Digital Commons Network^™

A High-Throughput Gene Silencing Approach For Studying The Interaction Between Perennial Ryegrass (Lolium Perenne) And The Fungal Endophyte Neotyphodium Lolii, S. Felitti, P. Tian, D. Edwards, G. C. Spangenberg

IGC Proceedings (1997-2023)

Perennial ryegrass (Lolium perenne L.) and its fungal endophyte (Neotyphodium lolii) are known to establish a mutualistic association that impacts on the agronomic productivity of endophyte-infected ryegrass pastures. To study this interaction at the molecular level, a genomic resource consisting of 13,964 endophyte ESTs has been generated. However, the functions of a large proportion of these genes remain to be elucidated. Recent work has demonstrated the potential for RNA-mediated gene silencing to suppress gene expression in a sequence specific manner thus allowing for the subsequent analysis of gene function.

Synthesis, Characterization, And Evaluation Of Amphiphilic Cell-Penetrating Peptides As Sirna Delivery Tools For Cancer Therapy, Muhammad Imran Sajid

Pharmaceutical Sciences (PhD) Dissertations

Post-transcriptional gene silencing (PTGS), also termed as RNA interference (RNAi) possess a great therapeutic potential. Three siRNA-based products have been recently approved that have developed a renewed interest in the scientific community to explore this alternative therapeutic area rigorously. However, several challenges are limiting their use as a widespread therapeutic agent. The limitations include their membrane impermeability, short half-life, elimination by the kidney, entrapment by the reticuloendothelial system, sequestration by plasma proteins, endosomal trap, and off-target effects.

Several delivery systems and transfection agents have been investigated to address these challenges. Still, most of the systems suffer from toxicity and low …

Rna Interference For Emerald Ash Borer Suppression: Ecotoxicological Assessment And Delivery Methods, Flavia Pampolini

Theses and Dissertations--Entomology

The emerald ash borer (EAB), Agrilus planipennis (Coleoptera: Buprestidae), is a highly invasive phloem-feeding insect native to Asia. It has killed millions of ash trees (Fraxinus spp.) since its accidental introduction into North America, causing profound economic and ecological impacts. RNA interference (RNAi) or double-stranded RNA (dsRNA)-mediated gene silencing is an emerging biotechnology that is developing as an innovative tool for pest management. Exogenous dsRNA triggers the RNAi pathway, silences genes, and disrupts protein function, causing insect mortality. RNAi has proven effective in reducing target gene expression and causing mortality in EAB; however, two aspects stand as barriers …

Micelles And Lipid Nanoparticles: Catalysis And Biomedical Application., Faisal Ibrahim

Electronic Theses and Dissertations

RNA-based therapeutics is a rapidly expanding field due to its enormous potential for treatment of diseases through knockdown of genes or expression of therapeutic proteins. However, due to the overall negative-charge of an RNA molecule, RNA-based therapeutics must rely on delivery systems to overcome the various biological barriers for ultimate release of an RNA payload into the cytosol. Over the past three decades, the development of lipid-based RNA delivery systems, especially lipid nanoparticles (LNPs), have been comprehensively studied due to their unique properties. LNPs represent the most widely used delivery systems for RNA-based therapeutics, as evidenced by the clinical approvals …

Resistance To Aflatoxin Accumulation In Maize Mediated By Host-Induced Gene Silencing Of Aspergillus Flavus Alkaline Protease And O-Methyltransferase-A Genes, Olanike Omotola Omolehin

LSU Doctoral Dissertations

Aspergillus flavus is a soil-borne fungal pathogen that infects maize and produces aflatoxins. In the current study, portions of the alkaline protease (alk) and the O-methyl transferase (omtA) genes, which are key in A. flavus virulence and aflatoxin biosynthesis, respectively, were targeted for suppression through an RNAi (RNA interference) approach known as Host-Induced Gene Silencing (HIGS). Separate RNAi vectors were designed to carry regions of the alk and omtA gene fragments (Alk-RNAi and OmtA-RNAi) and introduced into B104 maize zygotic embryos. Eight and six transformation events were positive for the alk and omtA transgene, respectively. …

Emerald Ash Borer Specific Gene Silencing Has No Effect On Non-Target Organisms, Flavia Pampolini, Lynne K. Rieske

Entomology Faculty Publications

The sequence complementarity of the RNA interference (RNAi) pathway allows for targeted suppression of genes essential for insect survival, and enables development of pest management strategies specific to a given species while reducing the likelihood of adversely impacting non-target organisms (NTOs). The feasibility of manipulating the RNAi pathway to cause mortality in the highly invasive emerald ash borer (EAB) has been demonstrated. Here the spectrum of activity of three double stranded RNAs (dsRNAs) targeting the genes hsp, shi, and sn-rnp in EAB was evaluated in model insects representing five functional guilds including herbivore, predator, detritivore, pollinator, parasitoid; …

Invasive Species Control And Resolution Of Wildlife Damage Conflicts: A Framework For Chemical And Genetically Based Management Methods, Larry Clark, John Eisemann, John Godwin, Katherine Horak, Kevin Oh, Jeanette R. O'Hare, Antoinette J. Piaggio, Kim M. Pepin, Emily W. Ruell

USDA Wildlife Services: Staff Publications

Vertebrate wildlife damage management relates to developing and employing methods to mitigate against damage caused by wildlife in the areas of food production, property damage, and animal or human health and safety. Of the many management tools available, chemical methods (e.g., toxicants) draw the most attention owing to issues related to environmental burden, species specificity, and humaneness. Research and development focusing on RNA interference and gene drives may be able to address the technical aspects of performance goals. However, there remain many questions about regulation, environmental risk, and societal acceptance for these emerging biological technologies. Here we focus on the …

Improving Transgenic Rnai In Plants, Daai Zhang

University of Wollongong Thesis Collection 2017+

Double-stranded RNA (dsRNA)-induced gene silencing, or RNA interference (RNAi), is a conserved gene control mechanism in eukaryotes that has been exploited extensively as a tool for gene knockdown. In plants, RNAi has been achieved mainly through the expression of transgenes encoding long hairpin-shaped RNA (hpRNA), which has proven to be a powerful tool in gene function studies and crop improvement. A typical hpRNA transgene construct is comprised of a perfect inverted repeat with a sense and antisense sequence of the target gene, separated by a spacer sequence. A number of studies from us and others have indicated that hpRNA transgenes …

Structure, Function And Potential Application Studies Of Selenium Substituted Nucleic Acids, Ziyuan Fang

Chemistry Dissertations

Nucleic Acids are the most important macromolecules in living systems. They directly participate in storing, transferring and expressing the genetic information, thereby controlling and regulating the function of living systems. Therefore, nucleic acid research will give us molecular insights into lives. Meanwhile, many novel research methods based on nucleic acids have been developed. Moreover, nucleic acid-based therapeutics have been developed rapidly over the past several years, leading to a revolution on drug discovery and disease study at the molecular level and the genetic level. Consequently, the structure and function studies on nucleic acids and protein-nucleic acid complexes have attracted tremendous …

Targeting Cdk6 And Bcl2 Exploits The "Myb Addiction" Of Ph+ Acute Lymphoblastic Leukemia, Marco De Dominici, Patrizia Porazzi, Angela Rachele Soliera, Samanta A. Mariani, Sankar Addya, Paolo Fortina, Luke F. Peterson, Orietta Spinelli, Alessandro Rambaldi, Giovanni Martinelli, Anna Ferrari, Ilaria Iacobucci, Bruno Calabretta

Department of Cancer Biology Faculty Papers

Philadelphia chromosome–positive acute lymphoblastic leukemia (Ph^þ ALL) is currently treated with BCR-ABL1 tyrosine kinase inhibitors (TKI) in combination with chemotherapy. However, most patients develop resistance to TKI through BCR-ABL1–dependent and –independent mechanisms. Newly developed TKI can target Ph^þ ALL cells with BCR-ABL1–dependent resistance; however, overcoming BCR-ABL1–independent mechanisms of resistance remains challenging because transcription factors, which are difficult to inhibit, are often involved. We show here that (i) the growth of Ph^þ ALL cell lines and primary cells is highly dependent on MYB-mediated transcriptional upregulation of CDK6, cyclin D3, and BCL2, and (ii) restoring their expression in MYB-silenced …

Tomato Spotted Wilt Virus Nss Protein Supports Infection And Systemic Movement Of A Potyvirus And Is A Symptom Determinant, Hernan Garcia-Ruiz, Sergio M. Gabriel Peralta, Patricia A. Harte-Maxwell

Department of Plant Pathology: Faculty Publications

Plant viruses are inducers and targets of antiviral RNA silencing. To condition susceptibility, most plant viruses encode silencing suppressor proteins that interfere with antiviral RNA silencing. The NSs protein is an RNA silencing suppressor in orthotospoviruses, such as the tomato spotted wilt virus (TSWV). The mechanism of RNA silencing suppression by NSs and its role in virus infection and movement are poorly understood. Here, we cloned and tagged TSWV NSs and expressed it from a GFP-tagged turnip mosaic virus (TuMV-GFP) carrying either a wild-type or suppressor-deficient (AS9) helper component proteinase (HC-Pro). When expressed in cis, NSs restored pathogenicity and promoted …

Susceptibility Genes To Plant Viruses, Hernan Garcia Ruiz

Department of Plant Pathology: Faculty Publications

Plant viruses use cellular factors and resources to replicate and move. Plants respond to viral infection by several mechanisms, including innate immunity, autophagy, and gene silencing, that viruses must evade or suppress. Thus, the establishment of infection is genetically determined by the availability of host factors necessary for virus replication and movement and by the balance between plant defense and viral suppression of defense responses. Host factors may have antiviral or proviral activities. Proviral factors condition susceptibility to viruses by participating in processes essential to the virus. Here, we review current advances in the identification and characterization of host factors …

Regulated Transcriptional Silencing Promotes Germline Stem Cell Differentiation In Drosophila Melanogaster, Pooja Flora

Legacy Theses & Dissertations (2009 - 2024)

Germ cells are the only cell in an organism that have the capacity to give rise to a new organism and are passed from one generation to the next. Therefore, to maintain this unique ability of totipotency and immortality, germ cells execute specific functions, such as, repression of a somatic program and contour a germ line-specific pre- and post-transcriptional gene regulatory landscape. In many sexually reproducing organisms, germ cells are formed during the earliest stages of embryogenesis and undergoes several stages of development to eventually get encapsulated by the somatic cells of the gonad. Once, in the gonad, the germ …

Small Rna-Dependent Gene Silencing In The Green Alga Chlamydomonas Reinhardtii: Functions And Mechanisms, Eun Jeong Kim

School of Biological Sciences: Dissertations, Theses, and Student Research

Small RNAs (sRNAs), ~20-30 nucleotides in length, are non-coding RNAs that play essential roles in the regulation of gene expression in eukaryotes. They lead to inactivation of cognate sequences at the post-transcriptional level via a variety of mechanisms involved in translation inhibition and/or RNA degradation.

In the Chlorophyta Chlamydomonas reinhardtii, however, the molecular machinery responsible for sRNA-mediated translational repression remains unclear. To address the mechanisms of translation inhibition by sRNA, we have isolated an RNAi defective mutant (Mut26), which contains a deletion of the gene encoding the homolog of CCR4 in Chlamydomonas. We investigated the expression of …

Intrinsic And Innate Defenses Of Neurons: Détente With The Herpesviruses, Lynn Enquist, David A. Leib

Dartmouth Scholarship

Neuroinvasive herpesviruses have evolved to efficiently infect and establish latency in neurons. The nervous system has limited capability to regenerate, so immune responses therein are carefully regulated to be nondestructive, with dependence on atypical intrinsic and innate defenses. In this article we review studies of some of these noncanonical defense pathways and how herpesvirus gene products counter them, highlighting the contributions that primary neuronal in vitro models have made to our understanding of this field.

Development Of Gene Silencing Technique For Crop Protection Against Soil-Borne Fungal Disease, Guo Huishan, Gao Feng, Zhao Jianhua, Zhang Bosen

Bulletin of Chinese Academy of Sciences (Chinese Version)

Crop disease caused by soil-borne fungal pathogens is one of the major threatens to agriculture nowadays. Due to the lack of efficient control method, it is becoming a key factor to restrict sustainable development of agricultural production in China. Gene silencing (or RNA silencing, RNAi) is an important pathway in eukaryotes that regulates gene expression based on sequence homology. Gene silencingbased technology has been widely used as a new strategy for plant protection. In this review, we summarized occurrence and general prevention method of crop disease caused by soil-borne fungi, and introduced recent advances and applications of RNA silencing in …

Mechanisms, Applications, And Perspectives Of Antiviral Rna Silencing In Plants / Mecanismos, Aplicaciones Y Perspectivas Del Silenciamiento Génico De Virus En Plantas, Hernan Garcia-Ruiz, Mayra Teresa Garcia Ruiz, Sergio Manuel Gabriel Peralta, Cristina Betzabeth Miravel Gabriel, Kaoutar El-Mounadi

Department of Plant Pathology: Faculty Publications

Viral diseases of plants cause important economic losses due to reduction in crop quality and quantity to the point of threatening food security in some countries. Given the reduced availability of natural sources, genetic resistance to viruses has been successfully engineered for some plant-virus combinations. A sound understanding of the basic mechanisms governing plant-virus interactions, including antiviral RNA silencing, is the foundation to design better management strategies and biotechnological approaches to engineer and implement antiviral resistance in plants. In this review, we present current molecular models to explain antiviral RNA silencing and its application in basic plant research, biotechnology and …

Inheritance Of Virulence In The Root Rot Pathogen Phytophthora Sojae, Sirjana Devi Shrestha

Electronic Thesis and Dissertation Repository

The oomycete Phytophthora sojae causes stem and root rot of soybean plants. The interaction of pathogen avirulence (Avr) and host resistance (R)-genes determine the disease outcome. The Avr3a mRNA transcript level is variable among P. sojae strains and determines virulence towards the R-gene Rps3a. To study the inheritance of virulence, genetic crosses and self-fertilizations were performed. A cross between P. sojae strains ACR10 and P7076 causes transgenerational gene silencing of Avr3a allele, and this effect is meiotically stable up to the F₅ generation. However, test-crosses of F₁ (Avr3a^ACR10/Avr3a …

Silencing Of The Fibroblast Growth Factor 21 Gene Is An Underlying Cause Of Acinar Cell Injury In Mice Lacking Mist1, Charis L. Johnson, Rashid Mehmood, Scott W. Laing, Camilla V. Stepniak, Alexei Kharitonenkov, Christopher L. Pin

Paediatrics Publications

Fibroblast growth factor 21 (FGF21) is a key regulator of metabolism under conditions of stress such as starvation, obesity, and hypothermia. Rapid induction of FGF21 is also observed in experimental models of pancreatitis, and FGF21 reduces tissue damage observed in these models, suggesting a nonmetabolic function. Pancreatitis is a debilitating disease with significant morbidity that greatly increases the risk of pancreatic ductal adenocarcinoma. The goals of this study were to examine the regulation and function of FGF21 in acinar cell injury, specifically in a mouse model of pancreatic injury (Mist1-/-). Mist1-/- mice exhibit acinar cell disorganization, decreased acinar cell communication …

Tumor Necrosis Factor-Alpha Is Produced By Dying Retinal Neurons And Is Required For Müller Glia Proliferation During Zebrafish Retinal Regeneration, Craig M. Nelson, Kristin M. Ackerman, Patrick O'Hayer, Travis J. Bailey, Ryne A. Gorsuch, David R. Hyde

Biology

Intense light exposure causes photoreceptor apoptosis in dark-adapted adult albino zebrafish (Danio rerio). Subsequently, Müller glia increase expression of the Achaete-scute complex-like 1a (Ascl1a) and Signal transducer and activator of transcription 3 (Stat3) transcription factors and re-enter the cell cycle to yield undifferentiated neuronal progenitors that continue to proliferate, migrate to the outer nuclear layer, and differentiate into photoreceptors. A proteomic analysis of light-damaged retinal homogenates, which induced Müller glia proliferation when injected into an undamaged eye, revealed increased expression of tumor necrosis factor α (TNFα) signaling proteins relative to undamaged retinal homogenates. TNFα expression initially increased in apoptotic photoreceptors …

De Novo Orfs In Drosophila Are Important To Organismal Fitness And Evolved Rapidly From Previously Non-Coding Sequences, Josephine A. Reinhardt, Betty M. Wanjiru, Alicia T. Brant, Perot Saelao, David J. Begun, Corbin D. Jones

Biology

How non-coding DNA gives rise to new protein-coding genes (de novo genes) is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution …

Pax3 Expression, Protein Modifications And Downstream Target Gene Profiling In Melanocytes And Melanoma Cells, Danielle Bartlett

Theses: Doctorates and Masters

PAX3 is a transcription factor. It plays a major role in the development of melanocytes in the embryo. As a result of alternative splicing, the gene gives rise to eight different transcripts which encode proteins that have differing structures and are therefore likely to activate different downstream target genes. The presence of post-translational modifications has also been shown to alter the functions of the proteins.

PAX3 regulates the maintenance of undifferentiated melanoblasts and mediates pathways involved in proliferation, migration and survival. It has been shown to be expressed in melanoblasts, adult melanocytes, naevi and in most melanoma cells. This implies …

Roles Of The Drosophila Sk Channel (Dsk) In Courtship Memory, Ahmad N. Abou Tayoun, Claudio Pikielny, Patrick J. Dolph

Dartmouth Scholarship

A role for SK channels in synaptic plasticity has been very well-characterized. However, in the absence of simple genetic animal models, their role in behavioral memory remains elusive. Here, we take advantage of Drosophila melanogaster with its single SK gene (dSK) and well-established courtship memory assay to investigate the contribution of this channel to memory. Using two independent dSK alleles, a null mutation and a dominant negative subunit, we show that while dSK negatively regulates the acquisition of short-term memory 30 min after a short training session, it is required for normal long-term memory 24 h after extended …

Efficacy Of A Novel Molecular Tool In Silencing Arabidopsis Genes, Chase Purnell, Vibha Srivastava, M. Aydin Akbudak, Scott J. Nicholson

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

RNA interference (RNAi), a pathway capable of silencing genes, has until recently only been achievable in the laboratory by the use of one method, expression of inverted repeat sequences of DNA. These constructs generate a double-stranded RNA, which in turn induce post-transcriptional silencing of other genes that bear sequence homology with the transgene. This approach of targeted gene silencing is extremely useful for studying the function of genes and engineering new traits in both plants and animals. It has recently been discovered that a transgene lacking the polyadenylation signal, called a truncated transgene, is also capable of inducing RNAi in …

The Hippo Pathway Member Yap Plays A Key Role In Influencing Fate Decisions In Muscle Satellite Cells, Robert Judson, Annie Tremblay, Paul Knopp, Robert White, Roby Urcia, Cosimo De Bari, Peter Zammit, Fernando Camargo, Henning Wackerhage

Research outputs 2012

Satellite cells are the resident stem cells of skeletal muscle. Mitotically quiescent in mature muscle, they can be activated to proliferate and generate myoblasts to supply further myonuclei to hypertrophying or regenerating muscle fibres, or self-renew to maintain the resident stem cell pool. Here, we identify the transcriptional co-factor Yap as a novel regulator of satellite cell fate decisions. Yap expression increases during satellite cell activation and Yap remains highly expressed until after the differentiation versus self-renewal decision is made. Constitutive expression of Yap maintains Pax7+ and MyoD+ satellite cells and satellite cell-derived myoblasts, promotes proliferation but prevents differentiation. In …