A method of providing meaningful, self-descripting metadata to REST return JSON data

A method of providing meaningful, self-descripting metadata to REST return JSON data This document describes a method where REST data can be wrapped in a well-defined metadata format which enables convenient self-documenting return values and also enables programmatically discovering and utilizing new REST service entry points

Detection QTLs for Grain Quality Traits and Yield in Two BILs Population of Rice

. Rice, the second most important crop after wheat, has been cultivated in Iran. Marketing conditions and quality traits after yield are the most important factors to adopt of new varieties. Therefore in recent years Iranian scientists decided to training on breeding improved high yield varieties with good grain quality.Quantitative trait loci (QTLs) yield and grain quality traits of rice (Oryza sativa L.) with additive, epistatic, and QTL × environment (QE) interaction effects were studied using a mixed-model-based composite interval mapping (MCIM) method and two populations of Back cross inbred lines (BILs) with a common maternal parent.In each of the populations two or three main effects of QTLs were detected for yield, amylose content, gel consistency and gelatinization temperature. Some identified QTL clusters suggested pleiotropic effects could control these traits. The phenotypic variation of AAE and AA QTLs effects were smaller than main QTLs. We conclude that the major genes and some minor and modifier genes controlled rice grain quality and yield components. The information obtained in this study have used to manipulating the QTLs for these traits by molecular marker-assisted selection and the best lines with excellent quality and high yield recognize

MIF-induced stromal PKCβ/IL8 is essential in human acute myeloid leukemia

Acute myeloid leukemia (AML) cells exhibit a high level of spontaneous apoptosis when cultured in vitro but have a prolonged survival time in vivo, indicating that tissue microenvironment plays a critical role in promoting AML cell survival. In vitro studies have shown that bone marrow-mesenchymal stromal cells (BM-MSC) protect AML blasts from spontaneous and chemotherapy-induced apoptosis. Here we report a novel interaction between AML blasts and BM-MSC which benefits AML proliferation and survival. We initially examined the cytokine profile in cultured human AML compared to AML cultured with BMMSC and found that macrophage-migration inhibitory factor (MIF) was highly expressed by primary AML, and that interleukin-8 (IL-8) was increased in AML/BM-MSC co-cultures. Recombinant MIF increased IL-8 expression in BM-MSC via its receptor CD74. Moreover, the MIF inhibitor ISO-1 inhibited AML-induced IL-8 expression by BM-MSC as well as BMMSC- induced AML survival. Protein kinase C β (PKCβ) regulated MIF-induced IL-8 in BMMSC. Finally, targeted IL-8 shRNA inhibited BM-MSC-induced AML survival. These results describe a novel, bidirectional, pro-survival mechanism between AML blasts and BM-MSC. Furthermore, they provide biologic rationale for therapeutic strategies in AML targeting the microenvironment, specifically MIF and IL-8

Acute myeloid leukemia induces pro-tumoral p16INK4a driven senescence in the bone marrow microenvironment

Acute myeloid leukemia (AML) is an age-related disease that is highly dependent on the bone marrow (BM) microenvironment. With increasing age, tissues accumulate senescent cells, characterized by an irreversible arrest of cell proliferation and the secretion of a set of proinflammatory cytokines, chemokines, and growth factors, collectively known as the senescence-associated secretory phenotype (SASP). Here, we report that AML blasts induce a senescent phenotype in the stromal cells within the BM microenvironment and that the BM stromal cell senescence is driven by p16INK4a expression. The p16INK4a-expressing senescent stromal cells then feed back to promote AML blast survival and proliferation via the SASP. Importantly, selective elimination of p16INK4a 1 senescent BM stromal cells in vivo improved the survival of mice with leukemia. Next, we find that the leukemia-driven senescent tumor microenvironment is caused by AML-induced NOX2-derived superoxide. Finally, using the p16-3MR mouse model, we show that by targeting NOX2 we reduced BM stromal cell senescence and consequently reduced AML proliferation. Together, these data identify leukemia-generated NOX2-derived superoxide as a driver of protumoral p16INK4a-dependent senescence in BM stromal cells. Our findings reveal the importance of a senescent microenvironment for the pathophysiology of leukemia. These data now open the door to investigate drugs that specifically target the “benign” senescent cells that surround and support AML

Laboratory Assessment of Potential Impacts to Dungeness Crabs from Disposal of Dredged Material from the Columbia River

Dredging of the Columbia River navigation channel has raised concerns about dredging-related impacts on Dungeness crabs (Cancer magister) in the estuary, mouth of the estuary, and nearshore ocean areas adjacent to the Columbia River. The Portland District, U.S. Army Corps of Engineers engaged the Marine Sciences Laboratory (MSL) of the U.S. Department of Energy’s Pacific Northwest National Laboratory to review the state of knowledge and conduct studies concerning impacts on Dungeness crabs resulting from disposal during the Columbia River Channel Improvement Project and annual maintenance dredging in the mouth of the Columbia River. The present study concerns potential effects on Dungeness crabs from dredged material disposal specific to the mouth of the Columbia River

Evolution of regulatory networks associated with traits under selection in cichlids

Background Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species. Here we use a novel approach for comparative GRN analysis in vertebrate species to study GRN evolution in representative species of the most striking examples of adaptive radiations, the East African cichlids. We previously demonstrated how the explosive phenotypic diversification of East African cichlids can be attributed to diverse molecular mechanisms, including accelerated regulatory sequence evolution and gene expression divergence. Results To investigate these mechanisms across species at a genome-wide scale, we develop a novel computational pipeline that predicts regulators for co-extant and ancestral co-expression modules along a phylogeny, and candidate regulatory regions associated with traits under selection in cichlids. As a case study, we apply our approach to a well-studied adaptive trait—the visual system—for which we report striking cases of network rewiring for visual opsin genes, identify discrete regulatory variants, and investigate their association with cichlid visual system evolution. In regulatory regions of visual opsin genes, in vitro assays confirm that transcription factor binding site mutations disrupt regulatory edges across species and segregate according to lake species phylogeny and ecology, suggesting GRN rewiring in radiating cichlids. Conclusions Our approach reveals numerous novel potential candidate regulators and regulatory regions across cichlid genomes, including some novel and some previously reported associations to known adaptive evolutionary traits

20% More Eelgrass in Puget Sound by 2020: Restoration Site Selection

As part of a larger program by the state of Washington to restore the Puget Sound ecosystem, we are engaged in a selection process to locate specific areas where eelgrass could be restored or enhanced to meet the goal of 20% more eelgrass by 2020, amounting to a ~4,000 ha increase in areal eelgrass coverage. Embedded in this goal is the establishment and development of meadows that are resilient to the effects of climate change and anthropogenic and natural disturbances. We hypothesize that: (1) many sites are recruitment limited; (2) eelgrass has been lost in some areas because of temporary disturbance; and (3) there may be broader stresses limiting eelgrass in subregions of Puget Sound. Our approach utilizes an understanding of eelgrass growth requirements coupled with hydrodynamic and water quality models, an eelgrass growth model, field observations, and test plantings. We are using these results along with spatial data and stressor information collected as part of regional assessments of nearshore ecosystem condition to identify restoration sites. We are also working with local governments to determine actions that could be taken to improve conditions for eelgrass within their jurisdictions to maximize the success and long-term viability of planted meadows. The models revealed differences in the predicted growth rate of eelgrass among regions. In general, northern Puget Sound and Strait of Juan de Fuca provided the best conditions, whereas Hood Canal and southern Puget Sound were relatively less suitable for eelgrass. Field visits were conducted at 23 sites where the eelgrass model predicted good growing conditions but where eelgrass does not presently exist based on available information. From among these sites we selected five sites for test planting. Test plantings, modeling and jurisdictional information will form the basis to develop strategies for larger recovery efforts

Representing the function and sensitivity of coastal interfaces in earth system models

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ward, N. D., Megonigal, J. P., Bond-Lamberty, B., Bailey, V. L., Butman, D., Canuel, E. A., Diefenderfer, H., Ganju, N. K., Goni, M. A., Graham, E. B., Hopkinson, C. S., Khangaonkar, T., Langley, J. A., McDowell, N. G., Myers-Pigg, A. N., Neumann, R. B., Osburn, C. L., Price, R. M., Rowland, J., Sengupta, A., Simard, M., Thornton, P. E., Tzortziou, M., Vargas, R., Weisenhorn, P. B., & Windham-Myers, L. Representing the function and sensitivity of coastal interfaces in earth system models. Nature Communications, 11(1), (2020): 2458, doi:10.1038/s41467-020-16236-2.Between the land and ocean, diverse coastal ecosystems transform, store, and transport material. Across these interfaces, the dynamic exchange of energy and matter is driven by hydrological and hydrodynamic processes such as river and groundwater discharge, tides, waves, and storms. These dynamics regulate ecosystem functions and Earth’s climate, yet global models lack representation of coastal processes and related feedbacks, impeding their predictions of coastal and global responses to change. Here, we assess existing coastal monitoring networks and regional models, existing challenges in these efforts, and recommend a path towards development of global models that more robustly reflect the coastal interface.Funding for this work was provided by Pacific Northwest National Laboratory (PNNL) Laboratory Directed Research & Development (LDRD) as part of the Predicting Ecosystem Resilience through Multiscale Integrative Science (PREMIS) Initiative. PNNL is operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830. Additional support to J.P.M. was provided by the NSF-LTREB program (DEB-0950080, DEB-1457100, DEB-1557009), DOE-TES Program (DE-SC0008339), and the Smithsonian Institution. This manuscript was motivated by discussions held by co-authors during a three-day workshop at PNNL in Richland, WA: The System for Terrestrial Aquatic Research (STAR) Workshop: Terrestrial-Aquatic Research in Coastal Systems. The authors thank PNNL artist Nathan Johnson for preparing the figures in this manuscript and Terry Clark, Dr. Charlette Geffen, and Dr. Nancy Hess for their aid in organizing the STAR workshop. The authors thank all workshop participants not listed as authors for their valuable insight: Lihini Aluwihare (contributed to biogeochemistry discussions and development of concept for Fig. 3), Gautam Bisht (contributed to modeling discussion), Emmett Duffy (contributed to observational network discussions), Yilin Fang (contributed to modeling discussion), Jeremy Jones (contributed to biogeochemistry discussions), Roser Matamala (contributed to biogeochemistry discussions), James Morris (contributed to biogeochemistry discussions), Robert Twilley (contributed to biogeochemistry discussions), and Jesse Vance (contributed to observational network discussions). A full report on the workshop discussions can be found at https://www.pnnl.gov/publications/star-workshop-terrestrial-aquatic-research-coastal-systems