Exploring unfrequent events with accelerated molecular dynamics simulations: from photochemistry to drug design

La meva incorporació al grup de recerca del Prof. McCammon (University of California San Diego) en qualitat d’investigador post doctoral amb una beca Beatriu de Pinós, va tenir lloc el passat 1 de desembre de 2010; on vaig dur a terme les meves tasques de recerca fins al darrer 1 d’abril de 2012. El Prof. McCammon és un referent mundial en l’aplicació de simulacions de dinàmica molecular (MD) en sistemes biològics d’interès humà. La contribució més important del Prof. McCammon en la simulació de sistemes biològics és el desenvolupament del mètode de dinàmiques moleculars accelerades (AMD). Les simulacions MD convencionals, les quals estan limitades a l’escala de temps del nanosegon (~10-9s), no son adients per l’estudi de sistemes biològics rellevants a escales de temps mes llargues (μs, ms...). AMD permet explorar fenòmens moleculars poc freqüents però que son clau per l’enteniment de molts sistemes biològics; fenòmens que no podrien ser observats d’un altre manera. Durant la meva estada a la “University of California San Diego”, vaig treballar en diferent aplicacions de les simulacions AMD, incloent fotoquímica i disseny de fàrmacs per ordinador. Concretament, primer vaig desenvolupar amb èxit una combinació dels mètodes AMD i simulacions Car-Parrinello per millorar l’exploració de camins de desactivació (interseccions còniques) en reaccions químiques fotoactivades. En segon lloc, vaig aplicar tècniques estadístiques (Replica Exchange) amb AMD en la descripció d’interaccions proteïna-lligand. Finalment, vaig dur a terme un estudi de disseny de fàrmacs per ordinador en la proteïna-G Rho (involucrada en el desenvolupament de càncer humà) combinant anàlisis estructurals i simulacions AMD. Els projectes en els quals he participat han estat publicats (o estan encara en procés de revisió) en diferents revistes científiques, i han estat presentats en diferents congressos internacionals. La memòria inclosa a continuació conté més detalls de cada projecte esmentat.

Influence of physico-chemical material characteristics on staphylococcal biofilm formation--a qualitative and quantitative in vitro analysis of five different calcium phosphate bone grafts.

Various compositions of synthetic calcium phosphates (CaP) have been proposed and their use has considerably increased over the past decades. Besides differences in physico-chemical properties, resorption and osseointegration, artificial CaP bone graft might differ in their resistance against biofilm formation. We investigated standardised cylinders of 5 different CaP bone grafts (cyclOS, chronOS (both β-TCP (tricalcium phosphate)), dicalcium phosphate (DCP), calcium-deficient hydroxyapatite (CDHA) and α-TCP). Various physico-chemical characterisations e.g., geometrical density, porosity, and specific surface area were investigated. Biofilm formation was carried out in tryptic soy broth (TSB) and human serum (SE) using Staphylococcus aureus (ATCC 29213) and S. epidermidis RP62A (ATCC 35984). The amount of biofilm was analysed by an established protocol using sonication and microcalorimetry. Physico-chemical characterisation showed marked differences concerning macro- and micropore size, specific surface area and porosity accessible to bacteria between the 5 scaffolds. Biofilm formation was found on all scaffolds and was comparable for α-TCP, chronOS, CDHA and DCP at corresponding time points when the scaffolds were incubated with the same germ and/or growth media, but much lower for cyclOS. This is peculiar because cyclOS had an intermediate porosity, mean pore size, specific surface area, and porosity accessible to bacteria. Our results suggest that biofilm formation is not influenced by a single physico-chemical parameter alone but is a multi-step process influenced by several factors in parallel. Transfer from in vitro data to clinical situations is difficult; thus, advocating the use of cyclOS scaffolds over the four other CaP bone grafts in clinical situations with a high risk of infection cannot be clearly supported based on our data.

Study of common database feeding with results coming from different analytical methods in the framework of illicit drugs chemical profiling

Analytical results harmonisation is investigated in this study to provide an alternative to the restrictive approach of analytical methods harmonisation which is recommended nowadays for making possible the exchange of information and then for supporting the fight against illicit drugs trafficking. Indeed, the main goal of this study is to demonstrate that a common database can be fed by a range of different analytical methods, whatever the differences in levels of analytical parameters between these latter ones. For this purpose, a methodology making possible the estimation and even the optimisation of results similarity coming from different analytical methods was then developed. In particular, the possibility to introduce chemical profiles obtained with Fast GC-FID in a GC-MS database is studied in this paper. By the use of the methodology, the similarity of results coming from different analytical methods can be objectively assessed and the utility in practice of database sharing by these methods can be evaluated, depending on profiling purposes (evidential vs. operational perspective tool). This methodology can be regarded as a relevant approach for database feeding by different analytical methods and puts in doubt the necessity to analyse all illicit drugs seizures in one single laboratory or to implement analytical methods harmonisation in each participating laboratory.

Purification of recombinant proteins by chemical removal of the affinity tag.

The efficient removal of a N- or C-terminal purification tag from a fusion protein is necessary to obtain a protein in a pure and active form, ready for use in human or animal medicine. Current techniques based on enzymatic cleavage are expensive and result in the presence of additional amino acids at either end of the proteins, as well as contaminating proteases in the preparation. Here we evaluate an alternative method to the one-step affinity/protease purification process for large-scale purification. It is based upon the cyanogen bromide (CNBr) cleavage at a single methionine placed in between a histidine tag and a Plasmodium falciparum antigen. The C-terminal segment of the circumsporozoite polypeptide was expressed as a fusion protein with a histidine tag in Escherichia coli purified by Ni-NAT agarose column chromatography and subsequently cleaved by CNBr to obtain a polypeptide without any extraneous amino acids derived from the cleavage site or from the affinity purification tag. Thus, a recombinant protein is produced without the need for further purification, demonstrating that CNBr cleavage is a precise, efficient, and low-cost alternative to enzymatic digestion, and can be applied to large-scale preparations of recombinant proteins.

The politics of contaminated sites management : institutional regime change and actor's mode of participation in the environmental management of the Bonfol Chemical Waste Landfill in Switzerland

By the end of the 1970s, contaminated sites had emerged as one of the most complex and urgent environmental issues affecting industrialized countries. The authors show that small and prosperous Switzerland is no exception to the pervasive problem of sites contamination, the legacy of past practices in waste management having left some 38,000 contaminated sites throughout the country. This book outlines the problem, offering evidence that open and polycentric environmental decision-making that includes civil society actors is valuable. They propose an understanding of environmental management of contaminated sites as a political process in which institutions frame interactions between strategic actors pursuing sometimes conflicting interests. In the opening chapter, the authors describe the influences of politics and the power relationships between actors involved in decision-making in contaminated sites management, which they term a "wicked problem." Chapter Two offers a theoretical framework for understanding institutions and the environmental management of contaminated sites. The next five chapters present a detailed case study on environmental management and contaminated sites in Switzerland, focused on the Bonfol Chemical Landfill. The study and analysis covers the establishment of the landfill under the first generation of environmental regulations, its closure and early remediation efforts, and the gambling on the remediation objectives, methods and funding in the first decade of the 21st Century. The concluding chapter discusses the question of whether the strength of environmental regulations, and the type of interactions between public, private, and civil society actors can explain the environmental choices in contaminated sites management. Drawing lessons from research, the authors debate the value of institutional flexibility for dealing with environmental issues such as contaminated sites.

Matters Relating to a Forced Move of, Use of a Chemical Agent on and Withdrawal of Medication for Inmate Craig Gardner, 1994

Case Number 91-151 Craig Gardner, an inmate in the Iowa prison system, was the subject of a force move by correctional officers while incarcerated at the Iowa State Penitentiary (ISP). This action involved the use of a chemical agent. This investigation began as a review of the use of a chemical agent in a forced cell move on June 30, 1991.

Érosion des sols au Cap Vert : étude des processus et quantification à l’échelle de trois bassins versants de l’île de Santiago

Erosão dos solos em Cabo Verde: estudo dos processos e quantificação à escala de três bacias hidrográficas O arquipélago de Cabo Verde é constituído por 10 ilhas vulcânicas pertence à zona do Sahel que se estende do Atlântico ao Mar Vermelho. Desde então, várias décadas, Cabo Verde é afectado pela desertificação causada principalmente pela recessão climatica e a erosão do solo. Esses fatores, aliados à alta pressão humana sobre os recursos, a topografia acidentada e chuvas tropicais por vezes torrenciais, causam sérios danos aos solos. No entanto, desde sua independência em 1975, o Governo realizou um amplo programa de arborização, recuperação de áreas degradadas e a correcção dos leitos das ribeiras. No entanto, a investigação, muito pouco foi realizada para avaliar as acções de protecção e conservação do solo e da água. Portanto, não há dados sobre o problema da degradação das terras nem balanços. Como parte deste trabalho, foram estudados vários factores que controlam a erosão do solo pela água. Especificamente, buscou-se diferenciar os efeitos das actividades humanas, incluindo a agricultura, os factores climáticos, como chuva e geração de escoamento. Também estabeleceu os primeiros balanços das exportações de matérias em suspensão e em solução no contexto do arquipélago de Cabo Verde. O estudo foi realizado em três bacias hidrográficas da ilha de Santiago, Cabo Verde. Estas três bacias hidrográficas (Longueira, Grande e Godim) estão localizadas na parte central da ilha de Santiago e representam os diversos tipos de uso da terra e as diferentes zonas bioclimaticas da ilha. Existe um gradiente climático entre as três bacias hidrográficas. Na verdade, Longueira que abrange uma área de 4,18 km2, tem um declive médio de 47 %, uma zona florestada de 69% e uma área agrícola de 17 %. Grande com uma área de 1,87 km2, é localizada numa zona sub humida com um declive médio de 50%, é essencialmente agrícola. Godim, com uma área de 2,0 km2, é localizado numa zona semi-árida com um declive médio de 32%, é particularmente uma zona agricola. Para estes três bacias hidrográficas, as cheias foram medidas e amostradas de 2004 a 2009. A bacia de Longueira teve um maior acompanhamento, nomeadamente em termos de amostragem e monitoramento dos escoamentos. Em cada amostra foram feitas a determinação da concentração de matérias em suspensão e a análise dos principais elementos quimicos. Os resultados mostram que a erosão mecânica nas três bacias hidrográficas é caracterizada por uma forte variabilidade espacial e temporal. Durante o período de 2005-2009, o balanço anual média para as bacias hidrográficas de Longueira, Grande e Godim é: 4266, 157 e 10,1 t.km2.an-1, respectivamente. A estação das chuvas de 2006 foi a mais erosiva para as três bacias, particularmente em Longueira, com 2 cheias excepcionais, que têm gerado uma concentração média de sólidos em suspensão superior a 100 g / l. Porém, as estações do ano de 2005 e 2008 foram de uma forma geral menos erosivas porque as concentrações médias não inferiores a 20 g / l. Além disso, não houve cheias para as temporadas 2005 e 2007 para a bacia do Godim. Na bacia de Longueira, o estudo dos fenómenos de histerese na caracterização das cheias mostrou que a evolução temporal das exportações de sólidos em suspensão durante a temporada é fortemente influenciada pelas atividades agrícolas. Na verdade, a primeira cheia causou uma exportação maciça de sedimento disponível e localizado no leito da ribeira. Assim, a segunda cheia exportou menos sedimentos. Um mês após as primeiras chuvas, a prática da monda que reduz a densidade da cobertura vegetal e destructura a camada superficial do solo, gerou uma grande quantidade de sedimento que novamente permitiu uma exportação muito forte de sedimentos durante a terceira forte cheia. Os resultados da erosão química na bacia de Longueira indicam que a taxa de erosão é de 45 t.km2.an-1 com uma forte variabilidade temporal. Na verdade, as temporadas de 2006 e 2007 são as mais erosivas, enquanto 2005 teve uma exportação de matérias disolvidas baixa. A utilização do modelo EMMA (End- Members Mixing Analysis) mostra que os escoamentos hipodermico e profundo, alimentandos os fluxos de elementos dissolvidos são os principais factores da erosão química. É mostrado que esses fluxos causam mais de 90% dos fluxos de erosão química. O escoamento superficial, que contribui com cerca de 70% na formação das cheias, é o maior factor da erosão mecânica do solo.

Nature, evolution and characterisation of rhizospheric chemical exudates affecting root herbivores

Similar to aboveground herbivores, root-feeding insects must locate and identify suitable resources. In the darkness of soil, they mainly rely on root chemical exudations and, therefore, have evolved specific behaviours. Because of their impact on crop yield, most of our knowledge in belowground chemical ecology is biased towards soil-dwelling insect pests. Yet the increasing literature on volatile-mediated interactions in the ground underpins the great importance of chemical signalling in this ecosystem and its potential in pest control. Here, we explore the ecology and physiology of these chemically based interactions. An evolutionary approach reveals interesting patterns in the response of insects to particular classes of volatile or water-soluble organic compounds commonly emitted by roots. Food web analyses reasonably support that volatiles are used as long-range cues whereas water-soluble molecules serve in host acceptance/rejection by the insect; however, data are still scarce. As a case study, the chemical ecology of Diabrotica virgifera virgifera is discussed and applications of belowground signalling in pest management are examined. Soil chemical ecology is an expanding field of research and will certainly be a hub of our understanding of soil communities and subsequently of the management of belowground ecosystem services.

Morphological, chemical and developmental aspects of the Dufour gland in some eusocial bees (Hymenoptera, Apidae): a review

Morphological, chemical and developmental aspects of the Dufour gland in some eusocial bees (Hymenoptera, Apidae): a review. The present revision focused on the more recent data about the Dufour gland in some eusocial bees, taking in account general aspects of its morphology, secretion chemical nature, bio-synthetic pathway and development. Many functions have been attributed to this gland in eusocial bees, but none are convincing. With the new data about this gland, not only the secretion chemical pathway of the Dufour gland may be reasonable understood, as its function in some eusocial bees, especially Apis mellifera Linné, 1758, which has been extensively studied in the last years.

Erosão dos solos em Cabo Verde - Estudos dos Processos e Quantificação de Três Bacias na Ilha de Santiago

L’archipel du Cap Vert constitué de 10 îles volcaniques appartient à la zone sahélienne qui s’étend de l’atlantique jusqu’à la mer rouge. Depuis, plusieurs décennies le Cap Vert est affecté par la désertification causée en grande partie par la récession climatique et l’érosion des sols. Ces facteurs, associés à la forte pression anthropique sur les ressources, à l’orographie accidentée et à des pluies tropicales parfois diluviennes, provoquent de sérieuses pertes du patrimoine foncier. Cependant, depuis son Indépendance en 1975, le Gouvernement a mené un vaste programme d’arborisation, de restauration des terres et d’aménagement des cours d’eau. Pourtant, très peu de recherches ont été menées pour évaluer les actions de protection et de conservation des sols et des eaux. Par conséquent, il n’existe quasiment pas de données sur la problématique de la dégradation des terres ni de bilans. Dans le cadre de ce travail, nous avons étudié les différents facteurs qui contrôlent l’érosion hydrique des sols. Nous avons plus particulièrement cherché à différencier les effets des activités humaines, notamment agricoles, de ceux des facteurs climatiques comme les précipitations et la génération des écoulements. Nous avons également établi les premiers bilans d’exportations de matières en suspension et en solution dans le contexte de l’archipel du Cap Vert. L’étude a été menée à l’échelle de trois bassins versants de l’ile de Santiago Cap-Vert. Ces trois bassins versant (Longueira, Grande et Godim) sont localisés dans la partie centrale de l’île de Santiago et représentatifs des divers modes d’occupation du sol et des différents climats de l’île. Il existe un gradient climatique entre les trois bassins versants. En effet, Longueira qui présente une superficie de 4,18 km2, une pente moyenne de 47 %, se localise dans une zone humide couverte à 69 % par une forêt et une surface agricole de 17 %. Grande avec une superficie de 1,87 km2, se localise en zone sub humide pour une pente moyenne de 50 %, il est essentiellement agricole. Godim, avec une superficie de 2,0 km2, se localise en zone semi aride, il est particulièrement agricole et sa pente moyenne est de 32 %. Pour ces trois bassins versants, les écoulements de crue à l’exutoire ont été mesurés et échantillonnés de 2004 à 2009. Le bassin versant de Longueira a fait l’objet d’un suivi plus poussé, notamment en termes de fréquence d’échantillonnage et de suivi des écoulements hors crue. Sur chaque échantillon nous avons procédé à la détermination de la concentration des matières en suspension ainsi qu’à l’analyse des éléments majeurs. Les résultats obtenus montrent que l’érosion mécanique dans les 3 bassins versants est caractérisée par une forte variabilité spatiale et temporelle. Sur la période 2005-2009, le bilan moyen annuel pour les bassins versants de Longueira, Grande et Godim est de : 4266, 157 et 10,1 t.km2.an-1 respectivement. La saison humide 2006 a été la plus érosive pour l’ensemble des trois bassins versants et particulièrement dans Longueira avec 2 crues exceptionnelles qui ont généré une concentration moyenne de matières en suspension supérieure à 100 g/l. En revanche, les saisons 2005 et 2008 ont été dans l’ensemble peu érosives car les concentrations moyennes ne dépassèrent pas 20 g/l. Par ailleurs, il n’y a pas eu de lames d’eau écoulées pour les saisons 2005 et 2007 pour le bassin de Godim. Sur le bassin de Longueira, l’étude des phénomènes d’hystérésis permet de caractériser chaque crue et de montrer que l’évolution temporelle des exportations de matières en suspension au cours de la saison est fortement influencée par les activités agricoles. En effet, la première crue provoque l’exportation massive des sédiments disponibles et localisés dans le lit du cours d’eau. En conséquence, la seconde est moins exportatrice de sédiments. Un mois après les premières pluies, les activités de sarclage diminuent la densité du couvert végétal et destructurent la partie superficielle des sols, ce qui provoque à nouveau une très forte exportation de sédiments lors de la troisième crue. Les résultats de l’érosion chimique sur le bassin de Longueira indiquent que le taux d’érosion chimique moyen s’élève à 45 t.km2.an-1 avec une forte variabilité temporelle. En effet, les saisons les plus humides de 2006 et 2007 sont les plus exportatrices de matières en solution, alors que 2005 a eu une faible exportation. L’utilisation du modèle de mélanges EMMA (End-Members Mixing Analysis) montre que les écoulements hypodermique et profond, qui alimentent le cours d’eau en éléments dissous, sont les principaux facteurs de l’érosion chimique. On montre ainsi que les écoulements hors crue sont à l’origine de plus de 90% des flux d’érosion chimique. L’écoulement superficiel, qui contribue à environ 70 % du débit du cours d’eau en crue, constitue un facteur de premier plan de l’érosion mécanique des sols.

Improved statistical analysis of low abundance phenomena in bimodal bacterial populations.

Accurate detection of subpopulation size determinations in bimodal populations remains problematic yet it represents a powerful way by which cellular heterogeneity under different environmental conditions can be compared. So far, most studies have relied on qualitative descriptions of population distribution patterns, on population-independent descriptors, or on arbitrary placement of thresholds distinguishing biological ON from OFF states. We found that all these methods fall short of accurately describing small population sizes in bimodal populations. Here we propose a simple, statistics-based method for the analysis of small subpopulation sizes for use in the free software environment R and test this method on real as well as simulated data. Four so-called population splitting methods were designed with different algorithms that can estimate subpopulation sizes from bimodal populations. All four methods proved more precise than previously used methods when analyzing subpopulation sizes of transfer competent cells arising in populations of the bacterium Pseudomonas knackmussii B13. The methods' resolving powers were further explored by bootstrapping and simulations. Two of the methods were not severely limited by the proportions of subpopulations they could estimate correctly, but the two others only allowed accurate subpopulation quantification when this amounted to less than 25% of the total population. In contrast, only one method was still sufficiently accurate with subpopulations smaller than 1% of the total population. This study proposes a number of rational approximations to quantifying small subpopulations and offers an easy-to-use protocol for their implementation in the open source statistical software environment R.

Study of the variability in chemical composition of bark layers of Quercus Suber L. from different production areas

Cork is the bark of the cork oak tree (Quercus suber L), a renewable and biodegradable raw bioresource concentrated mainly in the Mediterranean region. Development of its potential uses as a biosorbent will require the investigation of its chemical composition; such information can be of help to understand its interactions with organic pollutants. The present study investigates the summative chemical composition of three bark layers (back, cork, and belly) of five Spanish cork samples and one cork sample from Portugal. Suberin was the main component in all the samples (21.1 to 53.1%), followed by lignin (14.8 to 31%), holocellulose (2.3 to 33.6%), extractives (7.3 to 20.4%), and ash (0.4 to 3.3%). The Kruskal-Wallis test was used to determine whether the variations in chemical composition with respect to the production area and bark layers were significant. The results indicate that, with respect to the bark layer, significant differences were found only for suberin and holocellulose contents: they were higher in the belly and cork than in the back. Based on the results presented, cork is a material with a lot of potential because of its heterogeneity in chemical composition

Chemical labelling of oyster shells used for time-calibrated high-resolution Mg/Ca ratios: A tool for estimation of past seasonal temperature variations

The geochemical compositions of biogenic carbonates are increasingly used for palaeoenvironmental reconstructions. The skeletal delta O-18 temperature relationship is dependent on water salinity, so many recent studies have focused on the Mg/Ca and Sr/Ca ratios because those ratios in water do not change significantly on short time scales. Thus, those elemental ratios are considered to be good palaeotemperature proxies in many biominerals, although their use remains ambiguous in bivalve shells. Here, we present the high-resolution Mg/Ca ratios of two modern species of juvenile and adult oyster shells, Crassostrea gigas and Ostrea edulis. These specimens were grown in controlled conditions for over one year in two different locations. In situ monthly Mn-marking of the shells has been used for day calibration. The daily Mg/Ca.ratios in the shell have been measured with an electron microprobe. The high frequency Mg/Ca variation of all specimens displays good synchronism with lunar cycles, suggesting that tides strongly influence the incorporation of Mg/Ca into the shells. Highly significant correlation coefficients (0.70<R<0.83, p<0.0001) between the Mg/Ca ratios and the seawater temperature are obtained only for juvenile C. gigas samples, while metabolic control of Mg/Ca incorporation and lower shell growth rates preclude the use of the Mg/Ca ratio in adult shells as a palaeothermometer. Data from three juvenile C. gigas shells from the two study sites are selected to establish a relationship: T = 3.77Mg/Ca + 1.88, where T is in degrees C and Mg/Ca in mmol/mol. (c) 2012 Elsevier B.V. All rights reserved.