C-reactive protein (CRP) is an acute phase protein produced by hepatocytes whose serum concentration increases in inflammatory conditions including cardiovascular complications. Statins that are used in the treatment of cardiovascular diseases to reduce cholesterol also lower serum CRP levels. In human hepatoma Hep3B cells, CRP is induced in response to cytokines IL-6 and IL-1β. The objective of the study was to determine the mechanism of regulation of CRP gene expression in Hep3B cells in response to cytokines and to determine the effect of statins on CRP expression. Key findings of our research were: 1. IL-1β-activated NF-κB p50/p65 acted synergistically with IL-6-activated C/EBPβ in inducing CRP transactivation through the proximal CRP promoter. 2. A NF-κB site was localized in the proximal CRP promoter centered at position -69 overlapping the known OCT-1/HNF-1/HNF-3 sites. 3. The synergy between IL-6 and IL-1β in inducing CRP gene expression was partially mediated through the NF-κB site. 4. In the absence of C/EBPβ, a complex containing C/EBPζ and RBP-Jκ was formed at the C/EBP-p50-site. 5. Overexpressed C/EBPζ repressed both (IL-6+IL-1β)-induced and C/EBPβ-induced CRP expression. 6. OCT-1 repressed (IL-6+IL-1β)-induced CRP transactivation through the proximal CRP promoter. 7. Statins reduce cytokine-induced CRP gene expression at the transcriptional level. These findings led us to conclude that: 1. CRP transcription is determined by the relative levels of various transcription factors such as C/EBPβ, C/EBPζ, NF-κB and OCT-1 and their interaction with the proximal CRP promoter. 2. Inhibition of CRP transcription by statins is not due to an anti-inflammatory effect but due to the direct effect on CRP gene expression.

The hepatitis B virus (HBV) is a common virus, with two billion people infected worldwide. It causes approximately 600,000 deaths each year, despite the availability of an effective vaccine since 1982. Maize as a platform for oral vaccination can supply a heat stable vaccine, which does not require syringes or trained personnel to administer. The Hepatitis B Surface antigen was transformed into maize and this seed was used to evaluate expression levels through the breeding process. The transgene was transferred into two elite maize inbreds by backcrossing. Highest expressing ears were selected each generation until approximately 99% commercial parent was obtained with a single gene coding for the vaccine present. Selected individuals were crossed to create hybrid plants. This work was done to create high expressing high yielding lines that could be used as a plant-based oral vaccine for Hepatitis B.

This study focuses on a secondary contact zone between two sister species of woodrat, Neotoma fuscipes (dusky-footed woodrat) and N. macrotis (big-eared woodrat). Along the Nacimiento River, on the border of southern Monterey and northern San Luis Obispo counties, the ranges of these sister species of woodrats meet and overlap forming a secondary contact zone. The zone of secondary contact is estimated to include a 500-meter (~1,650 linear feet) portion of the Nacimiento River riparian corridor. This research examines quantifiable morphological change that is likely associated with heightened inter-specific competition within the contact zone. When in sympatry the sister species may compete for resources indirectly through exploitative competition, or directly through contest competition, or through a combination of these two processes. The prediction that heightened competition has resulted in distinctive morphological character shifts between allopatric and sympatric populations was tested my examining size and shape of adult woodrats along a 20-kilometer transect. It was confirmed that adults woodrats of the two sister taxa are morphologically distinct (N = 602) and that the phallus morphology was indeed a reliable means to identify adult male woodrats as to species (p < 0.0001, N = 331). A two model approach was used to examine convergence and divergence in size and shape of woodrats across the transect. Neotoma fuscipes exhibited a statistically significant divergerence from N. macrotis with regard to breadth of rostrum (p < 0.0001, N = 414) in a region of sympatry along the Nacimiento River. Based on the results on one statistical model, N. macrotis exhibited a statistically significant convergence with regard to body-size (p = 0.0240, N = 587) and length of hind foot (p < 0.0001, N = 563) towards those of N. fuscipes between zones of sympatry and allopatry. Alternatively, based on the results of a second statistical model that accounted for environmental variation within the system both species exhibited a statistically significant divergence with regard to body-size (p = 0.0054, N = 587) and towards that of N. fuscipes between zones of sympatry and allopatry. Also, N. macrotis exhibited a statistically significant convergence with regard to length of ear (p = 0.0022, N = 563) towards that of N. fuscipes. Based on the results of both models, detectable re-patterning of size-independent traits was observed to varying degrees. The morphological character shifts between sympatric populations and allopatric populations of woodrats suggest that ecological interactions between the species are occuring. Specifically, across the contact zone, patterns of variation in body-size and other morphological character traits are consistent with expectations of a combination of contest and exploitative competition.

Chenopodium pallidicaule, known commonly as cañahua, is a semi-domesticated crop grown in high-altitude regions of the Andes. It is an A-genome diploid (2n = 2x = 18) relative of the allotetraploid (AABB) Chenopodium quinoa and shares many of its nutritional benefits. Both species contain a complete protein, a low glycemic index, and offer a wide variety of nutritionally important vitamins and minerals. Due to its minor crop status, few genomic resources for its improvement have been developed. Here we present a fully annotated, reference-quality assembly of cañahua. The reference assembly was developed using a combination of established techniques, including multiple rounds of Hi-C based proximity-guided assembly. The final assembly consists of 4,633 scaffolds with 96.6% of the assembly contained in nine scaffolds representing the nine haploid chromosomes of the species. Repetitive element analysis classified 52.3% of the assembly as repetitive, with the most common (27.3% of assembly) identified as LTR retrotransposons. MAKER annotation of the assembly yielded 22,832 putative genes with an average length of 4.6 Kb. When compared with quinoa, strong patterns of synteny support the hypothesis that cañahua is a close A-genome diploid relative, and thus potentially a model diploid species for genetic analysis and improvement of quinoa. Resequencing and phylogenetic analysis of a diversity panel of 30 cañahua accessions collected from across the Altiplano suggests that coordinated efforts are needed to enhance genetic diversity conservation within ex situ germplasm collections.

Plant diseases remain a major obstruction to meeting the world’s increased demand for soybean oil and protein. Reducing the losses caused by diseases in order to improve crop production is a high priority for agricultural research. The need for novel strategies for plant disease control cannot be overstated. In the present study, selected defense-related genes were silenced and/or overexpressed in soybean using a virus-based vector and the resultant plants were tested for their responses to pathogens. The first part of the study focused on Rps1k (Resistance to Phytophthora sojae) gene. The two conserved domains encoding ‘P-Loop NTPase’ and ‘PLN03210’ of Rps1k were independently overexpressed. Stem inoculation assays for the overexpressing plants showed significant resistance to virulent races; 90% standing plants compared to 10% in controls. Lesion length was greatly restricted only in case of plants overexpressing ‘PLN03210’. Simultaneous silencing of Rps1k-1 and Rps1k-2 resulted in remarkable susceptibility to avirulent races when tested by a detached-leaf assay. The second part of the study entailed silencing/overexpression of the chlorophyllase genes GmCLH1 and GmCLH2 and testing the responses of the silenced/overexpressing plants to the sudden death pathogen Fusarium virguliforme. Four weeks post root inoculation, GmCLH2-silenced plants showed enhanced resistance while the GmCLH2-overexpressing plants exhibited markedly increased susceptibility when compared to empty vector control. RT-PCR assay of PR genes revealed elevated expression of PR2 and PR4 in GmCLH2-silenced plants. In the third part of the study, soybean plants silenced for a leucine-rich repeat receptor-like kinase (GmRLK3) gene were examined for their responses to different pathogens. Silencing of GmRLK3 enhanced susceptibility to infection with Alternaria tenuissima or Sclerotinia sclerotiorum as revealed by rapid disease progress on treated leaves. Surprisingly, silencing of GmRLK3 in known susceptible soybean cultivars rendered the silenced plants resistant to P. sojae. The ensuing partial resistance to P. sojae was consistent with results of RT-PCR assays that showed a significant increase in the transcript level of the osmotin-encoding gene (PR5a) in the GmRLK3-silenced plants. PR5a is considered a marker for systemic acquired resistance.

Environmental toxicants are ubiquitous throughout the environment as a result of human activity. Among these toxicants, environmental estrogens are a category of particular concern due to their environmental prevalence and potency in altering reproductive traits. While many studies have addressed the detrimental effects of environmental estrogens on both aquatic and terrestrial organisms, few have analyzed the potential for these compounds to alter mitochondrial function. Mitochondria are the primary energy-generating system for all eukaryotic life, supporting all aspects of development, metabolism, and growth. Each cell within the body contains many mitochondria which in turn contain multiple copies of their own DNA genome, mitochondrial DNA (mtDNA). Mutations in mtDNA are responsible for a wide range of human diseases such as metabolic syndromes, cancers, and obesity. Among these mitochondrial diseases many are characterized by increased levels of heteroplasmy, multiple mitochondrial DNA haplotypes within an individual. Increased heteroplasmy can alter normal mitochondrial function and influence disease initiation and progression. To date, no studies have investigated the effects of synthetic estrogens on mitochondrial genome stability. Synthetic estrogens have the capacity to bind to estrogen receptors and initiate estrogenic responses through translocation into the mitochondrion. Despite our knowledge about the relationship of heteroplasmy and disease, we still do not have a complete grasp of the mechanisms of heteroplasmic induction. Here we report our analysis of the effects of 17α-ethynylestradiol (EE2) exposure in three studies to investigate its effect on mitochondrial genome stability. Data analysis reveals a statistically significant relationship between EE2 exposure and increased heteroplasmic frequency.

Smith-Magenis Syndrome (SMS; OMIM #182290) is a multiple congenital abnormality and intellectual disability (ID) disorder caused by either an interstitial deletion of the 17p11.2 region containing the retinoic acid induced-1 (RAI1) gene or a mutation of the RAI1 gene. Individuals diagnosed with SMS typically present characteristics such as ID, self-injurious behavior, sleep disturbance, ocular and otolaryngological abnormalities, craniofacial and skeletal abnormalities, neurological and behavioral abnormalities, as well as other systemic defects and manifestations. Previous work by Vyas in 2009 showed temporal expression of rai1 in zebrafish embryos as early as 9 hpf. We hypothesize that there is maternal rai1 expression as early as zero hours post fertilization in wild type embryos. Using end-point PCR, we found that in fact there is maternal rai1 expression is detectable as early as 2 hours post fertilization (hpf) in wild type zebrafish embryos. Furthermore, we quantified rai1 expression using qPCR and found that rai1 expression declines significantly after 6 hpf. We hypothesize that a down regulation of rai1 or loss of rai1 will lead to morphological phenotypes, especially if that loss of rai1 function occurs during the earliest stages of zebrafish embryogenesis. Using a rai1morpholino oligonucleotide (MO), we found a loss of rai1 expression did not induce a morphological phenotype in in wild type embryos; furthermore, we also found that a loss of maternal rai1 expression did not induce a morphological phenotype as well. Utilizing a mutant rai1 zebrafish line, we found that both rai1 +/fh370 progeny nor rai1 fh370/fh370 progeny exhibited a morphological phenotype and that downstream targets such as bdnf were not affected by a reduction or complete loss of rai1. Prior research has shown that retinoic acid (RA) can induce rai1 expression. We hypothesize that RA can induce expression of rai1 during zebrafish embryogenesis. Using wild type fish and a rai1 in situ hybridization probe, we found that RA treatment at 25 hpf induced expression of rai1. The construction of a rai1 overexpression vector used for overexpression studies was started. Further development of GFP expression vector and zebrafish rai1 antibody are needed to determine if the morpholino is reducing rai1 protein expression.

Plants are threatened by global change, increasing variability in weather patterns, and associated abiotic stress. Consequently, there is an urgent need to enhance our ability to predict plant community dynamics, shifts in species distributions, and physiological responses to environmental challenges. By building a fundamental understanding of plant stress tolerance, it may be possibly to protect the ecological services, economic industries, and communities that depend on plants. Dehydration tolerance (DhT) is an important mechanism of water stress tolerance with promising translational applications. Here, I take advantage natural variation in DhT to gain a deeper insight into this complex trait. In addition, I address questions related to the causes and consequences of sexual dimorphisms in DhT. Understanding sexual dimorphisms in stress tolerance is critical because these dimorphisms can drive spatial segregation of the sexes, biased sex ratios, and may ultimately reduce sexual reproduction and population persistence. This work takes an integrated approach, addressing DhT on multiple scales from ecology, to physiology, to genomics in the tropical liverwort Marchantia inflexa. Initially, I tested for correlations between DhT and environmental dryness, sex differences in DhT, and genetic vs. plastic contributions to DhT variability. I found that patterns of variation in DhT are associated with environmental variability, including complex sexual dimorphisms, and derive from a combination of plasticity and genetic differences in DhT. Subsequently, I leveraged the variability in DhT to identify candidate DhT enhancing genes. In M. inflexa intraspecific differences in DhT are impacted by baseline variability among plants, as well as unique gene expression responses initiated during drying. In parallel, I assembled a draft genome assembly for M. inflexa, which was employed to investigate questions of sex chromosome evolution and sexual dimorphism in DhT. Finally, the bacteriome of M. inflexa was characterized and found to be extremely diverse and variable. Collectively, this work adds to a growing understanding of DhT and highlights the importance of sampling approaches that seek to comprehensively describe variability in DhT. I detected complex patterns of variability in DhT among populations and the sexes of M. inflexa, which were used to gain insight into the genetic intricacies of DhT.

Obesity is a major health problem in the United States and worldwide. It increases the risk for type-2 diabetes and cardiovascular diseases. A chronic low-grade inflammation occurring in white adipose tissue (WAT) is causally linked to the development of insulin resistance (IR), metabolic syndrome and obesity-associated chronic diseases. The aim of this dissertation research was to elucidate the WAT function in metabolic syndrome using genetic (overexpression of an adipose pro-inflammatory hormone, angiotensinogen) and nutritional manipulations/approaches (caloric restriction and omega-3 fatty acids), with specific emphasis on the role of inflammation. Previous research indicates that WAT renin-angiotensin system (RAS) is overactivated in obesity. However, its role in the pathogenesis of IR is hitherto unknown. Using mice overexpressing angiotensinogen (Agt), the only precursor for the hypertensive hormone angiotensin (Ang) II, in WAT, we showed that adipose-specific RAS overactivation leads to systemic IR. This is at least in part due to Ang II, NADPH oxidase and NF-kB-dependent increases in WAT inflammation. Caloric restriction is the main dietary intervention to treat obesity-associated metabolic disorders. While most health agencies recommend a low-fat diet, energy-restricted high-fat diets (HFR) are also claimed to be effective in this regard. Here, we show that weight loss due to HFR is accompanied by improvements of IR but only partial resolution of WAT inflammation. Further, this diet negatively impacted the adipokine profile supporting the current recommendations for low-fat diets. Dietary interventions targeted at reducing WAT inflammation have not been explored in detail. Eicosapentaenoic acid (EPA) is an omega-3 polyunsaturated fatty acid of marine origin with anti-inflammatory properties. We show that EPA is able to both prevent and reverse high-fat diet-induced IR and hepatic steatosis via modulation of WAT inflammation. In conclusion, primary changes occurring in WAT, such as overexpression of Agt, can lead to WAT inflammation and systemic IR. Moreover, nutritional interventions targeting at reducing adiposity (caloric restriction) and inflammation (EPA) can both lead to improvements in systemic IR. Our findings support the current recommendation of low-fat diets for improvement in metabolic profile and show that dietary modulation of WAT function can be used to improve metabolic derangements in obesity.

Lambdoid phages suppress transcription termination to fully express their genes. Antitermination of early gene expression in most lambdoid phages is mediated by an interaction between the N protein and a number of host-encoded factors. Bacteriophage HK022 does not rely on a protein for antitermination. To promote full expression of early phage genes, the transcripts of the HK022 put sites interact directly with RNA polymerase to convert it to a termination resistant form. Bacteriophage HK639 also uses RNA-mediated antitermination. However, it only possesses a single put-like element in its left operon. Because most lambdoid phages, including HK022, have antiterminator elements in each of their early operons, the presence of a single antitermination site in HK639 was unexpected. We have shown that host genes involved in promoting protein-mediated antitermination are not required for HK639 growth. We have also shown that expression of the left operon is essential for lytic growth. Replacement of the left operon promoter, PL, and the putL antitermination sequence prevented HK639 phage release. A similar construct that only replaced putL also prevented phage release. These results suggest that antitermination is required for HK639 excision and/or lytic growth. To distinguish between a defect in phage excision versus a defect in lytic growth, the mutations were crossed onto lytically growing phage. Recombinant phages could not be recovered which suggests a defect in lytic growth is preventing phage release. Additional replacements of left operon sequences suggest that antitermination is not the only requirement for lytic growth. A 2,161bp deletion (HK639 genome coordinates 30,888-33,048) and a 1,736bp deletion (HK639 genome coordinates 29,152- 30,887) downstream of the HK639 putL site also prevented phage release, whereas a 1,746bp deletion (HK639 genome coordinates 29,151-27,406) did not. These results suggest that the deleted HK639 left operon sequences are required for lytic growth. BLAST analysis did not provide insight into the function of the deleted genes. Although the function of many of the HK639 left operon genes is unknown, their importance in phage growth can now be verified by complementation analysis. Our results suggest that HK639 may use a novel mechanism to control the expression of its early genes.