As the COVID-19 outbreak spreads, there is a growing need for a compilation of conserved RNA genome regions in the SARS-CoV-2 virus along with their structural propensities to guide development of ...antivirals and diagnostics. Here we present a first look at RNA sequence conservation and structural propensities in the SARS-CoV-2 genome. Using sequence alignments spanning a range of betacoronaviruses, we rank genomic regions by RNA sequence conservation, identifying 79 regions of length at least 15 nt as exactly conserved over SARS-related complete genome sequences available near the beginning of the COVID-19 outbreak. We then confirm the conservation of the majority of these genome regions across 739 SARS-CoV-2 sequences subsequently reported from the COVID-19 outbreak, and we present a curated list of 30 "SARS-related-conserved" regions. We find that known RNA structured elements curated as Rfam families and in prior literature are enriched in these conserved genome regions, and we predict additional conserved, stable secondary structures across the viral genome. We provide 106 "SARS-CoV-2-conserved-structured" regions as potential targets for antivirals that bind to structured RNA. We further provide detailed secondary structure models for the extended 5' UTR, frameshifting stimulation element, and 3' UTR. Lastly, we predict regions of the SARS-CoV-2 viral genome that have low propensity for RNA secondary structure and are conserved within SARS-CoV-2 strains. These 59 "SARS-CoV-2-conserved-unstructured" genomic regions may be most easily accessible by hybridization in primer-based diagnostic strategies.
Variational autoencoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single nonlinear embedding. In this work, we illustrate how this ...nonlinear latent embedding can be used as a collective variable for enhanced sampling and present a simple modification that allows us to rapidly perform sampling in multiple related systems. We first demonstrate our method is able to describe the effects of force field changes in capped alanine dipeptide after learning about a model using AMBER99. We further provide a simple extension to variational dynamics encoders that allows the model to be trained in a more efficient manner on larger systems by encoding the outputs of a linear transformation using time-structure based independent component analysis (tICA). Using this technique, we show how such a model trained for one protein, the WW domain, can efficiently be transferred to perform enhanced sampling on a related mutant protein, the GTT mutation. This method shows promise for its ability to rapidly sample related systems using a single transferable collective variable, enabling us to probe the effects of variation in increasingly large systems of biophysical interest.
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IJS, KILJ, NUK, PNG, UL, UM
The size, shape, and connectivity of water bodies (lakes, ponds, and wetlands) can have important effects on ecological communities and ecosystem processes, but how these characteristics are ...influenced by land use and land cover change over broad spatial scales is not known. Intensive alteration of water bodies during urban development, including construction, burial, drainage, and reshaping, may select for certain morphometric characteristics and influence the types of water bodies present in cities. We used a database of over one million water bodies in 100 cities across the conterminous United States to compare the size distributions, connectivity (as intersection with surface flow lines), and shape (as measured by shoreline development factor) of water bodies in different land cover classes. Water bodies in all urban land covers were dominated by lakes and ponds, while reservoirs and wetlands comprised only a small fraction of the sample. In urban land covers, as compared to surrounding undeveloped land, water body size distributions converged on moderate sizes, shapes toward less tortuous shorelines, and the number and area of water bodies that intersected surface flow lines (i.e., streams and rivers) decreased. Potential mechanisms responsible for changing the characteristics of urban water bodies include: preferential removal, physical reshaping or addition of water bodies, and selection of locations for development. The relative contributions of each mechanism likely change as cities grow. The larger size and reduced surface connectivity of urban water bodies may affect the role of internal dynamics and sensitivity to catchment processes. More broadly, these results illustrate the complex nature of urban watersheds and highlight the need to develop a conceptual framework for urban water bodies.
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BFBNIB, FZAB, GIS, IJS, INZLJ, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZRSKP
Quantifying global soil respiration (RSG) and its response to temperature change are critical for predicting the turnover of terrestrial carbon stocks and their feedbacks to climate change. ...Currently, estimates of RSG range from 68 to 98 Pg C year−1, causing considerable uncertainty in the global carbon budget. We argue the source of this variability lies in the upscaling assumptions regarding the model format, data timescales, and precipitation component. To quantify the variability and constrain RSG, we developed RSG models using Random Forest and exponential models, and used different timescales (daily, monthly, and annual) of soil respiration (RS) and climate data to predict RSG. From the resulting RSG estimates (range = 66.62–100.72 Pg), we calculated variability associated with each assumption. Among model formats, using monthly RS data rather than annual data decreased RSG by 7.43–9.46 Pg; however, RSG calculated from daily RS data was only 1.83 Pg lower than the RSG from monthly data. Using mean annual precipitation and temperature data instead of monthly data caused +4.84 and −4.36 Pg C differences, respectively. If the timescale of RS data is constant, RSG estimated by the first‐order exponential (93.2 Pg) was greater than the Random Forest (78.76 Pg) or second‐order exponential (76.18 Pg) estimates. These results highlight the importance of variation at subannual timescales for upscaling to RSG. The results indicated RSG is lower than in recent papers and the current benchmark for land models (98 Pg C year−1), and thus may change the predicted rates of terrestrial carbon turnover and the carbon to climate feedback as global temperatures rise.
Quantifying different sources of variability in global soil respiration estimates helped to constrain soil respiration projections. We developed global soil respiration models using Random Forest and exponential models and used different timescales (daily, monthly, and annual) of soil respiration and climate data to predict global soil respiration. We found global soil respiration is closer to 70‐81 Pg C yr‐1. These results highlight the need for understanding and capturing the relevant timescale for upscaling fine‐scale temporal measures to broad‐scale global flux estimates. Assuming a lower global soil respiration could substantially change the carbon‐climate feedback under global warming.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Therapeutic mRNAs and vaccines are being developed for a broad range of human diseases, including COVID-19. However, their optimization is hindered by mRNA instability and inefficient protein ...expression. Here, we describe design principles that overcome these barriers. We develop an RNA sequencing-based platform called PERSIST-seq to systematically delineate in-cell mRNA stability, ribosome load, as well as in-solution stability of a library of diverse mRNAs. We find that, surprisingly, in-cell stability is a greater driver of protein output than high ribosome load. We further introduce a method called In-line-seq, applied to thousands of diverse RNAs, that reveals sequence and structure-based rules for mitigating hydrolytic degradation. Our findings show that highly structured "superfolder" mRNAs can be designed to improve both stability and expression with further enhancement through pseudouridine nucleoside modification. Together, our study demonstrates simultaneous improvement of mRNA stability and protein expression and provides a computational-experimental platform for the enhancement of mRNA medicines.
The inclusion of winter annual cereal cover crops (WCC) in grain crop rotations is a common management practice promoted to protect soil resources and enhance water quality. However, the effects of ...long-term incorporation of WCC into no-till grain crop rotations on soil physical properties are not well established. We evaluated the long-term effects of WCC on soil physical properties after 13 yr of use at three locations in Maryland, USA. Continuous maize (Zea mays L.) was the summer grain crop. In the control treatment, maize was followed by winter fallow and in the WCC treatment, cereal rye (Secale cereal L.) was planted as a WCC in the off-season. We examined aggregate stability, total and labile organic matter, soil bulk density (BD), air permeability (AP), water infiltration rate (WIR), and hydraulic conductivity (HC), during the growing and off-season. Aggregate stability increased under the WCC treatment but there were no increases in total organic matter and labile organic matter. Only during the winter sampling season at the two Coastal Plain locations, soils under WCC displayed improved soil physical properties in comparison with the same soils under winter fallow. The heavier-textured soils at the Piedmont location exhibited no consistent differences attributable to WCC.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Zeolitic imidazolate frameworks (ZIFs) have been widely investigated for numerous applications including energy storage, heterogeneous catalysis, and greenhouse gas adsorption. Much of the early work ...has focused on the bulk properties of microcrystalline ZIFs. Herein, we focus on identifying the nature of the surface of ZIF-8 by studying a supported ZIF-8 nanoparticle film using surface characterization techniques. We have experimentally identified the presence of a zinc-rich surface terminated by carbonates and water/hydroxyl groups (in addition to the expected methylimidazole terminations) using X-ray photoelectron spectroscopy (XPS). The thermal stability of ZIF-8 thin films was also investigated using scanning electron microscopy (SEM) and temperature-programmed reaction spectroscopy (TPRS). We determined the onset of decomposition of ZIF-8 thin films to be approximately 630 K using TPRS in an ultrahigh vacuum (UHV) environment. This work presents the first characterization steps needed to study the evolution of ZIF surfaces in situ using surface characterization techniques. Such techniques are capable of determining reaction products and tracking intermediates and surface evolution in gas adsorption/reaction studies of thin films.
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Altering root morphology of rice (Oryza sativa L.) cultivars could improve yields in drought-prone upland ecosystems. Marker-assisted backcross breeding was used to introgress four QTLs for root ...traits into an upland rice cultivar. The QTLs had previously been identified under experimental conditions in a different genetic background. The introgressed lines and the recurrent parent were grown for 6 years by resource-poor farmers in upland sites in Eastern India and yields recorded. In combination the QTLs significantly increased yield by 1 t ha⁻¹ under relatively favourable field conditions. In less favourable trials, the QTL effects were not detected due to greater heterogeneity in soil–water availability in very low yielding environments and consequent yield variability. Root studies under controlled conditions showed that lines with the introgressions had longer roots throughout tillering than the recurrent parent (14 cm longer 2 weeks after sowing). Therefore, both improved roots and increased yield can be attributed to the introgression of QTLs. This is the first demonstration that marker-assisted backcross breeding (MABC) to introgress multiple root QTLs identified under controlled conditions is an effective strategy to improve farmers’ yields of upland rice. The strategy was used to breed a novel upland rice cultivar that has been released in India as Birsa Vikas Dhan 111.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
9.
Ecological homogenization of urban USA Groffman, Peter M; Cavender-Bares, Jeannine; Bettez, Neil D ...
Frontiers in ecology and the environment,
February 2014, Volume:
12, Issue:
1
Journal Article
Peer reviewed
Open access
A visually apparent but scientifically untested outcome of land-use change is homogenization across urban areas, where neighborhoods in different parts of the country have similar patterns of roads, ...residential lots, commercial areas, and aquatic features. We hypothesize that this homogenization extends to ecological structure and also to ecosystem functions such as carbon dynamics and microclimate, with continental-scale implications. Further, we suggest that understanding urban homogenization will provide the basis for understanding the impacts of urban land-use change from local to continental scales. Here, we show how multi-scale, multi-disciplinary datasets from six metropolitan areas that cover the major climatic regions of the US (Phoenix, AZ; Miami, FL; Baltimore, MD; Boston, MA; Minneapolis-St Paul, MN; and Los Angeles, CA) can be used to determine how household and neighborhood characteristics correlate with land-management practices, land-cover composition, and landscape structure and ecosystem functions at local, regional, and continental scales.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
A marker-assisted back-crossing (MABC) breeding programme was conducted to improve the root morphological traits, and thereby drought tolerance, of the Indian upland rice variety, Kalinga III. This ...variety, the recurrent parent in the MABC, had not previously been used for quantitative trait locus (QTL) mapping. The donor parent was Azucena, an upland japonica variety from Philippines. Five segments on different chromosomes were targeted for introgression; four segments carried QTLs for improved root morphological traits (root length and thickness) and the fifth carried a recessive QTL for aroma. Some selection was made at non-target regions for recurrent parent alleles. We describe the selection made in three backcross (BC) generations and two further crosses between BC₃ lines to pyramid (stack) all five target segments. Pyramids with four root QTLs were obtained in eight generations, completed in 6 years using 3,000 marker assays in a total of 323 lines. Twenty-two near-isogenic lines (NILs) were evaluated for root traits in five field experiments in Bangalore, India. The target segment on chromosome 9 (RM242-RM201) significantly increased root length under both irrigated and drought stress treatments, confirming that this root length QTL from Azucena functions in a novel genetic background. No significant effects on root length were found at the other four targets. Azucena alleles at the locus RM248 (below the target root QTL on chromosome 7) delayed flowering. Selection for the recurrent parent allele at this locus produced early-flowering NILs that were suited for upland environments in eastern India.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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