Prediction of subplastidial localization of chloroplast proteins from spectral count data - Comparison of machine learning algorithms

To study chloroplast metabolism and functions, subplastidial localization is a prerequisite to achieve protein functional characterization. As the accurate localization of many chloroplast proteins often remains hypothetical, we set up a proteomics strategy in order to assign the accurate subplastidial localization. A comprehensive study of Arabidopsis thaliana chloroplast proteome has been carried out in our group [1], involving high performance mass spectrometry analyses of highly fractionated chloroplasts. In particular, spectral count data were acquired for the three major chloroplast sub-fractions (stroma, thylakoids and envelope) obtained by sucrose gradient purification. As the distribution of spectral counts over compartments is a fair predicator of relative abundance of proteins [2], it was justified to propose a prime statistical model [1] relating spectral counts to subplastidial localization. This predictive model was based on a logistic regression, and demonstrated an accuracy rate of 84% for chloroplast proteins. In the present work, we conducted a comparative study of various machine learning techniques to generate a predictive model of subplastidial localization of chloroplast proteins based on spectral count data

Clustering Libraries of Compounds into Families: Asymmetry-Based Similarity Measure to Categorize Small Molecules

International audienceClustering Libraries of Compounds into Families: Asymmetry-Based Similarity Measure to Categorize Small Molecule

Criteria for deterministic single-photon emission in two-dimensional atomic crystals

The deterministic production of single-photons from two dimensional materials promises to usher in a new generation of photonic quantum devices. In this work, we outline criteria by which single-photon emission can be realised in two dimensional materials: spatial isolation, spectral filtering and low excitation of quantum emitters. We explore how these criteria can be fulfilled in atomically thin transition metal dichalcogenides, where excitonic physics dictates the observed photoemission. In particular, we model the effect of defects and localised strain, in accordance with the most common experimental realisations, on the photon statistics of emitted light. Moreover, we demonstrate that an optical cavity has a negative impact on the photon statistics, suppressing the single-photon character of the emission by diminishing the effect of spectral filtering on the emitted light. Our work provides a theoretical framework revealing criteria necessary to facilitate single-photon emission in two-dimensional materials and thus can guide future experimental studies in this field

DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics.

UNLABELLED: DAPAR and ProStaR are software tools to perform the statistical analysis of label-free XIC-based quantitative discovery proteomics experiments. DAPAR contains procedures to filter, normalize, impute missing value, aggregate peptide intensities, perform null hypothesis significance tests and select the most likely differentially abundant proteins with a corresponding false discovery rate. ProStaR is a graphical user interface that allows friendly access to the DAPAR functionalities through a web browser. AVAILABILITY AND IMPLEMENTATION: DAPAR and ProStaR are implemented in the R language and are available on the website of the Bioconductor project (http://www.bioconductor.org/). A complete tutorial and a toy dataset are accompanying the packages. CONTACT: [email protected], [email protected], [email protected] (ChloroTypes), ANR-10-INBS-08 (ProFI project, ‘Infrastructures Nationales en Biologie et Sante´’, ‘Investissements d’Avenir’), European Union FP7 program (Prime-XS Project, Contract no. 262067), Prospectom project (Mastodons 2012 CNRS Challenge), Biotechnology and Biological Sciences Research Council (Strategic Longer and Larger Grant ID: BB/L002817/1)This is the final version of the article. It first appeared from Oxford University Press via https://doi.org/10.1093/bioinformatics/btw58

Seismic Constraints on the Thickness and Structure of the Martian Crust from InSight

NASA¿s InSight mission [1] has for the first time placed a very broad-band seismometer on the surface of Mars. The Seismic Experiment for Interior Structure (SEIS) [2] has been collecting continuous data since early February 2019. The main focus of InSight is to enhance our understanding of the internal structure and dynamics of Mars, which includes the goal to better constrain the crustal thickness of the planet [3]. Knowing the present-day crustal thickness of Mars has important implications for its thermal evolution [4] as well as for the partitioning of silicates and heat-producing elements between the different layers of Mars. Current estimates for the crustal thickness of Mars are based on modeling the relationship between topography and gravity [5,6], but these studies rely on different assumptions, e.g. on the density of the crust and upper mantle, or the bulk silicate composition of the planet and the crust. The resulting values for the average crustal thickness differ by more than 100%, from 30 km to more than 100 km [7]. New independent constraints from InSight will be based on seismically determining the crustal thickness at the landing site. This single firm measurement of crustal thickness at one point on the planet will allow to constrain both the average crustal thickness of Mars as well as thickness variations across the planet when combined with constraints from gravity and topography [8]. Here we describe the determination of the crustal structure and thickness at the InSight landing site based on seismic receiver functions for three marsquakes compared with autocorrelations of InSight data [9].We acknowledge NASA, CNES, partner agencies and institutions (UKSA, SSO,DLR, JPL, IPGP-CNRS, ETHZ, IC, MPS-MPG) and the operators of JPL, SISMOC, MSDS, IRIS-DMC and PDS for providing SEED SEIS data. InSight data is archived in the PDS, and a full list of archives in the Geosciences, Atmospheres, and Imaging nodes is at https://pds-geosciences.wustl.edu/missions/insight/. This work was partially carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration. ©2021, California Institute of Technology. Government sponsorship acknowledge

Surface waves and crustal structure on Mars

We detected surface waves from two meteorite impacts on Mars. By measuring group velocity dispersion along the impact-lander path, we obtained a direct constraint on crustal structure away from the InSight lander. The crust north of the equatorial dichotomy had a shear wave velocity of approximately 3.2 kilometers per second in the 5- to 30-kilometer depth range, with little depth variation. This implies a higher crustal density than inferred beneath the lander, suggesting either compositional differences or reduced porosity in the volcanic areas traversed by the surface waves. The lower velocities and the crustal layering observed beneath the landing site down to a 10-kilometer depth are not a global feature. Structural variations revealed by surface waves hold implications for models of the formation and thickness of the martian crust.D.K., S.C., D.G., J.C., C.D., A. K., S.C.S., N.D., and G.Z. were supported by the ETH+ funding scheme (ETH+02 19-1: “Planet Mars”). Marsquake Service operations at ETH Zürich were supported by ETH Research grant ETH-06 17-02. N.C.S. and V.L. were supported by NASA PSP grant no. 80NSSC18K1628. Q.H. and E.B. are funded by NASA grant 80NSSC18K1680. C.B. and J.L. were supported by NASA InSight PSP grant no. 80NSSC18K1679. S.D.K. was supported by NASA InSight PSP grant no. 80NSSC18K1623. P.L., E.B., M.D., H.S., E.S., M.W., Z.X., T.W., M.P., R.F.G. were supported by CNES and the Agence Nationale de la Recherche (ANR-19-CE31-0008-08 MAGIS) for SEIS operation and SEIS Science analysis. A.H., C.C. and W.T.P. were supported by the UKSA under grant nos. ST/R002096/1, ST/ W002523/1 and ST/V00638X/1. Numerical computations of McMC Approach 2 were performed on the S-CAPAD/DANTE platform (IPGP, France) and using the HPC resources of IDRIS under the allocation A0110413017 made by GENCI. A.H. was supported by the UKSA under grant nos. ST/R002096/1 and ST/W002523/1. F.N. was supported by InSight PSP 80NSSC18K1627. I.J.D. was supported by NASA InSight PSP grant no. 80NSSC20K0971. L.V.P. was funded by NASANNN12AA01C with subcontract JPL-1515835. The research was carried out in part by W.B.B., M.G. and M.P.P. at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004)Peer reviewe

The interior of Mars as seen by InSight (Invited)

InSight is the first planetary mission dedicated to exploring the whole interior of a planet using geophysical methods, specifically seismology and geodesy. To this end, we observed seismic waves of distant marsquakes and inverted for interior models using differential travel times of phases reflected at the surface (PP, SS...) or the core mantle-boundary (ScS), as well as those converted at crustal interfaces. Compared to previous orbital observations1-3, the seismic data added decisive new insights with consequences for the formation of Mars: The global average crustal thickness of 24-75 km is at the low end of pre-mission estimates5. Together with the the thick lithosphere of 450-600 km5, this requires an enrichment of heat-producing elements in the crust by a factor of 13-20, compared to the primitive mantle. The iron-rich liquid core is 1790-1870 km in radius6, which rules out the existence of an insulating bridgmanite-dominated lower mantle on Mars. The large, and therefore low-density core needs a high amount of light elements. Given the geochemical boundary conditions, Sulfur alone cannot explain the estimated density of ~6 g/cm3 and volatile elements, such as oxygen, carbon or hydrogen are needed in significant amounts. This observation is difficult to reconcile with classical models of late formation from the same material as Earth. We also give an overview of open questions after three years of InSight operation on the surface of Mars, such as the potential existence of an inner core or compositional layers above the CM