73 research outputs found

    ATHENA Research Book, Volume 2

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    ATHENA European University is an association of nine higher education institutions with the mission of promoting excellence in research and innovation by enabling international cooperation. The acronym ATHENA stands for Association of Advanced Technologies in Higher Education. Partner institutions are from France, Germany, Greece, Italy, Lithuania, Portugal and Slovenia: University of Orléans, University of Siegen, Hellenic Mediterranean University, Niccolò Cusano University, Vilnius Gediminas Technical University, Polytechnic Institute of Porto and University of Maribor. In 2022, two institutions joined the alliance: the Maria Curie-Skłodowska University from Poland and the University of Vigo from Spain. Also in 2022, an institution from Austria joined the alliance as an associate member: Carinthia University of Applied Sciences. This research book presents a selection of the research activities of ATHENA University's partners. It contains an overview of the research activities of individual members, a selection of the most important bibliographic works of members, peer-reviewed student theses, a descriptive list of ATHENA lectures and reports from individual working sections of the ATHENA project. The ATHENA Research Book provides a platform that encourages collaborative and interdisciplinary research projects by advanced and early career researchers

    Studying the Biliary Tree using Organoid-Technology

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    Italian Proteomics Association, 5th Annual National Conference Abstract Volume

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    Abstract volume of the Italian Proteomics Association 5th Annual national conferenc

    Global occurrence of pine wilt disease: biological interactions and integrated management

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    Plant pathogens cause severe losses in a wide range of crops and forestry plant species worldwide, being a major obstacle toward achieving sustainable agriculture and forestry. In forests, pathogens can affect sustainable management by affecting economic trade and serious ecological losses can occur, such as the ability to store carbon, reduce flood risk or purify water (Boyd et al., 2013). Ranking in the top ten of the most damaging plant-parasitic nematodes worldwide, the migratory endoparasitic nematode Bursaphelenchus xylophilus (pinewood nematode, PWN) is the causal agent of Pine wilt disease (PWD) being responsible for the tremendous decline of conifers species in Eurasian conifer forests”

    Studying the Biliary Tree using Organoid-Technology

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    La spectrométrie de masse : un couteau suisse pour disséquer la structure et la fonction du spermatoprotéasome

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    Le protéasome est le complexe enzymatique protéolytique principal de la cellule. Son cœur catalytique (20S) est formé de quatre anneaux heptamériques. Son activité et sa spécificité de substrat peuvent être régulées par les complexes 19S, PA28alphaß, PA28gamma et PA200 ainsi que par des sous-unités 20S alternatives. La spermatogenèse est un processus de différenciation des cellules germinales mâles: les spermatogonies (SPG) se transforment en spermatocytes (SPC), en spermatides (SPT) puis en spermatozoïdes. Ce processus requière une protéolyse intense. Le spermatoprotéasome (spt20S) est spécifique des gamètes en développement et essentiel à la spermatogenèse. Il diffère du protéasome standard (std20S) par la sous-unité alpha4s qui remplace la sous-unité constitutive alpha4. Le spt20S joue un rôle important avec PA200 dans la progression de la méiose, mais les mécanismes qui le rendent différent du std20S restent inconnus. Nous avons établi des stratégies protéomiques complémentaires pour caractériser les complexes du protéasome immunopurifiés à partir de testicules. L'analyse Top-Down de protéasome purifié, nous a permis de montrer pour la première fois qu'alpha4s et alpha4 portent les mêmes MPTs. La protéomique Bottom-Up, nous a permis de comparer les immunopurifications (IPs) de protéasomes totaux avec celles obtenues avec un anticorps spécifique du stp20S que nous avons développé. Nous avons établi qu'alpha4 et alpha4s ne coexistent pas dans le même 20S, bien qu'ils soient presque également abondants dans les testicules. Nous avons également trouvé plus de 19S et de PA200 liés au spt20S qu'au std20S. Les autres protéines préférentiellement associées au spt20S incluent PI31 et Fbxo7 qui sont cruciales pour la fertilité et d'importants médiateurs du transport du protéasome et de l'ancrage des E3 ligases - deux processus qui semblent cruciaux pour la fonction du spt20S pendant la spermatogenèse. Nous avons ensuite obtenu des cellules germinales à différents stades de la différenciation et l'analyse protéomique des lysats ainsi que des IPs, nous a permis d'établir un interactome dynamique du protéasome tout au long de la spermatogenèse. Nous avons observé un changement total du std20S au spt20S entre les SPG pré-méiotiques et les SPC/SPT méiotiques et post-méiotiques. Un changement d'expression semble responsable, plutôt qu'une incorporation préférentielle d'alpha4s. En entrant dans la méiose, l'association de PA200 avec le protéasome a augmenté 7 fois, confirmant son importance dans le développement des gamètes. Bien que PA200 soit d'après la littérature le principal activateur du spt20S, nous montrons que le 19S est est en réalité majoritaire, lié à 60% des 20S dans les SPC - une activation du protéasome sans précédent. De nombreux partenaires du spt20S sont identifiés à la fois dans les cellules germinales et dans les testicules entiers, montrant la robustesse de nos méthodes. Ceux-ci incluent des protéines synaptonémales, de nombreuses protéines impliquées dans l'ubiquitylation, le cycle cellulaire et la progression méiotique ainsi que le transport cellulaire, en accord avec les fonctions du spt20S proposées dans la littérature. Le passage d'alpha4 à alpha4s semble crucial pour la méiose, mais quelles sont les bases moléculaires de cette transition ? L'échange hydrogène-deutérium nous a permis de montrer pour la première fois que les deux protéasomes présentent des interfaces d'interaction différentes : alpha4s contient des régions plus flexibles qu'alpha4. Cette découverte est confirmée par des pull-down in vitro montrant que le 19S se lie plus fortement au spt20S qu'au std20S, expliquant la hausse d'activité protéolytique pendant la méiose. L'activité trypsique du spt20S est plus élevée que celle du std20S in vitro, ce qui pourrait refléter la nécessité de dégradation des histones. Globalement, nos données révèlent un processus de régulation du spt20S qui est plus complexe que ce qui avait été suggéré précédemment et jettent les bases des différences structurales et fonctionnelles entre le spt20S et le std20S.The proteasome is the main enzymatic complex for targeted proteolysis in the cell. Its core complex (20S) consists of four stacked heptameric rings and requires activator complexes: 19S, PA28alphaß, PA28gamma and PA200, which regulate 20S activity and substrate specificity. Alternative 20S subunits exist to further modulate the proteasome activity. Spermatogenesis is a process of male germ cell differentiation, where spermatogonia (SPG) transform through spermatocyte (SPC), then spermatid (SPT) stages, to become spermatozoa. This process requires intense proteolysis. The spermatoproteasome (spt20S) is specific to the developing gametes and essential for spermatogenesis. It differs from the standard proteasome (std20S) by only one subunit - alpha4s, which replaces the constitutive alpha4 subunit. Together with PA200, the spt20S plays an important role in meiosis progression, however, the mechanisms that make it different compared to std20S remain unknown. We established complementary proteomic pipelines for characterisation of proteasome complexes in the testes, combining immunopurification (IP) and mass spectrometry (MS) analysis. Our Top-Down analysis of purified proteasome, showed for the first time that both alpha4 and alpha4s carry the same PTMs. Using Bottom-Up proteomics we compared the interactome of total proteasomes with that of the spt20S only, obtained using a specific antibody we developed for this purpose. We established that alpha4 and alpha4s do not co-exist in the same 20S, although they are almost equally abundant in the testes.  We also measured that 19S and PA200 regulators were bound in higher ratios to the spt20S compared to std20S. Among other preferentially-associated proteins of spt20S were PI31 and Fbxo7, both shown to be crucial for fertility. They mediate proteasome transport and docking of E3 ligases - both processes that could be crucial for spt20S function. We then obtained germ cells at different differentiation stages and performed a proteomics analysis of both lysates and IP-ed proteasome complexes, to establish a dynamic image of the proteasome throughout spermatogenesis. We observed a complete shift from std20S to spt20S between pre-meiotic SPG and meiotic and post-meiotic SPC and SPT cells. We explained this by a shift in expression, rather than preferential incorporation of alpha4s. Upon entering meiosis, the PA200 association with core proteasome increased 7-fold, marking its importance in gamete development. Although PA200 was represented in literature as the main spt20S interactor, we show that 19S was undoubtedly stoichiometrically dominant, occupying 60% of the existing 20S in SPCs - an unprecedented proteasome activation. Identified spt20S-interacting proteins largely correlated with previous interactome analysis on the whole testes, showing robustness of our methods. We identified synaptonemal proteins bound exclusively to spt20S and numerous proteins involved in ubiquitylation, cell cycle and meiotic progression as well as cellular transport, which fits the current model of spt20S role, proposed by earlier work. The shift from alpha4 to alpha4s in meiosis was shown to be crucial, but what is the molecular basis for this transition? The hydrogen-deuterium exchange experiment coupled to MS helped us to show for the first time that the two proteasomes exhibit different binding interfaces: alpha4s contains regions that are more flexible compared to alpha4. We further supported this finding with pull-down assays, which showed that 19S binds more strongly to the spt20S than to std20S, which would explain the increase in proteolytic activity required during meiosis. The spt20S showed a higher tryptic activity compared to the std20S in vitro, which might reflect a particular need for histone degradation. Altogether, our data reveal a more complex process of spt20S regulation than previously suggested and set the basis for structural and functional differences between the spt20S and std20S

    Case series of breast fillers and how things may go wrong: radiology point of view

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    INTRODUCTION: Breast augmentation is a procedure opted by women to overcome sagging breast due to breastfeeding or aging as well as small breast size. Recent years have shown the emergence of a variety of injectable materials on market as breast fillers. These injectable breast fillers have swiftly gained popularity among women, considering the minimal invasiveness of the procedure, nullifying the need for terrifying surgery. Little do they know that the procedure may pose detrimental complications, while visualization of breast parenchyma infiltrated by these fillers is also deemed substandard; posing diagnostic challenges. We present a case series of three patients with prior history of hyaluronic acid and collagen breast injections. REPORT: The first patient is a 37-year-old lady who presented to casualty with worsening shortness of breath, non-productive cough, central chest pain; associated with fever and chills for 2-weeks duration. The second patient is a 34-year-old lady who complained of cough, fever and haemoptysis; associated with shortness of breath for 1-week duration. CT in these cases revealed non thrombotic wedge-shaped peripheral air-space densities. The third patient is a 37‐year‐old female with right breast pain, swelling and redness for 2- weeks duration. Previous collagen breast injection performed 1 year ago had impeded sonographic visualization of the breast parenchyma. MRI breasts showed multiple non- enhancing round and oval shaped lesions exhibiting fat intensity. CONCLUSION: Radiologists should be familiar with the potential risks and hazards as well as limitations of imaging posed by breast fillers such that MRI is required as problem-solving tool

    Characterization of alar ligament on 3.0T MRI: a cross-sectional study in IIUM Medical Centre, Kuantan

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    INTRODUCTION: The main purpose of the study is to compare the normal anatomy of alar ligament on MRI between male and female. The specific objectives are to assess the prevalence of alar ligament visualized on MRI, to describe its characteristics in term of its course, shape and signal homogeneity and to find differences in alar ligament signal intensity between male and female. This study also aims to determine the association between the heights of respondents with alar ligament signal intensity and dimensions. MATERIALS & METHODS: 50 healthy volunteers were studied on 3.0T MR scanner Siemens Magnetom Spectra using 2-mm proton density, T2 and fat-suppression sequences. Alar ligament is depicted in 3 planes and the visualization and variability of the ligament courses, shapes and signal intensity characteristics were determined. The alar ligament dimensions were also measured. RESULTS: Alar ligament was best depicted in coronal plane, followed by sagittal and axial planes. The orientations were laterally ascending in most of the subjects (60%), predominantly oval in shaped (54%) and 67% showed inhomogenous signal. No significant difference of alar ligament signal intensity between male and female respondents. No significant association was found between the heights of the respondents with alar ligament signal intensity and dimensions. CONCLUSION: Employing a 3.0T MR scanner, the alar ligament is best portrayed on coronal plane, followed by sagittal and axial planes. However, tremendous variability of alar ligament as depicted in our data shows that caution needs to be exercised when evaluating alar ligament, especially during circumstances of injury

    Biomechanical Spectrum of Human Sport Performance

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    Writing or managing a scientific book, as it is known today, depends on a series of major activities, such as regrouping researchers, reviewing chapters, informing and exchanging with contributors, and at the very least, motivating them to achieve the objective of publication. The idea of this book arose from many years of work in biomechanics, health disease, and rehabilitation. Through exchanges with authors from several countries, we learned much from each other, and we decided with the publisher to transfer this knowledge to readers interested in the current understanding of the impact of biomechanics in the analysis of movement and its optimization. The main objective is to provide some interesting articles that show the scope of biomechanical analysis and technologies in human behavior tasks. Engineers, researchers, and students from biomedical engineering and health sciences, as well as industrial professionals, can benefit from this compendium of knowledge about biomechanics applied to the human body

    Deciphering the interplay of molecular alterations underpinning renal cell carcinoma by label-free mass spectrometry and clinical proteomics: A systems medicine approach for precision diagnosis

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    Renal neoplasia is the 14th most common tumor type diagnosed worldwide. With a vast heterogeneity, renal neoplasia encompasses different subtypes. 90% of the neoplasms arise from the epithelial layer of the nephron and vary from benign renal masses (renal oncocytoma, RO) to more indolent or aggressive cancers (renal cell carcinomas, RCC). As RCC subtypes, clear cell (ccRCC) subtype is the most predominant subtype, followed by papillary (pRCC) and chromophobe (chRCC). Despite the different outcomes, some overlapped histological and morphological features difficult their differentiation and diagnosis. Therefore, new approaches for a clear and accurate diagnosis are still needed. To achieve this goal, renal tissue biopsies diagnosed with ccRCC (n = 7), pRCC (n = 5), chRCC (n = 5), RO (n = 5) and normal adjacent tissue (NAT, n= 5) were enrolled in this study. As a very resourceful tool for proteome analysis and biomarker discovery, mass spectrometry (MS)-based methods were used to interrogate the proteome of each tumor in order to undisclosed differences trough which to develop faster and accurate diagnostics. The results achieved with this doctoral thesis include i) the accomplishment of an effective ultrasonic workflow to recover the proteome of optimal cutting temperature (OCT)-embedded tissues, ii) a novel analytical approach based on MALDI-MS profiling to distinguish chRCC from RO, iii) a 109-protein panel to discriminate between chRCC and RO and NAT, iv) a top 24-protein panel to diagnose ccRCC, pRCC, chRCC and RO based on absolute concentration values, v) the translation and validation of three promising biomarkers by immunohistochemical analysis, and vi) an approach for phosphopeptide enrichment. This work brings new insights into the different mechanisms underlying formation of these tumors as well as it provides valuable information to improve clinical diagnosis by opening new avenues for immunohistochemistry and mass spectrometry-based approaches
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