STRANgE,integrated physical–biological–mechanical system for recovery in of the “oil spill” in Antarctic environment

Throughout the last century the increasing human activities in Antarctic region, particularly research expeditions, fishing, and tourism amplified the risk of oils spills at these high latitudes of the meridional hemisphere. A number of studies have been focused on chronic hydrocarbon contamination near Antarctic research stations revealing the presence and persistence of these human-derived contaminants. Marine ship-source oil spills in Antarctic region can have significant impacts on the marine environment. The key factors to effectively fight oil spills are a careful selection and proper use of the equipment and materials best suited to the critical local conditions. Despite the significant advances in the field of environmental recovery after an “oil spill” episode, research has recently shown that the usual techniques are often less effective than expected. This issue become much more relevant in the Antarctic case, not only for the incomparable environmental value of the Antarctic region but also for the extreme environmental conditions and the great distances from properly equipped centers, that make unfeasible sending naval vessels. Scope of the STRANgE Project is the preliminary design of a prototype floating platform, parachutable by plane, able to intervene as quickly as possible for the containment, removal and treatment/storage of the oil slick. New sorbent nanostructured materials and specialized Antarctic bacteria applications constitute the main innovations of this Project.     

Inhibition of Bovine Kidney Low Molecular Mass Phosphotyrosine Protein Phosphatase by Uric Acid

Uric acid inhibited 50% of the activity of bovine kidney low molecular mass phosphotyrosine protein phosphatase at concentrations of 1.0, 0.4, 1.3, and 0.2 mM, respectively for p -nitrophenyl phosphate (p -NPP), flavine mononucleotide, β -naphthyl phosphate and tyrosine phosphate (Tyr-P) as substrates. The mixed type inhibition of p -NPP hydrolysis was fully reversible, with K ic and K iu values of 0.4 and 1.1 mM, respectively; the inhibition by uric acid shifted the pH optimum from 5.0 to 6.5. When Tyr-P was the substrate, competitive inhibition was observed with a K i value of 0.05 mM. Inhibition studies by uric acid in the presence of thiol compounds, and preincubation studies in the presence of inorganic phosphate suggest that the interaction of uric acid with the enzyme occurred at the active site, but did not involve SH residues, and that the mechanism of inhibition depended on the structure of the substrates.     

Body mass explains characteristic scales of habitat selection in terrestrial mammals

Niche theory in its various forms is based on those environmental factors that permit species persistence, but less work has focused on defining the extent, or size, of a species' environment: the area that explains a species' presence at a point in space. We proposed that this habitat extent is identifiable from a characteristic scale of habitat selection, the spatial scale at which habitat best explains species' occurrence. We hypothesized that this scale is predicted by body size. We tested this hypothesis on 12 sympatric terrestrial mammal species in the Canadian Rocky Mountains. For each species, habitat models varied across the 20 spatial scales tested. For six species, we found a characteristic scale; this scale was explained by species' body mass in a quadratic relationship. Habitat measured at large scales best-predicted habitat selection in both large and small species, and small scales predict habitat extent in medium-sized species. The relationship between body size and habitat selection scale implies evolutionary adaptation to landscape heterogeneity as the driver of scale-dependent habitat selection.     

Binding of abscisic acid to human LANCL2

The phytohormone abscisic acid (ABA) is the central regulator of abiotic stress in plants and plays important roles during plant growth and development. In animal cells, ABA was shown to be an endogenous hormone, acting as a stress signal and stimulating cell functions involved in inflammatory responses and in insulin release. Recently, we demonstrated that Lanthionine synthetase component C-like protein 2 (LANCL2) is required for ABA binding to the plasmamembrane of granulocytes and for the activation of the signaling pathway triggered by ABA in human granulocytes and in rat insulinoma cells. In order to investigate whether ABA activates LANCL2 via direct interaction, we performed specific binding studies on human LANCL2 recombinant protein using different experimental approaches (saturation binding, scintillation proximity assays, dot blot experiments and affinity chromatography). Altogether, results indicate that human recombinant LANCL2 binds ABA directly and provide the first demonstration of ABA binding to a mammalian ABA receptor.     

Evidences of a natively unfolded state for the human topoisomerase IB N-terminal domain

The N-terminal domain of human topoisomerase IB has been expressed, purified and characterized by spectroscopic techniques. CD spectra as a function of concentration and pH indicate that the domain does not possess any defined secondary structure. The protein is probably in a natively unfolded state since its denaturation curve is indicative of a non-cooperative transition. Evidence of a partially folded structure comes from the fluorescence spectrum of ANS, whose intensity increases in presence of the domain. Indication of a partial structural arrangement of the domain comes also from the endogenous fluorescence of tryptophans that is centred at 350 nm in the native and shifts to 354 nm in the fully denaturated protein. Interestingly despite the poor structural degree, as also confirmed by a predictive approach, the domain efficiently binds DNA, suggesting that the absence of a defined 3D structure has a functional meaning that permits the domain to be available for the interaction with different molecular partners.     

Question 5: On the Chemical Reality of the RNA World

The discovery of catalytic RNA has revolutionised modern molecular biology and bears important implications for the origin of Life research. Catalytic RNA, in particular self-replicating RNA, prompted the hypothesis of an early “RNA world” where RNA molecules played all major roles such information storage and catalysis. The actual role of RNA as primary actor in the origin of life has been under debate for a long time, with a particular emphasis on possible pathways to the prebiotic synthesis of mononucleotides; their polymerization and the possibility of spontaneous emergence of catalytic RNAs synthesised under plausible prebiotic conditions. However, little emphasis has been put on the chemical reality of an RNA world; in particular concerning the chemical constrains that such scenario should have met to be feasible. This paper intends to address those concerns with regard to the achievement of high local RNA molecules concentration and the aetiology of unique sequence under plausible prebiotic conditions. Presented at: International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

Breast cancer stem cells rely on fermentative glycolysis and are sensitive to 2-deoxyglucose treatment

A number of studies suggest that cancer stem cells are essential for tumour growth, and failure to target these cells can result in tumour relapse. As this population of cells has been shown to be resistant to radiation and chemotherapy, it is essential to understand their biology and identify new therapeutic approaches. Targeting cancer metabolism is a potential alternative strategy to counteract tumour growth and recurrence. Here we applied a proteomic and targeted metabolomic analysis in order to point out the main metabolic differences between breast cancer cells grown as spheres and thus enriched in cancer stem cells were compared with the same cells grown in adherent differentiating conditions. This integrated approach allowed us to identify a metabolic phenotype associated with the stem-like condition and shows that breast cancer stem cells (BCSCs) shift from mitochondrial oxidative phosphorylation towards fermentative glycolysis. Functional validation of proteomic and metabolic data provide evidences for increased activities of key enzymes of anaerobic glucose fate such as pyruvate kinase M2 isoform, lactate dehydrogenase and glucose 6-phopshate dehydrogenase in cancer stem cells as well as different redox status. Moreover, we show that treatment with 2-deoxyglucose, a well known inhibitor of glycolysis, inhibits BCSC proliferation when used alone and shows a synergic effect when used in combination with doxorubicin. In conclusion, we suggest that inhibition of glycolysis may be a potentially effective strategy to target BCSCs.One of the main problems in the therapy of breast tumour is long-term relapse. This can in part be explained by failure to eradicate a subset of cells within the tumour that are then capable of sustaining tumour growth. These cells share a number of features with stem cells and have therefore been called cancer stem cells (CSCs). CSCs have been isolated from a variety of solid tumours, including breast cancer¹ and appear to have role in resistance to treatment as well as in metastasis formation.² Indeed, CSCs present several intrinsic mechanisms of resistance to conventional antitumour drugs and radiation therapy such the overexpression of adenosine triphosphate (ATP)-binding cassette (ABC) drug transporters, activation of survival pathways, increased production of anti-apoptotic factors, higher defences against oxidative stress, and efficient repair of DNA damage.³ Therefore the development and validation of new therapeutic strategies targeting CSCs is urgently needed to improve clinical outcome.Recently, the interest on studying cancer metabolism and the so called Warburg effect has grown as targeting specific metabolic pathways might be a promising approach to cancer therapy.^{4, 5} Warburg effect defines cancer dependence on fermentative glycolysis allowing for the diversion of key metabolites into cellular biosynthetic pathways in proliferating cancer cells,⁶ including CSC, and it has been suggested that it can be exploited to develop new pharmacological treatments that can counteract the chemo-resistance of these cells.^{7, 8}It has also been suggested that metabolic changes may have a causal role in inducing different phenotypic states of cancer cells. As an example, Dong et al.⁹ have shown that silencing of the gluconeogenic enzyme fructose-1,6-biphosphatase that activates fermentative glycolysis results in a stem-like phenotype. Despite their importance, the metabolic features of CSCs still remains largely unknown. Recently, it has been shown that CSCs isolated from several solid tumours display significant alteration of energy metabolism and are more glycolytic compared with more differentiated tumour cells^{10, 11, 12, 13}or normal stem cells.¹⁴ However, this is still a controversial issue as previous studies have shown that CSCs are less glycolytic than the differentiated ones.¹⁵Here, using an integrated proteomic and targeted metabolomic approach, we show that the metabolism of breast cancer stem cells (BCSCs) grown as spheres is strongly linked to fermentative glycolysis compared with the same cells grown in adherent differentiating conditions (spheroid-derived adherent cells (SDACs)). On the basis of these evidences, we sought to test the effect of a well-characterized glycolytic inhibitor, 2-deoxy-D-glucose (2-DG),^{16, 17} alone or in combination with the widely used chemotherapeutic doxorubicin (Doxo) on BCSCs'' growth and proliferation. Our results indicate that BCSCs are highly sensitive to 2-DG that also shows a synergic effect with Doxo treatment.     

Overexpression of guanylate cyclase activating protein 2 in rod photoreceptors in vivo leads to morphological changes at the synaptic ribbon

Guanylate cyclase activating proteins are EF-hand containing proteins that confer calcium sensitivity to retinal guanylate cyclase at the outer segment discs of photoreceptor cells. By making the rate of cGMP synthesis dependent on the free intracellular calcium levels set by illumination, GCAPs play a fundamental role in the recovery of the light response and light adaptation. The main isoforms GCAP1 and GCAP2 also localize to the synaptic terminal, where their function is not known. Based on the reported interaction of GCAP2 with Ribeye, the major component of synaptic ribbons, it was proposed that GCAP2 could mediate the synaptic ribbon dynamic changes that happen in response to light. We here present a thorough ultrastructural analysis of rod synaptic terminals in loss-of-function (GCAP1/GCAP2 double knockout) and gain-of-function (transgenic overexpression) mouse models of GCAP2. Rod synaptic ribbons in GCAPs-/- mice did not differ from wildtype ribbons when mice were raised in constant darkness, indicating that GCAPs are not required for ribbon early assembly or maturation. Transgenic overexpression of GCAP2 in rods led to a shortening of synaptic ribbons, and to a higher than normal percentage of club-shaped and spherical ribbon morphologies. Restoration of GCAP2 expression in the GCAPs-/- background (GCAP2 expression in the absence of endogenous GCAP1) had the striking result of shortening ribbon length to a much higher degree than overexpression of GCAP2 in the wildtype background, as well as reducing the thickness of the outer plexiform layer without affecting the number of rod photoreceptor cells. These results indicate that preservation of the GCAP1 to GCAP2 relative levels is relevant for maintaining the integrity of the synaptic terminal. Our demonstration of GCAP2 immunolocalization at synaptic ribbons at the ultrastructural level would support a role of GCAPs at mediating the effect of light on morphological remodeling changes of synaptic ribbons.