Design and synthesis of short antimicrobial peptides for plant protection. Study of their mode of action

Aquesta tesi doctoral està basada en el desenvolupament de nous agents antimicrobians derivats del pèptid híbrid cecropina A-melitina WKLFKKILKVL-NH2 (Pep3) que siguin sostenibles i útils per al control de malalties de plantes. Es van dissenyar i sintetitzar més de 133 anàlegs de Pep3 mitjançant química combinatòria. Es van obtenir anàlegs de Pep3 amb una elevada activitat contra fitopatògens i que presentaven baixa toxicitat. Els millors anàlegs van presentar eficàcies comparables amb pesticides de referència en la prevenció d'infeccions causades per fitopatògens. Es va estudiar el mecanisme d'acció de KKLFKKILKYL-NH2 (BP100) investigant la seva interacció amb models de membrana mitjançant tècniques espectroscòpiques. Es va observar la capacitat de BP100 a induir la permeabilització, la neutralització, i l'agregació de vesícules lipídiques aniòniques a una determinada concentració llindar. Es va deduir una equació que relaciona la CMI d'un pèptid antimicrobià amb la constant de partició i la concentració llindar en la membrana.

Synthesis, structure and reactivity of novel CuI, CuII and CuIII complexes containing triaza and hexaaza macrocyclic ligands

El treball de tesi s'emmarca dins del camp de la bioinorgànica, disciplina que estudia les propietats estructurals i de reactivitat dels centres actius dels enzims, servint-se de models síntètics de baix pes molecular per tal d'intentar reproduïr la reactivitat presentada per l'enzim i conèixer els mecanismes de reacció a nivell molecular que tenen lloc en els processos biològics.1 Més concretament el treball posa especial èmfasi en els processos d'activació d'oxigen molecular que tenen lloc en les metaloproteïnes de Coure del Tipus 3, com són l'hemocianina i la tirosinasa, ambdues presentant un complex dinuclear de Cu(I)) en el centre actiu de la forma reduïda, capaç d'activar l'O2 cap a espècies de tipus peròxid.2 Un altre camp d'interès ha estat l'estudi dels processos d'activació d'enllaços C-H no activats en hidrocarburs, tant per la seva importàcia a nivell industrial com per comprendre els mecanismes intrínsecs d'aquesta activació a través de metalls de trancisió.3,4 Durant el treball de tesi presentat s'ha desenvolupat la síntesi de nous complexes de Coure(I), Coure(II) y Cu(III) utilitzant lligands macrocíclics de tipus triaza i hexaaza, i s'han estudiat la seves propietats estructurals així com la seva reactivitat. La reacció dels lligands triazacíclics H32m, H2Me33m i H33m amb sals de coure(II) dóna lloc a una reacció de desproporció de Cu(II) per obtenir-se en quantitats equimolars un complex organometàl·lic de Cu(III) i un complex de Cu(I). La caracterizació estructural exhaustiva dels complexes del tipus aryl-Cu(III) evidencia la formació d'un enllaç organometàl·lic entre l'àtom de Cu(III) i el carboni més próxim de l'anell aromàtic del lligand. Aquesta reacció, a més de representar una nova forma de desproporció en la química del Cu, suposa l'activació d'un enllaç C-H aromàtic a temperatura ambient que, mitjançant l'estudi cinètic d'aquesta desproporció per espectroscòpia UV-Vis, dels càlcul de l'efecte cinètic isotòpic utilitzant el lligand deuterat en el C-H de l'anell, juntament amb el recolzament teòrics dels càlculs DFT per a la optimització de geometries d'intermedis de reacció, ens permeten proposar un mecanisme de reacció pel nostre sistema, on l'activació de l'enllaç C-H aromàtic transcorre per la formació d'un enllaç de tipus agòstic C-H ? Cu(II),5 seguit de la desprotonació del C-H aromàtic per acció d'una base i posterior transferència electrònica per obtenir el complex organometàlic de Cu(III) i el complex de de Cu(I). En quant a la reactivitat d'aquests complexes organometàl·lics aryl-Cu(III) s'ha observat que una base en medi aquós causa la inestabilitat d'aquests compostos, evolucionant cap a la inserció d'un àtom d'oxigen sobre la posició activada de l'anell aromàtic, per a donar lloc a un complex dinuclear de Cu(II) amb dos grups fenoxo actuant de pont entre els àtoms metàl·lics. La reacció transcorre per un intermedi colorejat, caracteritzat com el complex ayl-Cu(III) monodesprotonat en una de les seves amines benzíliques, els quals s'observen igualment en la reacció dels correponents complexos de Cu(I) amb oxigen molecular (O2). És en els nostres sistemes en els quals es descriu per primera vegada la participació d'intermedis organometàl·lics Cu(III)-C en processos d'hidroxilació aromàtica, tals com el desenvolupat per l'enzim tirosinasa o per alguns dels seus models químics de síntesi.6,7,8 S'han estudiat les propietats magnètiques dels quatre bis(fenoxo)complexes de Cu(II) descrits, obtenint-se uns acoplaments de tipus antiferromagnètic o ferromagnètic de diversa magnitud, depenent del solapament orbitalari a l'enllaç Cu-O, a través del qual es produeix el superintercanvi. Nous complexos de Cu(I) sintetitzats amb lligands hexaazamacrocíclics han estat estudiats, i posant especial èmfasi a la seva reactivitat respecta a l'activació d'oxigen molecular (O2). S'ha observat una reactivitat diferenciada segons la concentració de complex de Cu(I) utilitzada, de manera que a altes concentracions s'obté un carbonato complex tetranuclear de Cu(II) per fixació de CO2 atmosfèric, mentre que a baixes concentracions s'observa la hidroxilació aromàtica intramolecular d'un dels anells benzílics del lligand, reacció que presumiblement transcorre per atac electrofílic d'un peroxo complex intermedi sobre el sistema ? de l'anell.6 Els resultats obtinguts en aquest treball ens mostren la facilitat per activar enllaços C-H aromàtics per metalls de transició de la primera sèrie (Cu, Ni) quan aquests estan suficientment pròxims a l'enllaç C-H, en unes condicions de reacció molt suaus (1atm., temperatura ambient). Els nous complexos organometàl·lics Aryl-Cu(III) són el producte d'una nova reacció de desproporció de Cu(II), així com un posició aromàtica activada que podria ser el punt de partida per l'estudi de funcionalització selectiva d'aquests grups aromàtics.

Demographic models and the management of endangered species: a case study of the critically endangered Seychelles magpie robin

1. Demographic models are assuming an important role in management decisions for endangered species. Elasticity analysis and scope for management analysis are two such applications. Elasticity analysis determines the vital rates that have the greatest impact on population growth. Scope for management analysis examines the effects that feasible management might have on vital rates and population growth. Both methods target management in an attempt to maximize population growth. 2. The Seychelles magpie robin Copsychus sechellarum is a critically endangered island endemic, the population of which underwent significant growth in the early 1990s following the implementation of a recovery programme. We examined how the formal use of elasticity and scope for management analyses might have shaped management in the recovery programme, and assessed their effectiveness by comparison with the actual population growth achieved. 3. The magpie robin population doubled from about 25 birds in 1990 to more than 50 by 1995. A simple two-stage demographic model showed that this growth was driven primarily by a significant increase in the annual survival probability of first-year birds and an increase in the birth rate. Neither the annual survival probability of adults nor the probability of a female breeding at age 1 changed significantly over time. 4. Elasticity analysis showed that the annual survival probability of adults had the greatest impact on population growth. There was some scope to use management to increase survival, but because survival rates were already high (> 0.9) this had a negligible effect on population growth. Scope for management analysis showed that significant population growth could have been achieved by targeting management measures at the birth rate and survival probability of first-year birds, although predicted growth rates were lower than those achieved by the recovery programme when all management measures were in place (i.e. 1992-95). 5. Synthesis and applications. We argue that scope for management analysis can provide a useful basis for management but will inevitably be limited to some extent by a lack of data, as our study shows. This means that identifying perceived ecological problems and designing management to alleviate them must be an important component of endangered species management. The corollary of this is that it will not be possible or wise to consider only management options for which there is a demonstrable ecological benefit. Given these constraints, we see little role for elasticity analysis because, when data are available, a scope for management analysis will always be of greater practical value and, when data are lacking, precautionary management demands that as many perceived ecological problems as possible are tackled.

Synthesis and structure-activity relationship studies of CD4 down-modulating cyclotriazadisulfonamide (CADA) analogues

HIV attachment via the CD4 receptor is an important target for developing novel approaches to HIV chemotherapy. Cyclotriazadisulfonamide (CADA) inhibits HIV at submicromolar levels by specifically down-modulating cell-surface and intracellular CD4. An effective five-step synthesis of CADA in 30% overall yield is reported. This synthesis has also been modified to produce more than 50 analogues. Many tail-group analogues have been made by removing the benzyl tail of CADA and replacing it with various alkyl, acyl, alkoxycarbonyl and aminocarbonyl substituents. A series of sidearm analogues, including two unsymmetrical compounds, have also been prepared by modifying the CADA synthesis, replacing the toluenesulfonyl sidearms with other sulfonyl groups. Testing 30 of these compounds in MT-4 cells shows a wide range of CD4 down-modulation potency, which correlates with ability to inhibit HIV-1. Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were constructed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) approaches. The X-ray crystal structures of four compounds, including CADA, show the same major conformation of the central 12-membered ring. The solid-state structure of CADA was energy minimized and used to generate the remaining 29 structures, which were similarly minimized and aligned to produce the 3D-QSAR models. Both models indicate that steric bulk of the tail group, and, to a lesser extent, the sidearms mainly determine CD4 down-modulation potency in this series of compounds.

Synthesis of heterosulfamates. Search for structure-taste relationships

Thirty one new sodium heterosulfamates, RNHSO3Na, where the R portion contains mainly thiazole, benzothiazole, thiadiazole and pyridine ring structures, have been synthesized and their taste portfolios have been assessed. A database of 132 heterosulfamates ( both open-chain and cyclic) has been formed by combining these new compounds with an existing set of 101 heterosulfamates which were previously synthesized and for which taste data are available. Simple descriptors have been obtained using (i) measurements with Corey-Pauling-Koltun (CPK) space- filling models giving x, y and z dimensions and a volume VCPK, (ii) calculated first order molecular connectivities ((1)chi(v)) and (iii) the calculated Spartan program parameters to obtain HOMO, LUMO energies, the solvation energy E-solv and V-SPART AN. The techniques of linear (LDA) and quadratic (QDA) discriminant analysis and Tree analysis have then been employed to develop structure-taste relationships (SARs) that classify the sweet (S) and non-sweet (N) compounds into separate categories. In the LDA analysis 70% of the compounds were correctly classified ( this compares with 65% when the smaller data set of 101 compounds was used) and in the QDA analysis 68% were correctly classified ( compared to 80% previously). TheTree analysis correctly classified 81% ( compared to 86% previously). An alternative Tree analysis derived using the Cerius2 program and a set of physicochemical descriptors correctly classified only 54% of the compounds.

One’s own soundtrack: affective music synthesis

Computer music usually sounds mechanical; hence, if musicality and music expression of virtual actors could be enhanced according to the user’s mood, the quality of experience would be amplified. We present a solution that is based on improvisation using cognitive models, case based reasoning (CBR) and fuzzy values acting on close-to-affect-target musical notes as retrieved from CBR per context. It modifies music pieces according to the interpretation of the user’s emotive state as computed by the emotive input acquisition componential of the CALLAS framework. The CALLAS framework incorporates the Pleasure-Arousal-Dominance (PAD) model that reflects emotive state of the user and represents the criteria for the music affectivisation process. Using combinations of positive and negative states for affective dynamics, the octants of temperament space as specified by this model are stored as base reference emotive states in the case repository, each case including a configurable mapping of affectivisation parameters. Suitable previous cases are selected and retrieved by the CBR subsystem to compute solutions for new cases, affect values from which control the music synthesis process allowing for a level of interactivity that makes way for an interesting environment to experiment and learn about expression in music.

Uncertainty in climate change impacts on basin-scale freshwater resources – preface to the special issue: the QUEST-GSI methodology and synthesis of results

This paper presents a preface to this Special Issue on the results of the QUEST-GSI (Global Scale Impacts) project on climate change impacts on catchment-scale water resources. A detailed description of the unified methodology, subsequently used in all studies in this issue, is provided. The project method involved running simulations of catchment-scale hydrology using a unified set of past and future climate scenarios, to enable a consistent analysis of the climate impacts around the globe. These scenarios include "policy-relevant" prescribed warming scenarios. This is followed by a synthesis of the key findings. Overall, the studies indicate that in most basins the models project substantial changes to river flow, beyond that observed in the historical record, but that in many cases there is considerable uncertainty in the magnitude and sign of the projected changes. The implications of this for adaptation activities are discussed.

A comprehensive investigation of the synthesis of prebiotic galactooligosaccharides by whole cells of Bifidobacterium bifidum NCIMB 41171

The synthesis of galactooligosaccharides (GOS) by whole cells of Bifidobacterium bifidum NCIMB 41171 was investigated by developing a set of mathematical models. These were second order polynomial equations, which described responses related to the production of GOS constituents, the selectivity of lactose conversion into GOS, and the relative composition of the produced GOS mixture, as a function of the amount of biocatalyst, temperature, initial lactose concentration, and time. The synthesis reactions were followed for up to 36 h. Samples were withdrawn every 4 h, tested for β-galactosidase activity, and analysed for their carbohydrate content. GOS synthesis was well explained by the models, which were all significant (P < 0.001). The GOS yield increased as temperature increased from 40 °C to 60 °C, as transgalactosylation became more pronounced compared to hydrolysis. The relative composition of GOS produced changed significantly with the initial lactose concentration (P < 0.001); higher ratios of tri-, tetra-, and penta-galactooligosaccharides to transgalactosylated disaccharides were obtained as lactose concentration increased. Time was a critical factor, as a balanced state between GOS synthesis and hydrolysis was roughly attained in most cases between 12 and 20 h, and was followed by more pronounced GOS hydrolysis than synthesis.

How well can we simulate past climates? Evaluating the models using global palaeoenvironmental datasets.

Global syntheses of palaeoenvironmental data are required to test climate models under conditions different from the present. Data sets for this purpose contain data from spatially extensive networks of sites. The data are either directly comparable to model output or readily interpretable in terms of modelled climate variables. Data sets must contain sufficient documentation to distinguish between raw (primary) and interpreted (secondary, tertiary) data, to evaluate the assumptions involved in interpretation of the data, to exercise quality control, and to select data appropriate for specific goals. Four data bases for the Late Quaternary, documenting changes in lake levels since 30 kyr BP (the Global Lake Status Data Base), vegetation distribution at 18 kyr and 6 kyr BP (BIOME 6000), aeolian accumulation rates during the last glacial-interglacial cycle (DIRTMAP), and tropical terrestrial climates at the Last Glacial Maximum (the LGM Tropical Terrestrial Data Synthesis) are summarised. Each has been used to evaluate simulations of Last Glacial Maximum (LGM: 21 calendar kyr BP) and/or mid-Holocene (6 cal. kyr BP) environments. Comparisons have demonstrated that changes in radiative forcing and orography due to orbital and ice-sheet variations explain the first-order, broad-scale (in space and time) features of global climate change since the LGM. However, atmospheric models forced by 6 cal. kyr BP orbital changes with unchanged surface conditions fail to capture quantitative aspects of the observed climate, including the greatly increased magnitude and northward shift of the African monsoon during the early to mid-Holocene. Similarly, comparisons with palaeoenvironmental datasets show that atmospheric models have underestimated the magnitude of cooling and drying of much of the land surface at the LGM. The inclusion of feedbacks due to changes in ocean- and land-surface conditions at both times, and atmospheric dust loading at the LGM, appears to be required in order to produce a better simulation of these past climates. The development of Earth system models incorporating the dynamic interactions among ocean, atmosphere, and vegetation is therefore mandated by Quaternary science results as well as climatological principles. For greatest scientific benefit, this development must be paralleled by continued advances in palaeodata analysis and synthesis, which in turn will help to define questions that call for new focused data collection efforts.

Vertical structure and physical processes of the Madden-Julian oscillation: synthesis and summary

The "Vertical structure and physical processes of the Madden-Julian oscillation (MJO)" project comprises three experiments, designed to evaluate comprehensively the heating, moistening and momentum associated with tropical convection in general circulation models (GCMs). We consider here only those GCMs that performed all experiments. Some models display relatively higher or lower MJO fidelity in both initialized hindcasts and climate simulations, while others show considerable variations in fidelity between experiments. Fidelity in hindcasts and climate simulations are not meaningfully correlated. The analysis of each experiment led to the development of process-oriented diagnostics, some of which distinguished between GCMs with higher or lower fidelity in that experiment. We select the most discriminating diagnostics and apply them to data from all experiments, where possible, to determine if correlations with MJO fidelity hold across scales and GCM states. While normalized gross moist stability had a small but statistically significant correlation with MJO fidelity in climate simulations, we find no link with fidelity in medium-range hindcasts. Similarly, there is no association between timestep-to-timestep rainfall variability, identified from short hindcasts, and fidelity in medium-range hindcasts or climate simulations. Two metrics that relate precipitation to free-tropospheric moisture--the relative humidity for extreme daily precipitation, and variations in the height and amplitude of moistening with rain rate--successfully distinguish between higher- and lower-fidelity GCMs in hindcasts and climate simulations. To improve the MJO, developers should focus on relationships between convection and both total moisture and its rate of change. We conclude by offering recommendations for further experiments.

Climate variability and human impact in South America during the last 2000 years: synthesis and perspectives from pollen records

An improved understanding of present-day climate variability and change relies on high-quality data sets from the past 2 millennia. Global efforts to model regional climate modes are in the process of being validated against, and integrated with, records of past vegetation change. For South America, however, the full potential of vegetation records for evaluating and improving climate models has hitherto not been sufficiently acknowledged due to an absence of information on the spatial and temporal coverage of study sites. This paper therefore serves as a guide to high-quality pollen records that capture environmental variability during the last 2 millennia. We identify 60 vegetation (pollen) records from across South America which satisfy geochronological requirements set out for climate modelling, and we discuss their sensitivity to the spatial signature of climate modes throughout the continent. Diverse patterns of vegetation response to climate change are observed, with more similar patterns of change in the lowlands and varying intensity and direction of responses in the highlands. Pollen records display local-scale responses to climate modes; thus, it is necessary to understand how vegetation–climate interactions might diverge under variable settings. We provide a qualitative translation from pollen metrics to climate variables. Additionally, pollen is an excellent indicator of human impact through time. We discuss evidence for human land use in pollen records and provide an overview considered useful for archaeological hypothesis testing and important in distinguishing natural from anthropogenically driven vegetation change. We stress the need for the palynological community to be more familiar with climate variability patterns to correctly attribute the potential causes of observed vegetation dynamics. This manuscript forms part of the wider LOng-Term multi-proxy climate REconstructions and Dynamics in South America – 2k initiative that provides the ideal framework for the integration of the various palaeoclimatic subdisciplines and palaeo-science, thereby jump-starting and fostering multidisciplinary research into environmental change on centennial and millennial timescales.

Interior point algorithm for linear programming used in transmission network synthesis

This article presents a well-known interior point method (IPM) used to solve problems of linear programming that appear as sub-problems in the solution of the long-term transmission network expansion planning problem. The linear programming problem appears when the transportation model is used, and when there is the intention to solve the planning problem using a constructive heuristic algorithm (CHA), ora branch-and-bound algorithm. This paper shows the application of the IPM in a CHA. A good performance of the IPM was obtained, and then it can be used as tool inside algorithm, used to solve the planning problem. Illustrative tests are shown, using electrical systems known in the specialized literature. (C) 2005 Elsevier B.V. All rights reserved.

Generating VHDL-AMS models of digital-to-analogue converters from MATLAB (R)/SIMULINK (R)

Today, the trend within the electronics industry is for the use of rapid and advanced simulation methodologies in association with synthesis toolsets. This paper presents an approach developed to support mixed-signal circuit design and analysis. The methodology proposed shows a novel approach to the problem of developing behvioural model descriptions of mixed-signal circuit topologies, by construction of a set of subsystems, that supports the automated mapping of MATLAB (R)/SINIULINK (R) models to structural VHDL-AMS descriptions. The tool developed, named (MSSV)-S-2, reads a SIMULINK (R) model file and translates it to a structural VHDL-AMS code. It also creates the file structure required to simulate the translated model in the SystemVision (TM). To validate the methodology and the developed program, the DAC08, AD7524 and AD5450 data converters were studied and initially modelled in MATLAB (R)/SIMULINK (R). The VHDL-AMS code generated automatically by (MSSV)-S-2, (MATLAB (R)/SIMULINK (R) to SystemVision (TM)), was then simulated in the SystemVision (TM). The simulation results show that the proposed approach, which is based on VHDL-AMS descriptions of the original model library elements, allows for the behavioural level simulation of complex mixed-signal circuits.

Effect of green Coffea arabica L. seed oil on extracellular matrix components and water-channel expression in in vitro and ex vivo human skin models

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

On non-linear dynamics and an optimal control synthesis of the action potential of membranes (ideal and non-ideal cases) of the Hodgkin-Huxley (HH) mathematical model

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)