The VIMOS VLT Deep Survey - First epoch VVDS-Deep survey: 11564 spectra with 17.5<=IAB<=24, and the redshift distribution over 0< z <=5

This paper presents the ``First Epoch'' sample from the VIMOS VLT Deep Survey (VVDS). The VVDS goals, observations, data reduction with VIPGI, and redshift measurement with KBRED are discussed. Data have been obtained with the VIsible Multi Object Spectrograph (VIMOS) on the ESO-VLT UT3, allowing to observe ~600 slits simultaneously at R~230. A total of 11564 objects have been observed in the VVDS-02h and VVDS-CDFS Deep fields over a total area of 0.61deg^2, selected solely on the basis of apparent magnitude 17.5 <=I_{AB} <=24. The VVDS covers the redshift range 0 < z <= 5. It is successfully going through the ``redshift desert'' 1.5<z<2.2, while the range 2.2<z<2.7 remains of difficult access because of the VVDS wavelength coverage.A total of 9677 galaxies have a redshift measurement, 836 are stars, 90 are AGNs, and a redshift could not be measured for 961 objects. There are 1065 galaxies with a measured redshift z>1.4. The survey reaches a redshift measurement completeness of 78% overall (93% including less reliable objects), with a spatial sampling of the population of galaxies of 25% and ~30% in the VVDS-02h and VVDS-CDFS. The redshift accuracy measured from repeated observations with VIMOS and comparison to other surveys is ~276km/s. From this sample we present for the first time the redshift distribution of a magnitude limited spectroscopic sample down to IAB=24. The redshift distribution has a median of z=0.62, z=0.65, z=0.70, and z=0.76, for magnitude limited samples with IAB<=22.5, 23, 23.5, and 24. A high redshift tail above redshift 2 and up to redshift 5 becomes readily apparent for IAB>23.5, probing the bright star forming population of galaxies. This sample provides an unprecedented dataset to study galaxy evolution over 90% of the life of the universeComment: 30 pages, accepted 22-Feb-05 in A&

Automatic Tuning Matching Cycler (ATMC) in situ NMR spectroscopy as a novel approach for real-time investigations of Li- and Na-ion batteries.

We have developed and explored the use of a new Automatic Tuning Matching Cycler (ATMC) in situ NMR probe system to track the formation of intermediate phases and investigate electrolyte decomposition during electrochemical cycling of Li- and Na-ion batteries (LIBs and NIBs). The new approach addresses many of the issues arising during in situ NMR, e.g., significantly different shifts of the multi-component samples, changing sample conditions (such as the magnetic susceptibility and conductivity) during cycling, signal broadening due to paramagnetism as well as interferences between the NMR and external cycler circuit that might impair the experiments. We provide practical insight into how to conduct ATMC in situ NMR experiments and discuss applications of the methodology to LiFePO4 (LFP) and Na3V2(PO4)2F3 cathodes as well as Na metal anodes. Automatic frequency sweep (7)Li in situ NMR reveals significant changes of the strongly paramagnetic broadened LFP line shape in agreement with the structural changes due to delithiation. Additionally, (31)P in situ NMR shows a full separation of the electrolyte and cathode NMR signals and is a key feature for a deeper understanding of the processes occurring during charge/discharge on the local atomic scale of NMR. (31)P in situ NMR with "on-the-fly" re-calibrated, varying carrier frequencies on Na3V2(PO4)2F3 as a cathode in a NIB enabled the detection of different P signals within a huge frequency range of 4000 ppm. The experiments show a significant shift and changes in the number as well as intensities of (31)P signals during desodiation/sodiation of the cathode. The in situ experiments reveal changes of local P environments that in part have not been seen in ex situ NMR investigations. Furthermore, we applied ATMC (23)Na in situ NMR on symmetrical Na-Na cells during galvanostatic plating. An automatic adjustment of the NMR carrier frequency during the in situ experiment ensured on-resonance conditions for the Na metal and electrolyte peak, respectively. Thus, interleaved measurements with different optimal NMR set-ups for the metal and electrolyte, respectively, became possible. This allowed the formation of different Na metal species as well as a quantification of electrolyte consumption during the electrochemical experiment to be monitored. The new approach is likely to benefit a further understanding of Na-ion battery chemistries.The collaboration with Marco Braun (NMR Service GmbH, Erfurt, DE) on NMR probehead design and manufacturing is gratefully acknowledged. We acknowledge Baris Key, Rangeet Bhattacharrya and Revolution NMR LLC (Fort Collins, CO, USA) for the development of the first generation in situ NMR probes. We thank David Bennett (Bruker Biospin, Rheinstetten, DE), Andrew J. Pell (Cambridge, UK), and Peter Grice (Cambridge, UK) for fruitful discussions and Nathan Pitt (Cambridge, UK) for technical support. C.P.G. and Z.L. acknowledge Prof. Yong Yang (Xiamen, China) and his group for ongoing collaborations on Na3V2(PO4)2F3. O.P. and P.M.B. gratefully acknowledge financial support through a Marie Skłodowska-Curie Individual Fellowship (H2020-MSCA-IF-2014-EF, #655444) and FP7 Marie Curie International Incoming Fellowship, respectively. Research was supported in part by the NorthEast Center for Chemical Energy Storage (NECCES), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award # DE-SC0012583 (LFP materials, H.L., and N.M.T.), and by the Assistant Secretary for Energy Efficiency and Renewable Energy, Office of Vehicle Technologies of the U.S. Department of Energy, under contract no. DE-AC02-05CH11231, under the Batteries for Advanced Transportation Technologies Program subcontract 7057154 (Na metal).This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.jmr.2016.02.00

Medically Biodegradable Hydrogenated Amorphous Silicon Microspheres

[EN] Hydrogenated amorphous silicon colloids of low surface area (<5 m(2)/g) are shown to exhibit complete in-vitro biodegradation into orthosilicic acid within 10-15 days at 37 degrees C. When converted into polycrystalline silicon colloids, by high temperature annealing in an inert atmosphere, microparticle solubility is dramatically reduced. The data suggests that amorphous silicon does not require nanoscale porosification for full in-vivo biodegradability. This has significant implications for using a-Si:H coatings for medical implants in general, and orthopedic implants in particular. The high sphericity and biodegradability of submicron particles may also confer advantages with regards to contrast agents for medical imaging.This work has been partially supported by the Spanish CICyT projects, FIS2009-07812, Consolider CSD2007-046, MAT2009-010350 and PROMETEO/2010/043.Shabir, Q.; Pokale, A.; Loni, A.; Johnson, DR.; Canham, L.; Fenollosa Esteve, R.; Tymczenko, MK.... (2011). Medically Biodegradable Hydrogenated Amorphous Silicon Microspheres. Silicon. 3(4):173-176. https://doi.org/10.1007/s12633-011-9097-4S17317634Salonen J, Kaukonen AM, Hirvonen J, Lehto VP (2008) J Pharmaceutics 97:632–53Anglin EJ, Cheng L, Freeman WR, Sailor MJ (2008) Adv Drug Deliv Rev 60:1266–77O’Farrell N, Houlton A, Horrocks BR (2006) Int J Nanomedicine 1:451–72Canham LT (1995) Adv Mater 7:1037, PCT patent WO 97/06101,1999Park JH, Gui L, Malzahn G, Ruoslahti E, Bhatia SN, Sailor MJ (2009) Nature Mater 8:331–6Cullis AG, Canham LT, Calcott PDJ (1997) J Appl Phys 82:909–66Canham LT, Reeves CR (1996) Mat Res Soc Symp 414:189–90Edell DJ, Toi VV, McNeil VM, Clark LD (1992) IEEE Trans Biomed Eng 39:635–43Fenollosa R, Meseguer F, Tymczenko M (2008) Adv Mater 20:95Fenollosa R, Meseguer F, Tymczenko M, Spanish Patent P200701681, 2007Pell LE, Schricker AD, Mikulec FV, Korgel BA (2004) Langmuir 20:6546Xifré-Perez E, Fenollosa R, Meseguer F (2011) Opt Express 19:3455–63Fenollosa R, Ramiro-Manzano F, Tymczenko M, Meseguer F (2010) J Mater Chem 20:5210Xifré-Pérez E, Domenech JD, Fenollosa R, Muñoz P, Capmany J, Meseguer F (2011) Opt Express 19–4:3185–92Rodriguez I, Fenollosa R, Meseguer F, Cosmetics & Toiletries 2010;42–49Ramiro-Manzano F, Fenollosa R, Xifré-Pérez E, Garín M, Meseguer F (2011) Adv Mater 23:3022–3025. doi: 10.1002/adma.201100986Iler RK (1979) Chemistry of silica: solubility, polymerization, colloid & surface properties & biochemistry. Wiley, New YorkTanaka K, Maruyama E, Shimado T, Okamoto H (1999) Amorphous silicon. Wiley, New York, NYPatterson AL (1939) Phys Rev 56:978–82Canham LT, Reeves CL, King DO, Branfield PJ, Gabb JG, Ward MC (1996) Adv Mater 8:850–2Iler RK In: Chemistry of silica: solubility, polymerization, colloid & surface properties &Biochemistry. Wiley, New York, NYFinnie KS, Waller DJ, Perret FL, Krause-Heuer AM, Lin HQ, Hanna JV, Barbe CJ (2009) J Sol-Gel Technol 49:12–8Zhao D, Huo Q, Feng J, Chmelka BF, Stucky GD (1998) J Am Chem Soc 120:6024–36Fan D, Akkaraju GR, Couch EF, Canham LT, Coffer JL (2010) Nanoscale 1:354–61Tasciotti E, Godin B, Martinez JO, Chiappini C, Bhavane R, Liu X, Ferrari M (2011) Mol Imaging 10:56–

Genetic Analysis of Anti-Amoebae and Anti-Bacterial Activities of the Type VI Secretion System in Vibrio cholerae

A type VI secretion system (T6SS) was recently shown to be required for full virulence of Vibrio cholerae O37 serogroup strain V52. In this study, we systematically mutagenized each individual gene in T6SS locus and characterized their functions based on expression and secretion of the hemolysin co-regulated protein (Hcp), virulence towards amoebae of Dictyostelium discoideum and killing of Escherichia coli bacterial cells. We group the 17 proteins characterized in the T6SS locus into four categories: twelve (VipA, VipB, VCA0109–VCA0115, ClpV, VCA0119, and VasK) are essential for Hcp secretion and bacterial virulence, and thus likely function as structural components of the apparatus; two (VasH and VCA0122) are regulators that are required for T6SS gene expression and virulence; another two, VCA0121 and valine-glycine repeat protein G 3 (VgrG-3), are not essential for Hcp expression, secretion or bacterial virulence, and their functions are unknown; the last group is represented by VCA0118, which is not required for Hcp expression or secretion but still plays a role in both amoebae and bacterial killing and may therefore be an effector protein. We also showed that the clpV gene product is required for Dictyostelium virulence but is less important for killing E. coli. In addition, one vgrG gene (vgrG-2) outside of the T6SS gene cluster was required for bacterial killing but another (vgrG-1) was not. However, a bacterial killing defect was observed when vgrG-1 and vgrG-3 were both deleted. Several genes encoded in the same putative operon as vgrG-1 and vgrG-2 also contribute to virulence toward Dictyostelium but have a smaller effect on bacterial killing. Our results provide new insights into the functional requirements of V. cholerae's T6SS in the context of secretion as well as killing of bacterial and eukaryotic phagocytic cells

In situ size sorting in CVD synthesis of Si microspheres

[EN] Silicon microspheres produced in gas-phase by hot-wall CVD offer unique quality in terms of sphericity, surface smoothness, and size. However, the spheres produced are polydisperse in size, which typically range from 0.5 mu m to 5 mu m. In this work we show through experiments and calculations that thermophoretic forces arising from strong temperature gradients inside the reactor volume effectively sort the particles in size along the reactor. These temperature gradients are shown to be produced by a convective gas flow. The results prove that it is possible to select the particle size by collecting them in a particular reactor region, opening new possibilities towards the production by CVD of size-controlled high-quality silicon microspheres.The authors acknowledge financial support from the following projects: ENE2013-49984-EXP, MAT2012-35040, MAT2015-69669-P and ESP2014-54256-C4-2-R of the Spanish Ministry of Economy and Competitiveness (MINECO), and PROMETEOII/2014/026 of the Regional Valencian Government.Garín Escrivá, M.; Fenollosa Esteve, R.; Kowalski, L. (2016). In situ size sorting in CVD synthesis of Si microspheres. Scientific Reports. 6:1-10. https://doi.org/10.1038/srep38719S110

An Epigenetic Switch Involving Overlapping Fur and DNA Methylation Optimizes Expression of a Type VI Secretion Gene Cluster

Type VI secretion systems (T6SS) are macromolecular machines of the cell envelope of Gram-negative bacteria responsible for bacterial killing and/or virulence towards different host cells. Here, we characterized the regulatory mechanism underlying expression of the enteroagregative Escherichia coli sci1 T6SS gene cluster. We identified Fur as the main regulator of the sci1 cluster. A detailed analysis of the promoter region showed the presence of three GATC motifs, which are target of the DNA adenine methylase Dam. Using a combination of reporter fusion, gel shift, and in vivo and in vitro Dam methylation assays, we dissected the regulatory role of Fur and Dam-dependent methylation. We showed that the sci1 gene cluster expression is under the control of an epigenetic switch depending on methylation: fur binding prevents methylation of a GATC motif, whereas methylation at this specific site decreases the affinity of Fur for its binding box. A model is proposed in which the sci1 promoter is regulated by iron availability, adenine methylation, and DNA replication

Burkholderia Type VI Secretion Systems Have Distinct Roles in Eukaryotic and Bacterial Cell Interactions

Bacteria that live in the environment have evolved pathways specialized to defend against eukaryotic organisms or other bacteria. In this manuscript, we systematically examined the role of the five type VI secretion systems (T6SSs) of Burkholderia thailandensis (B. thai) in eukaryotic and bacterial cell interactions. Consistent with phylogenetic analyses comparing the distribution of the B. thai T6SSs with well-characterized bacterial and eukaryotic cell-targeting T6SSs, we found that T6SS-5 plays a critical role in the virulence of the organism in a murine melioidosis model, while a strain lacking the other four T6SSs remained as virulent as the wild-type. The function of T6SS-5 appeared to be specialized to the host and not related to an in vivo growth defect, as ΔT6SS-5 was fully virulent in mice lacking MyD88. Next we probed the role of the five systems in interbacterial interactions. From a group of 31 diverse bacteria, we identified several organisms that competed less effectively against wild-type B. thai than a strain lacking T6SS-1 function. Inactivation of T6SS-1 renders B. thai greatly more susceptible to cell contact-induced stasis by Pseudomonas putida, Pseudomonas fluorescens and Serratia proteamaculans—leaving it 100- to 1000-fold less fit than the wild-type in competition experiments with these organisms. Flow cell biofilm assays showed that T6S-dependent interbacterial interactions are likely relevant in the environment. B. thai cells lacking T6SS-1 were rapidly displaced in mixed biofilms with P. putida, whereas wild-type cells persisted and overran the competitor. Our data show that T6SSs within a single organism can have distinct functions in eukaryotic versus bacterial cell interactions. These systems are likely to be a decisive factor in the survival of bacterial cells of one species in intimate association with those of another, such as in polymicrobial communities present both in the environment and in many infections

Rapid Proton-Detected NMR Assignment for Proteins with Fast Magic Angle Spinning

Using a set of six 1H-detected triple-resonance NMR experiments, we establish a method for sequence-specific backbone resonance assignment of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of 5–30 kDa proteins. The approach relies on perdeuteration, amide 2H/1H exchange, high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling the use of automated analysis. The method is validated with five examples of proteins in different condensed states, including two microcrystalline proteins, a sedimented virus capsid, and two membrane-embedded systems. In comparison to contemporary 13C/15N-based methods, this approach facilitates and accelerates the MAS NMR assignment process, shortening the spectral acquisition times and enabling the use of unsupervised state-of-the-art computational data analysis protocols originally developed for solution NMR