ALBERT

Description: Coinductive definitions, such as that of an infinite stream, may often be described by elegant logic programs, but ones for which SLD-refutation is of no value as SLD-derivations fall into infinite loops. Such definitions give rise to questions of lazy corecursive derivations and parallelism, as execution of such logic programs can have both recursive and corecursive features at once. Observational and coalgebraic semantics have been used to study them abstractly. The programming developments have often occurred separately and have usually been implementation-led. Here, we give a coherent semantics-led account of the issues, starting with abstract category theoretic semantics, developing coalgebra to characterize naturally arising trees and proceeding towards implementation of a new dialect, CoALP, of logic programming, characterised by guarded lazy corecursion and parallelism.

Description: : Intrinsically disordered proteins (IDPs) play central roles in many biological processes. Consequently, an accurate description of the disordered state is an important step towards a comprehensive understanding of a number of important biological functions. In this work we describe a new web server, Mollack, for the automated construction of unfolded ensembles that uses both experimental and molecular simulation data to construct models for the unfolded state. An important aspect of the method is that it calculates a quantitative estimate of the uncertainty in the constructed ensemble, thereby providing an objective measure of the quality of the final model. Overall, Mollack facilitates structure-function studies of disordered proteins. Availability and Implementation: http://cmstultz-mollack.mit.edu Contact: cmstultz@mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Candida albicans is a dimorphic yeast commonly found on human mucosal membranes that switches from yeast to hyphal morphology in response to environmental factors. The change to hyphal growth requires histone H3 modifications by the yeast-specific histone acetyltransferase Rtt109. In addition to its role in morphogenesis, Rtt109-dependent acetylation of histone H3 lysine residues 9 and 56 has regulatory functions during DNA replication and repair. Boric acid (BA) is a broad-spectrum agent that specifically inhibits C. albicans hyphal growth, locking the fungus in its harmless commensal yeast state. The present study characterizes the effect of BA on C. albicans histone acetylation in respect to specificity, time-course and significance. We demonstrate that sublethal concentrations of BA reduce H3K9/H3K56 acetylation, both on a basal level and in response to genotoxic stress. Acetylation at other selected histone sites were not affected by BA. qRT-PCR expression analysis of the DNA repair gene Rad51 indicated no elevated level of genotoxic stress during BA exposure. A forward-mutation analysis demonstrated the BA does not increase spontaneous or induced mutations . The findings suggest that DNA repair remains effective even when histone H3 acetylation decreases and dispels the notion that BA treatment impairs genome integrity in yeast.

Description: Carbonatite and silicate rocks occurring within a single magmatic complex may originate through liquid immiscibility. We thus experimentally determined carbonatite/silicate melt partition coefficients ( D carbonate melt/silicate melt , hereafter D ) for 45 elements to understand their systematics as a function of melt composition and to provide a tool for identifying the possible conjugate nature of silicate and carbonatite magmas. Static and, when necessary, centrifuging piston cylinder experiments were performed at 1–3 GPa, 1150–1260°C such that two well-separated melts resulted. Bulk compositions had Na K, Na ~ K, and Na K; for the latter we also varied bulk H 2 O (0–4 wt %) and SiO 2 contents. Oxygen fugacities were between iron–wüstite and slightly below hematite–magnetite and were not found to exert significant control on partitioning. Under dry conditions alkali and alkaline earth elements partition into the carbonatite melt, as did Mo and P ( D Mo 〉8, D P = 1·6–3·3). High field strength elements (HFSE) prefer the silicate melt, most strongly Hf ( D Hf = 0·04). The REE have partition coefficients around unity with D La/Lu = 1·6–2·3. Transition metals have D 〈 1 except for Cu and V ( D Cu ~ 1·3, D V = 0·95–2). The small variability of the partition coefficients in all dry experiments can be explained by a comparable width of the miscibility gap, which appears to be flat-topped in our dry bulk compositions. For all carbonatite and silicate melts, Nb/Ta and Zr/Hf fractionate by factors of 1·3–3·0, in most cases much more strongly than in silicate–oxide systems. With the exception of the alkalis, partition coefficients for the H 2 O-bearing systems are similar to those for the anhydrous ones, but are shifted in favour of the carbonatite melt by up to an order of magnitude. An increase of bulk silica and thus SiO 2 in the silicate melt (from 35 to 69 wt %) has a similar effect. Two types of trace element partitioning with changing melt composition can be observed. The magnitude of the partition coefficients increases for the alkalis and alkaline earths with the width of the miscibility gap, whereas partition coefficients for the REE shift by almost two orders of magnitude from partitioning into the silicate melt ( D La = 0·47) to strongly partitioning into the carbonatite melt ( D La = 38), whereas D La / D Lu varies by only a factor of three. The partitioning behavior can be rationalized as a function of ionic potential ( Z / r ). Alkali and alkaline earth elements follow a trend, the slope of which depends on the K/Na ratio and H 2 O content. Contrasting the sodic and potassic systems, alkalis have a positive correlation in D vs Z / r space in the potassic case and Cs to K partition into the silicate melt in the presence of H 2 O. For the divalent third row transition metals on the one hand and for the tri- and tetravalent REE and HFSE on the other, two trends of negative correlation of D vs Z / r can be defined. Nevertheless, the highest ionic strength network-modifying cations (V, Nb, Ta, Ti and Mo) do not follow any trend; understanding their behavior would require knowledge of their bonding environment in the carbonatite melt. Strong partitioning of REE into the carbonatite melt ( D REE = 5·8–38·0) occurs only in H 2 O-rich compositions for which carbonatites unmix from evolved alkaline melts with the conjugate silicate melt being siliceous. We thus speculate that upon hydrous carbonatite crystallization, the consequent saturation in fluids may lead to hydrothermal systems concentrating REE in secondary deposits.

Description: We introduce the moduli space of spectral curves of constant mean curvature (CMC) cylinders of finite type in the round unit 3-sphere. The subset of spectral curves of mean-convex Alexandrov embedded cylinders is explicitly determined using a combination of integrable systems and geometric analysis techniques. We prove that these cylinders are surfaces of revolution. As a consequence, all mean-convex Alexandrov embedded CMC tori in the 3-sphere are surfaces of revolution.

Description: Comet 67P/Churyumov-Gerasimenko (67P) was imaged with the 2 m telescope at Mt. Wendelstein Observatory in the Alps. Coma and tail monitoring was performed during 51 nights between 2015 August 22 and 2016 May 9. The images through r and i Sloan Digital Sky Survey (SDSS) filters show the dust distribution around the comet, while images in the SDSS g filter also indicate the presence of coma gas in early 2015 September. The dust colour of 67P implies intrinsic reddening of 9 per cent/100 nm. After maximum, shortly after perihelion passage, the dust activity decreased with a heliocentric exponent of 4.1–4.2 from late 2015 September until 2016 May. The opposition surge during early 2016 can be explained by a linear light scattering phase function (β ~ 0.04) or an asteroid-like HG-type phase function ( G ~ 0.15). The radial brightness profile indicates a ‘quasi-steady-state’ dust coma from late September to the end of 2015. Dust fragmentation during about a month after perihelion may be responsible for radial coma profiles with slopes below unity, while dust accumulation due to very slow dust expansion velocity may result in steeper than unity profiles during 2016. Three fan-shape dust structures are characterized in the coma of 67P. A short dust ejection event on 2015 August 22–23 has produced a dust arc-let and jet feature in the coma. In 2015 September, the appearance of cometary dust tail is dominated by the young dust produced around perihelion. The older dust dominates the tail appearance as of 2015 mid-November.

Description: We present a simple observation showing that the heat kernel on a locally finite graph behaves for short times $t$ roughly like $t^d$ , where $d$ is the combinatorial distance. This is very different from the classical Varadhan-type behavior on manifolds. Moreover, this also gives that short-time behavior and global behavior of the heat kernel are governed by two different metrics whenever the degree of the graph is not uniformly bounded.

Description: Palmitoylation, the dynamic post-translational addition of the lipid, palmitate, to proteins by Asp-His-His-Cys-containing palmitoyl acyltransferase (PAT) enzymes, modulates protein function and localization and plays a key role in the nervous system. Huntingtin-interacting protein 14 (HIP14), a well-characterized neuronal PAT, has been implicated in the pathogenesis of Huntington disease (HD), a fatal neurodegenerative disease associated with motor, psychiatric and cognitive symptoms, caused by a CAG expansion in the huntingtin gene ( HTT ). Mice deficient for Hip14 expression develop neuropathological and behavioural features similar to HD, and the catalytic activity of HIP14 is impaired in HD mice, most likely due to the reduced interaction of HIP14 with HTT. Huntingtin-interacting protein 14-like (HIP14L) is a paralog of HIP14, with identical domain structure. Together, HIP14 and HIP14L are the major PATs for HTT. Here, we report the characterization of a Hip14l -deficient mouse model, which develops adult-onset, widespread and progressive neuropathology accompanied by early motor deficits in climbing, impaired motor learning and reduced palmitoylation of a novel HIP14L substrate: SNAP25. Although the phenotype resembles that of the Hip14 –/– mice, a more progressive phenotype, similar to that of the YAC128 transgenic mouse model of HD, is observed. In addition, HIP14L interacts less with mutant HTT than the wild-type protein, suggesting that reduced HIP14L-dependent palmitoylation of neuronal substrates may contribute to the pathogenesis of HD. Thus, both HIP14 and HIP14L may be dysfunctional in the disease.

Description: We report observations of four weak absorption lines of the interstellar CN A 2 -X 2 + (3,0) band: R 1 (0) 6951.8 Å, R Q 21 (0) 6927.3 Å, R 2 (1)+ R Q 1 (1) 6926.7 Å, Q R 12 (1)+Q 1 (1) 6953.6 Å, and show that they provide reasonable information on column densities in sightlines towards early-type stars. The (3,0) band is always very weak and thus the saturation effect is negligible, which is particularly useful for the sightlines where the near UV-range CN bands are very strong, i.e. saturated.