Kinetic analysis of an efficient DNA-dependent TNA polymerase.

alpha-l-Threofuranosyl nucleoside triphosphates (tNTPs) are tetrafuranose nucleoside derivatives and potential progenitors of present-day beta-d-2'-deoxyribofuranosyl nucleoside triphosphates (dNTPs). Therminator DNA polymerase, a variant of the 9 degrees N DNA polymerase, is an efficient DNA-directed threosyl nucleic acid (TNA) polymerase. Here we report a detailed kinetic comparison of Therminator-catalyzed TNA and DNA syntheses. We examined the rate of single-nucleotide incorporation for all four tNTPs and dNTPs from a DNA primer-template complex and carried out parallel experiments with a chimeric DNA-TNA primer-DNA template containing five TNA residues at the primer 3'-terminus. Remarkably, no drop in the rate of TNA incorporation was observed in comparing the DNA-TNA primer to the all-DNA primer, suggesting that few primer-enzyme contacts are lost with a TNA primer. Moreover, comparison of the catalytic efficiency of TNA synthesis relative to DNA synthesis at the downstream positions reveals a difference of no greater than 5-fold in favor of the natural DNA substrate. This disparity becomes negligible when the TNA synthesis reaction mixture is supplemented with 1.25 mM MnCl(2). These results indicate that Therminator DNA polymerase can recognize both a TNA primer and tNTP substrates and is an effective catalyst of TNA polymerization despite changes in the geometry of the reactants

High fidelity TNA synthesis by Therminator polymerase

Therminator DNA polymerase is an efficient DNA-dependent TNA polymerase capable of polymerizing TNA oligomers of at least 80 nt in length. In order for Therminator to be useful for the in vitro selection of functional TNA sequences, its TNA synthesis fidelity must be high enough to preserve successful sequences. We used sequencing to examine the fidelity of Therminator-catalyzed TNA synthesis at different temperatures, incubation times, tNTP ratios and primer/template combinations. TNA synthesis by Therminator exhibits high fidelity under optimal conditions; the observed fidelity is sufficient to allow in vitro selection with TNA libraries of at least 200 nt in length

Applying the FAO-56 Dual \u3ci\u3eK\u3csub\u3ec\u3c/sub\u3e\u3c/i\u3e Method for Irrigation Water Requirements over Large Areas of the Western U.S.

The FAO-56 dual crop coefficient procedure was used to determine evapotranspiration (ET) and net irrigation water requirements for all agricultural areas of the states of Idaho and Nevada and in a western U.S. study on effects of climate change on future irrigation water requirements. The products of the applications are for use by state governments for water rights management, irrigation system planning and design, wastewater application system design and review, hydrologic water balances, and groundwater modeling. The products have been used by the U.S. federal government for assessing impacts of current and future climate change on irrigation water demands. The procedure was applied to data from more than 200 weather station locations across the state of Idaho, 200 weather station locations across the state of Nevada, and eight major river basins in the western U.S. for available periods of weather records. Estimates were made over daily, monthly, and annual time intervals. Methods from FAO-56 were employed for calculating reference ET and crop coefficients (Kc), with ET calculations performed for all times of the calendar year including winter. Expressing Kc as a function of thermal-time units allowed application across a wide range of local climates and elevations. The ET estimates covered a wide range of agricultural crops grown in the western U.S. plus a number of native plant systems, including wetlands, rangeland, and riparian trees. Evaporation was estimated for three types of open-water surfaces ranging from deep reservoirs to small farm ponds

Universal amplitudes in the FSS of three-dimensional spin models

In a MC study using a cluster update algorithm we investigate the finite-size scaling (FSS) of the correlation lengths of several representatives of the class of three-dimensional classical O(n) symmetric spin models on a column geometry. For all considered models we find strong evidence for a linear relation between FSS amplitudes and scaling dimensions when applying antiperiodic instead of periodic boundary conditions across the torus. The considered type of scaling relation can be proven analytically for systems on two-dimensional strips with periodic bc using conformal field theoryComment: 4 pages, RevTex, uses amsfonts.sty, 3 Figure

Youth Savings Groups in Africa: They’re a Family Affair

Based on fieldwork in Tanzania, Zambia, Uganda, and Ghana, in the paper we provide new evidence that young people’s engagement with savings groups in Africa is deeply embedded in networks of family and social relations. Savings group members rely on money that is given to them by partners and family members to make savings contributions to the groups, while they also transfer some of their share-outs and loans to family members and friends. This is particularly true for younger members. As such we argue that the socially embedded nature of young people's engagement with savings group needs to be taken into account. The tension between the primary focus on the individual within youth saving programming, and the socially embedded nature of their engagement, has important implications for programme design, implementation and evaluation

Natural climate solutions

Our thanks for inputs by L. Almond, A. Baccini, A. Bowman, S. CookPatton, J. Evans, K. Holl, R. Lalasz, A. Nassikas, M. Spalding, M. Wolosin, and expert elicitation respondents. Our thanks for datasets developed by the Hansen lab and the NESCent grasslands working group (C. Lehmann, D. Griffith, T. M. Anderson, D. J. Beerling, W. Bond, E. Denton, E. Edwards, E. Forrestel, D. Fox, W. Hoffmann, R. Hyde, T. Kluyver, L. Mucina, B. Passey, S. Pau, J. Ratnam, N. Salamin, B. Santini, K. Simpson, M. Smith, B. Spriggs, C. Still, C. Strömberg, and C. P. Osborne). This study was made possible by funding from the Doris Duke Charitable Foundation. Woodbury was supported in part by USDA-NIFA Project 2011-67003-30205 Data deposition: A global spatial dataset of reforestation opportunities has been deposited on Zenodo (https://zenodo.org/record/883444). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1710465114/-/DCSupplemental.Peer reviewedPublisher PD

The c2d Spitzer Spectroscopic Survey Of Ices Around Low-Mass Young Stellar Objects. I. H2O And The 5-8 Mu M Bands

To study the physical and chemical evolution of ices in solar-mass systems, a spectral survey is conducted of a sample of 41 low-luminosity YSOs (L similar to 0.1-10 L-circle dot) using 3-38 mu m Spitzer and ground-based spectra. The sample is complemented with previously published Spitzer spectra of background stars and with ISO spectra of well-studied massive YSOs (L similar to 10(5) L-circle dot). The long-known 6.0 and 6.85 mu m bands are detected toward all sources, with the Class 0-type YSOs showing the deepest bands ever observed. The 6.0 mu m band is often deeper than expected from the bending mode of pure solid H2O. The additional 5-7 mu m absorption consists of five independent components, which, by comparison to laboratory studies, must be from at least eight different carriers. Much of this absorption is due to simple species likely formed by grain surface chemistry, at abundances of 1%-30% for CH3OH, 3%-8% for NH3, 1%-5% for HCOOH, similar to 6% for H2CO, and similar to 0.3% for HCOO- relative to solid H2O. The 6.85 mu m band has one or two carriers, of which one may be less volatile than H2O. Its carrier(s) formed early in the molecular cloud evolution and do not survive in the diffuse ISM. If an NH4+- containing salt is the carrier, its abundance relative to solid H2O is similar to 7%, demonstrating the efficiency of low-temperature acid-base chemistry or cosmic-ray-induced reactions. Possible origins are discussed for enigmatic, very broad absorption between 5 and 8 mu m. Finally, the same ices are observed toward massive and low-mass YSOs, indicating that processing by internal UV radiation fields is a minor factor in their early chemical evolution.NWO SpinozaNOVAEuropean Research Training Network PLANETS HPRN-CT-2002-00308NASA Origins NAG5-13050NASA Hubble Fellowship 01201.01NASA NAS 5-26555Astronom

NLRX1 suppresses tumorigenesis and attenuates histiocytic sarcoma through the negative regulation of NF-κB signaling

Histiocytic sarcoma is an uncommon malignancy in both humans and veterinary species. Research exploring the pathogenesis of this disease is scarce; thus, diagnostic and therapeutic options for patients are limited. Recent publications have suggested a role for the NLR, NLRX1, in acting as a tumor suppressor. Based on these prior findings, we hypothesized that NLRX1 would function to inhibit tumorigenesis and thus the development of histiocytic sarcoma. To test this, we utilized Nlrx1−/− mice and a model of urethane-induced tumorigenesis. Nlrx1−/− mice exposed to urethane developed splenic histiocytic sarcoma that was associated with significant up-regulation of the NF-λB signaling pathway. Additionally, development of these tumors was also significantly associated with the increased regulation of genes associated with AKT signaling, cell death and autophagy. Together, these data show that NLRX1 suppresses tumorigenesis and reveals new genetic pathways involved in the pathobiology of histiocytic sarcoma