CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Jatropha curcas L. is a plant native to America and belongs to the Euphorbiaceae family. Currently it is gaining economical interest mainly because it is an oilseed crop with potential to produce biodiesel. However, presence of phorbol esters (a class of diterpenes) that are the major toxic constituents of the seeds, limits a better usage of the plant, by making the use of the residue, obtained after the oil extraction from the seeds, unfeasible for animal feed, due to its pro-carcinogenic activity and inflammatory action. Proteomic analysis of the plastids isolated from developing seeds of Jatropha is important because the synthesis of fatty acid as well as phorbol esters, the two most attractive compounds in the study of Jatropha curcas, occur in plastids. Proteomic analysis of this organelle is crucial to better understand and explore not only the biosynthetic pathway of these two compounds but other metabolic pathways , and addtionaly providing foundation for researchs that aimed to develope genotypes with more suitable characteristics for industrial applications. In this study, we performed a proteomic analysis of plastids isolated from the endosperm of developing Jatropha curcas seeds that were in the initial stage of deposition of protein and lipid reserves. Proteins extracted from the plastids were digested with trypsin, and the peptides were applied to an EASY-nano LC system coupled online to an ESI-LTQ-Orbitrap Velos mass spectrometer, and this led to the identification of 1103 proteins representing 804 protein groups, of which 923 were considered as true identifications, and this considerably expands the repertoire of J. curcas proteins identified so far. Of the identified proteins, only five are encoded in the plastid genome, and none of them are involved in photosynthesis, evidentiating the nonphotosynthetic nature of the isolated plastids. Homologues for 824 out of 923 identified proteins were present in three different plastids proteins databases i.e. PPDB, SUBA and PlProt, while homologues for 13 proteins were not found in any of these three databases but were marked as plastidial by at least one of the three prediction programs used (TargetP, ChloroP and PlantMPloc). Functional classification showed that proteins belonging to amino acids metabolism comprise the main functional class, followed by carbohydrate, energy, and lipid metabolisms. The small and large subunits of Rubisco were identified, and their presence in plastids is considered to be an adaptive feature counterbalancing for the loss of one-third of the carbon as CO2 as a result of the conversion of carbohydrate to oil through glycolysis. While several enzymes involved in the biosynthesis of several precursors of diterpenoids were identified, we were unable to identify any terpene synthase/cyclase, which suggests that the plastids isolated from the endosperm of developing seeds do not synthesize phorbol esters. In conclusion, this study provides insights into the major biosynthetic pathways and certain unique features of the plastids from the endosperm of developing seeds at the whole proteome level. / O pinhÃo manso (Jatropha curcas L.) à uma planta nativa da AmÃrica, pertencente à famÃlia Euphorbiaceae. Atualmente, ela desperta interesse econÃmico principalmente por se tratar de uma oleaginosa com potencial para a produÃÃo de biodiesel. Entretanto, a presenÃa de Ãsteres de forbol (uma classe de diterpeno), que sÃo os principais constituintes tÃxicos das sementes, limita uma melhor utilizaÃÃo dessa planta, por inviabilizar o uso do resÃduo de extraÃÃo do Ãleo das sementes na alimentaÃÃo animal, bem como, por apresentar atividade prÃ-carcinogÃnica e aÃÃo inflamatÃria. A anÃlise proteÃmica de plastÃdeos, isolados de sementes em desenvolvimento de pinhÃo manso, à uma importante vertente de estudo, pois tanto a sÃntese de Ãcidos graxos como dos Ãsteres de forbol, os dois compostos mais atrativos no estudo de Jatropha curcas, ocorrem nos plastÃdeos. O estudo proteÃmico dessa organela torna-se crucial para melhor compreender e explorar nÃo somente as vias biossintÃticas desses dois compostos, como de outras vias metabÃlicas, alÃm de proporcionar um conjunto de dados que pode ser utilizado em pesquisas voltadas para o desenvolvimento de genÃtipos com caracterÃsticas mais adequadas para aplicaÃÃes industriais. No presente trabalho, realizou-se uma anÃlise proteÃmica de plastÃdeos isolados do endosperma de sementes em desenvolvimento do pinhÃo manso, que estavam nos estÃgios iniciais de deposiÃÃo de lipÃdios e proteÃnas de reserva (25-30DAA), confirmados por meio de anÃlises histolÃgica e histoquÃmica. As proteÃnas extraÃdas dos plastÃdeos foram digeridas com tripsina e os peptÃdeos foram aplicados no sistema de nano-LC EASYII acoplado online ao espectrÃmetro de massa nano ESI LTQ-Orbitrap velos, o que resultou na identificaÃÃo 1103 proteÃnas, representando 804 grupos de proteÃnas, dos quais 923 foram consideradas identificaÃÃes verdadeiras. Isso expandiu consideravelmente o repertÃrio de proteÃnas do pinhÃo manso atà agora identificas. Dentre as proteÃnas identificadas, apenas 5 sÃo codificadas pelo genoma plastidial, e nenhuma delas està envolvida na fotossÃntese, o que evidencia a natureza nÃo fotossintÃtica dos plastÃdeos isolados. HomÃlogos de 824, dentre as 923 proteÃnas identificadas, estavam presentes nos bancos de dados PPDB, SUBA e PlProt, enquanto homÃlogos para 13 proteÃnas nÃo foram encontrados em nenhum dos trÃs bancos de dados plastidiais, mas foram detectados como plastidiais por pelo menos um dos trÃs programas de prediÃÃo de localizaÃÃo subcelular utilizados (TargetP, ChloroP, PlantMPloc). A classificaÃÃo funcional mostrou que a maioria das proteÃnas identificadas pertencia ao metabolismo dos aminoÃcidos, seguido dos metabolismos dos carboidratos, energÃtico e dos lipÃdios. As subunidades maiores e menores da Rubisco foram identificadas, e sua presenÃa nos plastÃdeos foi considerada uma caracterÃstica adaptativa para contrabalancear a perda de um terÃo do carbono na forma de CO2 como um resultado da conversÃo de carboidratos em Ãleo atravÃs da glicÃlise. Apesar de enzimas envolvidas na biossÃntese de diversos precursores dos diterpenÃides terem sido identificadas, nÃo foi detectado nenhuma terpeno sintase/ciclase, o que sugere que os plastÃdeos isolados do endosperma de sementes em desenvolvimento nÃo sintetizam Ãsteres de forbol, apesar de uma grande quantidade desse composto ser encontrada neste tecido. Como conclusÃo, o presente trabalho proporciona insights sobre as principais vias biossÃntÃticas, e sobre caracterÃsticas peculiares dos plastideos isolados do endosperma de sementes em desenvolvimento.

<div>The use of computational approaches to understand kinase substrate preference has been a powerful tool in the search to develop artificial peptide probes to monitor kinase activity, however, most of these efforts focus on a small portion of the human kinome. The use of high throughput techniques to identify known kinase substrates plays an important role in development of sensitive protein kinase activity assays.</div><div>The KINATEST-ID pipeline is an example of a computational tool that uses known kinase substrate sequence information to identify kinase substrate preference. This approach was used to design three artificial substrates for ABL, JAK2 and SRC family kinases. These biosensors were used to design ELISA and lanthanide-based assays to monitor in vitro kinase activity. The KINATEST-ID pipeline relies on a high number of reported kinase substrates to predict artificial substrate sequences, however, not all kinases have the sufficient number of known substrates to make an accurate prediction. </div><div>The adaptation of kinase assay linked with phosphoproteomics technique was used to increase the number of known FLT3 kinase variant substrate sequences. Subsequently, a set of data formatting tools were developed to curate the mass spectrometry data to become compatible with a command line version of the KINATEST-ID pipeline modules. This approach was used to design seven pan-FLT3 artificial substrate (FAStides) sequences. The pair of FAStides that were deemed the most sensitive toward FLT3 kinase phosphorylation were assayed in increasing concentrations of clinically relevant tyrosine kinase inhibitors. </div><div>To improve the automation of the mass spectrometry data analysis and formatting for use with the KINATEST-ID pipeline, a streamlined process was developed within a bioinformatic platform, GalaxyP. The data formatting tools used to process the FLT3 mass spectrometry data were converted into compatible versions to execute within the GalaxyP framework. This process was used to design four BTK artificial substrates (BAStide) to monitor kinase activity. Additionally, one of the BAStide sequences was designed in the lanthanide chelating motif to develop an antibody-free activity assay for BTK. </div><div>Lastly, a multicolored time resolved lanthanide assay was designed by labeling SYK artificial substrate and a SRC family artificial substrate to measure the activity of both kinases in the same kinase reaction. This highlighted the functionality of lanthanide-based time resolved assays for potential multiplexing assay development. </div><div><br></div>

The major goal of this study was to develop an experimental proteomics approach for deciphering protein complexes and protein interaction networks in the budding and fission yeasts. Key steps of the employed analytical routine, including the purification of complexes and mass spectrometric identification of their subunits, were investigated in detail. Archiving, storage and handling of polyacylamide gels, visualization of protein bands and their effect on the efficiency of in-gel digestion and mass spectrometric identification of proteins were quantitatively evaluated. It was further demonstrated that a combination of several mass spectrometric techniques based on MALDI and ES ionization provided complementary data and enabled comprehensive characterization of protein digests. The optimized analytical procedures were employed in deciphering protein complexes and protein interaction networks in the budding and fission yeasts. A combination of Tandem Affinity Purification (TAP) and mass spectrometric identification of gel separated protein subunits is generic and robust strategy that provided accurate and reproducible data. The evaluation of TAP success rate, reproducibility and typical protein background presented in this work is based on TAP tagging and immunoprecepitation of 75 genes in S. cerevisiae and 22 in S. pombe. The molecular composition of characterized protein complexes was compared with protein-protein interactions uncovered by other established methods, such as yeast two hybrid screens or proteome-wide purification of protein complexes. We found that repetitive purification of protein complexes using different subunits as baits is crucially important for confident charting of proteomic environments. Accurate dissection of individual protein complexes and identification of their proteomic hyperlinks enabled to consider proteomic environments in the phylogenetic perspective and paved the way to reliable projection of proteomics data obtained in lower eukaryotic model organisms to higher eukaryotes, including humans.

<p>  </p> <p>Cyclic dinucleotides (CDNs) such as the bacterial CDNs (cyclic-di-AMP, cyclic-di-GMP and 3’3’cyclic GMP-AMP) and mammalian CDN, 2’3’-cGAMP, are essential immune response second messenger signaling molecules. These CDNs act via Stimulator of interferon genes (STING)-TANK Binding Kinase 1 (TBK1)-Interferon Regulatory Factor 3 (IRF3) pathway. However, data from our lab and others indicate that beyond the classical STING-TBK1-IRF3 pathway, CDNs also regulate other signaling axes related to both inflammatory and non-inflammatory pathways. But, a global view of how these CDNs affect signaling in diverse cells or through non-STING pathways is lacking. There is also paucity of data on CDN modulated kinases and no global assessment of phosphorylation events that follow cyclic GMP AMP synthase (cGAS)-STING axis stimulation in immune cells. Herein, I have used a proteomics approach to determine signaling pathways regulated by bacterial CDNs, c-di-GMP and c-di-AMP in human gingival fibroblasts such as pathways related to nucleotide excision repair (NER) which ordinarily do not channel through STING (Chapter 3). Additionally, with the use of phosphoproteomics and bioinformatics, this project accomplished a system-wide phosphorylation analyses of T cells treated with 2’3’cGAMP and showed that 2’3’cGAMP impact various, yet unreported critical kinases (E.g. LCK, ZAP70, ARG2) and signaling pathways important for T cell function (Chapter 4). Asides known interferon signaling, these differentially phosphorylated kinases were involved in T cell receptor (TCR) signaling, myeloid cell differentiation, cell cycle regulation, and regulation of double strand break repair. </p> <p>Another area of interest addressed by this project is the discovery of novel antibacterial agents against multi-drug resistant (MDR) bacteria. Thus, in Chapters 5 and 6, I show the identification, antibacterial activity and characterization of <strong>HSD1835</strong> and <strong>HSD1919 </strong>as novel SF5 and SCF-containing membrane active compounds, highly potent against preformed MDR biofilms with fast bactericidal activity against persister bacteria. Plus, an exciting addition to the fight against MDR bacteria in Chapter 7, the discovery of <strong>HSD1624</strong> and analogs, which are able to re-sensitize MDR and colistin resistant bacteria such as <em>Pseudomonas aeruginosa</em> from a colistin MIC of 1024 μg/mL to 0.03 μg/mL (64000-fold reduction). Ultimately, these compounds could be translated into anti-biofilm and, anti-MDR bacteria therapeutics, preventing repeated surgeries due to infections, and saving lives. </p>

<p dir="ltr">Adipose tissue is characterized by the dominant presence of adipocytes, specialized cells adept at lipid metabolism. These adipocytes act as critical nodes, coordinating the complex processes of energy storage and mobilization according to the body's metabolic requirements. Within the adipocyte population of mammals, there are three main subtypes: white, beige, and brown adipocytes. White adipocytes are primarily dedicated to the sequestration of energy in the form of triglycerides. Conversely, beige and brown adipocytes are distinguished by their capacity for thermogenesis, the process of dissipating nutritional energy as heat. The contemporary challenge of chronic overnutrition has precipitated a global surge in obesity and cardiometabolic diseases. Addressing this issue necessitates the maintenance of white adipocyte homeostasis and the enhancement of the quantity and function of thermogenic adipocytes, which are imperative for mitigating the global obesity epidemics.</p><p dir="ltr">Mitochondrion, a multifunctional organelle, is integral to a broad spectrum of cellular processes, including anabolic and catabolic metabolism, bioenergetics, and signal transduction, all of which are essential for maintaining cellular functions and homeostasis. The efficacy of mitochondrial operations is intrinsically linked to their membrane dynamics. In this study, transmission electron microscopy and mass spectrometry were employed to investigate the proteins implicated in the cold-induced mitochondrial membrane remodeling in brown adipocytes. Through this approach, a poorly characterized protein, Family with Sequence Similarity 210 Member A (FAM210A), was identified as a mitochondrial inner membrane protein that is induced by cold stimulation. Subsequent loss-of-function experiments were conducted to elucidate the role of FAM210A in adipocytes. Mice with adipose-specific deletion of <i>Fam210a</i> (<i>Fam210a</i>^<em>AKO</em>) exhibited compromised mitochondrial cristae structure and a reduced thermogenic capacity in brown adipose tissue (BAT), resulting in an increased susceptibility to lethal hypothermia during acute cold challenge. Moreover, in mice with inducible ablation of <i>Fam210a</i> in adipocytes (<i>Fam210</i>^{<em>iAKO</em>}), mitochondrial alterations in BAT were negligible at thermoneutral conditions; however, they exhibited defective cold-induced mitochondrial cristae remodeling, culminating in a progressive loss of cristae and diminished mitochondrial density. Mechanistically, it was determined that FAM210A interacts with mitochondrial protease YME1L and modulates its activity toward OMA1 and OPA1 cleavage, thus compromising cold-induced mitochondrial remodeling in BAT.</p><p dir="ltr">Additionally, this research delved into the role of FAM210A in adipocytes in response to dietary stress by feeding mice with high-fat diet (HFD). The study found a consistent correlation between FAM210A expression and OPA1 cleavage in adipocytes under HFD challenge. Mice lacking FAM210A in all adipocytes and subjected to HFD exhibited lipoatrophy in white adipose tissue (WAT) and a downregulation of genes associated with adipogenesis and lipid metabolism. In contrast, mice with a brown adipocyte-specific ablation of <i>Fam210a </i>(<i>Fam210a</i>^<em>UKO</em>) displayed no significant change in WAT mass but had enlarged livers. Crucially, both <i>Fam210a</i>^<em>AKO</em> and <i>Fam210a</i>^<em>UKO</em> mice presented increased WAT inflammation, deteriorated glucose tolerance, and exacerbated insulin resistance. These findings underscore the pivotal role of FAM210A in brown adipose tissue (BAT) in the preservation of WAT homeostasis and the regulation of systemic glucose clearance in diet-induced obesity.</p><p dir="ltr">In summary, these studies characterize the mitochondrial dynamics in brown adipocytes in response to cold stress, identify a new cold-induced mitochondrial protein, FAM210A, and uncover its functions in adipocytes under cold and dietary stresses. These findings highlight the importance of mitochondrial remodeling in the adaptive response of adipocytes to evolving metabolic demands. This work establishes FAM210A as a key regulator of mitochondrial cristae remodeling, shedding light on the mechanisms that govern mitochondrial plasticity in adipocytes.</p>

The oncoprotein MDM2 has an integral role in cancer development via multiple signalling pathways. Two proteomic mass spectrometry screens, label-free with spectral counting quantitation and 8-plex iTRAQ were used to identify proteins up or downregulated over time by the MDM2 targeting drug Nutlin. A subset of previously identified MDM2 binding partners were identified as altered after Nutlin treatment, along with proteins which have not as yet been linked to MDM2 or p53. Proteins altered two hours after Nutlin treatment were screened for sequence similarity to an MDM2 binding consensus motif based on the BOX-I region of p53. Peptides corresponding to this motif were validated for MDM2 binding, and the mode of binding investigated using competition ELISA and thermal denaturation assays. Known MDM2 ligands such as Nutlin were shown to have a range of effects on the binding of these newly identified MDM2 peptides, which may be attributed to allosteric regulation of MDM2. The effects of Nutlin on two full length proteins identified by the MS screens, CypB and NPM, were confirmed in vivo. In vitro binding of MDM2 to CypB and PK, which contain BOX-I like motifs, was also demonstrated validating proteomic mass spectrometry screens as a method to identify new protein-protein interactions. To further investigate the potential of linear motifs to modulate protein-protein interactions, a peptide aptamer targeting the protein AGR2 was tested for effect on AGR2 and p53 in a cancer cell line.

BACKGROUND:Marek's Disease (MD) is a hyperproliferative, lymphomatous, neoplastic disease of chickens caused by the oncogenic Gallid herpesvirus type 2 (GaHV-2 / MDV). Like several human lymphomas the neoplastic MD lymphoma cells overexpress the CD30 antigen (CD30hi) and are in minority, while the non-neoplastic cells (CD30lo) form the majority of population. MD is a unique natural in-vivo model of human CD30hi lymphomas with both natural CD30hi lymphomagenesis and spontaneous regression. The exact mechanism of neoplastic transformation from CD30lo expressing phenotype to CD30hi expressing neoplastic phenotype is unknown. Here, using microarray, proteomics and Systems Biology modeling / we compare the global gene expression of CD30lo and CD30hi cells to identify key pathways of neoplastic transformation. We propose and test a specific mechanism of neoplastic transformation, and genetic resistance, involving the MDV oncogene Meq, host gene products of the Nuclear Factor Kappa B (NF-kappaB) family and CD30 / we also identify a novel Meq protein interactome.RESULTS:Our results show that a) CD30lo lymphocytes are pre-neoplastic precursors and not merely reactive lymphocytes / b) multiple transformation mechanisms exist and are potentially controlled by Meq / c) Meq can drive a feed-forward cycle that induces CD30 transcription, increases CD30 signaling which activates NF-kappaB, and, in turn, increases Meq transcription / d) Meq transcriptional repression or activation of the CD30 promoter generally correlates with polymorphisms in the CD30 promoter distinguishing MD-lymphoma resistant and susceptible chicken genotypes e) MDV oncoprotein Meq interacts with proteins involved in physiological processes central to lymphomagenesis.CONCLUSIONS:In the context of the MD lymphoma microenvironment (and potentially in other CD30hi lymphomas as well), our results show that the neoplastic transformation is a continuum and the non-neoplastic cells are actually pre-neoplastic precursor cells and not merely immune bystanders. We also show that NF-kappaB is a central player in MDV induced neoplastic transformation of CD30-expressing lymphocytes in vivo. Our results provide insights into molecular mechanisms of neoplastic transformation in MD specifically and also herpesvirus induced lymphoma in general.

Plant cells are routinely exposed to various pathogens and environmental stresses that cause cell wall perturbations. Little is known of the mechanisms that plant cells use to sense these disturbances and transduce corresponding signals to regulate cellular responses to maintain cell wall integrity. Previous studies in rice have shown that removal of the cell wall leads to substantial chromatin reorganization and histone modification changes concomitant with cell wall re-synthesis. But the genes and proteins that regulate these cellular responses are still largely unknown. Here we present an examination of the nuclear proteome differential expression in response to removal of the cell wall in rice suspension cells using multiple nuclear proteome extraction methods. A total of 382 nuclear proteins were identified with two or more peptides, including 26 transcription factors. Upon removal of the cell wall, 142 nuclear proteins were up regulated and 112 were down regulated. The differentially expressed proteins included transcription factors, histones, histone domain containing proteins, and histone modification enzymes. Gene ontology analysis of the differentially expressed proteins indicates that chromatin & nucleosome assembly, protein-DNA complex assembly, and DNA packaging are tightly associated with cell wall removal. Our results indicate that removal of the cell wall imposes a tremendous challenge to the cells. Consequently, plant cells respond to the removal of the cell wall in the nucleus at every level of the regulatory hierarchy.

BACKGROUND: A systems toxicology investigation comparing and integrating transcriptomic and proteomic results was conducted to develop holistic effects characterizations for the wildlife bird model, Northern bobwhite (Colinus virginianus) dosed with the explosives degradation product 2-amino-4,6-dinitrotoluene (2A-DNT). A subchronic 60d toxicology bioassay was leveraged where both sexes were dosed via daily gavage with 0, 3, 14, or 30 mg/kg-d 2A-DNT. Effects on global transcript expression were investigated in liver and kidney tissue using custom microarrays for C. virginianus in both sexes at all doses, while effects on proteome expression were investigated in liver for both sexes and kidney in males, at 30 mg/kg-d. RESULTS: As expected, transcript expression was not directly indicative of protein expression in response to 2A-DNT. However, a high degree of correspondence was observed among gene and protein expression when investigating higher-order functional responses including statistically enriched gene networks and canonical pathways, especially when connected to toxicological outcomes of 2A-DNT exposure. Analysis of networks statistically enriched for both transcripts and proteins demonstrated common responses including inhibition of programmed cell death and arrest of cell cycle in liver tissues at 2A-DNT doses that caused liver necrosis and death in females. Additionally, both transcript and protein expression in liver tissue was indicative of induced phase I and II xenobiotic metabolism potentially as a mechanism to detoxify and excrete 2A-DNT. Nuclear signaling assays, transcript expression and protein expression each implicated peroxisome proliferator-activated receptor (PPAR) nuclear signaling as a primary molecular target in the 2A-DNT exposure with significant downstream enrichment of PPAR-regulated pathways including lipid metabolic pathways and gluconeogenesis suggesting impaired bioenergetic potential. CONCLUSION: Although the differential expression of transcripts and proteins was largely unique, the consensus of functional pathways and gene networks enriched among transcriptomic and proteomic datasets provided the identification of many critical metabolic functions underlying 2A-DNT toxicity as well as impaired PPAR signaling, a key molecular initiating event known to be affected in di- and trinitrotoluene exposures.

Cystic fibrosis (CF) lung disease is characterised by early airways infection and inflammation, chronic suppuration, frequent infective exacerbations and an increased influx of acute, and chronic inflammatory cells. The inflammatory process involves activation of many cell types including neutrophils, macrophages and epithelial cells, and leads ultimately to the development of progressive respiratory failure and death. Accurate assessment of the inflammatory process is a crucial part of disease monitoring and should allow appropriate evaluation of therapeutic interventions so as to maximize control of the respiratory sequelae of the disorder. Lung function markers such as FEV1 are insensitive and indirect. Direct but invasive methods such as fibreoptic bronchoscopy and biopsy are limited in application, repeatability and safety. Non-invasive methods of assessment are, therefore, attractive. Exhaled Breath Gases, Exhaled Breath Condensate and Induced Sputum provide potential for such measures. These techniques are safe, simple, repeatable and could assess all airways and can be used in children as young as 6 years. We hypothesised that biomarkers of inflammation in Cystic Fibrosis Lung Disease are measurable in samples collected noninvasively, and can be developed into clinically useful assays. These assays would have the ability to reflect the level of inflammation in the CF lungs as well as holding the potential to act as surrogate markers of CFTR function. Methods Non-invasive markers of inflammation in Cystic Fibrosis lung disease Methods. Exhaled breath gases, exhaled breath condensate, bronchoalveolar lavage fluid and induced sputum were investigated using a number of analysis techniques to identify the markers which best discriminated CF from non CF subjects. Analysis techniques used were electrochemical cells, chemiluminescene, ELISA, EIA, ion selective probes and mass spectrometry. Results Markers found to discriminate CF from non CF subjects were EBC pH and ammonium, and 38 proteomic markers were found in induced sputum. 21 proteomic markers were found in bronchoalveolar lavage fluid. One biomarker has been identified with confidence, Calgranulin A. Discussion A large component of the work of this thesis was focussed on exhaled breath condensate. Two markers, pH and Ammonium were different between the CF and control groups. The measurement of EBC pH and ammonium as markers of inflammation should be used in future gene therapy trials as they are cheap, quick and simple to perform Using clean techniques free from contamination, no proteins are repeatedly detectable in EBC using highly sensitive SELDI techniques. This technique reflects the highest sensitivity of any available proteomics instrument and therefore until new technologies become available, it would be incorrect to assay any proteins in EBC. The induced sputum proteomics study identified 38 independent markers of CF lung inflammation Therefore, sampling by collection of induced sputum should be used in gene therapy trials. The endpoints should be assessed by a combination of SELDI as an endpoint and by ELISA where this is available. The marker Calgranulin is likely to report on neutrophil recruitment to the lung. It is anticipated that this will be a sensitive marker of inflammation in the lung and it also has the potential to report on successful of gene transfer as it is raised in heterozygote carriers as well as homozygotes with CF. Therefore, the non-invasive technique induced sputum coupled to proteomic analysis would have the ability to reflect the level of inflammation in CF subjects and may also report on CFTR function.