Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells.

BACKGROUND: Conserved non-coding sequences in the human genome are approximately tenfold more abundant than known genes, and have been hypothesized to mark the locations of cis-regulatory elements. However, the global contribution of conserved non-coding sequences to the transcriptional regulation of human genes is currently unknown. Deeply conserved elements shared between humans and teleost fish predominantly flank genes active during morphogenesis and are enriched for positive transcriptional regulatory elements. However, such deeply conserved elements account for <1% of the conserved non-coding sequences in the human genome, which are predominantly mammalian. RESULTS: We explored the regulatory potential of a large sample of these 'common' conserved non-coding sequences using a variety of classic assays, including chromatin remodeling, and enhancer/repressor and promoter activity. When tested across diverse human model cell types, we find that the fraction of experimentally active conserved non-coding sequences within any given cell type is low (approximately 5%), and that this proportion increases only modestly when considered collectively across cell types. CONCLUSIONS: The results suggest that classic assays of cis-regulatory potential are unlikely to expose the functional potential of the substantial majority of mammalian conserved non-coding sequences in the human genome.

Brain natriuretic peptide is able to stimulate cardiac progenitor cell proliferation and differentiation in murine hearts after birth.

Brain natriuretic peptide (BNP) contributes to heart formation during embryogenesis. After birth, despite a high number of studies aimed at understanding by which mechanism(s) BNP reduces myocardial ischemic injury in animal models, the actual role of this peptide in the heart remains elusive. In this study, we asked whether BNP treatment could modulate the proliferation of endogenous cardiac progenitor cells (CPCs) and/or their differentiation into cardiomyocytes. CPCs expressed the NPR-A and NPR-B receptors in neonatal and adult hearts, suggesting their ability to respond to BNP stimulation. BNP injection into neonatal and adult unmanipulated mice increased the number of newly formed cardiomyocytes (neonatal: +23 %, p = 0.009 and adult: +68 %, p = 0.0005) and the number of proliferating CPCs (neonatal: +142 %, p = 0.002 and adult: +134 %, p = 0.04). In vitro, BNP stimulated CPC proliferation via NPR-A and CPC differentiation into cardiomyocytes via NPR-B. Finally, as BNP might be used as a therapeutic agent, we injected BNP into mice undergoing myocardial infarction. In pathological conditions, BNP treatment was cardioprotective by increasing heart contractility and reducing cardiac remodelling. At the cellular level, BNP stimulates CPC proliferation in the non-infarcted area of the infarcted hearts. In the infarcted area, BNP modulates the fate of the endogenous CPCs but also of the infiltrating CD45(+) cells. These results support for the first time a key role for BNP in controlling the progenitor cell proliferation and differentiation after birth. The administration of BNP might, therefore, be a useful component of therapeutic approaches aimed at inducing heart regeneration.

Chemistry, isotope values (δD, δ18O, δ34S(SO4)) and temperatures of the water inflows in two Gotthard tunnels, Swiss Alps

Water inflows in the Gotthard Highway Tunnel and in the Gotthard Exploration Tunnel are meteoric waters infiltrating at different elevations, on both sides of an important orographic divide. Limited interaction of meteoric waters with gneissic rocks produces Ca-HCO3 and Na-Ca-HCO3 waters, whereas prolonged interaction of meteoric waters with the same rocks generates Na-HCO3 to Na-SO4 waters. Waters circulating in Triassic carbonate-evaporite rocks have a Ca-SO4 composition. Calcium-Na-SO4 waters are also present. They can be produced through interaction of either Na-HCO3 waters with anhydrite or Ca-SO4 waters with a local gneissic rock, as suggested by reaction path modeling. An analogous simulation indicates that Na-HCO3 waters are generated through interaction of Ca-HCO3 waters with a local gneissic rock. The two main SO4-sources present in the Alps are leaching of upper Triassic sulfate minerals and oxidative dissolution of sulfide minerals of crystalline rocks. Values of delta S-34(SO4) < <similar to>+ 9 parts per thousand, are due to oxidative dissolution of sulfide minerals, whereas delta S-34(SO4) > similar to+ 9 parts per thousand are controlled either by bacterial SO4 reduction or leaching of upper Triassic sulfate minerals. Most waters have temperatures similar to the expected values for a geothermal gradient of 22 degreesC/km and are close to thermal equilibrium with rocks. However relatively large, descending flows of cold waters and ascending flows of warm waters are present in both tunnels and determine substantial cooling and heating, respectively, of the interacting rocks. The most import upflow zone of warm, Na-rich waters is below Guspisbach, in the Gotthard Highway Tunnel, at 6.2-9.0 km from the southern portal. These warm waters have equilibrium temperatures of 65-75 degreesC and therefore constitute an important low-enthalpy geothermal resource. (C) 2001 Elsevier Science Ltd. All rights reserved.

Pheomelanin-based colouration is correlated with indices of flying strategies in the barn owl

Resource polymorphism refers to individuals from the same population foraging in alternative habitats or on alternative food. Food specialization can be associated with adaptations such as colour polymorphism, with pale and dark colours conferring differential camouflage in different habitats. Pale and dark-reddish pheomelanic Barn Owls (Tyto alba) forage on different prey species in closed and open habitats, respectively. We show here that darker-reddish owls have heavier stomach content when found dead, and their 5th secondary wing feather is more deeply anchored inside the integument. These correlations suggest that their feathers bend less when flying, and that darker-reddish Barn Owls are able sustain more intense flying than their paler conspecifics.

Tumor-reactive, SSX-2-specific CD8+ T cells are selectively expanded during immune responses to antigen-expressing tumors in melanoma patients.

The SSX-2 gene encodes a tumor-specific antigen expressed in neoplasms of various histological types. By analyzing a tumor-infiltrated lymph node of a melanoma patient bearing an SSX-2-expressing tumor, we have recently identified the first SSX-2-derived CD8(+) T-cell epitope, that corresponds to peptide SSX-2(41-49), and is recognized by specific CTL in an HLA-A2 restricted fashion. Here, we have used fluorescent HLA-A2/SSX-2(41-49) peptide multimeric complexes to analyze the response to SSX-2(41-49) in melanoma patients and healthy donors. Multimer(+) CD8(+) T cells were readily detected in the majority of patients bearing SSX-2-expressing tumors and, at lower proportions, in patients with nonexpressing tumors and healthy donors. Importantly, isolated A2/SSX-2(41-49) multimer(+) CD8(+) T cells exhibited a large functional heterogeneity in terms of antigen recognition and tumor reactivity. SSX-2-specific CTLs isolated from tumor-infiltrated lymph node of antigen-expressing patients as well as from the corresponding peripheral blood mononuclear cells exhibited high functional avidity of antigen recognition and efficiently recognized antigen-expressing tumors. In contrast, SSX-2-specific CTLs isolated from patients with undetectable responses in the tumor-infiltrated lymph node, as well as from healthy donors, recognized the antigen with decreased functional avidity and were not tumor reactive. Together, these data indicate that CD8(+) T-cell responses to SSX-2(41-49) frequently occur in SSX-2-expressing melanoma patients and suggest that SSX-2(41-49)-specific CTLs of high avidity and tumor reactivity are selectively expanded during immune responses to SSX-2-expressing tumors in vivo.

Tumor necrosis factor-α activates estrogen signaling pathways in endometrial epithelial cells via estrogen receptor α.

The pro-inflammatory cytokine TNF-α and the female hormone estrogen have been implicated in the pathophysiology of two common gynecological diseases, endometriosis and endometrial adenocarcinoma. Here we describe a novel capacity of TNF-α to activate ER signaling in endometrial epithelial cells. TNF-α induced luciferase expression in the absence and presence of estradiol and also augmented expression of the estrogen-regulated genes c-fos, GREB1, and progesterone receptor. Furthermore, TNF-α mediated ER transcriptional activity is dependent on the Extracellular Regulated Kinase (ERK) 1/2 pathway. Co-treatment with a pure ER antagonist resulted in an inhibition of this TNF-α-induced ERE luciferase activity and gene expression, demonstrating that this cytokine signals through ERs. Additional investigations confirmed that TNF-α acts specifically via ERα. Taken together, these data provide a rationale for the potential use of inhibitors of TNF-α and estrogen production/activity in combination for the treatment of endometrial pathologies.

Ricercando tra i Registri

My final project is to show the development of the language and the style of the double bass and its change of role through different influences. To accomplish this I decided to make an analytic overview of those double bass players that started to use a different and not traditional approach on the instrument. Later, I focused on the bassists and composers who influenced me the most in the latest period of my study career by partly analysing their playing and their composition. Another part of my work was concerned with creating a personal connection with those musicians, who I consider idols of mine. I did this through interviews, to try to understand their creative process on the instrument and in the composition and to deeply comprehend their personal point of view about the evolution of the double bass. At the same time my interest for the compositional aspect was growing together with the necessity to discover my own voice as a musician. Subsequently I made an analysis of my compositions to underline and to get conscious about my personal influences and evolution. Concluding from this, I have created a complete overview and deepened my understanding for the modern approach in Jazz double bass.

Cellular distribution of glucose and monocarboxylate transporters in human brain white matter and multiple sclerosis lesions.

To ensure efficient energy supply to the high demanding brain, nutrients are transported into brain cells via specific glucose (GLUT) and monocarboxylate transporters (MCT). Mitochondrial dysfunction and altered glucose metabolism are thought to play an important role in the progression of neurodegenerative diseases, including multiple sclerosis (MS). Here, we investigated the cellular localization of key GLUT and MCT proteins in human brain tissue of non-neurological controls and MS patients. We show that in control brain tissue GLUT and MCT proteins were abundantly expressed in a variety of central nervous system cells, particularly in microglia and endothelial cells. In active MS lesions, GLUTs and MCTs were highly expressed in infiltrating leukocytes and reactive astrocytes. Astrocytes manifest increased MCT1 staining and maintain GLUT expression in inactive lesions, whereas demyelinated axons exhibit significantly reduced GLUT3 and MCT2 immunoreactivity in inactive lesions. Finally, we demonstrated that the co-transcription factor peroxisome proliferator-activated receptor gamma co-activator 1-alpha (PGC-1α), an important protein involved in energy metabolism, is highly expressed in reactive astrocytes in active MS lesions. Overexpression of PGC-1α in astrocyte-like cells resulted in increased production of several GLUT and MCT proteins. In conclusion, we provide for the first time a comprehensive overview of key nutrient transporters in white matter brain samples. Moreover, our data demonstrate an altered expression of these nutrient transporters in MS brain tissue, including a marked reduction of axonal GLUT3 and MCT2 expression in chronic lesions, which may impede efficient nutrient supply to the hypoxic demyelinated axons thereby contributing to the ongoing neurodegeneration in MS. GLIA 2014;62:1125-1141.

Enhanced generation of specific tumor-reactive CTL in vitro by selected Melan-A/MART-1 immunodominant peptide analogues.

The Melan-A/MART-1 gene, which is expressed by normal melanocytes as well as by most fresh melanoma samples and melanoma cell lines, codes for Ags recognized by tumor-reactive CTL. HLA-A*0201-restricted Melan-A-specific CTL recognize primarily the Melan-A(27-35) (AAGIGILTV) and the Melan-A(26-35) (EAAGIGILTV) peptides. The sequences of these two peptides are not necessarily optimal as far as binding to HLA-A*0201 is concerned, since both lack one of the dominant anchor amino acid residues (leucine or methionine) at position 2. In this study we introduced single amino acid substitutions in either one of the two natural peptide sequences with the aim of improving peptide binding to HLA-A*0201 and/or recognition by specific CTL. Surprisingly, analogues of the Melan-A(27-35) peptide, which bound more efficiently than the natural nonapeptide to HLA-A*0201, were poorly recognized by tumor-reactive CTL. In contrast, among the Melan-A(26-35) peptide analogues tested, the peptide ELAGIGILTV was not only able to display stable binding to HLA-A2.1 but was also recognized more efficiently than the natural peptide by two short-term cultured tumor-infiltrated lymph node cell cultures as well as by five of five tumor-reactive CTL clones. Moreover, in vitro generation of tumor-reactive CTL by stimulation of PBMC from HLA-A*0201 melanoma patients with this particular peptide analogue was much more efficient than that observed with either one of the two natural peptides. These results suggest that the Melan-A(26-35) peptide analogue ELAGIGILTV may be more immunogenic than the natural peptides in HLA-A*0201 melanoma patients and should thus be considered as a candidate for future peptide-based vaccine trials.

Selective accumulation of mature DC-Lamp+ dendritic cells in tumor sites is associated with efficient T-cell-mediated antitumor response and control of metastatic dissemination in melanoma.

The clinical relevance of dendritic cells (DCs) at the tumor site remains a matter of debate concerning their role in the generation of effective antitumor immunity in human cancers. We performed a comprehensive immunohistochemical analysis using a panel of DC-specific antibodies on regressing tumor lesions and sentinel lymph nodes (SLNs) in melanoma patients. Here we show in a case report involving spontaneous regression of metastatic melanoma that the accumulation of DC-Lamp+ DCs, clustered with tumor cells and lymphocytes, is associated with local expansion of antigen-specific memory effector CTLs. These findings were extended in a series of 19 melanoma-positive SLNs and demonstrated a significant correlation between the density of DC-Lamp+ DC infiltrates in SLNs with the absence of metastasis in downstream lymph nodes. This study, albeit performed in a limited series of patients, points to a pivotal role of mature DCs in the local expansion of efficient antitumor T-cell-mediated immune responses at the initial sites of metastasis and may have important implications regarding the prognosis, staging, and immunotherapy of melanoma patients.

Neutrophil-derived APRIL concentrated in tumor lesions by proteoglycans correlates with human B-cell lymphoma aggressiveness.

A PRoliferation-Inducing TNF Ligand (APRIL) costimulates B-cell activation. When overexpressed in mice, APRIL induces B-cell neoplasia, reminiscent of human B-cell chronic lymphoid leukemia (B-CLL). We analyzed APRIL expression in situ in human non-Hodgkin lymphomas. APRIL up-regulation was only observed in high-grade B-cell lymphomas, diffuse large B-cell lymphoma (DLBCL), and Burkitt lymphoma (BL). Up-regulation was seen in 46% and 20% of DLBCL and BL, respectively. In DLBCL, neutrophils, constitutively producing APRIL and infiltrating the tumor tissue, were the main cellular source of APRIL. Rare DLBCL cases showed a predominance of histiocytes or mesenchymal cells as APRIL source. APRIL secreted by neutrophils accumulated on tumor cells via proteoglycan binding. In addition to proteoglycans, DLBCL tumor cells expressed the APRIL signaling receptor, TACI and/or BCMA, indicating that these tumor cells are fully equipped to respond to APRIL. A retrospective clinical analysis revealed a significant correlation between high expression of APRIL in tumor lesions and decreased overall patient survival rate. Hence, APRIL produced by inflammatory cells infiltrating lymphoma lesions may increase tumor aggressiveness and affect disease outcome.

O Erro, uma Análise Necessária: sua Implicação no Ensino da Língua Portuguesa em Cabo Verde

O trabalho de investigação que ora se apresenta entronca nas preocupações do dia a dia enquanto profissional e dirigente da educação que tem experimentado e acompanhado de perto a prática pedagógica e docente. Por esses imperativos, senti-me na obrigação de procurar uma resposta, refletir sobre as dificuldades do ensino da língua portuguesa e perceber melhor esses obstáculos, nomeadamente o erro linguístico nas práticas letivas, as causas subjacentes e, eventualmente, a quota-parte de responsabilidades dos outros intervenientes no processo, nomeadamente, dos professores de língua portuguesa e do próprio sistema. Nesta sequência, o presente estudo aborda o erro como conceito, marcado pela polissemia da sua definição, abordado pelas múltiplas metodologias de ensino, mas também como elemento central no ensino e aprendizagem de uma língua segunda, no ensino básico, em contextos de coabitação de línguas muito próximas como o português e a língua cabo-verdiana; pretendemos também elencar os procedimentos e atitudes dos atores no processo, bem como os meios didático-pedagógicos essenciais com vista a sua deteção, análise e tratamento do mesmo. A aprendizagem de uma língua segunda como o português, num contexto como o de Cabo Verde, constitui uma tarefa complexa e por vezes demorada, que não pode ser resumida a atos corriqueiros e previsíveis de sala de aula, ignorando as necessidades, disposições e interesses dos aprendentes que são colocados perante uma encruzilhada, o de aprender uma língua que não é sua, mas que não pode recusar. A aparente aproximação entre as duas línguas constitui um obstáculo acrescido, por propiciar a interferência, principal causa do erro, apesar do avanço verificado no desenvolvimento de metodologias e materiais de apoio que auxiliam e tornam mais eficiente o processo de aquisição de uma língua segunda. Para operacionalização do assunto foi elaborado um estudo com recurso à análise de erros, em quarenta e um (41) textos produzidos por alunos do 6.º ano de escolaridade de cinco escolas do ensino básico do Tarrafal, Cabo Verde, com o intuito de recolher informações, analisá-las e, após uma reflexão sobre os resultados, concluir sobre as suas implicações no ensino aprendizagem da língua portuguesa.

O ensino e o uso do conjuntivo no terceiro ciclo em Cabo Verde: estudo de caso realizado na escola secundaria Manuel Lopes - Praia

Neste trabalho analisamos um conteúdo gramatical - o modo conjuntivo num contexto de aprendizagem formal, seguindo duas vias: a teórica, em que fizemos uma abordagem sobre as perspectivas de vários gramáticos; a prática, que se traduz na análise de um corpus. Desenvolvemos esta análise com base nas produções escritas dos aprendentes do terceiro ciclo, na Escola Secundária Manuel Lopes, Praia, com o objectivo de fazer uma abordagem crítica respeitante ao ensino do Português Língua Segunda, em particular, ao ensino e uso do conjuntivo na supracitada língua em Cabo Verde. Com efeito, foram abordadas questões relativas às teorias de aquisição/aprendizagem segundo as perspectivas de diversos autores. A análise dos textos escritos orientou-nos para o levantamento e estudo dos erros de uso do conjuntivo e para termos uma noção do perfil sociolinguístico dos aprendentes. A descrição linguística efectuada conduziu-nos a uma reflexão sobre as formas de tratamento e de recuperação dos erros . Os resultados sugerem que o insucesso na aprendizagem do Português Língua Segunda deve-se a factores vários, entre os quais, sociolinguísticos e políticos. Nesta sequência, perspectivamos a superação de erros mediante estratégias e sugestões metodológicas para um ensino eficaz do conjuntivo em Português Língua Segunda, neste país.

SwissParam: a fast force field generation tool for small organic molecules.

The drug discovery process has been deeply transformed recently by the use of computational ligand-based or structure-based methods, helping the lead compounds identification and optimization, and finally the delivery of new drug candidates more quickly and at lower cost. Structure-based computational methods for drug discovery mainly involve ligand-protein docking and rapid binding free energy estimation, both of which require force field parameterization for many drug candidates. Here, we present a fast force field generation tool, called SwissParam, able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field, but in a functional form that is compatible with the CHARMM force field. Output files can be used with CHARMM or GROMACS. The topologies and parameters generated by SwissParam are used by the docking software EADock2 and EADock DSS to describe the small molecules to be docked, whereas the protein is described by the CHARMM force field, and allow them to reach success rates ranging from 56 to 78%. We have also developed a rapid binding free energy estimation approach, using SwissParam for ligands and CHARMM22/27 for proteins, which requires only a short minimization to reproduce the experimental binding free energy of 214 ligand-protein complexes involving 62 different proteins, with a standard error of 2.0 kcal mol(-1), and a correlation coefficient of 0.74. Together, these results demonstrate the relevance of using SwissParam topologies and parameters to describe small organic molecules in computer-aided drug design applications, together with a CHARMM22/27 description of the target protein. SwissParam is available free of charge for academic users at www.swissparam.ch.

Melanoma cell expression of Fas(Apo-1/CD95) ligand: implications for tumor immune escape.

Malignant melanoma accounts for most of the increasing mortality from skin cancer. Melanoma cells were found to express Fas (also called Apo-1 or CD95) ligand (FasL). In metastatic lesions, Fas-expressing T cell infiltrates were proximal to FasL+ tumor cells. In vitro, apoptosis of Fas-sensitive target cells occurred upon incubation with melanoma tumor cells; and in vivo, injection of FasL+ mouse melanoma cells in mice led to rapid tumor formation. In contrast, tumorigenesis was delayed in Fas-deficient lpr mutant mice in which immune effector cells cannot be killed by FasL. Thus, FasL may contribute to the immune privilege of tumors.