Mapping Weekly Rangeland Vegetation Productivity Using MODIS Algorithms

The great spatial extent of rangelands combined with recent emphasis on rangeland health has prompted a need for more efficient and cost effective management tools. The Moderate Resolution Imaging Spectroradiometer (MODIS) sensor of the Earth Observing System (EOS) will offer improved and more timely monitoring of rangeland vegetation, and, unlike any previous satellite sensor, the publicly available MODIS data stream will include estimates of rangeland productivity. These estimations of rangeland productivity can be used regionally for measuring biomass production and will be available every eight-days, with global coverage at 1- km^ resolution. MODIS derived estimates of rangeland productivity combine remote sensing information with daily meteorological data as inputs to a mathematical model of photosynthetic conversion of solar radiation into plant carbohydrates. Vegetation productivity is .a measure of rangeland vegetation vigor and growth capacity, which are important components of rangeland management and health assessment. Using MODIS data, it will be possible to characterize rangeland vegetation seasonality, estimate herbage quantity and, monitor the rates and trends of change in primary production. Consistent, objective and frequent productivity estimates will be available for even the most inaccessible rangelands. Potential applications of weekly and annual productivity estimates are demonstrated on the Shoshone BLM Administrative District and a larger portion of the Interior Northwestern United States. Productivity estimates were derived using Advanced Very High-Resolution Radiometer data as a surrogate for the MODIS data stream. Shrub and grassland vegetation seasonality for 1991 was characterized. Herbage quantity was estimated from the 1993 shrub and grassland regional net primary production. A 5-year average productivity from 1990 - 1994 and departures from that average were calculated for the years 1991 and 1993. The measures of departure indicated that 1991 was regionally less productive and 1993 more productive than the five year average. Collaboration between rangeland scientists and managers is necessary to realize the potential for EOS-derived vegetation productivity as a management tool. Future research will include field calibration of the productivity algorithms and exploration of new techniques for using EOS-derived productivity measures for rangeland management. Measures of rangeland productivity could become part of an integrated rangeland system analysis. This may permit differentiation between anthropogenic, biotic, and abiotic factors as the primary cause of declining productivity. Other research may include customization of biome properties for selected regions

Estimating climate change effects on net primary production of rangelands in the United States

The potential effects of climate change on net primary productivity (NPP) of U.S. rangelands were evaluated using estimated climate regimes from the A1B, A2 and B2 global change scenarios imposed on the biogeochemical cycling model, Biome-BGC from 2001 to 2100. Temperature, precipitation, vapor pressure deficit, day length, solar radiation, CO2 enrichment and nitrogen deposition were evaluated as drivers of NPP. Across all three scenarios, rangeland NPP increased by 0.26 % year−1 (7 kg C ha−1 year−1) but increases were not apparent until after 2030 and significant regional variation in NPP was revealed. The Desert Southwest and Southwest assessment regions exhibited declines in NPP of about 7 % by 2100, while the Northern and Southern Great Plains, Interior West and Eastern Prairies all experienced increases over 25 %. Grasslands dominated by warm season (C4 photosynthetic pathway) species showed the greatest response to temperature while cool season (C3 photosynthetic pathway) dominated regions responded most strongly to CO2 enrichment. Modeled NPP responses compared favorably with experimental results from CO2 manipulation experiments and to NPP estimates from the Moderate Resolution Imaging Spectroradiometer (MODIS). Collectively, these results indicate significant and asymmetric changes in NPP for U.S. rangelands may be expected

Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes

Human cytomegalovirus (HCMV) infects most of the population worldwide, persisting throughout the host's life in a latent state with periodic episodes of reactivation. While typically asymptomatic, HCMV can cause fatal disease among congenitally infected infants and immunocompromised patients. These clinical issues are compounded by the emergence of antiviral resistance and the absence of an effective vaccine, the development of which is likely complicated by the numerous immune evasins encoded by HCMV to counter the host's adaptive immune responses, a feature that facilitates frequent super-infections. Understanding the evolutionary dynamics of HCMV is essential for the development of effective new drugs and vaccines. By comparing viral genomes from uncultivated or low-passaged clinical samples of diverse origins, we observe evidence of frequent homologous recombination events, both recent and ancient, and no structure of HCMV genetic diversity at the whole-genome scale. Analysis of individual gene-scale loci reveals a striking dichotomy: while most of the genome is highly conserved, recombines essentially freely and has evolved under purifying selection, 21 genes display extreme diversity, structured into distinct genotypes that do not recombine with each other. Most of these hyper-variable genes encode glycoproteins involved in cell entry or escape of host immunity. Evidence that half of them have diverged through episodes of intense positive selection suggests that rapid evolution of hyper-variable loci is likely driven by interactions with host immunity. It appears that this process is enabled by recombination unlinking hyper-variable loci from strongly constrained neighboring sites. It is conceivable that viral mechanisms facilitating super-infection have evolved to promote recombination between diverged genotypes, allowing the virus to continuously diversify at key loci to escape immune detection, while maintaining a genome optimally adapted to its asymptomatic infectious lifecycle

Gene Network Disruptions and Neurogenesis Defects in the Adult Ts1Cje Mouse Model of Down Syndrome

Background: Down syndrome (DS) individuals suffer mental retardation with further cognitive decline and early onset Alzheimer's disease. Methodology/Principal Findings: To understand how trisomy 21 causes these neurological abnormalities we investigated changes in gene expression networks combined with a systematic cell lineage analysis of adult neurogenesis using the Ts1Cje mouse model of DS. We demonstrated down regulation of a number of key genes involved in proliferation and cell cycle progression including Mcm7, Brca2, Prim1, Cenpo and Aurka in trisomic neurospheres. We found that trisomy did not affect the number of adult neural stem cells but resulted in reduced numbers of neural progenitors and neuroblasts. Analysis of differentiating adult Ts1Cje neural progenitors showed a severe reduction in numbers of neurons produced with a tendency for less elaborate neurites, whilst the numbers of astrocytes was increased. Conclusions/Significance: We have shown that trisomy affects a number of elements of adult neurogenesis likely to result in a progressive pathogenesis and consequently providing the potential for the development of therapies to slow progression of, or even ameliorate the neuronal deficits suffered by DS individuals.Chelsee A. Hewitt, King-Hwa Ling, Tobias D. Merson, Ken M. Simpson, Matthew E. Ritchie, Sarah L. King, Melanie A. Pritchard, Gordon K. Smyth, Tim Thomas, Hamish S. Scott and Anne K. Vos

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data