Study of nanostructured targets for plasma production via laser ablation

Metal nanowires (NWs) - nanostructures 20-100 nm in diameter and up to tens of micrometers long - behave as waveguides when irradiated with light with wavelength much greater than their diameter. This is due to collective excitations of free electrons (plasmons) in the metal which couple to light and travel on the surface of the nanowire. This effect can be used to efficiently absorb laser pulses to produce dense and hot plasma on special nanostructured targets with metal nanowires vertically aligned on the surface. In this thesis work, nanostructured targets with different parameters (length, diameter, metal and fabrication process) have been irradiated with infrared laser light. X-ray flux emitted by the cooling plasma is measured during irradiation, and the depth of craters formed on the target is measured later. This data is used to choose which target parameters are best for plasma production. Different targets are compared with each other and against a control, non-nanostructured (bulk) target. As will be shown, highly significant (> 5 sigma) differences are found between targets with different nanostructures, and between nanostructured and bulk target. This differences are very difficult to explain whithout accounting for the nanostructures in the targets. Therefore, data collected and analized in this thesis work supports the hypotesys that nanostructured targets perform better than bulk targets for laser plasma production purposes, and provides useful indications for optimization of NWS' parameters.

Fibroblast growth factors:new insights, new targets in the management of diabetes

The fibroblast growth factor (FGF) family consists of 22 evolutionarily and structurally related proteins (FGF1 to FGF23; with FGF15 being the rodent ortholog of human FGF19). Based on their mechanism of action, FGFs can be categorized into intracrine, autocrine/paracrine and endocrine subgroups. Both autocrine/paracrine and endocrine FGFs are secreted from their cells of origin and exert their effects on target cells by binding to and activating specific single-pass transmembrane tyrosine kinase receptors (FGFRs). Moreover, FGF binding to FGFRs requires specific cofactors, namely heparin/heparan sulfate proteoglycans or Klothos for autocrine/paracrine and endocrine FGF signaling, respectively. FGFs are vital for embryonic development and mediate a broad spectrum of biological functions, ranging from cellular excitability to angiogenesis and tissue regeneration. Over the past decade certain FGFs (e.g. FGF1, FGF10, FGF15/FGF19 and FGF21) have been further recognized as regulators of energy homeostasis, metabolism and adipogenesis, constituting novel therapeutic targets for obesity and obesity-related cardiometabolic disease. Until recently, translational research has been mainly focused on FGF21, due to the pleiotropic, beneficial metabolic actions and the relatively benign safety profile of its engineered variants. However, increasing evidence regarding the role of additional FGFs in the regulation of metabolic homeostasis and recent developments regarding novel, engineered FGF variants have revitalized the research interest into the therapeutic potential of certain additional FGFs (e.g. FGF1 and FGF15/FGF19). This review presents a brief overview of the FGF family, describing the mode of action of the different FGFs subgroups, and focuses on FGF1 and FGF15/FGF19, which appear to also represent promising new targets for the treatment of obesity and type 2 diabetes.

Microglia as therapeutic targets in retinal degeneration: role of translocator protein (18 κDa) (TSPO) and minocycline.

Microglia are the resident immune cells of the central nervous system (CNS) and play an important role in innate immune defense as well as tissue homeostasis. Chronic microglial reactivity, microgliosis, is a general hallmark of inflammatory and degenerative diseases that affect the CNS, including the retina. There is increasing evidence that chronic microgliosis is more than just a bystander effect, but rather actively contributes to progression of degeneration through processes such as toxic nitric oxide (NO) production and even phagocytosis of stressed but viable photoreceptors. Therefore immunmodulation of microglia presents a possible therapeutic strategy for retinal degenerations. Notably, the expression of the mitochondrial translocator protein 18 (κDa) (TSPO) is highly elevated in reactive microglia as seen in several neuroinflammatory diseases such as Alzheimer’s disease, Parkinson’s disease and multiple sclerosis. Therefore it is used as a gliosis biomarker in the brain. Moreover TSPO ligands show potent effects in resolving neuroinflammatory brain disorders. However, TSPO expression in the eye had not been investigated before. Further, it was unknown whether TSPO ligands’ potent immunomodulatory effects could be used to treat retinal degenerations. To fill this gap, the study aimed to analyze whether TSPO is also a potential biomarker for degenerative processes in the retina. Moreover the thesis attempted to determine whether a specific TSPO ligand, XBD173, might modulate microglial reactivity and is a potent therapeutic, to treat retinal degenerative diseases. The findings revealed that TSPO is strongly upregulated in microglial cells of retinoschisin-deficient (RS1-/y) mice, a model of inherited retinal degeneration and in a murine light damage model. A co-localization of TSPO and microglia was furthermore detectable in human retinal sections, indicating a potential role for TSPO as a biomarker for retinal degenerations. In vitro assays showed that the TSPO ligand XBD173 effectively inhibited features of microglial activation such as morphological transformation into reactive phagocytes and enhanced expression of pro-inflammatory cytokines. XBD173 also reduced microglial migration and proliferation and reduced their neurotoxic potential on photoreceptor cells. In two independent mouse models of light-induced retinal degeneration, the treatment with XBD173 reduced accumulation of amoeboid, reactive microglia in the outer retina and attenuated degenerative processes, indicated by a nearly preserved photoreceptor layer. A further question addressed in this thesis was whether minocycline, an antibiotic with additional anti-inflammatory properties is able to reduce microglial neurotoxicity and to protect the retina from degeneration. Minocycline administration dampened microglial pro-inflammatory gene expression, NO production and neurotoxicity on photoreceptors. Interestingly, in addition to its immunomodulatory effect, minocycline also increased the viability of photoreceptors in a direct manner. In the light damage model, minocycline administration counter-acted microglial activation and blocked retinal degeneration. Taken together these results identified TSPO as a biomarker for microglial reactivity and as therapeutic target in the retina. Targeting TSPO with XBD173 was able to reverse microglial reactivity and could prevent degenerative processes in the retina. In addition, the study showed that the antibiotic minocycline effectively counter-regulates microgliosis and light-induced retinal degeneration. Considering that microgliosis is a major contributing factor for retinal degenerative disorders, this thesis supports the concept of a microglia-directed therapy to treat retinal degeneration.

Toward adaptive management of coastal MPAs: The influence of different conservation targets and costs on the design of no-take areas

There is still much discussion on the most appropriate location, size and shape of marine protected areas (MPAs). These three factors were analyzed for a small coastal MPA, the Luiz Saldanha Marine Park (LSMP), for which a very limited amount of local ecological information was available when implemented in 1998. Marxan was used to provide a number of near-optimal solutions considering different levels of protection for the various conservation features and different costs. These solutions were compared with the existing no-take area of the LSMP. Information on 11 habitat types and distribution models for 3 of the most important species for the local artisanal fisheries was considered. The human activities with the highest economic and ecological impact in the study area (commercial and recreational fishing and scuba diving) were used as costs. The results show that the existing no-take area is actually located in the best area. However, the no-take area offers limited protection to vagile fish and covers a very small proportion of some of the available habitats. An increase in the conservation targets led to an increase in the number of no-take areas. The comparative framework used in this study can be applied elsewhere, providing relevant information to local stakeholders and managers in order to proceed with adaptive management. (C) 2015 Elsevier B.V. All rights reserved.

Variability in the international normalised ratio (INR) in patients with antiphospholipid syndrome and positive lupus anticoagulant: should the INR targets be higher?

El síndrome antifosfolípido es un desorden autoinmune caracterizado por hipercoagulabilidad que requiere terapia anticoagulante como pilar fundamental, siendo la warfarina el tratamiento de elección en los casos que requieren manejo por largos periodos. Sin embargo, los pacientes con anticoagulante lúpico positivo representan un reto porque tienen mayor riesgo de presentar eventos trombóticos, sumado a que el seguimiento con el International Normalized Ratio (INR) no es confiable, ya que estos anticuerpos generan interferencia con las pruebas de laboratorio basadas en fosfolípidos, como es el caso del tiempo de protrombina (PT) con INR basal prolongado, incluso antes del inicio de la terapia anticoagulante. Por tal razón, se ilustra el caso de una paciente con síndrome antifosfolípido primario y anticoagulante lúpico positivo quien ha presentado múltiples episodios trombóticos, a pesar de recibir terapia anticoagulante. Además se hace una revisión de la literatura disponible y se postulan nuevas metas de INR en estos pacientes diferentes de las que se plantean actualmente.

Contrasting environment targets characteristics: development of the drought phenotyping network.

Introduction. Specific sites selecting criteria. Soil characteristics for establishment of a specific site. Main steps and recommendations for a specific site selection and placement. Climatic characterization.

Searching for novel targets to control wheat Head Blight Disease-I-Protein identification, 3D modeling and virtual screening.

2016

A preclinical study of spinal cord injury focused on cellular and molecular modifications as potential targets for innovative therapies

Spinal Cord Injury (SCI) is a devastating condition for human and animal health. In SCI particularly, neurons, oligodendrocytes precursor cells, and mature oligodendrocytes are highly vulnerable to the toxic microenvironment after the lesion and susceptible to the elevated levels of noxious stimuli. Thus the regenerative response of the organism in case of SCI is significantly reduced, and only little spontaneous amelioration is observed in lesioned patients during the early phases. This work mainly focuses on studying and characterizing the modification induced by the SCI in a preclinical animal model. We investigated the ECM composition in the spinal cord segments surrounding the primary lesion site at a gene expression level. We found Timp1 and CD44 as a crucial hub in the secondary cascade of SCI in both spinal cord segments surrounding the lesion site. Interestingly, a temporal and anatomical difference in gene expression, indicating a complex regulation of ECM genes after SCI that could be used as a tool for regenerative medicine. We also investigated the modification in synaptic plasticity-related gene expression in spinal and supraspinal areas involved in motor control. We confirmed the anatomical and temporal difference in gene expression in spinal cord tissue. This analysis suggests that a molecular mapping of the lesion-induced modification could be a useful tool for regenerative medicine. In the last part, we evaluated the efficacy of an implantable biopolymer loaded with an anti-inflammatory drug and a pro-myelinating agent on the acute phase of SCI in our preclinical model. We found a consistent reduction of the inflammatory state in the spinal lesion site and the cord's surrounding segments. Moreover, we found increased preservation of the spinal cord tissue with a related upregulation of neuronal and oligodendroglial markers after lesion. Our treatment showed effective ameliorating functional outcome and reducing the lesion extension in the chronic phase.

Modeling Alzheimer disease with iPSCs and mouse model for the identification of risk factors, new targets, and potential therapeutical strategies

Alzheimer's disease (AD) is the most common neurodegenerative disease in elderly. Donepezil is the first-line drug used for AD. In section one, the experimental activity was oriented to evaluate and characterize molecular and cellular mechanisms that contribute to neurodegeneration induced by the Aβ1-42 oligomers (Aβ1-42O) and potential neuroprotective effects of the hybrids feruloyl-donepezil compound called PQM130. The effects of PQM130 were compared to donepezil in a murine AD model, obtained by intracerebroventricular (i.c.v.) injection of Aβ1-42O. The intraperitoneal administration of PQM130 (0.5-1 mg/kg) after i.c.v. Aβ1-42O injection improved learning and memory, protecting mice against spatial cognition decline. Moreover, it reduced oxidative stress, neuroinflammation and neuronal apoptosis, induced cell survival and protein synthesis in mice hippocampus. PQM130 modulated different pathways than donepezil, and it is more effective in counteracting Aβ1-42O damage. The section two of the experimental activity was focused on studying a loss of function variants of ABCA7. GWA studies identified mutations in the ABCA7 gene as a risk factor for AD. The mechanism through which ABCA7 contributes to AD is not clear. ABCA7 regulates lipid metabolism and critically controls phagocytic function. To investigate ABCA7 functions, CRISPR/Cas9 technology was used to engineer human iPSCs and to carry the genetic variant Y622*, which results in a premature stop codon, causing ABCA7 loss-of-function. From iPSCs, astrocytes were generated. This study revealed the effects of ABCA7 loss in astrocytes. ABCA7 Y622* mutation induced dysfunctional endocytic trafficking, impairing Aβ clearance, lipid dysregulation and cell homeostasis disruption, alterations that could contribute to AD. Though further studies are needed to confirm the PQM130 neuroprotective role and ABCA7 function in AD, the provided results showed a better understanding of AD pathophysiology, a new therapeutic approach to treat AD, and illustrated an innovative methodology for studying the disease.

E-cadherin and Choline Kinase: two challenging drug discovery targets

The data presented in this thesis was generated using molecular biology, protein chemistry and X-ray crystallography techniques. However, while the methodologies employed are essentially the same, the research work presented here refers to two different proteins, which are part of different research projects in the laboratory. For this reason, the content of this thesis is divided in two independent parts, each provided with an introduction and a general overview of the research topic and state-ofthe- art, a materials and methods section discussing the techniques used and the protocols followed, and a section where the results are presented and discussed in detail. The first half of the thesis deals with the structural characterization of the complex between human E-cadherin and three different small molecule potential inhibitors identified via a fragment-based drug discovery (FBDD) screening campaign that was conducted using a library of commercially available small fluorinated chemical fragments. For this screening phase, we used 19F-NMR as readout. The NMR experiments were done by our collaborator Dr. Marina Veronesi at the D3 PharmaChemistry division of the Italian Institute of Technology (IIT) in Genova (Italy). Functional cell adhesion assays to validate the inhibitory effects of the fragments thus identified were carried out in collaboration with Prof. Frédéric André at the University of Marseille (France). The second half of the thesis describes the structural characterization of Plasmodium falciparum Choline Kinase (PfChoK), an important pharmaceutical target in the fight against malaria, as well as the biochemical characterization of a library of potential inhibitors of PfChoK. These inhibitors were synthetized in the group of Prof. Luisa Carlota López-Cara at the Department of Pharmaceutical and Organic Chemistry of the University of Granada (Spain) in the framework of an ongoing collaboration between the two groups.

Study of genes involved in her2-positive breast cancer progression for identification of new therapeutic targets

HER2 overexpression is observed in 20-30% of invasive breast carcinomas and it is correlated with poor prognosis. Although targeted therapies have revolutionized the treatment of HER2-positive breast cancer, a high number of patients presented primary or acquired resistance to monoclonal antibodies and tyrosine kinase inhibitors. Tumor heterogenicity, epithelial to mesenchymal transition (EMT) and cancer stem cells are key factors in target therapy resistance and tumor progression. The aim of this project was to discover alternative therapeutic strategies to over-come tumor resistance by harnessing immune system and looking for new targetable molecules. The results reported introduce a virus-like particles-based vaccine against HER2 as promising therapeutic approach to treat HER2-positive tumors. The high and persistent anti-HER2 antibody titers elicited by the vaccine significantly inhibited tumor growth and metastases onset. Furthermore, the polyclonal response induced by the vaccine also inhibited human HER2-positive breast cancer cells resistant to trastuzumab in vitro, suggesting its efficacy also on trastuzumab resistant tumors. To identify new therapeutic targets to treat progressed breast cancer, we took advantage from a dynamic model of HER2 expression obtained in our laboratory, in which HER2 loss and cancer progression were associated with the acquisition of EMT and stemness features. Targeting EMT-involved molecules, such as PDGFR-β, or the induction of epithelial markers, like E-cadherin, proved to be successful strategy to impair HER2-negative tumor growth. Density alterations, which might be induced by anti-HER2 target therapies, in cell culture condition of a cell line with a labile HER2 expression, caused HER2 loss probably as consequence of more aggressive subpopulations which prevail over the others. These subpopulations showed an increased EMT and stemness profile, confirming that targeting EMT-involved molecules or antigen expressed by cancer stem cells together with anti-HER2 target therapies is a valid strategy to inhibit HER2-positive cells and simultaneously prevent selection of more aggressive clone.

Identification Of Target Genes Using Gene Expression Profile Of Granulocytes From Patients With Chronic Myeloid Leukemia Treated With Tyrosine Kinase Inhibitors.

Differential gene expression analysis by suppression subtractive hybridization with correlation to the metabolic pathways involved in chronic myeloid leukemia (CML) may provide a new insight into the pathogenesis of CML. Among the overexpressed genes found in CML at diagnosis are SEPT5, RUNX1, MIER1, KPNA6 and FLT3, while PAN3, TOB1 and ITCH were decreased when compared to healthy volunteers. Some genes were identified and involved in CML for the first time, including TOB1, which showed a low expression in patients with CML during tyrosine kinase inhibitor treatment with no complete cytogenetic response. In agreement, reduced expression of TOB1 was also observed in resistant patients with CML compared to responsive patients. This might be related to the deregulation of apoptosis and the signaling pathway leading to resistance. Most of the identified genes were related to the regulation of nuclear factor κB (NF-κB), AKT, interferon and interleukin-4 (IL-4) in healthy cells. The results of this study combined with literature data show specific gene pathways that might be explored as markers to assess the evolution and prognosis of CML as well as identify new therapeutic targets.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.