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Predicting how forest carbon cycling will change in response to climate change and management depends on the collective knowledge from measurements across environmental gradients, ecosystem manipulations of global change factors, and mathematical models. Formally integrating these sources of knowledge through data assimilation, or model–data fusion, allows the use of past observations to constrain model parameters and estimate prediction uncertainty. Data assimilation (DA) focused on the regional scale has the opportunity to integrate data from both environmental gradients and experimental studies to constrain model parameters. Here, we introduce a hierarchical Bayesian DA approach (Data Assimilation to Predict Productivity for Ecosystems and Regions, DAPPER) that uses observations of carbon stocks, carbon fluxes, water fluxes, and vegetation dynamics from loblolly pine plantation ecosystems across the southeastern US to constrain parameters in a modified version of the Physiological Principles Predicting Growth (3-PG) forest growth model. The observations included major experiments that manipulated atmospheric carbon dioxide (CO2) concentration, water, and nutrients, along with nonexperimental surveys that spanned environmental gradients across an 8.6  ×  105 km2 region. We optimized regionally representative posterior distributions for model parameters, which dependably predicted data from plots withheld from the data assimilation. While the mean bias in predictions of nutrient fertilization experiments, irrigation experiments, and CO2 enrichment experiments was low, future work needs to focus modifications to model structures that decrease the bias in predictions of drought experiments. Predictions of how growth responded to elevated CO2 strongly depended on whether ecosystem experiments were assimilated and whether the assimilated field plots in the CO2 study were allowed to have different mortality parameters than the other field plots in the region. We present predictions of stem biomass productivity under elevated CO2, decreased precipitation, and increased nutrient availability that include estimates of uncertainty for the southeastern US. Overall, we (1) demonstrated how three decades of research in southeastern US planted pine forests can be used to develop DA techniques that use multiple locations, multiple data streams, and multiple ecosystem experiment types to optimize parameters and (2) developed a tool for the development of future predictions of forest productivity for natural resource managers that leverage a rich dataset of integrated ecosystem observations across a region.

The number of meiotic crossovers (COs) is tightly regulated within a narrow range, despite a large excess of molecular precursors. The factors that limit COs remain largely unknown. Here, using a genetic screen in Arabidopsis thaliana, we identified the highly conserved FANCM helicase, which is required for genome stability in humans and yeasts, as a major factor limiting meiotic CO formation. The fancm mutant has a threefold-increased CO frequency as compared to the wild type. These extra COs arise not from the pathway that accounts for most of the COs in wild type, but from an alternate, normally minor pathway. Thus, FANCM is a key factor imposing an upper limit on the number of meiotic COs, and its manipulation holds much promise for plant breeding.

Transgenic pigs have become an attractive research model in the field of translational research, regenerative medicine, and stem cell therapy due to their anatomic, genetic and physiological similarities with humans. The development of fluorescent proteins as molecular tags has allowed investigators to track cell migration and engraftment levels after transplantation. Here we describe the development of two transgenic pig models via SCNT expressing a fusion protein composed of eGFP and porcine Histone 2B (pH2B). This fusion protein is targeted to the nucleosomes resulting a nuclear/chromatin eGFP signal. The first model (I) was generated via random insertion of pH2B-eGFP driven by the CAG promoter (chicken beta actin promoter and rabbit Globin poly A; pCAG-pH2B-eGFP) and protected by human interferon-beta matrix attachment regions (MARs). Despite the consistent, high, and ubiquitous expression of the fusion protein pH2B-eGFP in all tissues analyzed, two independently generated Model I transgenic lines developed neurodegenerative symptoms including Wallerian degeneration between 3-5 months of age, requiring euthanasia. A second transgenic model (II) was developed via CRISPR-Cas9 mediated homology-directed repair (HDR) of IRES-pH2B-eGFP into the endogenous beta-actin (ACTB) locus. Model II transgenic animals showed ubiquitous expression of pH2B-eGFP on all tissues analyzed. Unlike the pCAG-pH2B-eGFP/MAR line, all Model II animals were healthy and multiple pregnancies have been established with progeny showing the expected Mendelian ratio for the transmission of the pH2B-eGFP. Expression of pH2B-eGFP was used to examine the timing of the maternal to zygotic transition after IVF, and to examine chromosome segregation of SCNT embryos. To our knowledge this is the first viable transgenic pig model with chromatin-associated eGFP allowing both cell tracking and the study of chromatin dynamics in a large animal model.

Mountaintop removal coal mining is the predominant form of surface mining in the Appalachian Region, USA and leads to elevated levels of chemical constituents in streams draining mined watersheds. This data set contains measurements of water chemistry in the mountaintop mined landscape of Central Appalachia, USA. These data were collected to determine the accumulation and transport of mercury (Hg) and selenium (Se) across environmental compartments in mountaintop mining-impacted waters as well as the impact of mountaintop mining on the aquatic-terrestrial subsidy. Samples were collected in summer 2017 and spring/summer 2018. Data predominantly include Se, THg, and methylmercury (MeHg) in the following environmental compartments at sites impacted and unimpacted by mountaintop removal coal mining: water, sediment, biofilm, larval cranefly, adult aquatic insects and spiders. Additional water parameters that have been found to vary across a gradient of mountaintop mining impact (total organic carbon [TOC], total nitrogen [TN], sulfate [SO4 ], nitrate [NO3 ], chloride [Cl], pH, sodium [Na], potassium [K], magnesium [Mg], calcium [Ca], manganese [Mn], sulfur [S], specific conductance) were also measured. The majority of sites represented are headwater streams, although some settling ponds below valley fills are included. This data set also includes taxonomic characterization of the adult aquatic insect community as well This article is protected by copyright. All rights reserved as measurements of spider density at a subset of sites. There are no copyright restrictions; please cite this data paper when the data are used in publications.

Hemlock woolly adelgid (HWA) is an exotic insect pest causing severe decimation of native hemlock trees. Extensive research has been conducted on the ecological impacts of HWA, but the exact physiological mechanisms that cause mortality are not known. Water relations, anatomy and gas exchange measurements were assessed on healthy and infested eastern (Tsuga canadensis) and Carolina (Tsuga caroliniana) hemlock trees. These data were then used in a mechanistic model to test whether the physiological responses to HWA infestation were sufficiently significant to induce changes in whole-plant water use and carbon uptake. The results indicated coordinated responses of functional traits governing water relations in infested relative to healthy trees. In response to HWA, leaf water potential, carbon isotope ratios, plant hydraulic properties and stomatal conductance were affected, inducing a reduction in tree water use by >40% and gross primary productivity by 25%. Anatomical changes also appeared, including the activation of traumatic cells. HWA infestation had a direct effect on plant water relations. Despite some leaf compensatory mechanisms, such as an increase in leaf hydraulic conductance and nitrogen content, tree water use and carbon assimilation were diminished significantly in infested trees, which could contribute to tree mortality.

UNLABELLED: ABSTRACT: BACKGROUND: Histiocytic malignancies in both humans and dogs are rare and poorly understood. While canine histiocytic sarcoma (HS) is uncommon in the general domestic dog population, there is a strikingly high incidence in a subset of breeds, suggesting heritable predisposition. Molecular cytogenetic profiling of canine HS in these breeds would serve to reveal recurrent DNA copy number aberrations (CNAs) that are breed and/or tumor associated, as well as defining those shared with human HS. This process would identify evolutionarily conserved cytogenetic changes to highlight regions of particular importance to HS biology. METHODS: Using genome wide array comparative genomic hybridization we assessed CNAs in 104 spontaneously occurring HS from two breeds of dog exhibiting a particularly elevated incidence of this tumor, the Bernese Mountain Dog and Flat-Coated Retriever. Recurrent CNAs were evaluated further by multicolor fluorescence in situ hybridization and loss of heterozygosity analyses. Statistical analyses were performed to identify CNAs associated with tumor location and breed. RESULTS: Almost all recurrent CNAs identified in this study were shared between the two breeds, suggesting that they are associated more with the cancer phenotype than with breed. A subset of recurrent genomic imbalances suggested involvement of known cancer associated genes in HS pathogenesis, including deletions of the tumor suppressor genes CDKN2A/B, RB1 and PTEN. A small number of aberrations were unique to each breed, implying that they may contribute to the major differences in tumor location evident in these two breeds. The most highly recurrent canine CNAs revealed in this study are evolutionarily conserved with those reported in human histiocytic proliferations, suggesting that human and dog HS share a conserved pathogenesis. CONCLUSIONS: The breed associated clinical features and DNA copy number aberrations exhibited by canine HS offer a valuable model for the human counterpart, providing additional evidence towards elucidation of the pathophysiological and genetic mechanisms associated with histiocytic malignancies. Extrapolation of data derived from canine histiocytic disorders to human histiocytic proliferation may help to further our understanding of the propagation and cancerization of histiocytic cells, contributing to development of new and effective therapeutic modalities for both species.

The geographical distribution of many crop species spans far beyond their centers of origin and the native range of their wild ancestors. Maize is exemplary of this adaptability, which has contributed to its agricultural... Understanding the evolutionary capacity of populations to adapt to novel environments is one of the major pursuits in genetics. Moreover, for plant breeding, maladaptation is the foremost barrier to capitalizing on intraspecific variation in order to develop new breeds for future climate scenarios in agriculture. Using a unique study design, we simultaneously dissected the population and quantitative genomic basis of short-term evolution in a tropical landrace of maize that was translocated to a temperate environment and phenotypically selected for adaptation in flowering time phenology. Underlying 10 generations of directional selection, which resulted in a 26-day mean decrease in female-flowering time, 60% of the heritable variation mapped to 14% of the genome, where, overall, alleles shifted in frequency beyond the boundaries of genetic drift in the expected direction given their flowering time effects. However, clustering these non-neutral alleles based on their profiles of frequency change revealed transient shifts underpinning a transition in genotype–phenotype relationships across generations. This was distinguished by initial reductions in the frequencies of few relatively large positive effect alleles and subsequent enrichment of many rare negative effect alleles, some of which appear to represent allelic series. With these genomic shifts, the population reached an adapted state while retaining 99% of the standing molecular marker variation in the founding population. Robust selection and association mapping tests highlighted several key genes driving the phenotypic response to selection. Our results reveal the evolutionary dynamics of a finite polygenic architecture conditioning a capacity for rapid environmental adaptation in maize.

Nutrient enrichment is a major global change component that often disrupts the relationship between aboveground biodiversity and ecosystem functions by promoting species dominance, altering trophic interactions, and reducing ecosystem stability. Emerging evidence indicates that nutrient enrichment also reduces soil biodiversity and weakens the relationship between belowground biodiversity and ecosystem functions, but the underlying mechanisms remain largely unclear. Here, we explore the effects of nutrient enrichment on soil properties, soil biodiversity, and multiple ecosystem functions through a 13-year field experiment. We show that soil acidification induced by nutrient enrichment, rather than changes in mineral nutrient and carbon (C) availability, is the primary factor negatively affecting the relationship between soil diversity and ecosystem multifunctionality. Nitrogen and phosphorus additions significantly reduce soil pH, diversity of bacteria, fungi and nematodes, as well as an array of ecosystem functions related to C and nutrient cycling. Effects of nutrient enrichment on microbial diversity also have negative consequences at higher trophic levels on the diversity of microbivorous nematodes. These results indicate that nutrient-induced acidification can cascade up its impacts along the soil food webs and influence ecosystem functioning, providing novel insight into the mechanisms through which nutrient enrichment influences soil community and ecosystem properties.Nutrient enrichment is a major global change component. Here the authors show that soil acidification induced by nutrient enrichment, rather than changes in mineral nutrient and carbon availability, modulates soil biodiversity-function relationships

Short-rotation woody crops (SRWC) grown for bioenergy production are considered a more sustainable feedstock than food crops such as corn and soybean. However, to be sustainable SRWC should be deployed on land not suitable for agriculture (e.g., marginal lands). Here we quantified productivity and energy yield of four SRWC candidate species grown at different planting densities (1250, 2500, 5000, and 10,000 trees ha −1 ) under a low-input regime on a marginal site in the Piedmont of North Carolina and responses to reduced water availability. By the end of the first growing season, 75 to 100% tree mortality occurred in all tested species ( Liquidambar styraciflua , Liriodendron tulipifera , and Populus nigra ) except American sycamore ( Platanus occidentalis ), the productivity of which was positively affected by planting density, but unaffected by the throughfall reduction treatment. After 4 years of growth, the 10,000 trees ha −1 sycamore treatment produced smaller individual trees but the largest amount of total tree biomass (23.2 ± 0.9 Mg ha −1 ), which, although greater, was not significantly different from the 5000 trees ha −1 treatment (19.6 ± 1.5 Mg ha −1 ). The two highest planting density treatments had similar aboveground net primary productivity (ANPP wood ) of 7.2 Mg ha −1  year −1 . By contrast, in the 1250 and 2500 trees ha −1 treatments, ANPP wood was significantly lower, ranging from 3.4 to 5.4 Mg ha −1  year −1 . Stem wood made up a majority of the biomass produced regardless of spacing density, but live branch biomass weight increased with decreasing planting density, comprising up to 31% of total aboveground biomass in the 1250 trees ha −1 treatment. Gross energy yield reached 140 GJ ha −1  year −1 for the 10,000 trees ha −1 treatment. Given this productivity, American sycamore could potentially yield 2400 (±380) L ethanol ha −1  year −1 over the first 4-year rotation. This study demonstrated that of the four species tested, only American sycamore grown on marginal land under low inputs (no fertilizer, no irrigation, limited weed control) had the capacity to successfully establish and maintain SRWC productivity, which might compare favorably with other fast-growing tree and grass species that typically require high inputs.

Auxin is a key regulator of plant growth and development. Within the root tip, auxin distribution plays a crucial role specifying developmental zones and coordinating tropic responses. Determining how the organ-scale auxin pattern is regulated at the cellular scale is essential to understanding how these processes are controlled. In this study, we developed an auxin transport model based on actual root cell geometries and carrier subcellular localizations. We tested model predictions using the DII-VENUS auxin sensor in conjunction with state-of-the-art segmentation tools. Our study revealed that auxin efflux carriers alone cannot create the pattern of auxin distribution at the root tip and that AUX1/LAX influx carriers are also required. We observed that AUX1 in lateral root cap (LRC) and elongating epidermal cells greatly enhance auxin's shootward flux, with this flux being predominantly through the LRC, entering the epidermal cells only as they enter the elongation zone. We conclude that the nonpolar AUX1/LAX influx carriers control which tissues have high auxin levels, whereas the polar PIN carriers control the direction of auxin transport within these tissues.