ALBERT

Description: The presence of potential microbial trace fossils (endolithic microborings) has been well documented in oceanic basaltic pillow lavas, hyaloclastites, tuffs, and transitional subglacial marine lavas in the past 30 yr. Despite their evident abundance in oceanic to subglacial environments, they have not been observed in continental basalts that were not erupted in marine or subglacial settings. To expand the record of putative endolithic microborings in volcanic rocks to nonmarine, continental lacustrine environments, we examined hydrovolcanic pyroclastic deposits in the Fort Rock volcanic field, central Oregon. This study presents the textures, mineralogy, and geochemistry of basaltic tuffs containing possible endolithic microborings comparable in morphology, size, and distribution to those described in earlier oceanic and subglacial basalt studies. We observed a variety of tubular and granular textures that show evidence of biogenic morphologies and behavior, and a primary geological context that expresses their age and syngenicity. Petrographic relationships with secondary phases (chabazite, nontronite, calcite) indicate that the construction of microtunnels occurred in saline, alkaline fluids at temperatures of 25–80 °C. In addition, positive correlations were observed between the extent of aqueous (abiotic) alteration and both the abundance of microtunnels and morphological type. These correlations suggest that microtunnels were more readily formed where there was greater abiotic alteration-fluid flux and that the resulting change in chemical composition of those fluids may have had a direct influence on the formation process or possibly the type of constructing microbe. This work adds to understanding of factors controlling microtunnel formation and is the first account of putative endolithic microborings in a continental lacustrine setting. This new information may also have implications in the search for habitable extraterrestrial environments, such as on Mars.

Description: Well defined productivity-precipitation relationships of ecosystems are needed as benchmarks for the validation of land-models used for future projections. The productivity-precipitation relationship may be studied in two ways: the spatial approach relates differences in productivity to those in precipitation among sites along a precipitation gradient (the spatial fit, with a steeper slope); the temporal approach relates inter-annual productivity changes to variation in precipitation within sites (the temporal fits, with flatter slopes). Precipitation-reduction experiments in natural ecosystems represent a complement to the fits, because they can reduce precipitation below the natural range and are thus well suited to study potential effects of climate drying. Here, we analyze the effects of dry treatments in eleven multi-year precipitation-manipulation experiments, focusing on changes in the temporal fit. We expected that structural changes in the dry treatments would occur in some experiments, thereby reducing the intercept of the temporal fit and displacing the productivity-precipitation relationship downward the spatial fit. The majority of experiments (72%) showed that dry treatments did not alter the temporal fit. This implies that current temporal fits are to be preferred over the spatial fit to benchmark land-model projections of productivity under future climate within the precipitation ranges covered by the experiments. Moreover, in two experiments, the intercept of the temporal fit unexpectedly increased due to mechanisms that reduced either water- or nutrient losses. The expected decrease of the intercept was observed in only one experiment, and only when distinguishing between the late and the early phases of the experiment. This implies that we currently do not know at which precipitation-reduction level or at which experimental duration structural changes will start to alter ecosystem productivity. Our study highlights the need for experiments with multiple, including more extreme, dry treatments, to identify the precipitation boundaries within which the current temporal fits remain valid. This article is protected by copyright. All rights reserved.

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: Fermi arcs are the surface manifestation of the topological nature of Weyl semimetals, enforced by the bulk-boundary correspondence with the bulk Weyl nodes. The surface of tantalum arsenide, similar to that of other members of the Weyl semimetal class, hosts nontopological bands that obscure the exploration of this correspondence. We use the spatial structure of the Fermi arc wave function, probed by scanning tunneling microscopy, as a spectroscopic tool to distinguish and characterize the surface Fermi arc bands. We find that, as opposed to nontopological states, the Fermi arc wave function is weakly affected by the surface potential: it spreads rather uniformly within the unit cell and penetrates deeper into the bulk. Fermi arcs reside predominantly on tantalum sites, from which the topological bulk bands are derived. Furthermore, we identify a correspondence between the Fermi arc dispersion and the energy and momentum of the bulk Weyl nodes that classify this material as topological. We obtain these results by introducing an analysis based on the role the Bloch wave function has in shaping quantum electronic interference patterns. It thus carries broader applicability to the study of other electronic systems and other physical processes.

Description: During opening of a new ocean, magma intrudes into the surrounding sedimentary basins. Heat provided by the intrusions matures the host rock, creating metamorphic aureoles potentially releasing large amounts of hydrocarbons. These hydrocarbons may migrate to the seafloor in hydrothermal vent complexes in sufficient volumes to trigger global warming, e.g., during the Paleocene-Eocene Thermal Maximum (PETM). Mound structures at the top of buried hydrothermal vent complexes observed in seismic data off Norway were previously interpreted as sediment volcanoes, and the amount of released hydrocarbon was estimated based on this interpretation. Here, we present new geophysical and geochemical data from the Gulf of California suggesting that such mound structures could in fact be edifices constructed by the growth of black smoker–type chimneys rather than sediment volcanoes. We have evidence for two buried and one active hydrothermal vent systems outside the rift axis. The active vent releases fluids of several hundred degrees Celsius containing abundant methane, mid-ocean ridge basalt–type helium, and precipitating solids up to 300 m high into the water column. Our observations challenge the idea that methane is emitted slowly from rift-related vents. The association of large amounts of methane with hydrothermal fluids that enter the water column at high pressure and temperature provides an efficient mechanism to transport hydrocarbons into the water column and atmosphere, lending support to the hypothesis that rapid climate change such as during the PETM can be triggered by magmatic intrusions into organic-rich sedimentary basins.

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: Amyloid fibrils are proteinaceous aggregates associated with diseases in humans and animals. The fibrils are defined by intermolecular interactions between the fibril-forming polypeptide chains, but it has so far remained difficult to reveal the assembly of the peptide subunits in a full-scale fibril. Using electron cryomicroscopy (cryo-EM), we present a...

Description: Rebun Island with Hamanaka and Funadomari among the 43 documented archaeological sites and the environmental archive stored in the Lake Kushu sediment proves to be one of the key areas to study the interplay between ecology, climate and human activities. This paper focuses on the potential of palaeobotanical records from Rebun Island for improving the chronological control and understanding of late Quaternary climate changes and habitation environments of northern hunter-gatherers in the Hokkaido Region of Japan. A set of 57 radiocarbon dates of the RK12 core (Lake Kushu) demonstrates that it represents a continuous environmental archive covering the last c . 17,000 years. The RK12 pollen record reflects distinct vegetation changes associated with the onset of the lateglacial warming about 15,000 cal. yr BP and the cold climate reversal after c . 13,000 cal. yr BP. The onset of the current Holocene interglacial after c . 11,700 cal. yr BP is marked by a major spread of trees. The middle Holocene ( c . 8000–4000 cal. yr BP) is characterized by a major spread of deciduous oak in the vegetation cover reflecting a temperature increase. A decline of oak and spread of fir and pine is recorded at c . 2000 cal. yr BP. After c . 1100 cal. yr BP, arboreal pollen percentages decrease, possibly linked to intensified usage of wood during the Okhotsk and Ainu culture periods. The results of diatom analysis suggest marshy or deltaic environments at the RK12 coring site prior to c . 10,500 cal. yr BP and a brackish lagoon between c . 10,500 and 7000 cal. yr BP. A freshwater lake developed after 6500 cal. yr BP, likely reflecting sea level stabilization and formation of the sand bar separating the Kushu depression from the sea. Plant macrofossil analysis shows use of various wild plants and also domesticated barley during the Okhotsk and Ainu periods.

Description: The NDP-forming acyl-CoA synthetases (ACDs) catalyze the conversion of various CoA thioesters to the corresponding acids, conserving their chemical energy in form of ATP. The ACDs are the major energy-conserving enzymes in sugar and peptide fermentation of hyperthermophilic archaea. They are considered to be primordial enzymes of ATP synthesis in...