The CELLULOSE SYNTHASE-LIKE A and CELLULOSE SYNTHASE-LIKE C families: recent advances and future perspectives

The CELLULOSE SYNTHASE (CESA) superfamily of proteins contains several sub-families of closely related CELLULOSE SYNTHASE-LIKE (CSL) sequences. Among these, the CSLA and CSLC families are closely related to each other and are the most evolutionarily divergent from the CESA family. Significant progress has been made with the functional characterization of CSLA and CSLC genes, which have been shown to encode enzymes with 1,4-β-glycan synthase activities involved in the biosynthesis of mannan and possibly xyloglucan backbones, respectively. This review examines recent work on the CSLA and CSLC families from evolutionary, molecular, and biochemical perspectives. We pose a series of questions, whose answers likely will provide further insight about the specific functions of members of the CSLA and CSLC families and about plant polysaccharide biosynthesis is general

Regularization of statistical inverse problems and the Bakushinskii veto

In the deterministic context Bakushinskii's theorem excludes the existence of purely data driven convergent regularization for ill-posed problems. We will prove in the present work that in the statistical setting we can either construct a counter example or develop an equivalent formulation depending on the considered class of probability distributions. Hence, Bakushinskii's theorem does not generalize to the statistical context, although this has often been assumed in the past. To arrive at this conclusion, we will deduce from the classic theory new concepts for a general study of statistical inverse problems and perform a systematic clarification of the key ideas of statistical regularization.Comment: 20 page

Minimax estimation of the Wigner function in quantum homodyne tomography with ideal detectors

We estimate the quantum state of a light beam from results of quantum homodyne measurements performed on identically prepared pulses. The state is represented through the Wigner function, a ``quasi-probability density'' on $\mathbb{R}^{2}$ which may take negative values and must respect intrinsic positivity constraints imposed by quantum physics. The data consists of $n$ i.i.d. observations from a probability density equal to the Radon transform of the Wigner function. We construct an estimator for the Wigner function, and prove that it is minimax efficient for the pointwise risk over a class of infinitely differentiable functions. A similar result was previously derived by Cavalier in the context of positron emission tomography. Our work extends this result to the space of smooth Wigner functions, which is the relevant parameter space for quantum homodyne tomography.Comment: 15 page

Dephosphorylated-uncarboxylated Matrix Gla protein concentration is predictive of vitamin K status and is correlated with vascular calcification in a cohort of hemodialysis patients.

Background: Matrix Gla protein (MGP) is known to act as a potent local inhibitor of vascular calcifications. However, in order to be active, MGP must be phosphorylated and carboxylated, with this last process being dependent on vitamin K. The present study focused on the inactive form of MGP (dephosphorylated and uncarboxylated: dp-ucMGP) in a population of hemodialyzed (HD) patients. Results found in subjects being treated or not with vitamin K antagonist (VKA) were compared and the relationship between dp-ucMGP levels and the vascular calcification score were assessed. Methods: One hundred sixty prevalent HD patients were enrolled into this observational cohort study, including 23 who were receiving VKA treatment. The calcification score was determined (using the Kauppila method) and dp-ucMGP levels were measured using the automated iSYS method. Results: dp-ucMGP levels were much higher in patients being treated with VKA and little overlap was found with those not being treated (5604 [3758; 7836] vs. 1939 [1419; 2841] pmol/L, p <0.0001). In multivariate analysis, treatment with VKA was the most important variable explaining variation in dp-ucMGP levels even when adjusting for all other significant variables. In the 137 untreated patients, dp-ucMGP levels were significantly (p < 0.05) associated both in the uni- and multivariate analysis with age, body mass index, plasma levels of albumin, C-reactive protein, and FGF-23, and the vascular calcification score. Conclusion: We confirmed that the concentration of dp-ucMGP was higher in HD patients being treated with VKA. We observed a significant correlation between dp-ucMGP concentration and the calcification score. Our data support the theoretical role of MGP in the development of vascular calcifications. We confirmed the potential role of the inactive form of MGP in assessing the vitamin K status of the HD patients

90m Optics Studies and Operation in the LHC

ISBN 978-3-95450-115-1 - http://accelconf.web.cern.ch/AccelConf/IPAC2012/papers/moppc006.pdfInternational audienceA high β* = 90 m optics was commissioned and used for first very forward physics operation in the LHC in 2011. The experience gained from working with this optics in 5 studies and operation periods in 2011 was very positive. The target β* = 90 m was reached by a de-squeeze from the standard 11 m injection and ramp optics on the first attempt and collisions and first physics results obtained in the second study. The optics was measured and corrected with good precision. The running conditions were very clean and allowed for measurements with roman pots very close to the beam

Multigene Phylogeny of Choanozoa and the Origin of Animals

Animals are evolutionarily related to fungi and to the predominantly unicellular protozoan phylum Choanozoa, together known as opisthokonts. To establish the sequence of events when animals evolved from unicellular ancestors, and understand those key evolutionary transitions, we need to establish which choanozoans are most closely related to animals and also the evolutionary position of each choanozoan group within the opisthokont phylogenetic tree. Here we focus on Ministeria vibrans, a minute bacteria-eating cell with slender radiating tentacles. Single-gene trees suggested that it is either the closest unicellular relative of animals or else sister to choanoflagellates, traditionally considered likely animal ancestors. Sequencing thousands of Ministeria protein genes now reveals about 14 with domains of key significance for animal cell biology, including several previously unknown from deeply diverging Choanozoa, e.g. domains involved in hedgehog, Notch and tyrosine kinase signaling or cell adhesion (cadherin). Phylogenetic trees using 78 proteins show that Ministeria is not sister to animals or choanoflagellates (themselves sisters to animals), but to Capsaspora, another protozoan with thread-like (filose) tentacles. The Ministeria/Capsaspora clade (new class Filasterea) is sister to animals and choanoflagellates, these three groups forming a novel clade (filozoa) whose ancestor presumably evolved filose tentacles well before they aggregated as a periciliary collar in the choanoflagellate/sponge common ancestor. Our trees show ichthyosporean choanozoans as sisters to filozoa; a fusion between ubiquitin and ribosomal small subunit S30 protein genes unifies all holozoa (filozoa plus Ichthyosporea), being absent in earlier branching eukaryotes. Thus, several successive evolutionary innovations occurred among their unicellular closest relatives prior to the origin of the multicellular body-plan of animals

Mechanistic Insights into Validoxylamine A 7\u27-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex

The pseudo-glycosyltransferase VldE catalyzes non-glycosidic C-N coupling between an unsaturated cyclitol and a saturated aminocyclitol with the conservation of the stereochemical configuration of the substrates to form validoxylamine A 7′-phosphate, the biosynthetic precursor of the antibiotic validamycin A. To study the molecular basis of its mechanism, the three-dimensional structures of VldE from Streptomyces hygroscopicus subsp. limoneus was determined in apo form, in complex with GDP, in complex with GDP and validoxylamine A 7′-phosphate, and in complex with GDP and trehalose. The structure of VldE with the catalytic site in both an open and closed conformation is also described. With these structures, the preferred binding of the guanine moiety by VldE, rather than the uracil moiety as seen in OtsA could be explained. The elucidation of the VldE structure in complex with the entirety of its products provides insight into the internal return mechanism by which catalysis occurs with a net retention of the stereochemical configuration of the donated cyclitol. © 2012 Cavalier et al

An elliptical tiling method to generate a 2-dimensional set of templates for gravitational wave search

Searching for a signal depending on unknown parameters in a noisy background with matched filtering techniques always requires an analysis of the data with several templates in parallel in order to ensure a proper match between the filter and the real waveform. The key feature of such an implementation is the design of the filter bank which must be small to limit the computational cost while keeping the detection efficiency as high as possible. This paper presents a geometrical method which allows one to cover the corresponding physical parameter space by a set of ellipses, each of them being associated to a given template. After the description of the main characteristics of the algorithm, the method is applied in the field of gravitational wave (GW) data analysis, for the search of damped sine signals. Such waveforms are expected to be produced during the de-excitation phase of black holes -- the so-called 'ringdown' signals -- and are also encountered in some numerically computed supernova signals.Comment: Accepted in PR

PHIL Accelerator at LAL - Diagnostic status

http://accelconf.web.cern.ch/AccelConf/BIW2010/papers/tupsm100.pdfInternational audienceThe "Photo-Injector at LAL" (PHIL : http://phil.lal.in2p3.fr/) is a new electron beam accelerator at LAL. This accelerator is dedicated to test and characterise electron photo-guns and high-frequency structures for future accelerator projects (like the next generation lepton colliders, CLIC, ILC). This machine has been designed to produce low energy (E<10 MeV), small emittance (epsilon < 10 pi.mm.mrad), high current (charge 2 nC/bunch) electrons bunch at low repetition frequency (frep<10Hz) [1]. The first beam has been obtained on the 4th of November 2009. This paper will describe the current status and the futures developments of the diagnostics devices on this machine

Phylogenomics Reshuffles the Eukaryotic Supergroups

Background. Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial. Methodology/Principle Findings. Here, we report the sequencing of expressed sequence tags (ESTs) for two species belonging to the supergroup Rhizaria and present the analysis of a unique dataset combining 29908 amino acid positions and an extensive taxa sampling made of 49 mainly unicellular species representative of all supergroups. Our results show a very robust relationship between Rhizaria and two main clades of the supergroup chromalveolates: stramenopiles and alveolates. We confirm the existence of consistent affinities between assemblages that were thought to belong to different supergroups of eukaryotes, thus not sharing a close evolutionary history. Conclusions. This well supported phylogeny has important consequences for our understanding of the evolutionary history of eukaryotes. In particular, it questions a single red algal origin of the chlorophyll-c containing plastids among the chromalveolates. We propose the abbreviated name ‘SAR’ (Stramenopiles+Alveolates+Rhizaria) to accommodate this new super assemblage of eukaryotes, which comprises the largest diversity of unicellular eukaryotes