302 research outputs found

    Characterizing the impact of the mutational landscape of SARS-CoV-2 on epitope presentation and CTL

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    La pandémie actuelle de COVID-19, causée par le coronavirus 2 du syndrome respiratoire aigu sévère (SRAS-CoV-2), a entraîné plus de 6 millions de décès et près de 680 millions de cas confirmés dans le monde. Depuis l'émergence du virus en décembre 2019, beaucoup d’efforts de recherche mondiaux ont visé à étudier la relation entre le SRAS-CoV-2 et l'immunité adaptative à médiation cellulaire. La caractérisation des réponses immunitaires à base de lymphocytes T CD4+ et CD8+ contre le SRAS-CoV-2 dans le contexte de mutations virales est d'une pertinence immédiate pour l’approfondissement de nos connaissances concernant l'immunité adaptative envers un virus en évolution, ainsi que l'amélioration de vaccins. Dans cette thèse, je passerai en revue les découvertes actuelles concernant la biologie du SRAS-CoV-2 et sa relation avec le système immunitaire adaptatif humain. Je discuterai ensuite les divers mécanismes par lesquels le SRAS-CoV-2, ainsi que d'autres virus, se sont avérés échapper l’immunité adaptative humoral et cellulaire. Enfin, je présenterai mes contributions à la compréhension du paysage mutationnel global du SRAS-CoV-2 et de sa capacité à échapper à la reconnaissance par les lymphocytes T CD8+. Dans ce travail, j'ai observé que le paysage mutationnel global du SRAS-CoV-2 était régi par des biais de mutation au cours de la première année de la pandémie, le plus répandu d’entre eux conduisant à la suppression de la proline. Il a ensuite été prédit que cette élimination globale de la proline conduirait à la perte d’épitopes reconnues par les cellules T CD8+ d'une manière dépendante sur les super-types HLA, avec la perte d'épitopes survenant préférentiellement dans le contexte du super-type HLA-B7. Le modèle développé dans ce travail propose un lien entre les biais mutationnels globaux du SRAS-CoV-2, les allèles HLA et l'évasion des lymphocytes T. Ce travail crée un cadre pour anticiper l'impact des variantes existantes et émergentes du SRAS-CoV- 2 envers la réponse immunitaire à base de lymphocytes T CD8+.The current COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has led to upwards of 6 million deaths and nearly 680 million confirmed cases worldwide. Since the emergence of the virus in December 2019, astounding global research efforts have been aimed at investigating the relationship between SARS-CoV-2 and cell-mediated adaptive immunity. Characterizing CD4+ and CD8+ T Lymphocyte responses to SARS-CoV-2 in the context of viral mutations is of immediate relevance to understanding the breadth of a population’s adaptive immunity to an evolving virus and is central to the improving existing vaccines. In this thesis, I will review all present findings pertaining to the biology of SARS-CoV-2 and its relationship with the human adaptive immune system. I will then discuss the various mechanisms by which SARS-CoV-2, along with other viruses, have been found to evade the various arms of the adaptive immune system. Finally, I will present my contributions to the understanding of the global mutational landscape of SARS-CoV-2 and its ability to evade recognition by CD8+ T lymphocytes. By investigating over 300,000 SARS-CoV-2 genomic sequences, I observed that the mutational landscape of SARS-CoV-2 was governed by mutation biases during the first year of the pandemic, with the most prevalent bias leading to the removal of proline. The observed global removal of Proline was predicted to lead to the loss of CD8+ T cell epitopes in an HLA-supertype-dependent manner, with the loss of epitopes occurring preferentially in the context of the HLA-B7 supertype. The model developed proposes a link between SARS-CoV-2 global mutational biases, HLA alleles and T cell evasion. This work creates a framework to anticipate the population-specific impact of existing and emerging SARS-CoV-2 variants on CD8+ T cell-based immunity

    프로테오지노믹스 기법을 이용한 폐암 바이오마커 연구

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    학위논문 (박사)-- 서울대학교 대학원 : 수의과대학 수의학과, 2019. 2. 조제열.정밀의료 패러다임의 등장 이후, 질환의 진단 및 치료를 위해서 바이오마커에 대한 수요는 높아지고있다. 가설기반연구는 전통적으로 당연하게 사용되오던 연구수행체계이지만, 바이오마커 발굴에서 필연적으로 마주치게되는 광범위한 스크리닝 작업에서는 효율성의 한계를 드러낸다. 오믹스기술의 등장과 함께 질환연구의 패러다임은 증거기반 대규모 타겟발굴방식으로 변화하고 있다. 단백질은 생체 기능조절에 직접적으로 관여하는 물질이기 때문에 바이오마커로 활용할 수 있는 가장 이상적인 물질로 여겨진다. 질량분석기를 이용한 단백체분석은 단백질을 직접 정성 및 정량할 수 있을 뿐만 아니라 매우 생산성이 높아 질환 바이오마커 발굴에 유용하다. 이 논문에서는 질량분석기를 이용하여 폐암 바이오마커의 발굴을 위한 고도화된 분석기법인 프로테오지노믹스 기법의 적용과, 스크리닝된 바이오마커후보 단백질의 정량검증 및 폐암 감별진단 조합마커의 생성연구에 대하여 알아본다. CHAPTER I에서는 인간염색체기반 단백체프로젝트 (C-HPP)의 일환으로 수행된 염색체9번에 대한 단백체연구가 포함되어있다. 미확인 단백질과 유전단백체에서 발견되지 않았던 시그니처를 밝혀내기 위해 LC-MS/MS분석과 RNA-seq 차세대염기분석기법을 적용하여 샘암종 폐암환자 5명의 정상-종양조직을 분석하였다. 염색체중심-인간단백체프로젝트의 2013년 리포트에서는 neXtProt 인간단백체 데이터베이스를 기준으로 염색체 9번에서 170개의 미확인 단백질이 있는 것으로 알려졌으며, 본 논문의 연구가 진행된 2015년에는 133개가 계속 미확인상태로 남아있었다. 본 논문의 단백체분석에서는 19개의 미확인 단백질을 동정할 수 있었으며, 그 중에서 염색체9번에 해당하는 단백질은 SPATA31A4 한 개 였다. RNA-seq분석으로는 샘종폐암조직 5개에서 공통적으로 검출되면서 정상조직에서는 검출되지 않는nonsynonymous SNP 5개 (CDH17, HIST1H1T, SAPCD2, ZNF695) 그리고 synonymous SNP 3개를 발굴할 수 있었다. 프로테오지노믹 분석을 위해서 각 시료별 RNA-seq데이터를 가공하여 맞춤형 데이터베이스를 구축하였다. 이렇게 생성된 시료맞춤형 데이터베이스를 단백체 질량분석데이터 검색에 활용하여 5개 유전자(LTF, HDLBP, TF, HBD, HLA-DRB5)에 해당하는 7개의 돌연변이를 검출하였다. 두 개의 돌연변이는 정상조직에서는 검출되지 않고 암조직에서만 검출되었다. 또한, 이 결과에서는 정상-암조직 모두에서 위유전자 (EEF1A1P5) 펩티드를 검출할 수 있었다. CHAPTER II에서는 다중반응검지법 (MRM) 을 이용한 단백질 바이오마커 검증과 조합마커 구성에 대한 연구를 서술하였다. 폐암과 다른 폐질환은 감별이 어렵기 때문에 폐암은 오진단 위험이 큰 질병이다. 따라서 혈청기반의 폐암감별진단 바이오마커개발의 필요성은 널리 인정되고있다. 이 단원에서는 폐암환자와 대조군폐질환 환자 198명의 혈청시료를 활용하여 일곱개의 폐암바이오마커 후보단백질을 나노유속 액체크로마토그래피-다중반응검지법으로 정량하였다. 후보단백질을 개별로 분석하였을 때에는 SERPINA4만이 통계적으로 유의성있게 혈중농도가 감소하는 것으로 나타났다. 다중반응검지법 전체데이터를 임상정보와 함께 로지스틱회귀모델에 적용하여 하나의 조합마커로 만들 수 있었다. 이 과정에서 개별마커로는 통계적인 유의성이 두드러지지 않지만 간섭효과를 만들어낼 수 있는 변수를 고려하여 모델링을 진행하였다. 최종적으로 SERPINA4, PON1, 나이를 조합하였을 때 가장 최적의 조합마커가 생성되었다. 이 조합마커는 AUC 0.915 의 감별진단 성능을 보여주었으며, 모델을 만드는데 사용되었던 시료와는 별개의 검증군에서도 성능은 유지되었다. 이와 같이 통계모델을 이용하여 생성한 조합마커는 개별 분자마커를 이용했을 경우보다 개선된 폐암 감별진단능력을 보여줄 수 있음을 제시한다.Biomarkers have been in high demand for disease diagnosis and therapeutics. Traditional hypothesis-based research has been challenging due to massive screening studies. Together with the emergence of omics technologies, currently, the paradigm for disease research has been moving toward evidence-based large-scale discovery studies. Proteins, as key effector molecules, can serve as ideal biomarkers for various diseases because they catalyze every biological function. Proteomics, which is represented by mass spectrometry (MS) technologies, stands as a solution for disease diagnosis and drug target discovery. CHAPTER I includes a portion of a report from of the human proteome project (HPP) related to chromosome 9 (Chr 9). To identify missing proteins (MPs) and their potential features in regard to proteogenomic view, both LC-MS/MS analysis and next-generation RNA sequencing (RNA-seq)-based tools were used for the clinical samples including adjacent non-tumor tissues. When the Chr 9 working group of the Chromosome-Centric Human Proteome Project (C-HPP) began this project, there were 170 remaining MPs encoded by Chr 9 (neXtProt 2013.09.26 rel.)currently, 133 MPs remain unidentified at present (neXtProt 2015.04.28 rel.). Proteome analysis in this study identified 19 missing proteins across all chromosomes and one MP (SPATA31A4) from Chr 9. RNA-seq analysis enable detection of RNA expression of 4 nonsynonymous (NS) SNPs (in CDH17, HIST1H1T, SAPCD2, and ZNF695) and 3 synonymous SNPs (in CDH17, CST1, and HNF1A) in all 5 tumor tissues but not in any of the adjacent normal tissues. By constructing a cancer patient sample-specific protein database based on individual RNA-seq data, and by searching the proteomics data from the same sample, 7 missense mutations in 5 genes (LTF, HDLBP, TF, HBD, and HLA-DRB5) were identified. Two of these mutations were found in tumor tissues but not in the paired normal tissues. Additionally, this study discovered peptides that were derived from the expression of a pseudogene (EEF1A1P5) in both tumor and normal tissues. In summary, this proteogenomic study of human primary lung tumor tissues enabled detection of additional missing proteins and revealed novel missense mutations and synonymous SNP signatures, some of which are predicted to be specific to lung cancer. CHAPTER II describes a study of the combination marker model using multiple reaction monitoring (MRM) quantitative data. Misdiagnosis of lung cancer remains a serious problem due to the difficulty of distinguishing lung cancer from other respiratory lung diseases. As a result, the development of serum-based differential diagnostic biomarkers is in high demand. In this study, 198 serum samples from non-cancer lung disease and lung cancer patients were analyzed using nLC-QqQ-MS to examine the diagnostic efficacy of seven lung cancer biomarker candidates. When the candidates were assessed individually, only SERPINEA4 showed statistically significant changes in the sera of cancer patient compared to those of control samples. The MRM results and clinical information were analyzed using logistic regression analysis to a select model for the best meta-marker, or combination of biomarkers for the differential diagnosis. Additionally, under consideration of statistical interaction, variables having a low significance as a single factor but statistically influencing the meta-marker model were selected. Using this probabilistic classification, the best meta-marker was determined to comprise two proteins SERPINA4 and PON1, with an age factor. This meta-marker showed an enhanced differential diagnostic capability (AUC=0.915) to distinguish the lung cancer from lung disease patient groups. These results suggest that a statistical model can determine optimal meta-markers, which may have better specificity and sensitivity than a single biomarker and may thus improve the differential diagnosis of lung cancer and lung disease patients.ABSTRACT_i CONTENTS_v LIST OF FIGURES_vii LIST OF TABLES_x ABBREVIATIONS_xii BACKGROUND_1 1. LUNG CANCER_1 2. BIOMARKER_7 3. MASS SPECTROMETRY BASED PROTEOMICS_12 4. PROTEOGENOMICS_24 5. TARGETED PROTEOMICS_33 CHAPTER I Proteogenomic Study: Variant Proteome and Transcriptome in Human Lung Adenocarcinoma Tissues_41 1. INTRODUCTION_42 2. MATERIALS AND METHODS_45 3. RESULTS AND DISCUSSION_53 4. CONCLUSION_81 CHAPTER II Multi-Panel Biomarker Development for the Efficient Discrimination of Lung Cancer for Other Lung Diseases_84 1. INTRODUCTION_85 2. MATERIALS AND METHODS_88 3. RESULTS_93 4. DISCUSSION_120 5. CONCLUSION_127 GENERAL CONCLUSION_129 REFERENCES_131 ABSTRACT IN KOREAN_154Docto

    Chemical Genetic Approaches for Elucidating Protease Function and Drug-Target Potential in Plasmodium Falciparum

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    Plasmodium falciparum is a protozoan parasite and the causative agent of malaria, which kills upwards of 1 million people annually. With the increasing prevalence of drug-resistant parasites, considerable interest now exists in the identification of new biological targets for the development of new malaria chemotherapeutics. However, given the genetic intractability inherent in studying P. falciparum, it is imperative that novel approaches be developed if we are to understand the role of essential enzymes. My work presented here focuses on the development and use of chemical tools to study malarial proteases, a class of enzymes that have been shown to play essential roles throughout the parasite lifecycle, but the majority of which though are still uncharacterized. In Chapter 2 I develop a novel set of activity-based probes (ABPs) based on the natural product metallo-aminopeptidase (MAP) inhibitor bestatin. I show the bestatin-based ABP allows the functional characterization of MAP activity within a complex proteome. In Chapter 3, I utilize an extended library of bestatin-based ABPs to define the function of two essential malarial MAPs, PfA-M1 and Pf-LAP. I find that PfA-M1 is necessary in the proteolysis of hemoglobin and that lethal inhibition starves parasites of amino acids. I also show that Pf-LAP has a role other than hemoglobin digestion, as parasites are susceptible to its inhibition prior to the onset of this process. In Chapter 4, I use a suite of specific small molecules to validate the P. falciparum signal peptide peptidase (PfSPP) as a drug target. This work shows that PfSPP is a druggable enzyme and that parasites are extremely vulnerable to its inhibition. Evidence is also presented that suggests this enzyme may play an important role in the parasite\u27s endoplasmic reticulum stress-response

    Structure-aided detection of functional innovation in protein phylogenies

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    Detection of positive selection in proteins is both a common and powerful approach for investigating the molecular basis of adaptation. In this thesis, I explore the use of protein three- dimensional (3D) structure to assist in prediction of historical adaptations in proteins. Building on a method first introduced by Wagner (Genetics, 2007, 176: 2451–2463), I present a novel framework called Adaptation3D for detecting positive selection by integrating sequence, structural, and phylogenetic information for protein families. Adaptation3D identifies possible instances of positive selection by reconstructing historical substitutions along a phylogenetic tree and detecting branch-specific cases of spatially clustered substitution. The Adaptation3D method was capable of identifying previously characterized cases of positive selection in proteins, as demonstrated through an analysis of the pathogenesis-related protein 5 (PR-5) phylogeny. It was then applied on a phylogenomic scale in an analysis of thousands of vertebrate protein phylogenetic trees from the Selectome database. Adaptation3D’s reconstruction of historical mutations in vertebrate protein families revealed several evolutionary phenomena. First, clustered mutation is widespread and occurs significantly more often than that expected by chance. Second, numerous top-scoring cases of predicted positive selection are consistent with existing literature on vertebrate protein adaptation. Third, in the vertebrate lineage, clustered mutation has occurred disproportionately in proteins from certain families and functional categories such as zinc-finger transcription factors (TFs). Finally, by separating paralogous and orthologous lineages, it was found that TF paralogs display significantly elevated levels of clustered mutation in their DNA-binding sites compared to orthologs, consistent with historical DNA-binding specificity divergence in newly duplicated TFs. Ultimately, Adaptation3D is a powerful framework for reconstructing structural patterns of historical mutation, and provides important insights into the nature of protein adaptation

    Characterization and identification of hypotensive, immunomodulatory, and metabolic disorder benefiting peptides from Atlantic mackerel (Scomber scombrus) hydrolysate separated based on molecular weight, charge, and hydrophobicity

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    L'hypertension artérielle est l'un des principaux facteurs de risque de syndrome cardiométabolique. En outre, l'inflammation chronique de bas grade joue également un rôle important dans la pathogenèse du syndrome. Il existe un lien entre l'apparition de la résistance à l 'insuline et l'hypertension qui peut initier le diabète de type 2 et l'obésité. Des peptides bioactifs terrestres et marins, des biomolécules de poissons en particulier, ont démontré des effets immunomodulateurs puissants ainsi que des effets hypotenseurs potentiels dans le traitement de ces facteurs de risque et de leurs complications associées. Notre hypothèse était que les fractions d'hydrolysat protéique de maquereau de l’Atlantique (Scromber scombrus) possèdent une activité biologique bénéfique sur l'hypertension. Le but de notre travail était de fractionner et d'identifier des peptides antihypertenseurs, immunomodulateurs et antiMetS basés sur diverses caractéristiques moléculaires de charge, de polarité et de taille. Les fractions ont été produites en utilisant la technique d'extraction en phase solide chromatographique (SPE), l'ultrafiltration baromembranaire (UF) et l'électrodialyse conditions expérimentales étaient l’utilisation des pH avec membrane UF (EDUF). Les 3, 6, 9, et des membranes de seuils de coupure (MWCO) de < 20 kDa pour l’EDUF et de MWCO de < 1 kDa pour l’UF. Selon nos résultats, parmi toutes les fractions hydrophobes obtenues par SPE il y avait une fraction ayant un effet antihypertenseur important, de 5 µg, et possédant des peptides antidémontrant une inhibition de 50% à une quantité inflammatoires, ayant une inhibition de 17% à une quantité de 10 µg de protéines. Par rapport au témoin négatif (Lipopolysaccharide) les peptides anioniques et cationiques des fractions d’EDUF à pH3 ainsi que l'hydrolysat de maquereau ont démontré des effets pro antiACE et anti-- inflammatoires significatifs jusqu'à 27%. La fraction inflammatoire la plus puissante était riche en acides aminés à chaîne latérale ramifiée et hydrophobe mais avait moins d’acides aminés chargés par rapport aux fractions proinflammatoires EDUF. Toutes les séquences possibles identifiées dans cette fraction sont courtes et ont des valeurs GRAVY positives. Cependant, l'hydrolysat et la fraction positivement du pH3 n'ont pas exercé d'effet antichargée MetS significatif chez les souris nourries au régime hypercalorique. En conclusion, la polarité et la charge de la fraction du maquereau de l’Atlantique sont les facteurs les plus importants pour l' immunomodulation et l'activité hypotensive des peptides. De plus, ces facteurs n'étaient pas suffisants pour réguler les déficiences métaboliques chez les souris obèses et résistantes à l'insuline induites par le régime alimentaire. Par conséquent, la compréhension du mécanisme d'action et la caractérisation approfondie des fractions bioactives seraient nécessaires pour une conclusion définitive et une application clinique du matériel.While, on the one hand, high blood pressure is one of the main risk factors of cardiometabolic syndrome, on the other hand, chronic low-grade inflammation similarly plays a significant role in the pathogenesis of the syndrome. Moreover, there is a link between the occurrence of insulin resistance and hypertension consequently initiating type 2 diabetes and obesity. Interestingly, terrestrial, and marine bioactive peptides, in particular fish biomolecules, have been reported as potent immunomodulators and or hypotensive material in the treatment of these risk factors and associated complications. Hence, our hypothesis was that Atlantic mackerel (Scomber scombrus) protein hydrolysate fractions possess beneficial biological activity on hypertension, inflammation, and other Metabolic Syndrome (MetS) factors. The aim of our work was to fractionate and identify antihypertensive, immunomodulating and anti-MetS peptides based on various molecule characteristics of charge, polarity, and size. Fractions were produced using chromatographic Solid Phase Extraction technique (SPE), pressure driven-Ultra Filtration (UF) and Electrodialysis with UF membrane (EDUF) under experimental conditions of pH 3, 6 and 9 with MWCO of < 1 kDa and < 20 kDa, respectively. According to the results of our in-vitro analysis the highly hydrophobic fraction of SPE was a potent antihypertensive, 50% inhibition at 5 µg, and anti-inflammatory product, 17% inhibition at 10 µg of protein, among all. Furthermore, in comparison to the negative control (Lipopolysaccharide), anionic and cationic peptides of pH3 EDUF as well as mackerel hydrolysate demonstrated significant pro-inflammatory effects up to 27%. The most potent anti-ACE and anti-inflammatory fraction was rather branched chain and hydrophobic amino acid rich with lesser charged amino acids compared to the EDUF pro-inflammatory fractions. All the identified possible sequences of the same fraction had rather small molecular mass with positive GRAVY values. Selected material, the hydrolysate and positively charged fraction of pH3, however, did not exert any significant anti-MetS effect in hypercaloric diet fed obese insulin resistant rats. In conclusion, polarity and charge of a fraction were the most important factors for immunomodulation and hypotensive activity of Atlantic mackerel peptides. Nevertheless, those factors were not sufficient enough to regulate metabolic impairments in diet-induced obese and insulin resistant rats. Accordingly, understanding the mechanism of action and thorough characterization of bioactive fractions would be required for a definite conclusion and clinical application of the material

    The structural basis of the Talin-KANK1 interaction that coordinates the actin and microtubule cytoskeletons at focal adhesions

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    Adhesion between cells and the extracellular matrix (ECM) is mediated by heterodimeric (alphabeta) integrin receptors that are intracellularly linked to the contractile actomyosin machinery. One of the proteins that control this link is talin, which organises cytosolic signalling proteins into discrete complexes on beta-integrin tails referred to as focal adhesions (FAs). The adapter protein KANK1 binds to talin in the region of FAs known as the adhesion belt. Here, we developed a novel crystallographic method to resolve the talin-KANK1 complex. This structure revealed that the talin binding KN motif of KANK1 has a novel fold, where a beta-turn stabilises the alpha-helical region, explaining its specific interaction with talin R7 and high affinity. Single point mutants in KANK1 identified from the structure abolished the interaction and enabled us to examine KANK1 enrichment in the adhesion belt. Strikingly, in cells expressing a constitutively active form of vinculin that keeps the FA structure intact even in the presence of myosin inhibitors, KANK1 localises throughout the entire FA structure even when actomyosin tension is released. We propose a model whereby actomyosin forces on talin eliminate KANK1 from talin binding in the centre of FAs while retaining it at the adhesion periphery

    Suppression and triggering of Arabidopsis immunity by Albugo species

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    Albugo species are obligate biotrophic phytopathogens. Like other biotrophs, they are anticipated to secrete effectors that can suppress or trigger plant defenses; the nature of Albugo effectors is currently unknown. Sequencing of A. laibachii isolate Nc14 (AlNc14) genome reveals 13032 genes encoded in a ~37 Mb genome. We analyze the effector complement of AlNc14 and find known effector classes but also classes unique to A. laibachii. Experiments reveal that CHXCs are a novel class of effectors that suppress host defense. We functionally characterize two predicted AlNc14 effectors in detail; CHXC1 a potential core effector conserved in other oomycete species, and SSP6, a fast-evolving effector specific to A. laibachii. CHXC1 encodes a nuclear localized HECT E3 ligase homolog, which suppresses host defenses dependent on cys651. We find 7 variants of SSP6 that are under diversifying selection. Two highly expressed variants SSP6-2c and SSP6-A are plasma membrane localized when expressed in planta. Interestingly, SSP6-2c but not SSP6-A, is able to enhance growth of P. infestans race blue 13 and suppress flg22-dependent ROS production. In Arabidopsis cells we find SSP6-2c localizes around AlNc14 haustoria. We propose that AlNc14 secretes the effectors SSP6-2c and CHXC1 into the plant cell to suppress defense and promote infection. Current methods to screen for virulence of effector candidates predominantly rely on measuring growth of bacterial pathogens. Quantitative assessment of resistance and susceptibility to eukaryotic pathogens is more difficult. We develop a semi-automated high-throughput system for assaying Hpa growth. We investigate the genetic basis of resistance to Albugo in Arabidopsis. We find that resistance to AlNc14 is linked to RAC1 and RAC3 in Ksk-1. In contrast, resistance to A. candida Nc2 (AcNc2) is linked to WRR4 in Col-0, Col-5 and Ksk-1. A second dominant locus, WRR5a/b in Col-5 also confers resistance to AlNc2. Thus, different R-genes and presumably different effectors govern resistance to AlNc14 and AcNc2.

    Mitocidal resistance in the ectoparasitic mite,Varroa destructor, and the relationship with its host Apis mellifera

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    The Western honeybee, Apis mellifera, is an economically important insect, responsible for a large portion of global pollination services. They live in densely populated colonies, which give the optimum chance for opportunistic pathogens and parasites to spread. Honeybees, like all organisms, are subject to a wide range of threats, from viruses to parasites. The immune response of A. mellifera to these threats relies on a fast acting non-adaptive immunity, with effectors such as cellular defences and the release of antimicrobial peptides. The defence against invading pathogens and parasites is important not only for the individual bee, but for the colony as a whole. Many bee diseases have been shown as capable of causing collapse of honeybee colonies. The first section of this thesis examines the occurrence and prevalence of four honeybee viruses (Deformed wing virus, Chronic bee paralysis virus, Acute bee paralysis virus, Israeli acute paralysis virus), the microsporidian parasite Nosema, and the parasitic tracheal mite, Acarapis woodi. The results from all seasons indicated a very low prevalence of the tracheal mite, with only 2% of the colonies testing postive in the Spring sampling, with none positive in the Summer or Autumn samples. Deformed wing virus was detected at very high levels throughout the year, with Israeli acute paralysis virus detected in the Autumn round of sampling in 3% of the tested colonies. The other two viruses were not detected. Levels of Nosema were also high throughout the year, at 18%, 6% and 12% of the colonies testing positive in the Spring, Summer and Autumn respectively. The results indicated no obvious disease variations present in the colonies tested from apiaries that lost more than 20% of their hives during the Winter post sampling than those that had lost less than 20%. The next section was to examine the mechanisms by which one of the most serious threats to the honeybee, the parasitic mite V. destructor, has developed resistance to pyrethroid chemicals. Varroa are thought to have a negative impact in the overall health and vitality of the bee, transmitting viruses through haemolymph feeding and possibly weakening the immune response of the bee. Proteomic analysis was used to compare the proteomic profile of sensitive and resistant mites, in order to observe any variations that may be conferring the resistant phenotype. The comparison showed that a number of proteins were detected at higher levels of abundance in the resistant mites, such as heat shock proteins and detoxifying enzymes such as aldehyde dehydrogenase. A number of proteins present at lower levels include cuticle proteins involved in cuticle structure. The altered levels of these proteins in the resistant Varroa could be conferring resistance through decreased penetration and increased metabolism of the pyrethroid. In the final section, the full effect that parasitization by Varroa has on the bee was examined. Parasitized Winter bees were compared to unparasitized and the proteomic profiles were analysed for changes. Hexmerin was present at lower levels in the bees that were parasitized, as was enolase-like protein. The decreased level of these proteins indicates Varroa parasitisation could lead to insufficient energy metabolism. Drone pupae that were parasitized by Varroa were compared to unparasitized drones using proteomic analysis. Cuticle proteins decreased in abundance which could indicate a compromised healing response following parasitization. A number of proteins involved in energy and nutrition such as hexamerin were also present at lower levels of abundance in the parasitized drone pupae. Similar proteins decreased in abundance in parasitized workers. Cuticle structure proteins were present at lower levels of abundance, with proteins involved in the stress response present at higher levels in the parasitized workers. Quantitative PCR analysis of parasitized drone and worker pupae indicated a reduced level of two immune genes – Abaecin and Defensin, with two other immune related genes increased in expression: Phenoloxidase and Hymenoptaecin. Changes in the expression of immune related genes following parasitization indicates that Varroa are affecting how the immune reposnse functions. To idenitify whether or not this change in the immune reponse was caused by salivary effectors secreted by the mite during feeding, the haemolymph from parasitized pupae was compared using label free proteomics to haemolymph from unparasitized pupae. A number of proteins were found exclusive to the parasitized haemolymph, including a mettalloendopeptidase which is found in other blood feeding insects and could be functioning in the digestion of haemolymph. Sox 14, a regulator of transcription, was also exclusively present in the parasitized haemolymph. The work presented throughout this thesis offers a comprehensive analysis of the diseases found in honeybee colonies, the effect that parasitization by Varroa has on adult and developing pupae, and analysis of the pyrethoid resistant phenotype. The results offer an explanation as to why Varroa are considered one of the most serious honeybee threats, and highlights the importance of controlling infestation levels in colonies
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