Assembly and disassembly of the Golgi Complex: two prodesses arranged in a cis to trans direction

We have studied the disassembly and assembly of two morphologically and functionally distinct parts of the Golgi complex, the cis/middle and trans cisterna/trans network compartments. For this purpose we have followed the redistribution of three cis/middle- (GMPc-1, GMPc-2, MG 160) and two trans- (GMPt-1 and GMPt-2) Golgi membrane proteins during and after treatment of normal rat kidney (NRK) cells with brefeldin A (BFA). BFA induced complete disassembly of the cis/middle- and trans-Golgi complex and translocation of GMPc and GMPt to the ER. Cells treated for short times (3 min) with BFA showed extensive disorganization of both cis/middle- and trans-Golgi complexes. However, complete disorganization of the trans part required much longer incubations with the drug. Upon removal of BFA the Golgi complex was reassembled by a process consisting of three steps: (a) exist of cis/middle proteins from the ER and their accumulation into vesicular structures scattered throughout the cytoplasm; (b) gradual relocation and accumulation of the trans proteins in the vesicles containing the cis/middle proteins; and (c) assembly of the cisternae, and reconstruction of the Golgi complex within an area located in the vicinity of the centrosome from which the ER was excluded. Reconstruction of the cis/middle-Golgi complex occurred under temperature conditions inhibitory of the reorganization of the trans-Golgi complex, and was dependent on microtubules. Reconstruction of the trans-Golgi complex, disrupted with nocodazole after selective fusion of the cis/middle-Golgi complex with the ER, occurred after the release of cis/middle-Golgi proteins from the ER and the assembly of the cis/middle cisternae.

Gp74 a membrane glycoprotein of the cis-Golgi network that cycles through the endoplasmic reticulum and intermediate compartment

A monoclonal antibody CC92 (IgM), raised against a fraction of rat liver enriched in Golgi membranes, recognizes a novel Endo H-resistant 74-kD membrane glycoprotein (gp74). The bulk of gp74 is confined to the cis-Golgi network (CGN). Outside the Golgi gp74 is found in tubulovesicular structures and ER foci. In cells incubated at 37 degrees C the majority of gp74 is segregated from the intermediate compartment (IC) marker p58. However, in cells treated with organelle perturbants such as low temperature, BFA, and [AIF4]- the patterns of the two proteins become indistinguishable. Both proteins are retained in the Golgi complex at 20 degrees C and in the IC at 15 degrees C. Incubation of cells with BFA results in relocation of gp74 to p58 positive IC elements. [AIF4]- induces the redistribution of gp74 from the Golgi to p58-positive vesicles and does not retard the translocation of gp74 to IC elements in cells treated with BFA. Disruption of microtubules by nocodazol results in the rapid disappearance of the Golgi elements stained by gp74 and redistribution of the protein into vesicle-like structures. The responses of gp74 to cell perturbants are in sharp contrast with those of cis/middle and trans-Golgi resident proteins whose location is not affected by low temperatures or [AIF4]-, are translocated to the ER upon addition of BFA, and stay in slow disintegrating Golgi elements in cells treated with nocodazol. The results suggest that gp74 is an itinerant protein that resides most of the time in the CGN and cycles through the ER/IC following the pathway used by p58.

Mutant Huntingtin impairs post-Golgi trafficking to lysosomes by delocalizing optineurin/Rab8 complex from the Golgi apparatus

Huntingtin regulates post-Golgi trafficking of secreted proteins. Here, we studied the mechanism by which mutant huntingtin impairs this process. Colocalization studies and Western blot analysis of isolated Golgi membranes showed a reduction of huntingtin in the Golgi apparatus of cells expressing mutant huntingtin. These findings correlated with a decrease in the levels of optineurin and Rab8 in the Golgi apparatus that can be reverted by overexpression of full-length wild-type huntingtin. In addition, immunoprecipitation studies showed reduced interaction between mutant huntingtin and optineurin/Rab8. Cells expressing mutant huntingtin produced both an accumulation of clathrin adaptor complex 1 at the Golgi and an increase of clathrin-coated vesicles in the vicinity of Golgi cisternae as revealed by electron microscopy. Furthermore, inverse fluorescence recovery after photobleaching analysis for lysosomal-associated membrane protein-1 and mannose-6-phosphate receptor showed that the optineurin/Rab8-dependent post-Golgi trafficking to lysosomes was impaired in cells expressing mutant huntingtin or reducing huntingtin levels by small interfering RNA. Accordingly, these cells showed a lower content of cathepsin D in lysosomes, which led to an overall reduction of lysosomal activity. Together, our results indicate that mutant huntingtin perturbs post-Golgi trafficking to lysosomal compartments by delocalizing the optineurin/Rab8 complex, which, in turn, affects the lysosomal function.

Cholesterol and Fatty Acids Regulate Dynamic Caveolin Trafficking through the Golgi Complex and between the Cell Surface and Lipid Bodies

Caveolins are a crucial component of plasma membrane (PM) caveolae but have also been localized to intracellular compartments, including the Golgi complex and lipid bodies. Mutant caveolins associated with human disease show aberrant trafficking to the PM and Golgi accumulation. We now show that the Golgi pool of mainly newly synthesized protein is detergent-soluble and predominantly in a monomeric state, in contrast to the surface pool. Caveolin at the PM is not recognized by specific caveolin antibodies unless PM cholesterol is depleted. Exit from the Golgi complex of wild-type caveolin-1 or -3, but not vesicular stomatitis virus-G protein, is modulated by changing cellular cholesterol levels. In contrast, a muscular dystrophy-associated mutant of caveolin-3, Cav3P104L, showed increased accumulation in the Golgi complex upon cholesterol treatment. In addition, we demonstrate that in response to fatty acid treatment caveolin can follow a previously undescribed pathway from the PM to lipid bodies and can move from lipid bodies to the PM in response to removal of fatty acids. The results suggest that cholesterol is a rate-limiting component for caveolin trafficking. Changes in caveolin flux through the exocytic pathway can therefore be an indicator of cellular cholesterol and fatty acid levels.

Outer membrane vesicles from cold-adapted antarctic bacteria

Many Gram-negative, cold-adapted bacteria from the Antarctic environment produce large amounts of extracellular matter with potential biotechnological applications. Transmission electron microscopy (TEM) analysis after high-pressure freezing and freeze substitution (HPF-FS) showed that this extracellular matter is structurally complex, appearing around cells as a netlike mesh, and composed of an exopolymeric substance (EPS) containing large numbers of outer membrane vesicles (OMVs). Isolation, purification and protein profiling via 1D SDS-PAGE confirmed the outer membrane origin of these Antarctic bacteria OMVs. In an initial attempt to elucidate the role of OMVs in cold-adapted strains of Gram-negative bacteria, a proteomic analysis demonstrated that they were highly enriched in outer membrane proteins and periplasmic proteins associated with nutrient processing and transport, suggesting that the OMVs may be involved in nutrient sensing and bacterial survival. OMVs from Gram-negative bacteria are known to play a role in lateral DNA transfer, but the presence of DNA in these vesicles has remained difficult to explain. A structural study of Shewanella vesiculosa M7T using TEM and Cryo-TEM revealed that this Antarctic Gram-negative bacterium naturally releases conventional one-bilayer OMVs, together with a more complex type of OMV, previously undescribed, which on formation drags along inner membrane and cytoplasmic content and can therefore also entrap DNA.

Outer membrane vesicles from cold-adapted antarctic bacteria

Many Gram-negative, cold-adapted bacteria from the Antarctic environment produce large amounts of extracellular matter with potential biotechnological applications. Transmission electron microscopy (TEM) analysis after high-pressure freezing and freeze substitution (HPF-FS) showed that this extracellular matter is structurally complex, appearing around cells as a netlike mesh, and composed of an exopolymeric substance (EPS) containing large numbers of outer membrane vesicles (OMVs). Isolation, purification and protein profiling via 1D SDS-PAGE confirmed the outer membrane origin of these Antarctic bacteria OMVs. In an initial attempt to elucidate the role of OMVs in cold-adapted strains of Gram-negative bacteria, a proteomic analysis demonstrated that they were highly enriched in outer membrane proteins and periplasmic proteins associated with nutrient processing and transport, suggesting that the OMVs may be involved in nutrient sensing and bacterial survival. OMVs from Gram-negative bacteria are known to play a role in lateral DNA transfer, but the presence of DNA in these vesicles has remained difficult to explain. A structural study of Shewanella vesiculosa M7T using TEM and Cryo-TEM revealed that this Antarctic Gram-negative bacterium naturally releases conventional one-bilayer OMVs, together with a more complex type of OMV, previously undescribed, which on formation drags along inner membrane and cytoplasmic content and can therefore also entrap DNA.

Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7

Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

Efficiency and environmental regulation: a 'complex situation'

Production of desirable outputs is often accompanied by undesirable by products that have damaging effects on the environment, and whose disposal is frequently regulated by public authorities. In this paper, we compute directional technology distance functions under particular assumptions concerning disposability of bads in order to test for the existence of what we call ‘complex situations’, where the biggest producer is not the greatest polluter. Furthermore, we show that how in such situations, environmental regulation could achieve an effective reduction in the aggregate level of bad outputs without reducing the production of good outputs. Finally, we illustrate our methodology with an empirical application to a sample of Spanish tile ceramic producers.

Empiricism in ecological economics: a perspective from complex systems theory

Economies are open complex adaptive systems far from thermodynamic equilibrium, and neo-classical environmental economics seems not to be the best way to describe the behaviour of such systems. Standard econometric analysis (i.e. time series) takes a deterministic and predictive approach, which encourages the search for predictive policy to ‘correct’ environmental problems. Rather, it seems that, because of the characteristics of economic systems, an ex-post analysis is more appropriate, which describes the emergence of such systems’ properties, and which sees policy as a social steering mechanism. With this background, some of the recent empirical work published in the field of ecological economics that follows the approach defended here is presented. Finally, the conclusion is reached that a predictive use of econometrics (i.e. time series analysis) in ecological economics should be limited to cases in which uncertainty decreases, which is not the normal situation when analysing the evolution of economic systems. However, that does not mean we should not use empirical analysis. On the contrary, this is to be encouraged, but from a structural and ex-post point of view.

Accuracy vs. simplicity: a complex trade-off

Inductive learning aims at finding general rules that hold true in a database. Targeted learning seeks rules for the predictions of the value of a variable based on the values of others, as in the case of linear or non-parametric regression analysis. Non-targeted learning finds regularities without a specific prediction goal. We model the product of non-targeted learning as rules that state that a certain phenomenon never happens, or that certain conditions necessitate another. For all types of rules, there is a trade-off between the rule's accuracy and its simplicity. Thus rule selection can be viewed as a choice problem, among pairs of degree of accuracy and degree of complexity. However, one cannot in general tell what is the feasible set in the accuracy-complexity space. Formally, we show that finding out whether a point belongs to this set is computationally hard. In particular, in the context of linear regression, finding a small set of variables that obtain a certain value of R2 is computationally hard. Computational complexity may explain why a person is not always aware of rules that, if asked, she would find valid. This, in turn, may explain why one can change other people's minds (opinions, beliefs) without providing new information.

Periodic orbits in complex Abel equation

"Vegeu el resum a l'inici del document del fitxer adjunt."

Propietats d'absorció bifotònica del tetrafenilporficè i el seu complex de palladi: potencials sensibilitzadors per a Teràpia Fotodinàmica bifotònica.

Estudi elaborat a partir d’una estada a la Universitat de Aarhus, Dinamarca, durant juliol 2006. En el present treball s’investiguen, per primer cop, les propietats de absorció bifotòniques del fotosensibilitzador 2,7,12,17-tetrafenilporficè (TPPo) i del seu complex de pal•ladi (II) (PdTPPo). Ambos compostos han rebut molta atenció com a possibles otosensibilitzadors per a Teràpia Fotodinàmica (TFD). S’utilitza la detecció de la fosforescència de l’oxigen singlet, centrada a 1270 nm i produïda per l’absorció de dos fotons, per quantificar la magnitud de la secció d’absorció bifotònica, "delta", dels porficèns estudiats. Els experiments se han dut a terme en el marge espectral 750-850 nm i a l’infraroig proper a 1100nm. Aquestes longituds d’ona corresponen a les zones d’absorció bifotònica en les bandes de Soret i Q. Les propietats bifotòniques obtingudes es comparen i contrasten amb les dades conegudes de la tetrafenilporfirina (TPP), isòmer estructural del tetrafenilporficè però amb més gran simetria, i es troba que en la banda de Soret (que coincideix amb la regió de la pell més transparent) els valors de delta per el TPPo i PdTPPo son aproximadament 2000 GM en el màxim, pràcticament cent vegades més grans que per la TPP. A més a més, aquestos valors son dos ordres de magnitud més grans que els obtinguts a l’irradiar a 1100 nm (bandes Q). Aquestes observacions es poden explicar mitjançant la amplificació per ressonància deguda a la presència de transicions monofotòniques ressonants en la regió de les bandes Q. Els elevats valors de "delta" obtinguts per els tetrafenilporficèns estudiats junt a les principals característiques que aquestos presenten (elevat rendiment de formació d’oxigen singlet, estabilitat química i fotoquímica, absència de citotoxicitat,...) qualifiquen al TPPo y PdTPPo com a possibles fotosensibilitzadors per a Teràpia Fotodinàmica Bifotònica.

Construcció i explotació d’un complex de turisme rural a la població d’Àreu (Pirineu de Lleida)

Aquest treball de fi de carrera pretén desenvolupar el pla de negoci per a la construcció i l’explotació d’un complex de turisme rural al Pallars Sobirà. El projecte compren l’enderroc de les construccions preexistents, construcció i posterior explotació d’apartaments d’ús turístic i una cafeteria a la població d’ Àreu. Dins el pla de negoci s’hi contemplen els plans comercial, financer, l’anàlisi del mercat i l’entorn i una acurada definició del servei que s’oferirà. Amb el treball es vol, doncs, aportar idees pràctiques i útils per a la consecució dels objectius plantejats en el projecte familiar.

Modelling of bird distribution under complex mediterranean landscape dynamics: open habitat birds and fire (MEDFIRE)

Report for the scientific sojourn at the Simon Fraser University, Canada, from July to September 2007. General context: landscape change during the last years is having significant impacts on biodiversity in many Mediterranean areas. Land abandonment, urbanisation and specially fire are profoundly transforming large areas in the Western Mediterranean basin and we know little on how these changes influence species distribution and in particular how these species will respond to further change in a context of global change including climate. General objectives: integrate landscape and population dynamics models in a platform allowing capturing species distribution responses to landscape changes and assessing impact on species distribution of different scenarios of further change. Specific objective 1: develop a landscape dynamic model capturing fire and forest succession dynamics in Catalonia and linked to a stochastic landscape occupancy (SLOM) (or spatially explicit population, SEPM) model for the Ortolan bunting, a species strongly linked to fire related habitat in the region. Predictions from the occupancy or spatially explicit population Ortolan bunting model (SEPM) should be evaluated using data from the DINDIS database. This database tracks bird colonisation of recently burnt big areas (&50 ha). Through a number of different SEPM scenarios with different values for a number of parameter, we should be able to assess different hypothesis in factors driving bird colonisation in new burnt patches. These factors to be mainly, landscape context (i.e. difficulty to reach the patch, and potential presence of coloniser sources), dispersal constraints, type of regenerating vegetation after fire, and species characteristics (niche breadth, etc).

Combinatorial Synthesis and Biological Evaluation of Inhibitors of D-Ala-D-Ala-Ligase

Report for the scientific sojourn carried out at the Max Planck Institut of Molecular Phisiology, Germany, from 2006 to 2008.The work carried out during this postdoctoral stage was focused on two different projects. Firstly, identification of D-Ala D-Ala Inhibitors and the development of new synthethic approaches to obtain lipidated peptides and proteins and the use of these lipidated proteins in biological and biophysical studies. In the first project, new D-Ala D-Ala inhibitors were identified by using structural alignments of the ATP binding sites of the bacterial ligase DDl and protein and lipid kinases in complex with ATP analogs. We tested a series of commercially available kinase inhibitors and found LFM-A13 and Tyrphostine derivatives to inhibit DDl enzyme activity. Based on the initial screening results we synthesized a series of malononitrilamide and salicylamide derivatives and were able to confirm the validity of these scaffolds as inhibitors of DDl. From this investigation we gained a better understanding of the structural requirements and limitations necessary for the preparation of ATP competitive DDl inhibitors. The compounds in this study may serve as starting points for the development of bi-substrate inhibitors that incorporate both, an ATP competitive and a substrate competitive moiety. Bisubstrate inhibitors that block the ATP and D-Ala binding sites should exhibit enhanced selectivity and potency profiles by preferentially inhibiting DDl over kinases. In the second project, an optimized synthesis for tha alkylation of cysteins using the thiol ene reaction was establisehd. This new protocol allowed us to obtain large amounts of hexadecylated cysteine that was required for the synthesis of differently lipidated peptides. Afterwards the synthesis of various N-ras peptides bearing different lipid anchors was performed and the peptides were ligated to a truncated N-ras protein. The influence of this differently lipidated N-ras proteins on the partioning and association of N-Ras in model membrane subdomains was studied using Atomic Force Microscopy.