CONFINED ANIMAL PRODUCTION AND MANURE NUTRIENTS

Using data from the Census of Agriculture on animal inventory and sales, we estimate manure nutrient production on farms with confined livestock. Using reported on-farm production of crops on these same farms, we estimate the nutrient uptake for major field crops and pastureland. This enables us to examine the balance between manure nutrient production and nutrient need measured by crop uptake at a farm level. Examination at alternative spatial scales, shows that 75 percent of counties in the U.S. have farms that produce more manure nutrients than can be assimilated on the farm of production (excess nitrogen).The vast majority of the counties that produce excess nitrogen have adequate land in the county to spread the manure at agronomic rates. Thus, proposed policies that focus on land application have the potential to limit manure nutrient movement to waterways in most areas, if properly managed. However, moving manure to crop farms that formerly had not used manure will increase costs. There were about 5 percent of counties where the manure nitrogen production levels from confined animal production exceeded half the nitrogen assimilative capacity of all the cropland and pastureland in the county. These areas have the greatest need for mechanisms to encourage off-farm solutions to utilize manure as a feedstock for commercial enterprises or central processing.Livestock Production/Industries,

CONFINED ANIMAL PRODUCTION AND MANURE NUTRIENTS

Census of agriculture data were used to estimate manure nutrient production and the capacity of cropland and pastureland to assimilate nutrients. Most farms (78 percent for nitrogen and 69 percent for phosphorus) have adequate land on which it is physically feasible to apply the manure produced onfarm at agronomic rates. (The costs of applying manure at these rates have not been assessed). Even so, manure that is produced on operations that cannot fully apply it to their own land at agronomic rates accounts for 60 percent of the Nation's manure nitrogen and 70 percent of the manure phosphorus. In these cases, most counties with farms that produce "excess" nutrients have adequate crop acres not associated with animal operations, but within the county, on which it is feasible to spread the manure at agronomic rates. However, barriers to moving manure to other farms need to be studied. About 20 percent of the Nation's onfarm excess manure nitrogen is produced in counties that have insufficient cropland for its application at agronomic rates (23 percent for phosphorus). For areas without adequate land, alternatives to local land application-such as energy production-will need to be developed.Manure, nutrients, manure nutrients, animal waste, confined livestock, confined animal feeding operation, CAFO, feedlot beef, dairy cows, swine, poultry, animal unit, manure nitrogen, manure phosphorus, water quality, Livestock Production/Industries,

Likelihood Ratio Test process for Quantitative Trait Locus detection

International audienceWe consider the likelihood ratio test (LRT) process related to the test of the absence of QTL (a QTL denotes a quantitative trait locus, i.e. a gene with quantitative effect on a trait) on the interval [0,T] representing a chromosome. The observation is the trait and the composition of the genome at some locations called ''markers''. We give the asymptotic distribution of this LRT process under the null hypothesis that there is no QTL on [0,T] and under local alternatives with a QTL at t* on [0,T]. We show that the LRT is asymptotically the square of some Gaussian process. We give a description of this process as an '' non-linear interpolated and normalized process ''. We propose a simple method to calculate the maximum of the LRT process using only statistics on markers and their ratio. This gives a new method to calculate thresholds for QTL detection

THEO Concept Mission: Testing the Habitability of Enceladus's Ocean

Saturn's moon Enceladus offers a unique opportunity in the search for life and habitable environments beyond Earth, a key theme of the National Research Council's 2013-2022 Decadal Survey. A plume of water vapor and ice spews from Enceladus's south polar region. Cassini data suggest that this plume, sourced by a liquid reservoir beneath the moon's icy crust, contain organics, salts, and water-rock interaction derivatives. Thus, the ingredients for life as we know it-- liquid water, chemistry, and energy sources-- are available in Enceladus's subsurface ocean. We have only to sample the plumes to investigate this hidden ocean environment. We present a New Frontiers class, solar-powered Enceladus orbiter that would take advantage of this opportunity, Testing the Habitability of Enceladus's Ocean (THEO). Developed by the 2015 Jet Propulsion Laboratory Planetary Science Summer School student participants under the guidance of TeamX, this mission concept includes remote sensing and in situ analyses with a mass spectrometer, a sub-mm radiometer-spectrometer, a camera, and two magnetometers. These instruments were selected to address four key questions for ascertaining the habitability of Enceladus's ocean within the context of the moon's geological activity: (1) How are the plumes and ocean connected? (2) Are the abiotic conditions of the ocean suitable for habitability? (3) How stable is the ocean environment? (4) Is there evidence of biological processes? By taking advantage of the opportunity Enceladus's plumes offer, THEO represents a viable, solar-powered option for exploring a potentially habitable ocean world of the outer solar system.Comment: JPL Summer School 201

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes—such as transcriptional profiles—at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS). Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions. We posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation. By decomposing many high content measurements into the effects of perturbations, their interactions, and diverse cell metadata, Perturb-seq dramatically increases the scope of pooled genomic assays. Keywords: single-cell RNA-seq; pooled screen; CRISPR; epistasis; genetic interaction

RNF43 is frequently mutated in colorectal and endometrial cancers

We report somatic mutations of RNF43 in over 18% of colorectal adenocarcinomas and endometrial carcinomas. RNF43 encodes an E3 ubiquitin ligase that negatively regulates Wnt signaling. Truncating mutations of RNF43 are more prevalent in microsatellite-unstable tumors and show mutual exclusivity with inactivating APC mutations in colorectal adenocarcinomas. These results indicate that RNF43 is one of the most commonly mutated genes in colorectal and endometrial cancers.National Human Genome Research Institute (U.S.) (Grant U54HG003067

Energy Flow in the Hadronic Final State of Diffractive and Non-Diffractive Deep-Inelastic Scattering at HERA

An investigation of the hadronic final state in diffractive and non--diffractive deep--inelastic electron--proton scattering at HERA is presented, where diffractive data are selected experimentally by demanding a large gap in pseudo --rapidity around the proton remnant direction. The transverse energy flow in the hadronic final state is evaluated using a set of estimators which quantify topological properties. Using available Monte Carlo QCD calculations, it is demonstrated that the final state in diffractive DIS exhibits the features expected if the interaction is interpreted as the scattering of an electron off a current quark with associated effects of perturbative QCD. A model in which deep--inelastic diffraction is taken to be the exchange of a pomeron with partonic structure is found to reproduce the measurements well. Models for deep--inelastic $ep$ scattering, in which a sizeable diffractive contribution is present because of non--perturbative effects in the production of the hadronic final state, reproduce the general tendencies of the data but in all give a worse description.Comment: 22 pages, latex, 6 Figures appended as uuencoded fil

SNP Genotyping Defines Complex Gene-Flow Boundaries Among African Malaria Vector Mosquitoes

Mosquitoes in the Anopheles gambiae complex show rapid ecological and behavioral diversification, traits that promote malaria transmission and complicate vector control efforts. A high-density, genome-wide mosquito SNP-genotyping array allowed mapping of genomic differentiation between populations and species that exhibit varying levels of reproductive isolation. Regions near centromeres or within polymorphic inversions exhibited the greatest genetic divergence, but divergence was also observed elsewhere in the genomes. Signals of natural selection within populations were overrepresented among genomic regions that are differentiated between populations, implying that differentiation is often driven by population-specific selective events. Complex genomic differentiation among speciating vector mosquito populations implies that tools for genome-wide monitoring of population structure will prove useful for the advancement of malaria eradication

Mutational heterogeneity in cancer and the search for new cancer genes

Major international projects are now underway aimed at creating a comprehensive catalog of all genes responsible for the initiation and progression of cancer. These studies involve sequencing of matched tumor–normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here, we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false positive findings that overshadow true driver events. Here, we show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumor-normal pairs and discover extraordinary variation in (i) mutation frequency and spectrum within cancer types, which shed light on mutational processes and disease etiology, and (ii) mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and allow true cancer genes to rise to attention

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes