Advances in next-generation sequencing and ribosomal profiling methods highlight that the proteome is likely orders of magnitude larger than previously thought. This expansion potentially occurs through translational recoding, a process that results in the expression of multiple variations of a protein from a single messenger RNA. Our laboratory demonstrated that cyclooxygenase-3/1b (COX-3/1b), a frameshifted, intron-1-retaining, alternative splice variant from the COX-1 gene, is multiply recoded, which results in the translation of at least seven different COX-3 proteins. Two of the recoded COX-3 proteins that we identified are active prostaglandin synthases and are inhibited by non-steroidal anti-inflammatory drugs (NSAIDs). Here we show that the other non-prostaglandin-generating recoded COX-3 proteins perform new roles in innate immunity, a process in which COX are known to generally function. Our analyses determined that these recoded COX-3 proteins bind at or near the amino-terminal region of ATG9a, a critical regulator of both canonical (i.e. digestive autophagy associated with mTORc inhibition and nutrient deprivation) and non-canonical (i.e. xenophagy involved in the innate immune response to invading organisms) autophagy. We further show that this process requires mTORc signaling activity, which opposes the digestive pathway. As a final confirmation of the biological relevance of these recoded COX-3 proteins and their central role in xenophagy, we demonstrate that expression of these COX-3 proteins in an encephalomyocarditis virus infection model system differentially affects infectious virion production. These COX-3 proteins also associate with recoded cytosolic nucleobindin around large, innate immune-related, large LC3-II positive structures (LLPSs). Through mutagenizing catalytic residues of recoded COX-3 proteins and drug assays, we determine LLPS formation is dependent on oxylipin generation.

Artemisinin-resistant Plasmodium falciparum parasites have been reported in the Greater Mekong Subregion since 2007. Artemisinin combination therapy (ACT) is the mainstay of antimalarial treatment and is responsible for decreases in malaria-related morbidity and mortality over the past fifteen years. The slowed parasite clearance rates following ACT indicates resistance to artemisinin derivatives. This resistance places increasing selective pressure for variants or traits that confer resistance to the partner drug used in combination and has led to the rapid failure of several partner drugs. While a single nucleotide polymorphism (SNP) in kelch13 has been shown to mediate some resistance phenotypes, the complete mechanism of artemisinin resistance is poorly understood. The known mechanisms of resistance hint at a connection to autophagy, an intracellular pathway that cells use to degrade waste molecules or organelles in response to stress and starvation, which is poorly characterized in Plasmodium. In this doctoral thesis project, I investigated the role of an autophagy-like mechanism in P. falciparum in the mechanism of artemisinin resistance. I found a SNP in autophagy-related gene 18 (atg18) that was associated with clinical delayed parasite clearance half-life following ACT. This gene encodes PfAtg18, a protein that I characterized as being similar to mammalian/yeast homologues in terms of structure, binding abilities, and ability to form puncta in response to stress. In order to investigate the contribution of the mutation in this protein, I edited the atg18 gene using CRISPR/Cas9 and screened the mutant and parent parasites against a drug library of over 6000 unique compounds. I discovered that while the SNP did not change the mutant parasite's susceptibility to any of the antimalarial compounds using a 72-hour drug pulse, it did alter the susceptibility to 227 other compounds. Further, I found that the SNP offers parasites a fitness advantage by allowing them to grow better in nutrient-limited settings. Finally, I determined that neither this atg18 SNP nor several polymorphisms in kelch13 modulate a dormancy phenotype that appears to be involved in the artemisinin-resistance mechanism.

No description available.

There is much observational evidence to suggest that patients with chronic kidney disease are biologically 'older' than their unaffected peers. This is most obviously seen with cardiovascular disease: young patients on haemodialysis have a relative risk of cardiovascular mortality similar to that of people over 50 years their senior in the general population. Moreover, there are striking analogies between the effects of physiological ageing and uraemia on the structure and function of the heart and vasculature. Despite this, little work has been published looking at whether these similarities are reflected at a molecular and cellular level. Two processes implicated in ageing are autophagy and senescence. There is much inferred evidence that these processes are affected by chronic kidney disease. The aim of this work was to investigate whether autophagy and senescence are indeed altered in the uraemic heart, whether these processes might be linked, and whether the findings of these enquiries might suggest their involvement in the pathogenesis of the prematurely aged cardiac phenotype. An in vitro model of the uraemic myocardium was created using rat cardiac myoblast cells exposed to the uraemic toxin indoxyl sulphate, and in vivo models using adenine-diet and subtotal (5/6) nephrectomy rodents. Autophagy was assayed using immunoblotting, PCR array, immunohistochemistry and fluorescence microscopy, and senescence by immunoblotting and as part of an ageing-dedicated PCR array. Though not achieving statistical significance, markers of autophagy activity appeared to be increased in rat cardiac myoblast cells exposed to indoxyl sulfate, and in cardiac tissue from adenine-diet rats. Interestingly markers of autophagy activity were significantly increased in hepatic tissue from subtotal nephrectomy rats. PCR of RNA purified from cardiac tissue from adenine-diet rats demonstrated an expression of ageing-related genes analogous to that in physiological ageing. Though limited by numbers, these findings present evidence to suggest that autophagy may be upregulated as a protective mechanism in the progeroid uraemic heart, a situation possibly comparable to that in physiological ageing. Changes in cardiac autophagy and ageing in uraemia present new avenues for translational research into pathological ageing in chronic kidney disease.

Human Papilloma Virus (HPV) is a conserved DNA virus, which infects mucosal and cutaneous epithelia. Although over 200 types of HPV have been identified which can infect humans, only around 15 high-risk (HR) types have been shown to be responsible for the development of cancer. HPV-16 is the most abundant HR-HPV type being responsible for almost 70% of cervical cancers. HPV-16 consists of 8 genes, the early genes (E1, E2, E4, E5 and the potential oncogenes E6 and E7) responsible for the infection, amplification and proliferation and the late genes (L1 and L2) responsible for the packaging and assembly of the virus. Autophagy, a physiological mechanism of intracellular digestion and recycling of unwanted cellular materials such as aggregated proteins and organelles has been shown to act as a first line defence against invading pathogens. An essential condition for this process is the formation of double membrane structures called the autophagosomes, which can engulf the pathogen or pathogenic proteins and digest them by fusing with endocytic vesicles (lysosomes). Beclin 1 and LC3 are vital proteins involved in the complicated process of the autophagosome formation while SQSTM1/p62 has a key role in the identification and transit of cargo into the forming autophagosomes. This novel work focuses on investigating the role of autophagy in HR-HPV related tumour development and progression in cervical epithelial cells both in vitro and ex vivo.

Decreased mitochondrial function is associated with aging and is an early step in Alzheimer's disease (AD). Autophagy also declines with age and is required for degradation of dysfunctional mitochondria but it is not known whether autophagosomal formation is overactive and/or degradation of autophagosomes is inhibited in AD. Although two-thirds of the 5 million Americans diagnosed with AD are women, without a clear mechanism. Since the role of gender and autophagy in AD is unclear, we wanted to know whether: A) decreased mitochondrial biogenesis precedes brain plaque formation, neuronal death and memory deficits B) autophagosomal formation is overactive and/or degradation of autophagosomes is inhibited in AD and C) deficits in mitochondrial biogenesis and autophagy occur earlier in life in the hippocampus/cortex of female AD-Tg, than male AD-Tg mice. To answer these questions, mitochondrial DNA (mtDNA), TFAM (transcription factor A mitochondrial) and two stages in autophagy, autophagosomal formation and degradation were measured in the hippocampus/cortex of non-transgenic (non-Tg) and the APP(Swe, DI)/NOS2-/- AD mouse model (AD-Tg) from 2 mo. through 12 mo. of age, when memory deficits develop. Male and female mice were evaluated for gender differences. By measuring mitochondrial gene copy number relative to nuclear gene copy number by qPCR, we found female specific decreases in mtDNA and TFAM protein levels in AD-Tg hippocampus/cortex, before 12 mo., when memory deficits develop. The male AD-Tg mice did not show any decline in the levels of mtDNA or TFAM protein through 12 mo. of age, indicating a decline in mitochondrial biogenesis earlier in life in female AD-Tg mice, than males. To determine whether autophagosomal formation is overactive and/or autophagosomal degradation is inhibited in AD, non-Tg and AD-Tg mouse neurons from 2-12 mo. of age were cultured and transfected with an adenovirus expressing the dual fusion protein, mCherry-GFP-LC3B. This system enables the distinction of early (autophagosomal formation) from late (autophagosomal degradation) stages of autophagy. Autophagosomal formation increased in female AD-Tg mice, while male AD-Tg neurons have decreased formation of autophagosomes, compared to non-Tg. Neurons from AD-Tg mice show deficits in degradation of autophagosomes by 2 mo. Our results show increased autophagosomal formation in female neurons with age and in our AD-like model without corresponding increases in degradation of autophagosomes. All together, our data indicates that the presence of familial APP mutations and knockout of NOS2 increases deficits in both mitochondrial biogenesis and autophagy in female mice, compared to males. These deficits occur before amyloid plaque formation and memory deficits, suggesting that mitochondrial and autophagic deficits may play a role in the higher incidence of AD in females.

Background: Autophagy is a conserved physiological process in the body that functions to maintain homeostasis via degradation and recycling of dysfunctional proteins and even entire organelles. It is typically triggered by nutritional stress and/or growth factor deprivation and ultimately results in the packaging of cellular components into autophagosomes. These autophagosomes then fuse with lysosomes to be degraded. Autophagy is suggested to play a significant role in cardiac remodeling, particularly following myocardial infarction (MI). Ataxia-telangiectasia mutated kinase (ATM) is a cell cycle checkpoint protein activated in response to DNA damage. Mutations in ATM cause a multi-systemic disease known as Ataxia-telangiectasia (AT). The present study aims to investigate the relationship between ATM and autophagy in the heart, particularly post-MI. Methods: Wild-type (WT) and ATM heterozygous (hKO; aged ~4 months) were injected with either bafilomycin (Baf; autophagy inhibitor) or rapamycin (Rap; autophagy activator) for 30 minutes. MI was then induced mice by ligation of the left anterior descending coronary artery. Heart function was measured using M-mode echocardiography 4 hours post-MI. For cellular analysis of autophagy, confluent cultures of cardiac fibroblasts were isolated from adult male rats and treated with KU-55933 (KU; specific ATM inhibitor) in serum-free media for 4 hours. Cardiac fibroblasts were also isolated from ATM WT, heterozygous (hKO), and knockout (KO) mice, grown to confluency, and serum-starved for 4 hours. Levels of microtubule-associated protein light chain 3-II (LC3-II), a marker for autophagy, was examined in the heart and cell lysates using western blots. Results: M-mode echocardiography revealed that MI decreases heart function in both genotypes as measured by decreased %FS and EF. No change in heart function was observed between WT-MI and hKO-MI groups following Baf treatment. Rap treatment resulted in the functional recovery of the heart in WT-MI, not in hKO-MI group. Levels of LC3-II protein were higher in hKO-sham versus WT-sham hearts. MI decreased LC3-II protein in hKO-MI, not in WT-MI group. Baf treatment further decreased LC3-II protein levels in hKO-MI group. LC3-II levels were lower in KU-treated rat cardiac fibroblasts when compared to control. Cardiac fibroblasts isolated from hKO and KO hearts exhibited decreased LC3-II levels versus those isolated from WT hearts. Conclusion: Although further investigations are needed to confirm our findings, these data provide evidence that ATM deficiency hinders improvement in heart function post-MI following activation of autophagy. ATM deficiency results in reduced autophagy post-MI, an effect that appears to be exaggerated following autophagy inhibition. ATM deficiency also reduces autophagy in rat and mouse cardiac fibroblasts.

Pancreatic ductal adenocarcinoma (PDAC) is among the most devastating of all cancers. It is responsible for only 3% of cancer cases annually but is the cause of over 7% of cancer related deaths. Despite the prevalence of this diseases there remains a scarcity of rational targeted chemotherapies. The most frequently observed driver mutation in PDAC is in the KRAS gene. KRAS is a GTPase protein in the RAS-RAF-MEK-ERK (MAPK) pathway. This pathway regulates vital functions necessary for cell proliferation, differentiation, and survival. Unfortunately, efforts to pharmacologically inhibit KRAS have been unsuccessful. PDAC can be subdivided into two classes: KRAS-dependent and KRAS-independent. KRAS-dependent cell lines acquire numerous genetic mutations yet still require sustained activity of the KRAS protein to survive. These two subtypes of PDAC have distinct genetic and morphological features. One such difference is expression of the Spleen tyrosine kinase (Syk), which is expressed at higher levels in KRAS-dependent cell lines. Syk is a non-receptor tyrosine kinase that functions downstream of KRAS and is an upstream activator of mTORC1. mTORC1 activity is associated with anabolic processes such as protein and lipid synthesis, while its suppression causes activation of the catabolic autophagy pathway. Like KRAS, mTORC1 has proven to be a poor drug target in clinical studies. This issue necessitates the discovery of other therapeutic targets in the pathway. Inhibiting Syk with the inhibitor PRT062607 (Syki) results in decreased mTORC1 activity, increased autophagy, and cell death. In this study we aim to identify compounds that act synergistically with Syki to produce an enhanced therapeutic effect. Synergy can be summarized as a combinational effect greater than the expected additive effect of each agent acting individually. We evaluated the effects of various drug combinations on cell viability and studied the impact of these compounds on the autophagy pathway. We found a synergistic killing effect when cells were treated with Syki and the iron-chelating agent Nocardimicin F (NCF). Live cell imaging assays showed that NCF is a strong activator of the autophagy pathway. Western Blot data suggest that NCF activates the autophagy pathway through a mechanism independent of mTORC1 suppression. Furthermore, our data suggest that the cytotoxicity of Nocardimicin does not result from induction of apoptosis. We hypothesize that cell death proceeds via an autophagy dependent mechanism called autosis. Autosis is a poorly understood process, however, is known to be dependent on the Na+/K+-ATPase. Our findings provide rationale for further study of the effects of iron-chelating compounds in PDAC and suggest that targeting the autophagy pathway is a viable therapeutic strategy.

Avian coccidiosis is caused by the intestinal protozoa Eimeria. The parasite's site of infection in the intestine is site specific. Eimeria acervulina mainly affects the duodenum, E. maxima the jejunum, and E. tenella the ceca. Lesions in the intestinal mucosa cause reduced feed efficiency and body weight gain in Eimeria-challenged chickens. My previous studies showed that the growth reduction may be due to changes in expression of digestive enzymes and nutrient transporters in the intestine. This can also lead to diminished intracellular pools of nutrients and inhibit pathogen replication. In this dissertation, further analysis of cellular events was performed. Expression of host defense peptides (HDPs), apoptosis and autophagy related genes were examined in Eimeria challenged broilers. The results showed that upon Eimeria infection, LEAP2 was consistently downregulated in the target tissues, while the avian beta-defensins (AvBDs) showed many variations in expression patterns. Downregulation of LEAP2 may be a mechanism for Eimeria to combat the host defense system, and to promote its survival inside the host cell. The in situ hybridization results showed that LEAP2 was expressed only along the villus in the small intestine and not in the crypt. This is the first time LEAP2 has been localized to epithelial cells of the chicken intestine. Eimeria infection can also induce an anti-apoptotic and anti-autophagy state in the host cells. This condition can be both favorable and unfavorable to parasite survival and replication inside the host cell. A comparison of gene expression between Ross and Eimeria resistant Fayoumi (line M5.1 and M15.2) chickens challenged with Eimeria maxima was conducted. The comparison among different lines of chickens showed differential gene expression patterns in lines with different resistance to Eimeria. The similar body weight reduction indicated that there may not be a significant Eimeria resistant line among the Ross, Fayoumi M5.1 and M15.2 birds. The interaction between Eimeria and the host cell is very complex. Studying the mechanisms behind the changes of gene expression during Eimeria infection may give rise to potential therapeutic targets of coccidiosis. / Ph. D.

Many studies in different eukaryotes have shown the importance of the vesicle-tethering exocyst complex for cellular processes dependent on intensive polarized secretion. The plant exocyst complex is crucial for regulation of cell polarity, morphogenesis, and defence. In land plants, gene encoding the EXO70 exocyst subunit multiplied into many paralogs, but only a few of them have been functionally described. In this thesis, the EXO70A2 isoform, a member of the EXO70.1 subfamily, was found to be the main EXO70 exocyst subunit involved in the canonical function of the exocyst complex in Arabidopsis pollen. EXO70A2 is important for several stages of pollen development-pollen grain maturation, germination, and pollen tube growth. Pollen-expressed EXO70A2 was the only EXO70 isoform able to substitute for the function of EXO70A1 in the sporophyte, but not vice-versa. This indicates partial functional redundancy of these two closely related isoforms and a high specificity for pollen-related processes. The finding that the exocyst is targeted to the plasma membrane via EXO70A1 subunit is further elaborated in the thesis. EXO70A1 binds plasma membrane via interactions with specific phospholipids that form a unique plasma membrane-lipid signature in plants. Other isoform, EXO70B1 from the EXO70.2 subfamily,...