Viruses of Asgard archaea

Asgardarchaeota encode many eukaryotic signature proteins and are widely considered to represent the closest archaeal relatives of eukaryotes. Whether similarities between Asgard archaea and eukaryotes extend to their viromes remains unknown. Here we present 20 metagenome-assembled genomes of Asgardarchaeota from deep-sea sediments of the basin off the Shimokita Peninsula, Japan. By combining CRISPR spacer search of metagenomic sequences with phylogenomic analysis, we identify three family-level groups of viruses associated with Asgard archaea. The first group, Verdandiviruses, includes tailed viruses of the realm Duplodnaviria, the second one, Skuldviruses, consists of viruses with predicted icosahedral capsids that belong to the realm Varidnaviria, and the third group, Wyrdviruses, is related to spindle-shaped viruses previously identified in other archaea. More than 90% of the proteins encoded by these putative viruses of Asgard archaea show no sequence similarity to proteins encoded by other known viruses. Nevertheless, all three proposed families consist of viruses typical of prokaryotes, providing no indication of a specific evolutionary relationship between viruses infecting Asgard archaea and eukaryotes. Verdandiviruses and skuldviruses are likely to be lytic, whereas wyrdviruses, similar to all other known spindle-shaped viruses, probably establish chronic infection and are released without host cell lysis. All three groups of viruses were identified in sediment samples from distinct geographical locations and are expected to play important roles in controlling the Asgard archaea populations in deep-sea ecosystems.

Eustatic, Climatic and Tectonic Controls on the Evolution of a Middle to Late Holocene Coastal Dune System in Shimokita, Northeast Japan

The Pacific coast of the Shimokita Peninsula, Northeast Japan, is occupied by one of the larger dune complexes in Japan. This coastal aeolian dune complex developed during the Holocene in a monsoon-influenced temperate climatic belt. The stratigraphic and sedimentological characteristics of outcrops, exposures and cores indicate that four generation of aeolian dunes are presented. These dunes developed during eustatic regression following the post-glacial sea-level highstand. Seaward shoreline movement, combined with strong winds from the Pacific Ocean, enhanced aeolian grain transport on the beach, resulting in the onset of dune growth and the consequent shrinkage of the coastal forest. Northeast Japan is located in a transitional zone affected largely by monsoonal circulation from Siberia and Southeast Asia. Thus, the regional climate is responsible for atmospheric changes on a hemispheric scale. Intensified monsoons contributed to flooding produced by rains and snow-melt. Steep increases in annual precipitation at 7200–6300, 4700–3600, 3050–2500, 1850–1100, and 550–200 calendar years before present (cal. yr. BP) increased the amount of surface erosion, causing a large volume of sediment discharge toward the coast. Shimokita has experienced frequent earthquakes and tsunamis, which have reduced dune landform relief by sediment displacement.

A Study of Variation of the 11-yr Solar Cycle before the onset of the Spoerer Minimum based on Annually measured 14C Content in tree Rings

ABSTRACTProxy-based observations of solar activity in the past have revealed long-term variations, such as the Gleissberg cycle (~88 yr), de Vries cycle (~200 yr), and the Hallstatt cycle (~2000 yr). Such long-term variations of solar activity sometimes cause the disappearance of sunspots for several decades. Currently, solar activity is becoming weaker, and there is a possibility that another long-term sunspot minimum could occur. However, the detailed mechanism of the weakening in solar activity is unknown, and the prediction of solar activity is ambiguous. In this study, we investigate the transitions of solar cycle length before the onset of the Spoerer Minimum, the longest grand minimum in the past 2000 yr. We measured the 14C content in an asunaro tree (Thujopsis dolabrata) excavated at Shimokita Peninsula from 1368–1420 CE using the compact AMS system at Yamagata University. It is found that the solar cycle lengthened to be 14–16 yr from 2 cycles before the onset of the Spoerer Minimum.

Differences in β-thujaplicin content of wood between plantation- and naturally grown Thujopsis dolabrata var. hondae (hinokiasunaro) trees in Shimokita Peninsula, Aomori, Japan

β-Thujaplicin (hinokitiol) is an important extractive of Thujopsis dolabrata var. hondae (hinokiasunaro) that confers high durability to its wood. We investigated differences in β-thujaplicin content in wood from plantation- and naturally grown trees of T. dolabrata var. hondae, and also examined growth rate and wood density. A total of 29 trees were collected from two natural forests and a plantation forest in the Shimokita Peninsula, Aomori, Japan. β-Thujaplicin content was determined for each heartwood sample by gas chromatography. The content ranged from 0.29 to 3.67 mg/g (oven-dry weight basis). β-thujaplicin content of plantation-grown trees was significantly higher than for naturally grown trees, though with a large variation. The effect of radial growth rate on β-thujaplicin content was minimal. We conclude that T. dolabrata var. hondae wood from both plantation and natural forest has similar durability. The coefficient of variation of β-thujaplicin content in each stand was higher than for other wood properties. This degree of tree-to-tree variation in the trait suggests that promising production with more durable wood could be achieved by selecting T. dolabrata var. hondae trees containing a high content of β-thujaplicin for plantations.

Statistical methods to enable practical on-site tomographic imaging of whole-core samples

Statistical methods enable the use of portable industrial scanners with sparse measurements, suitable for fast on-site whole-core X-ray computed tomography (CT), as opposed to conventional (medical) devices that use dense measurements. This approach accelerates an informed first-stage general assessment of core samples. To that end, this novel industrial tomographic measurement principle is feasible for rock-sample imaging, in conjunction with suitable forms of priors in Bayesian inversion algorithms. Gaussian, Cauchy, and total variation priors yield different inversion characteristics for similar material combinations. An evaluation of the inversion performance in rock samples considers, in a discrete form, conditional mean estimators, via Markov Chain Monte Carlo algorithms with noise-contaminated measurements. Additionally, further assessment indicates that this statistical approach better characterizes the attenuation contrast of rock materials, compared with simultaneous iterative reconstruction techniques. Benchmarking includes X-ray CT from numerical simulations of synthetic and measurement-based whole-core samples. To this end, we consider tomographic measurements of fine- to medium-grained sandstone core samples, with igneous-rich pebbles from the Miocene, off the Shimokita Peninsula in Japan, and fractured welded tuff from Big Bend National Park, Texas. Bayesian inversion results confirm that with only 16 radiograms, natural fractures with aperture of less than 2 mm wide are detectable. Additionally, reconstructed images found approximately spherical concretions of 6 mm diameter. To achieve similar results, filtered back projection techniques require hundreds of radiograms, only possible with conventional laboratory scanners.