Characterization of the 2'-5'-oligoadenylate synthetase ubiquitin-like family

The interferon-induced 2′–5′-oligoadenylate synthetases (OAS) are important for the antiviral activity of interferons. The human and murine OAS gene families each contain four genes: OAS1, OAS2, OAS3 and OASL, all having one or more conserved OAS units composed of five translated exons. The OASL gene has both an OAS unit and a C-terminus of two ubiquitin-like repeats. In this study, we demonstrate that murine Oasl1 protein is inactive while murine Oasl2 is active as an OAS. Further more, murine Oasl2 requires double-stranded RNA as co-factor. The affinity of murine Oasl2 for the double-stranded RNA activator is higher than that of human OAS1 (p42 isoform). We propose a model for the evolutionary origin of the murine Oasl1 and Oasl2 genes. The identification of a human orthologue (hOASL2) to the murine Oasl2 gene establishes that the OASL gene was duplicated prior to the radiation of the rodent and primate groups. We suggest that murine Oasl2, which has both enzymatic activity and a ubiquitin-like domain, is a functional intermediate between the active OAS species and the inactive human OASL1/murine Oasl1 proteins. In addition, we propose that murine Oasl1 appears to have gained a hitherto uncharacterized function independent of 2′–5′-linked oligoadenylate synthesis.     

Suppression of eukaryotic translation termination by selected RNAs

Using selection-amplification, we have isolated RNAs with affinity for translation termination factors eRF1 and eRF1.eRF3 complex. Individual RNAs not only bind, but inhibit eRF1-mediated release of a model nascent chain from eukaryotic ribosomes. There is also significant but weaker inhibition of eRF1-stimulated eRF3 GTPase and eRF3 stimulation of eRF1 release activity. These latter selected RNAs therefore hinder eRF1.eRF3 interactions. Finally, four RNA inhibitors of release suppress a UAG stop codon in mammalian extracts dependent for termination on eRF1 from several metazoan species. These RNAs are therefore new specific inhibitors for the analysis of eukaryotic termination, and potentially a new class of omnipotent termination suppressors with possible therapeutic significance.     

Distinct seasonal dynamics of responses to elevated CO2 in two understorey grass species differing in shade‐tolerance

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Effects of preheating on briquetting and subsequent hydrothermal pretreatment for enzymatic saccharification of wheat straw

Briquetting of plant biomass with low bulk density is an advantage for handling, transport, and storage of the material, and heating of the biomass prior to the briquetting facilitates the densification process and improves the physical properties of the briquettes. This study investigates the effects of preheating prior to briquetting of wheat straw (WS) on subsequent hydrothermal pretreatment and enzymatic conversion to fermentable sugars. WS (11% moisture content) was densified to briquettes under different conditions; without preheating or with preheating at 75 or 125°C for either 5 or 10 min. Subsequent hydrothermal pretreatment was done for both un-briquetted WS and for briquettes. Enzymatic saccharification was afterwards performed for all samples. The results showed that as expected, nonpretreated WS briquettes gave very low sugar yields (22–29% of the cellulose content), even though preheating at 125°C prior to briquetting (without pretreatment) improved sugar yields somewhat. When combined with pretreatment, briquetting with preheating showed neutral or negative effects on sugar yield. This result suggests that moderate preheating (75°C for 5 min) before briquetting improved bulk density and compressive resistance of briquettes without impeding subsequent enzymatic conversion. However, excessive preheating (75 or 125°C for 10 min) before briquetting may result in irreversible structural modifications that hinder the interaction between biomass and water during pretreatment, thereby decreasing the accessibility of cellulose to enzymatic saccharification.     

Recovery and virulence phenotyping of the historic ‘Stubbs collection’ of the yellow rust fungus Puccinia striiformis from wheat

A unique collection of spore samples of Puccinia striiformis, often referred to as the ‘Stubbs collection’, has been stored in liquid nitrogen from 18 to 45 years. A subset of samples representing 35 countries and 28 years was investigated to assess recovery rate, race identity and previously undetected virulence. A new method for recovery using an airbrush sprayer and Novec? 7100 for inoculating the host plants was highly successful. Ninety‐six percent of 231 isolates were recovered. Virulence phenotyping was done using differential sets of wheat genotypes representing specific‐resistance genes. A total of 181 samples represented single genotypes (isolates), whereas 40 samples consisted of at least two genotypes. Race identity was confirmed for 102 of 181 single‐genotype isolates. The virulence phenotype was updated for additional 44 isolates based on improved resolution of results because of updated and more informative wheat‐differential sets. The remaining 35 isolates showed discrepancies for one or more virulences when compared with past results. Additional virulences corresponding to Yr17, Yr25 and Yr27, respectively, which were not assayed originally, were discovered. The value of biological collections for research and plant breeding is discussed along with the challenges of maintaining collections of biotrophic microorganisms.     

Measuring Large-Scale Social Networks with High Resolution

This paper describes the deployment of a large-scale study designed to measure human interactions across a variety of communication channels, with high temporal resolution and spanning multiple years—the Copenhagen Networks Study. Specifically, we collect data on face-to-face interactions, telecommunication, social networks, location, and background information (personality, demographics, health, politics) for a densely connected population of 1 000 individuals, using state-of-the-art smartphones as social sensors. Here we provide an overview of the related work and describe the motivation and research agenda driving the study. Additionally, the paper details the data-types measured, and the technical infrastructure in terms of both backend and phone software, as well as an outline of the deployment procedures. We document the participant privacy procedures and their underlying principles. The paper is concluded with early results from data analysis, illustrating the importance of multi-channel high-resolution approach to data collection.     

Constraining oceanic oxygenation during the Shuram excursion in South China using thallium isotopes

Ediacaran sediments record an unusual global carbon cycle perturbation that has been linked to widespread oceanic oxygenation, the Shuram negative C isotope excursion (NCIE). However, proxy‐based estimates of global ocean redox conditions during this event have been limited largely due to proxy specificity (e.g., euxinic sediments for Mo and U isotopes). Modern global seawater documents a homogenous Tl isotope composition (ε²⁰⁵Tl = ?6.0) due to significant manganese oxide burial, which is recorded in modern euxinic sediments. Here, we provide new data documenting that sediments deposited beneath reducing but a non‐sulfidic water column from the Santa Barbara Basin (ε²⁰⁵Tl = ?5.6 ± 0.1) also faithfully capture global seawater Tl isotope values. Thus, the proxy utilization of Tl isotopes can extend beyond strictly euxinic settings. Second, to better constrain the global redox conditions during the Shuram NCIE, we measured Tl isotopes of locally euxinic and ferruginous shales of the upper Doushantuo Formation, South China. The ε²⁰⁵Tl values of these shales exhibit a decreasing trend from ≈?3 to ≈?8, broadly coinciding with the onset of Shuram NCIE. There are ε²⁰⁵Tl values (?5.1 to ?7.8) during the main Shuram NCIE interval that approach values more negative than modern global seawater. These results suggest that manganese oxide burial was near or even greater than modern burial fluxes, which is likely linked to an expansion of oxic conditions. This ocean oxygenation may have been an important trigger for the Shuram NCIE and evolution of Ediacaran‐type biota. Subsequently, Tl isotopes show an increasing trend from the modern ocean value to values near the modern global inputs or even heavier (ε²⁰⁵Tl ≈ ?2.5 ~ 0.4), occurring prior to recovery from the NCIE. These records may suggest that there was a decrease in the extent of oxygenated conditions in the global oceans during the late stage of the Shuram NCIE.     

Allocation of carbon to fine root compounds and their residence times in a boreal forest depend on root size class and season

Fine roots play a key role in the forest carbon balance, but their carbon dynamics remain largely unknown. We pulse labelled 50 m(2) patches of young boreal forest by exposure to (13)CO(2) in early and late summer. Labelled photosynthates were traced into carbon compounds of < 1 and 1-3 mm diameter roots (fine roots), and into bulk tissue of these and first-order roots (root tips). Root tips were the most strongly labelled size class. Carbon allocation to all size classes was higher in late than in early summer; mean residence times (MRTs) in starch increased from 4 to 11 months. In structural compounds, MRTs were 0.8 yr in tips and 1.8 yr in fine roots. The MRT of carbon in sugars was in the range of days. Functional differences within the fine root population were indicated by carbon allocation patterns and residence times. Pronounced allocation of recent carbon and higher turnover rates in tips are associated with their role in nutrient and water acquisition. In fine roots, longer MRTs but high allocation to sugars and starch reflect their role in structural support and storage. Accounting for heterogeneity in carbon residence times will improve and most probably reduce the estimates of fine root production.