Understanding the two-component sensing System of virulent bacteria

Report for the scientific sojourn carried out at the l’ Institute for Computational Molecular Science of the Temple University, United States, from 2010 to 2012. Two-component systems (TCS) are used by pathogenic bacteria to sense the environment within a host and activate mechanisms related to virulence and antimicrobial resistance. A prototypical example is the PhoQ/PhoP system, which is the major regulator of virulence in Salmonella. Hence, PhoQ is an attractive target for the design of new antibiotics against foodborne diseases. Inhibition of the PhoQ-mediated bacterial virulence does not result in growth inhibition, presenting less selective pressure for the generation of antibiotic resistance. Moreover, PhoQ is a histidine kinase (HK) and it is absent in animals. Nevertheless, the design of satisfactory HK inhibitors has been proven to be a challenge. To compete with the intracellular ATP concentrations, the affinity of a HK inhibidor must be in the micromolar-nanomolar range, whereas the current lead compounds have at best millimolar affinities. Moreover, the drug selectivity depends on the conformation of a highly variable loop, referred to as the “ATP-lid, which is difficult to study by X-Ray crystallography due to its flexibility. I have investigated the binding of different HK inhibitors to PhoQ. In particular, all-atom molecular dynamics simulations have been combined with enhanced sampling techniques in order to provide structural and dynamic information of the conformation of the ATP-lid. Transient interactions between these drugs and the ATP-lid have been identified and the free energy of the different binding modes has been estimated. The results obtained pinpoint the importance of protein flexibility in the HK-inhibitor binding, and constitute a first step in developing more potent and selective drugs. The computational resources of the hosting institution as well as the experience of the members of the group in drug binding and free energy methods have been crucial to carry out this work.

Distributed all-atom simulations of intrinsically unstructured proteins

The Computational Biophysics Group at the Universitat Pompeu Fabra (GRIB-UPF) hosts two unique computational resources dedicated to the execution of large scale molecular dynamics (MD) simulations: (a) the ACMD molecular-dynamics software, used on standard personal computers with graphical processing units (GPUs); and (b) the GPUGRID. net computing network, supported by users distributed worldwide that volunteer GPUs for biomedical research. We leveraged these resources and developed studies, protocols and open-source software to elucidate energetics and pathways of a number of biomolecular systems, with a special focus on flexible proteins with many degrees of freedom. First, we characterized ion permeation through the bactericidal model protein Gramicidin A conducting one of the largest studies to date with the steered MD biasing methodology. Next, we addressed an open problem in structural biology, the determination of drug-protein association kinetics; we reconstructed the binding free energy, association, and dissaciociation rates of a drug like model system through a spatial decomposition and a Makov-chain analysis. The work was published in the Proceedings of the National Academy of Sciences and become one of the few landmark papers elucidating a ligand-binding pathway. Furthermore, we investigated the unstructured Kinase Inducible Domain (KID), a 28-peptide central to signalling and transcriptional response; the kinetics of this challenging system was modelled with a Markovian approach in collaboration with Frank Noe’s group at the Freie University of Berlin. The impact of the funding includes three peer-reviewed publication on high-impact journals; three more papers under review; four MD analysis components, released as open-source software; MD protocols; didactic material, and code for the hosting group.

Edge detection by selection of pieces of level lines

We propose an edge detector based on the selection of wellcontrasted pieces of level lines, following the proposal ofDesolneux-Moisan-Morel (DMM) [1]. The DMM edge detectorhas the problem of over-representation, that is, everyedge is detected several times in slightly different positions.In this paper we propose two modifications of the originalDMM edge detector in order to solve this problem. The firstmodification is a post-processing of the output using a generalmethod to select the best representative of a bundle of curves.The second modification is the use of Canny’s edge detectorinstead of the norm of the gradient to build the statistics. Thetwo modifications are independent and can be applied separately.Elementary reasoning and some experiments showthat the best results are obtained when both modifications areapplied together.

One, two, (three), infinity: Newspaper and lab beauty-contest experiments

"Beauty-contest" is a game in which participants have to choose, typically, a number in [0,100], the winner being the person whose number is closest to a proportion of the average of all chosen numbers. We describe and analyze Beauty-contest experiments run in newspapers in UK, Spain, and Germany and find stable patterns of behavior across them, despite the uncontrollability of these experiments. These results are then compared with lab experiments involving undergraduates and game theorists as subjects, in what must be one of the largest empirical corroborations of interactive behavior ever tried. We claim that all observed behavior, across a wide variety of treatments and subject pools, can be interpretedas iterative reasoning. Level-1 reasoning, Level-2 reasoning and Level-3 reasoning are commonly observed in all the samples, while the equilibrium choice (Level-Maximum reasoning) is only prominently chosen by newspaper readers and theorists. The results show the empirical power of experiments run with large subject-pools, and open the door for more experimental work performed on the rich platform offered by newspapers and magazines.

Ex post bargaining, labor coordination and wage formation at the firm level

We lay out a model of wage bargaining with two leading features:bargaining is ex post to relevant investments and there isindividual bargaining in firms without a Union. We compareindividual ex post bargaining to coordinated ex post bargainingand we analyze the effects on wage formation. As opposed to exante bargaining models, the costs of destroying the employmentrelationship play a crucial role in determining wages. Highfiring costs in particular yield a rent for employees. Ourtheory points to a employer size-wage effect that is independentof the production function and market power. We derive a simpleleast squares specification from the theoretical model thatallow us to estimate components of the wage premium fromcoordination. We reject the hypothesis that labor coordinationdoes not alter the extensive form of the bargaining game. Laborcoordination substantially increases bargaining power butdecreases labor's ability to pose costly threats to the firm.

The pricing of academic journals: A two-sided market perspective

More and more academic journals adopt an open-access policy, by which articlesare accessible free of charge, while publication costs are recovered through authorfees. We study the consequences of this open access policy on a journal s qualitystandard. If the journal s objective was to maximize social welfare, open accesswould be optimal as long as the positive externalities generated by its diffusionexceed the marginal cost of distribution. However, we show that if an open accessjournal has a different objective (such as maximizing readers payoffs, the impactof the journal or its profit), it tends to choose a quality standard below the sociallyefficient level.

Analysis of the near-intrinsic and extrinsic photocapacitance due to the EL2 level in boron implanted GaAs

A detailed analysis of the photocapacitance signal at the near‐band and extrinsic energetic ranges in Schottky barriers obtained on horizontal Bridgman GaAs wafers, which were implanted with boron at different doses and annealed at several temperatures, has been carried out by using the optical isothermal transient spectroscopy, OITS. The optical cross sections have been determined as well as the quenching efficiency of the EL2 level which has been found to be independent of the annealing temperature. Moreover, the quenching relaxation presents two significant features: (i) a strong increase of the quenching efficiency from 1.35 eV on and (ii) a diminution of the quenching transient amplitude in relation with that shown by the fundamental EL2 level. In order to explain this behavior, different cases are discussed assuming the presence of several energy levels, the existence of an optical recuperation, or the association of the EL2 trap with two levels located, respectively, at Ev+0.45 eV and Ec−0.75 eV. The theoretical simulation, taking into account these two last cases, is in agreement with the experimental photocapacitance data at low temperature, as well as at room temperature where the EL2 filling phototransient shows an anomalous behavior. Moreover, unlike the previous data reported for the EL2 electron optical cross section, the values found using our experimental technique are in agreement with the behavior deduced from the theoretical calculation. The utilization of the OITS method has also allowed the determination of another level, whose faster optical contribution is often added to that of the EL2 level when the DLOS or standard photocapacitance is used.

Estimating slope and level change in N=1 designs

The current study proposes a new procedure for separately estimating slope change and level change between two adjacent phases in single-case designs. The procedure eliminates baseline trend from the whole data series prior to assessing treatment effectiveness. The steps necessary to obtain the estimates are presented in detail, explained, and illustrated. A simulation study is carried out to explore the bias and precision of the estimators and compare them to an analytical procedure matching the data simulation model. The experimental conditions include two data generation models, several degrees of serial dependence, trend, level and/or slope change. The results suggest that the level and slope change estimates provided by the procedure are unbiased for all levels of serial dependence tested and trend is effectively controlled for. The efficiency of the slope change estimator is acceptable, whereas the variance of the level change estimator may be problematic for highly negatively autocorrelated data series.

A system-level, molecular evolutionary analysis of mammalian phototransduction

Visual perception is initiated in the photoreceptor cells of the retina via the phototransduction system.This system has shown marked evolution during mammalian divergence in such complex attributes as activation time and recovery time. We have performed a molecular evolutionary analysis of proteins involved in mammalianphototransduction in order to unravel how the action of natural selection has been distributed throughout thesystem to evolve such traits. We found selective pressures to be non-randomly distributed according to both a simple protein classification scheme and a protein-interaction network representation of the signaling pathway. Proteins which are topologically central in the signaling pathway, such as the G proteins, as well as retinoid cycle chaperones and proteins involved in photoreceptor cell-type determination, were found to be more constrained in their evolution. Proteins peripheral to the pathway, such as ion channels and exchangers, as well as the retinoid cycle enzymes, have experienced a relaxation of selective pressures. Furthermore, signals of positive selection were detected in two genes: the short-wave (blue) opsin (OPN1SW) in hominids and the rod-specific Na+/Ca2+,K+ ion exchanger (SLC24A1) in rodents. The functions of the proteins involved in phototransduction and the topology of the interactions between them have imposed non-random constraints on their evolution. Thus, in shaping or conserving system-level phototransduction traits, natural selection has targeted the underlying proteins in a concerted manner.

Application of ultrasound in bone surgery: two case reports

The present study describes some of the applications of ultrasound in bone surgery, based on the presentation of two clinical cases. The Piezosurgery® ultrasound device was used (Tecnología Mectron Medical, Carasco, Italy). In one case the instrument was used to harvest a chin bone graft for placement in a bone defect at level 1.2, while in the other case a bony window osteotomy was made in the external wall of the maxillary sinus, in the context of a sinus membrane lift procedure. The Piezosurgery® device produces specific ultrasound frequency modulation (25-29 kHz), and has been designed to secure increased precision in application to bone surgery. This instrument produces selective sectioning of the mineralized bone structures, and causes less intra- and postoperative bleeding. One of the advantages of the Piezosurgery® device is that it can be used for maxillary sinus lift procedures in dental implant placement. In this context it considerably lessens the risk of sinus mucosa laceration by preparing the bony window in the external wall of the upper maxilla, and can be used to complete the lifting maneuver. The use of ultrasound in application to hard tissues can be regarded as a slow technique compared with the conventional rotary instruments, since it requires special surgical skill and involves a certain learning curve.

Deep incision in an Aptian carbonate succession indicates major sea-level fall in the Cretaceous

Long-term relative sea-level cycles (0 5 to 6 Myr) have yet to be fully understood for the Cretaceous. During the Aptian, in the northern Maestrat Basin (Eastern Iberian Peninsula), fault-controlled subsidence created depositional space, but eustasy governed changes in depositional trends. Relative sea-level history was reconstructed by sequence stratigraphic analysis. Two forced regressive stages of relative sea-level were recognized within three depositional sequences. The first stage is late Early Aptian age (intra Dufrenoyia furcata Zone) and is characterized by foreshore to upper shoreface sedimentary wedges, which occur detached from a highstand carbonate platform, and were deposited above basin marls. The amplitude of relative sea-level drop was in the order of tens of metres, with a duration of <1 Myr. The second stage of relative sea-level fall occurred within the Late Aptian and is recorded by an incised valley that, when restored to its pre-contractional attitude, was >2 km wide and cut 115 m down into the underlying Aptian succession. With the subsequent transgression, the incision was back-filled with peritidal to shallow subtidal deposits. The changes in depositional trends, lithofacies evolution and geometric relation of the stratigraphic units characterized are similar to those observed in coeval rocks within the Maestrat Basin, as well as in other correlative basins elsewhere. The pace and magnitude of the two relative sea-level drops identified fall within the glacio-eustatic domain. In the Maestrat Basin, terrestrial palynological studies provide evidence that the late Early and Late Aptian climate was cooler than the earliest part of the Early Aptian and the Albian Stage, which were characterized by warmer environmental conditions. The outcrops documented here are significant because they preserve the results of Aptian long-term sea-level trends that are often only recognizable on larger scales (i.e. seismic) such as for the Arabian Plate.

Deep incision in an Aptian carbonate succession indicates major sea-level fall in the Cretaceous

Long-term relative sea-level cycles (0 5 to 6 Myr) have yet to be fully understood for the Cretaceous. During the Aptian, in the northern Maestrat Basin (Eastern Iberian Peninsula), fault-controlled subsidence created depositional space, but eustasy governed changes in depositional trends. Relative sea-level history was reconstructed by sequence stratigraphic analysis. Two forced regressive stages of relative sea-level were recognized within three depositional sequences. The first stage is late Early Aptian age (intra Dufrenoyia furcata Zone) and is characterized by foreshore to upper shoreface sedimentary wedges, which occur detached from a highstand carbonate platform, and were deposited above basin marls. The amplitude of relative sea-level drop was in the order of tens of metres, with a duration of <1 Myr. The second stage of relative sea-level fall occurred within the Late Aptian and is recorded by an incised valley that, when restored to its pre-contractional attitude, was >2 km wide and cut 115 m down into the underlying Aptian succession. With the subsequent transgression, the incision was back-filled with peritidal to shallow subtidal deposits. The changes in depositional trends, lithofacies evolution and geometric relation of the stratigraphic units characterized are similar to those observed in coeval rocks within the Maestrat Basin, as well as in other correlative basins elsewhere. The pace and magnitude of the two relative sea-level drops identified fall within the glacio-eustatic domain. In the Maestrat Basin, terrestrial palynological studies provide evidence that the late Early and Late Aptian climate was cooler than the earliest part of the Early Aptian and the Albian Stage, which were characterized by warmer environmental conditions. The outcrops documented here are significant because they preserve the results of Aptian long-term sea-level trends that are often only recognizable on larger scales (i.e. seismic) such as for the Arabian Plate.

Cosmic censorship in two-dimensional gravity

A weak version of the cosmic censorship hypothesis is implemented as a set of boundary conditions on exact semiclassical solutions of two-dimensional dilaton gravity. These boundary conditions reflect low-energy matter from the strong coupling region and they also serve to stabilize the vacuum of the theory against decay into negative energy states. Information about low-energy incoming matter can be recovered in the final state but at high energy black holes are formed and inevitably lead to information loss at the semiclassical level.

First evidence for the two-body charmless baryonic decay

The results of a search for the rare two-body charmless baryonic decays TeX and TeX are reported. The analysis uses a data sample, corresponding to an integrated luminosity of 0.9 fb−1, of pp collision data collected by the LHCb experiment at a centre-of-mass energy of 7 TeV. An excess of TeX candidates with respect to background expectations is seen with a statistical significance of 3.3 standard deviations. This is the first evidence for a two-body charmless baryonic B 0 decay. No significant TeX signal is observed, leading to an improvement of three orders of magnitude over previous bounds. If the excess events are interpreted as signal, the 68.3% confidence level intervals on the branching fractions are $ TeX $ where the first uncertainty is statistical and the second is systematic.

Stable isotopes unveil habitat partitioning among the marine mammals off NW Africa and reveal unique trophic niches for two globally threatened species.

Stable isotope abundances of carbon (δ13C) and nitrogen (δ15N) in the bone of 13 species of marine mammals from the northwest coast of Africa were investigated to assess their positions in the local trophic web and their preferred habitats. Also, samples of primary producers and potential prey species from the study area were collected to characterise the local isotopic landscape. This characterisation indicated that δ13C values increased from offshore to nearshore and that δ15N was a good proxy for trophic level. Therefore, the most coastal species were Monachus monachus and Sousa teuszii, whereas the most pelagic were Physeter macrocephalus and Balaenoptera acutorostrata. δ15N values indicated that marine mammals located at the lowest trophic level were B. acutorostrata, Stenella coeruleoalba and Delphinus sp., and those occupying the highest trophic level were M. monachus and P. macrocephalus. The trophic level of Orcinus orca was similar to that of M. monachus, suggesting that O. orca preys on fish. Conservation of coastal and threatened species (M. monachus and S. teuszii) off NW Africa should be a priority because these species, as the main apex predators, cannot be replaced by other marine mammals.