Understanding the genetic regulation of the response to wounding and wound healing in fruiting plants is imperative to maintaining agricultural sustainability, preserving the quality of food supplies, and ensuring the economic viability of agriculture. Many genes are known to be induced by wounding, providing both structural repair and defense. The KED gene in tobacco (Nicotiana tabacum) has been shown to be induced by wounding. We have identified its homologue gene in tomato (Solanum lycopersicum) that we named SlKED. We have analyzed gene expression pattern of SlKED through tomato growth and development and in response to wounding as well as hormonal and inhibitor treatments. We found that the plant hormone ethylene played a major role in the expression of SlKED. To further identify evidence for physiological and transductional functions of KED and SlKED, the tobacco KED gene was introduced to tomato and overexpressed by the fruit tissue-active PUN1 promoter from pepper (Capsicum annuum,). The expression of this gene was compared to the expression of the native SlKED gene and other known wound response genes in both the wild-type and transgenic tomato plants. The upregulation of the native SlKED gene by wounding was significantly muted in the tobacco KED-expressing transgenic plants. The expression of other genes known to be associated with wound response transduction pathways was also altered. Our studies implicate the KED gene in defense mechanisms for mechanical stress in tomato plants. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection

Experimentally naive rats show variance in their locomotor reactivity to novelty, some displaying higher (HR) while others displaying lower (LR) reactivity, associated with vulnerability to stress. LRHR phenotype is proposed as an antecedent to the development of stress hyper responsiveness. Results presented here show emergence of antidepressive-like behavior following peripubertal-juvenile exposure to chronic variable physical (CVP) and chronic variable social stress (CVS) in HR rats, and depressive-like behavior following CVP in the LRs. The antidepressive-like behavior in HR rats was accompanied by increased levels of acetylated Histone3 (acH3) and acetylated Histone4 (acH4) at the hippocampal brain-derived neurotrophic factor (BDNF) P2 and P4 promoters respectively. This effect may mediate increased mossy fibre (MF) terminal field size, particularly the suprapyramidal mossy fibre projection volume (SP-MF), in the HR animals following both stress regimens. These findings show that chronic variable stress during adolescence induces individual differences in molecular, neuromorphological and behavioral parameters between LRs and HRs, which provides further evidence that individual differences in stress responsiveness is an important factor in resistance or vulnerability to stress-induced depression and/or anxiety. / by Ozge Oztan. / Thesis (Ph.D.)--Florida Atlantic University, 2013. / Includes bibliography. / Mode of access: World Wide Web. / System requirements: Adobe Reader.

Aging is a multifactoral biological process of progressive and deleterious changes partially attributed to a build up of oxidatively damaged biomolecules resulting from attacks by free radicals. Methionine sulfoxide reductases (Msrs) are enzymes that repair oxidized methionine (Met) residues found in proteins. Oxidized Met produces two enantiomers, Met-S-(o) and Met-R-(o), reduced by MsrA and MsrB respectively. Unlike other model organisms, our MsrA null fly mutant did not display increased sensitivity to oxidative stress or shortened lifespan, suggesting that in Drosophila, having either a functional copy of either Msr is sufficient. Here, two Msr mutant types were phenotypically assayed against isogenic controls. Results suggest that only the loss of both MsrA and MsrB produces increased sensitivity to oxidative stress and shortened lifespan, while locomotor defects became more severe with the full Msr knockout fly. / by Kelli Robbins. / Thesis (M.S.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web.

A principal fonte de proteínas para alimentação humana e animal é fornecida pelas sementes de cereais e leguminosas. O conteúdo de aminoácidos solúveis em endospermas de milho normal e mutantes opaco-2 e floury foram determinadas por HPLC. A análise indicou que a concentração total de aminoácidos solúveis variou entre os mutantes e seus tipos selvagens. Nos mutantes o10, o11 e o13, as concentrações foram aumentadas significativamente quando comparadas ao tipo selvagem W22, enquanto os mutantes o1, o2, o13, fl1 e fl2 exibiram baixas concentrações em relação ao seu respectivo tipo selvagem Oh43. Resultados similares foram obtidos para os mutantes o5, o7 e fl3 em relação aos seus tipos selvagens (B79, B37 e WT3, respectivamente). Para metionina, o mutante o2 e o tipo selvagem Oh43 apresentaram as mais altas concentrações deste aminoácido. Diferenças significativas não foram observadas para os outros aminoácidos analisados, tais como lisina e treonina. Os resultados sugerem que as altas concentrações sugeridas originalmente para estes mutantes devem ser devidas aos níveis destes aminoácidos incorporados nas proteínas de reserva, mas não na forma solúvel. / For human nutrition the main source of vegetable proteins are cereal and legume seeds. The content of total soluble amino acids in mature endosperms of wildtype and maize opaque and floury mutants have been determined by HPLC. The total absolute concentration of soluble amino acids among the mutants and their wild-type counterparts varied depending on the mutant. In the o10, o11 and o13 mutants the concentrations were significantly increased when compared to their wild-type counterpart W22, whereas the mutants o1, o2, o13, fl1 and fl2 exhibited lower concentrations when compared to the wild-type Oh43, Similar results were observed for o5, o7 and fl3 in relation to their specific wild-type counterparts (B79, B37 and WT3, respectively). For soluble methionine content, o2 and Oh43 exhibited the highest concentrations. Significant differences were not observed for other amino acids such as lysine and threonine. The results suggest that the high-lysine concentrations indicated originally for these mutants must be due to the amino acids incorporated into storage proteins, but not in the soluble form.

Tam Ka-ying. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 164-179). / Abstracts in English and Chinese. / Chapter Chapter one: --- Introduction --- p.4 / Chapter 1.1 --- Introduction of BRE --- p.4 / Chapter 1.1.1 --- Discovery of BRE --- p.4 / Chapter 1.1.2 --- cDNA sequence and amino acids sequence of BRE --- p.4 / Chapter 1.1.3 --- BRE expression level in Human and rat organs --- p.5 / Chapter 1.1.4 --- Expression of Human and mouse BRE in multiple isoforms --- p.6 / Chapter 1.1.4.1 --- BRE isoforms in Human --- p.6 / Chapter 1.1.4.2 --- BRE isoforms in mouse --- p.6 / Chapter 1.1.5 --- mRNA level of BRE upon stress --- p.7 / Chapter 1.1.6 --- BRE and steroidogenesis --- p.8 / Chapter 1.1.7 --- BRE and p55 tumor necrosis factor α (TNF) receptor --- p.9 / Chapter 1.1.8 --- BRE and NFkB activity --- p.9 / Chapter 1.1.9 --- Anti-apoptotic effect of BRE --- p.10 / Chapter 1.1.10 --- BRE enhances the growth of tumor cells --- p.12 / Chapter 1.1.11 --- BRE and its ubiquitination activity --- p.12 / Chapter 1.1.12 --- Regulation of Prohibitin and p53 expression and proliferation by BRE --- p.13 / Chapter 1.2 --- Regulation of transcription --- p.15 / Chapter 1.2.1 --- Cis-acting elements --- p.17 / Chapter 1.2.1.1 --- The TATA box --- p.18 / Chapter 1.2.1.2 --- The GC box and CAAT box --- p.18 / Chapter 1.2.1.3 --- The initiator (Inr) --- p.19 / Chapter 1.2.1.4 --- CpG islands --- p.20 / Chapter 1.2.2 --- Trans- acting protein factors --- p.21 / Chapter 1.2.2.1 --- Zinc finger domain --- p.21 / Chapter 1.2.2.2 --- Basic helix-turn-helix domain (bHLH) --- p.22 / Chapter 1.3 --- Hypothesis and Objectives --- p.23 / Chapter Chapter two: --- Materials and Methods --- p.25 / Chapter 2.1 --- Materials --- p.25 / Chapter 2.1.1 --- Primers used in polymerase chain reaction (PCR) and sequencing --- p.25 / Chapter 2.1.2 --- DNA clones used in the studies --- p.26 / Chapter 2.1.3 --- Materials for DNA manipulation --- p.27 / Chapter 2.1.4 --- Materials for protein manipulation --- p.28 / Chapter 2.1.5 --- Antibodies --- p.28 / Chapter 2.1.6 --- Chemical used in treatments --- p.29 / Chapter 2.1.7 --- Kits --- p.29 / Chapter 2.1.8 --- Culture media and reagents --- p.30 / Chapter 2.1.9 --- Instrumentation --- p.30 / Chapter 2.1.10 --- Bacterial strain used for transfection and cloning --- p.31 / Chapter 2.2 --- Methodologies --- p.36 / Chapter 2.2.1 --- Cell culture --- p.36 / Chapter 2.2.1.1 --- Monolayer cells --- p.36 / Chapter 2.2.1.2 --- Suspension cell --- p.36 / Chapter 2.2.2 --- Identification of the transcriptional start site (TSS) of BRE by RNA ligase- mediated rapid amplification of 5，and 3，cDNA ends (RLM-RACE) --- p.37 / Chapter 2.2.3 --- Preparation of the 5' untranslated region (UTR) fragments of BRE --- p.39 / Chapter 2.2.3.1 --- Polymerase chain reaction (PCR) with Taq polymerase --- p.39 / Chapter 2.2.3.2 --- Polymerase chain reaction (PCR) with PhusiońёØ high-fidelity DNA.… --- p.40 / Chapter 2.2.4 --- Construction of the reporter constructs --- p.42 / Chapter 2.2.5 --- Cell transfection --- p.42 / Chapter 2.2.6 --- Dual-luciferase reporter assay --- p.43 / Chapter 2.2.7 --- Western blotting --- p.44 / Chapter 2.2.8 --- Cell cycle analysis by flow cytometry --- p.45 / Chapter 2.2.9 --- BRE antibody production --- p.43 / Chapter Chapter Three: --- Identification of transcriptional start sites and promoter region for BRE --- p.52 / Chapter 3.1 --- Identification of the transcriptional start sites for BRE --- p.52 / Chapter 3.2 --- Computational analysis of the 5' region of BRE --- p.57 / Chapter 3.2.1 --- Putative transcriptional factor binding sites --- p.57 / Chapter 3.2.2 --- CpG island --- p.58 / Chapter 3.3 --- Identification of BRE promoter --- p.64 / Chapter Chapter Four: --- Characterization of transcriptional regulation of BRE --- p.70 / Chapter 4.1 --- Regulation of BRE promoter by genotoxic stimuli and retinoic acid --- p.71 / Chapter 4.1.1 --- Etoposide --- p.71 / Chapter 4.1.2 --- 4-nitroquinoline-l -oxide (4NQO) --- p.79 / Chapter 4.1.3 --- Retinoic acid (RA) --- p.87 / Chapter 4.2 --- Regulation of BRE promoter by p53 protein and gamma irradiation --- p.90 / Chapter 4.2.1 --- Co-transfection with p53 plasmid --- p.90 / Chapter 4.2.2 --- Gamma irradiation (y irradiation) --- p.96 / Chapter 4.2.2.1 --- γ irradiation treatment of HeLa cells --- p.96 / Chapter 4.2.2.2 --- γ irradiation treatment of Balb/c 3T3 cells --- p.99 / Chapter 4.3 --- Regulation of BRE promoter by BRE --- p.103 / Chapter 4.3.1 --- Co-transfection with V5-tagged BRE (GS-BRE) --- p.103 / Chapter 4.3 2 --- Co-transfection with untagged BRE (pcDNA3-BRE) --- p.107 / Chapter 4.4 --- Regulation of BRE promoter by culture condition --- p.110 / Chapter 4.4.1 --- Cell density --- p.110 / Chapter 4.4.2 --- Serum deprivation --- p.114 / Chapter 4.5 --- Regulation of BRE promoter by kinase inhibitors --- p.120 / Chapter Chapter Five: --- BRE and cell cycle analysis --- p.127 / Chapter 5.1 --- Cell synchronization in G1 phase by aphidicolin (APC) --- p.127 / Chapter 5.1.1 --- Flow analysis --- p.128 / Chapter 5.1.2 --- Luciferase reporter assay --- p.128 / Chapter 5.1.3 --- Western blot analysis --- p.129 / Chapter 5.2 --- Cell synchronization in G2/M phase by colchicine (COL) --- p.137 / Chapter 5.2.1 --- Flow analysis --- p.137 / Chapter 5.2.2 --- Luciferase reporter assay --- p.137 / Chapter 5.2.3 --- Western blot analysis --- p.138 / Chapter 5.3 --- Cell cycle analysis of the treatments investigated by luciferase assays --- p.144 / Chapter Chapter Six: --- Discussion --- p.149 / Chapter 6.1 --- Study of BRE expression --- p.149 / Chapter 6.2 --- Study of BRE regulation --- p.154 / Chapter 6.3 --- Conclusion --- p.163 / Reference --- p.164 / Appendix (Raw data and statistical information of luciferase assays)

Yiu Wai Han. / "June 2003." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (p. 146-156) / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

The Pentatricopeptide Repeat (PPR) gene family produces RNA-binding proteins that target organellar transcripts. The PPR family is expanded in land plants, with nearly 450 genes identified in Arabidopsis thaliana. In plants with a Cytoplasmic Male Sterility (CMS) phenotype, members of the PPR family can act as a RESTORER OF FERTILITY (Rf) and are part of a subset of genes called RESTORER OF FERTILITY-LIKE (RFL). Unlike other PPR transcripts, RFL transcripts are targets of both microRNA (miRNA) and trans-acting siRNA (tasiRNA) and produce secondary siRNA after initial miRNA- or tasiRNA-guided cleavage. We utilized the A. lyrata genome assembly and high-throughput sequencing of small RNA to examine the evolutionary dynamics of the PPR gene family and the pattern of small RNA targeting of RFL transcripts. We found an expanded set of 539 PPR genes in A. lyrata, 51 of which were in the RFL group, often in multiple collinear copies when compared to their A. thaliana orthologs. In-species RFL paralogs appear to be more related to one another than to their collinear orthologs, which is possible evidence of gene conversion or ectopic recombination. miRNA targeting of RFL transcripts is largely conserved with nearly two-thirds of all target sites maintained. TasiRNA targeting was less conserved with roughly one-third of comparable validated tasiRNA targets maintained in both species. However, when clusters of potential tasiRNA targets were considered, roughly two-thirds of target sites are conserved. Production of secondary siRNA from A. lyrata PPR transcripts is less well defined than in A. thaliana, with strong signals coming from phases that are not concordant with the miRNA- or tasiRNA-guided cleavage sites. / Graduation date: 2013

Nucleic acids have proven to be viable targets for small molecule drugs. While many examples of such drugs are detailed in the literature, only a select few have found practical use in a clinical setting. These currently employed nucleic acid targeting therapies suffer from either debilitating off-target side effects or succumb to a resistance mechanism of the target. The need for new small molecules that target nucleic acids is evident. However, designing a novel drug to bind to DNA or RNA requires a detailed understanding of exactly what binding environments each nucleic acid presents. In an effort to broaden this knowledge, the work presented in this thesis details the binding location and affinity of known and novel nucleic acid binding small molecules with targets ranging from simple RNA secondary structure all the way to the complex structure of ribosomal RNA. Specifically, it is shown that the anthracycline class of antineoplastics prefer to bind at or near mismatch base pairs in both physiologically relevant iron responsive element RNA hairpin constructs as well as DNA hairpin constructs presenting mismatched base pairs. Also characterized in this thesis is a novel class of topoisomerase II / histone deacetylase inhibitor conjugates that display a unique affinity for DNA over RNA. Finally, the novel class of macrolide-peptide conjugates, known as peptolides, are shown to retain potent translation inhibition of the prokaryotic ribosome. The binding pocket of the peptolides, including a crevice previously unreachable by macrolides that extends away from the peptidyl transferase center toward the subunit interface, is confirmed in detail via chemical footprinting of the 70S ribosome. Overall, the identification of a novel binding site for the anthracycline class of drugs and the characterization of the two novel drug designs presented in this thesis will undoubtedly aid in the effort to design and discover new molecules that aim for nucleic acid targets. For example, the anthracycline derivative topoisomerase II / histone deacetylase inhibitor conjugates, with their differential mode of nucleic acid binding, may prove to have a unique side effect profile in a therapeutic application. The peptolide compounds also have the potential to be applied as novel antibiotics as they bind to an area of the prokaryotic ribosome unrelated to known macrolide resistance mutations. Furthermore, as a result of the observation of this thesis work that some peptolides also posses eukaryotic translation inhibition capabilities, they could prove to be useful in preventing the growth of rapidly proliferating eukaryotic cells such as plasmodium, leishmania, or tumor cells. Additionally, different head groups could be utilized in creating new peptolides; for example, an oxazolidinone antibiotic could be employed to sample a different binding area of the ribosome.

Thesis (Ph. D.)--West Virginia University, 2001. / Title from document title page. Document formatted into pages; contains x, 152 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 119-149).

Clitellate annelids display conserved mechanisms of segmental ectodermal and mesodermal patterning. These tissues are generated by asymmetric divisions of large stem cells called teloblasts, elongating the ectoderm and mesoderm of the embryo. Each teloblast-derived lineage makes highly stereotyped contributions to the leech: the N, O, P, and Q contribute specific neurons, epidermis, and other ectodermal tissues along the ventral-to-dorsal axis of the embryo, respectively. The N and Q ectodermal lineages appear to be specified autonomously, but specification of the O and P lineages depends upon interactions with other, neighboring teloblast lineages. Until quite recently, there have been precious few teloblast lineage-specific markers, and virtually no molecular candidates for genes influencing the proper differentiation of any of these lineages. Here, I explore the possibility that members of the Pax-Six-Eyes absent-Dachshund network are involved in leech ectodermal patterning. I show that the leech Helobdella sp. Austin has two Pax6 paralogs, and demonstrate that Hau-Pax6A is expressed early in a subset of N-derived cells and O-derived cells. Next, I demonstrate that an ortholog of the six gene family, Hau-six1/2a, is expressed in the P lineage. I show through a series of cell ablations that Hau-six1/2a expression is regulated by neighboring teloblasts in a manner consistent with P fate induction, hinting that this transcription factor may be involved in P specification. The identification of these genes is a first step towards dissecting the molecular mechanisms of ectodermal teloblast differentiation in the leech embryo. The evolutionary context of the deployment of these genes is also discussed. In the appendices, I present two projects on the evolution of pigment patterns in Danio rerio and its relatives. In the first, I show that the larval melanin-containing pigment cells of Danio nigrofasciatus are uniquely redeployed into the adult pigment pattern, in contrast to seven related fishes. In the second, I show that variation in yellow pigment cell populations in different danio species may be dependent on variable signaling through the receptor tyrosine kinase fms pathway. / text