silks, kernels and cobs, causing substantial yield and quality losses both through herbivory and by vectoring pathogens. The long-term goal of this work is to elucidate the genetic and biochemical basis of a potentially novel CEW resistance source discovered in silk tissue of Piura 208, a Peruvian landrace of maize (PI 503849). We developed a quantitative CEW bioassay and tested it on four populations that contrast alleles from Piura 208 with those from GT119, a CEW-susceptible ...


A Functional Unfolded Protein Response Is Required For Normal Vegetative Development, Yan Bao, Diane C. Bassham, Stephen H. Howell Apr 2019

A Functional Unfolded Protein Response Is Required For Normal Vegetative Development, Yan Bao, Diane C. Bassham, Stephen H. Howell

Genetics, Development and Cell Biology Publications

The unfolded protein response (UPR) is activated in plants in response to endoplasmic reticulum stress and plays an important role in mitigating stress damage. Multiple factors act in the UPR, including the membrane-associated transcription factor, BASIC LEUCINE ZIPPER 17 (bZIP17), and the membrane-associated RNA splicing factor, INOSITOL REQUIRING ENZYME1 (IRE1). We have analyzed an Arabidopsis (Arabidopsis thaliana) ire1a ire1b bzip17 triple mutant, with defects in stress signaling, and found that the mutant is also impaired in vegetative plant growth under conditions without externally applied stress. This raised the possibility that the UPR functions in plant development in the same manner ...


Identification Of Transcription Factors That Regulate Atg8 Expression And Autophagy In Arabidopsis, Ping Wang, Trevor M. Nolan, Yanhai Yin, Diane C. Bassham Mar 2019

Identification Of Transcription Factors That Regulate Atg8 Expression And Autophagy In Arabidopsis, Ping Wang, Trevor M. Nolan, Yanhai Yin, Diane C. Bassham

Genetics, Development and Cell Biology Publications

Autophagy is a conserved catabolic process in eukaryotes that contributes to cell survival in response to multiple stresses and is important for organism fitness. In Arabidopsis thaliana, the core machinery of autophagy is well defined, but its transcriptional regulation is largely unknown. The ATG8 (autophagy-related 8) protein plays central roles in decorating autophagosomes and binding to specific cargo receptors to recruit cargo to autophagosomes. We propose that the transcriptional control of ATG8 genes is important during the formation of autophagosomes and therefore contributes to survival during stress. Here, we describe a yeast one-hybrid (Y1H) screen for transcription factors (TFs) that ...


Linking Autophagy To Abiotic And Biotic Stress Responses, Santiago Signorelli, Lukasz Pawel Tarkowski, Wim Van Den Ende, Diane C. Bassham Feb 2019

Linking Autophagy To Abiotic And Biotic Stress Responses, Santiago Signorelli, Lukasz Pawel Tarkowski, Wim Van Den Ende, Diane C. Bassham

Genetics, Development and Cell Biology Publications

Autophagy is a process in which cellular components are delivered to lytic vacuoles to be recycled and has been demonstrated to promote abiotic/biotic stress tolerance. Here, we review how the responses triggered by stress conditions can affect autophagy and its signaling pathways. Besides the role of SNF-related kinase 1 (SnRK1) and TOR kinases in the regulation of autophagy, abscisic acid (ABA) and its signaling kinase SnRK2 have emerged as key players in the induction of autophagy under stress conditions. Furthermore, an interplay between reactive oxygen species (ROS) and autophagy is observed, ROS being able to induce autophagy and autophagy ...


Synder: Inferring Genomic Orthologs From Synteny Maps, Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, Eve Syrkin Wurtele Feb 2019

Synder: Inferring Genomic Orthologs From Synteny Maps, Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, Eve Syrkin Wurtele

Genetics, Development and Cell Biology Publications

Ortholog inference is a key step in understanding the evolution and function of a gene or other genomic feature. Yet often no similar sequence can be identified, or the true ortholog is hidden among false positives. A solution is to consider the sequence's genomic context. We present the generic program, synder, for tracing features of interest between genomes based on a synteny map. This approach narrows genomic search-space independently of the sequence of the feature of interest. We illustrate the utility of synder by finding orthologs for the Arabidopsis thaliana 13-member gene family of Nuclear Factor YC transcription factor ...


Adult Neural Stem Cell Plasticity, Elizabeth J. Sandquist, Donald S. Sakaguchi Feb 2019

Adult Neural Stem Cell Plasticity, Elizabeth J. Sandquist, Donald S. Sakaguchi

Genetics, Development and Cell Biology Publications

Stem cells derived from adult tissues have long been considered multipotent, able to differentiate into a limited number of cell types found in their tissue of origin. Embryonic stem cells, in contrast, are pluripotent, which may differentiate into almost all cell types. With the ability to create induced pluripotent stem cells from somatic cells now available, the properties of multipotent stem cells are being re-evaluated. If adult cells may be reverted to pluripotent stem cells, can multipotent stem cells also be manipulated towards pluripotency? Advancements in biotechnology now allow for better methods to investigate stem cell plasticity, such as the ...


Multiple Variables At The Leukocyte Cell Surface Impact Fc Γ Receptor-Dependent Mechanisms, Kashyap R. Patel, Jacob T. Roberts, Adam W. Barb Feb 2019

Multiple Variables At The Leukocyte Cell Surface Impact Fc Γ Receptor-Dependent Mechanisms, Kashyap R. Patel, Jacob T. Roberts, Adam W. Barb

Biochemistry, Biophysics and Molecular Biology Publications

Fc γ receptors (FcγR) expressed on the surface of human leukocytes bind clusters of immunoglobulin G (IgG) to induce a variety of responses. Many therapeutic antibodies and vaccine-elicited antibodies prevent or treat infectious diseases, cancers and autoimmune disorders by binding FcγRs, thus there is a need to fully define the variables that impact antibody-induced mechanisms to properly evaluate candidate therapies and design new intervention strategies. A multitude of factors influence the IgG-FcγR interaction; one well-described factor is the differential affinity of the six distinct FcγRs for the four human IgG subclasses. However, there are several other recently described factors that ...


Development And Characterization Of An Immunologically Humanized And Cancer Xenograft Model In Pigs With Severe Combined Immunodeficiency (Scid), Adeline Nicole Boettcher Jan 2019

Development And Characterization Of An Immunologically Humanized And Cancer Xenograft Model In Pigs With Severe Combined Immunodeficiency (Scid), Adeline Nicole Boettcher

Graduate Theses and Dissertations

Swine with severe combined immunodeficiency (SCID) are an emerging large animal model for biomedical research. There have been several SCID pig models described since our first discovery of naturally occurring SCID with mutations in Artemis (DCLRE1C) in 2012. SCID animals are particularly useful in biomedical research due to their lack of T, B, and sometimes NK cells. Absence of the adaptive immune system allows for human cell and tissue xenotransplantation into these SCID animals. The works described within this thesis are categorized under four main goals: (1) further characterization of the immune system of Art-/- SCID pigs, (2) development of ...


Ectopic Expression Of The Arabidopsis Homomeric Acetyl-Coa Carboxylase, Troy Matthew Bunch Jan 2019

Ectopic Expression Of The Arabidopsis Homomeric Acetyl-Coa Carboxylase, Troy Matthew Bunch

Graduate Theses and Dissertations

A number of economic and environmental imperatives have spurred an increased demand for biologically sourced, chemically reduced forms of carbon. Fatty acids, and closely related derivatives, represent an abundant form of such biological carbon. The biosynthesis of these molecules requires acetyl-CoA as a primer substrate, and malonyl-CoA as the extender substrate. Malonyl-CoA is generated by the carboxylation of acetyl-CoA, a reaction catalyzed by acetyl-CoA carboxylase (ACCase), which is thought to be an important determinant of the rate limiting reaction of fatty acid biosynthesis. In Arabidopsis, as in most dicotyledonous plants, two distinct isozymes catalyze this reaction, a cytosolic homomeric form ...