Apatites in Gale Crater

ChemCam is an active remote sensing instrument suite that has operated successfully on MSL since landing Aug. 6th, 2012. It uses laser pulses to remove dust and to analyze rocks up to 7 m away. Laser-induced breakdown spectroscopy (LIBS) obtains emission spectra of materials ablated from the samples in electronically excited states. The intensities of the emission lines scale with the abundances of the related element. ChemCam is sensitive to most major rock-forming elements as well as to a set of minor and trace elements such as F, Cl, Li, P, Sr, Ba, and Rb. The measured chemical composition can then be used to infer the mineralogical composition of the ablated material. Here, we report a summary of inferred apatite detections along the MSL traverse at Gale Crater. We present the geologic settings of these findings and derive some interpretations about the formation conditions of apatite in time and space

Rigorous Formulation of Duality in Gravitational Theories

In this paper we evince a rigorous formulation of duality in gravitational theories where an Einstein like equation is valid, by providing the conditions under which the Hodge duals (with respect to the metric tensor g) of T^a and R_b^a may be considered as the torsion and curvature 2-forms associated with a connection D', part of a Riemann-Cartan structure (M,g',D'), in the cases g = g' and g does not equal g', once T^a and R_b^a are the torsion and curvature 2-forms associated with a connection D part of a Riemann-Cartan structure (M,g,D). A new form for the Einstein equation involving the dual of the Riemann tensor of D is also provided, and the result is compared with others appearing in the literature.Comment: 15 page

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

ABSTRACT:Journal ArticleSCOPUS: ar.jinfo:eu-repo/semantics/publishe

Iron Mobility during Diagenesis at Vera Rubin ridge, Gale Crater, Mars

The Curiosity rover investigated a topographic structure known as Vera Rubin ridge, associated with a hematite signature in orbital spectra. There, Curiosity encountered mudstones interpreted as lacustrine deposits, conformably overlying the 300 m‐thick underlying sedimentary rocks of the Murray formation at the base of Mount Sharp. While the presence of hematite (α‐Fe2O3) was confirmed in‐situ by both Mastcam and ChemCam spectral observations and by the CheMin instrument, neither ChemCam nor APXS observed any significant increase in FeOT (total iron oxide) abundances compared to the rest of the Murray formation. Instead, Curiosity discovered dark‐toned diagenetic features displaying anomalously high FeOT abundances, commonly observed in association with light‐toned Ca‐sulfate veins but also as crystal pseudomorphs in the host rock. These iron‐rich diagenetic features are predominantly observed in “grey” outcrops on the upper part of the ridge, which lack the telltale ferric signature of other Vera Rubin ridge outcrops. Their composition is consistent with anhydrous Fe‐oxide, as the enrichment in iron is not associated with enrichment in any other elements, nor with detections of volatiles. The lack of ferric absorption features in the ChemCam reflectance spectra and the hexagonal crystalline structure associated with dark‐toned crystals points toward coarse “grey” hematite. In addition, the host rock adjacent to these features appears bleached and show low‐FeOT content as well as depletion in Mn, indicating mobilization of these redox‐sensitive elements during diagenesis. Thus, groundwater fluid circulations could account for the remobilization of iron and recrystallization as crystalline hematite during diagenesis on Vera Rubin ridge

Integrating water exclusion theory into βcontacts to predict binding free energy changes and binding hot spots

10.1186/1471-2105-15-57BMC Bioinformatics151-BBMI

A relevant in vitro rat model for the evaluation of blood-brain barrier translocation of nanoparticles

Poly(MePEG2000cyanoacrylate-co-hexadecylcyanoacrylate) (PEG-PHDCA) nanoparticles have demonstrated their capacity to reach the rat central nervous system after intravenous injection. For insight into the transport of colloidal systems across the blood-brain barrier (BBB), we developed a relevant in vitro rat BBB model consisting of a coculture of rat brain endothelial cells (RBECs) and rat astrocytes. The RBECs used in our model displayed and retained structural characteristics of brain endothelial cells, such as expression of P-glycoprotein, occludin and ZO-1, and immunofluorescence studies showed the specific localization of occludin and ZO1. The high values of transendothelial electrical resistance and low permeability coefficients of marker molecules demonstrated the functionality of this model. The comparative passage of polyhexadecylcyanoacrylate and PEG-PHDCA nanoparticles through this model was investigated, showing a higher passage of PEGylated nanoparticles, presumably by endocytosis. This result was confirmed by confocal microscopy. Thanks to a good in vitro/in vivo correlation, this rat BBB model will help in understanding the mechanisms of nanoparticle translocation and in designing new types of colloidal carriers as brain delivery systems

Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques

This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had “opened” their “closed” structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge loop determination is comparable to that of manual inspection. This method has been implemented as a web-based tool, which requires two protein structures as the input and then the type and/or existence of DS relationships between the input structures are determined according to the A-D image-based structural alignments and the DS score. The proposed method is expected to trigger large-scale studies of this interesting structural phenomenon and facilitate related applications

Quantification of three macrolide antibiotics in pharmaceutical lots by HPLC: Development, validation and application to a simultaneous separation

A new validated high performance liquid chromatographic (HPLC) method with rapid analysis time and high efficiency, for the analysis of erythromycin, azithromycin and spiramycin, under isocratic conditions with ODB RP18 as a stationary phase is described. Using an eluent composed of acetonitrile –2-methyl-2-propanol –hydrogenphosphate buffer, pH 6.5, with 1.5% triethylamine (33:7: up to 100, v/v/v), delivered at a flow-rate of 1.0 mL min-1. Ultra Violet (UV) detection is performed at 210 nm. The selectivity is satisfactory enough and no problematic interfering peaks are observed. The procedure is quantitatively characterized and repeatability, linearity, detection and quantification limits are very satisfactory. The method is applied successfully for the assay of the studied drugs in pharmaceutical dosage forms as tablets and powder for oral suspension. Recovery experiments revealed recovery of 97.13–100.28%

Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction

The three-dimensional structures of proteins are stabilized by the interactions between amino acid residues. Here we report a method where four distances are calculated between any two side chains to provide an exact spatial definition of their bonds. The data were binned into a four-dimensional grid and compared to a random model, from which the preference for specific four-distances was calculated. A clear relation between the quality of the experimental data and the tightness of the distance distribution was observed, with crystal structure data providing far tighter distance distributions than NMR data. Since the four-distance data have higher information content than classical bond descriptions, we were able to identify many unique inter-residue features not found previously in proteins. For example, we found that the side chains of Arg, Glu, Val and Leu are not symmetrical in respect to the interactions of their head groups. The described method may be developed into a function, which computationally models accurately protein structures

Protein Design Using Continuous Rotamers

Optimizing amino acid conformation and identity is a central problem in computational protein design. Protein design algorithms must allow realistic protein flexibility to occur during this optimization, or they may fail to find the best sequence with the lowest energy. Most design algorithms implement side-chain flexibility by allowing the side chains to move between a small set of discrete, low-energy states, which we call rigid rotamers. In this work we show that allowing continuous side-chain flexibility (which we call continuous rotamers) greatly improves protein flexibility modeling. We present a large-scale study that compares the sequences and best energy conformations in 69 protein-core redesigns using a rigid-rotamer model versus a continuous-rotamer model. We show that in nearly all of our redesigns the sequence found by the continuous-rotamer model is different and has a lower energy than the one found by the rigid-rotamer model. Moreover, the sequences found by the continuous-rotamer model are more similar to the native sequences. We then show that the seemingly easy solution of sampling more rigid rotamers within the continuous region is not a practical alternative to a continuous-rotamer model: at computationally feasible resolutions, using more rigid rotamers was never better than a continuous-rotamer model and almost always resulted in higher energies. Finally, we present a new protein design algorithm based on the dead-end elimination (DEE) algorithm, which we call iMinDEE, that makes the use of continuous rotamers feasible in larger systems. iMinDEE guarantees finding the optimal answer while pruning the search space with close to the same efficiency of DEE. Availability: Software is available under the Lesser GNU Public License v3. Contact the authors for source code