Endorepellin remodels the endothelial transcriptome toward a pro-autophagic and pro-mitophagic gene signature.

Regulation of autophagy by proteolytically cleaved fragments of heparan sulfate proteoglycans is a novel and current research focus in tumor biology. Endorepellin is the C-terminal angiostatic fragment of the heparan sulfate proteoglycan perlecan and induces autophagy in endothelial cells. To further investigate this property, we used NanoString, a digital PCR platform for measuring pre-defined transcripts in biological samples to analyze a custom subset of 95 autophagy-related genes in human umbilical vein endothelial cells treated with ultrapure human recombinant endorepellin. We discovered an endorepellin-evoked pro-autophagic and pro-mitophagic gene expression signatures, which included two coordinately up-regulated mitochondrial-associated genes encoding the E3 ubiquitin protein ligase Parkin and the tumor suppressor mitostatin. Induction of both proteins required the tyrosine kinase activity of vascular endothelial growth factor receptor 2 (VEGFR2). Furthermore, we discovered that endorepellin evoked mitochondrial depolarization in endothelial cells via a specific interaction between its two proximal LG1/2 domains and VEGFR2. We also found that following loss of membrane potential, mitostatin and parkin interact and that mitostatin associates with the established Parkin receptor mitofusin-2. In conclusion, we have identified a critical role for endorepellin in remodeling the autophagic transcriptome and influencing mitochondrial homeostasis

The effect of mineral and organic nutrient input on yields and nitrogen balances in western Kenya

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Agriculture, Ecosystems & Environment 214 (2015): 10-20, doi:10.1016/j.agee.2015.08.006.Soil fertility declines constrain crop productivity on smallholder farms in sub-Saharan Africa. Government and non-government organizations promote the use of mineral fertilizer and improved seed varieties to redress nutrient depletion and increase crop yields. Similarly, rotational cropping with nitrogen (N)-fixing legume cover crops or trees is promoted to improve soil fertility and crop yields. We examined maize grain yields and partial N balances on 24 smallholder maize farms in western Kenya, where interventions have increased access to agricultural inputs and rotational legume technologies. On these farms, mineral fertilizer inputs ranged from 0 to 161 kg N ha-1 (mean = 48 kg N ha-1), and maize grain yields ranged from 1-7 tons ha-1 (mean = 3.4 t ha-1). Partial N balances ranged from large losses (-112 kg N ha-1) to large gains (93 kg N ha-1)with a mean of -3 kg N ha-1. Maize grain yields increased significantly with N inputs (from fertilizer and legumes) in 2012 but not in 2013 when rainfall was lower. Nitrogen inputs of 40 kg N ha-1 were required to produce 3 tons of maize ha-1. N balances varied both among farms and between years, highlighting the importance of tracking inputs and outputs on multiple farms over multiple years before drawing conclusions about nutrient management, soil fertility outcomes and food security. The addition of N from legume rotations was a strong predictor of grain yields and positive N balances in lower-yielding farms in both years. This suggested that legume rotations may be particularly important for buffering yields from climate variability and maintaining N balances in low rainfall years.This research was funded by an Earth Institute at Columbia University Cross-Cutting Initiative Grant, a National Science Foundation PIRE grant (IIA-0968211), and by the Bill and Melinda Gates Foundation (Gates Special Initiative Grant)

Structure and composition of altered riparian forests in an agricultural Amazonian landscape

Author Posting. © Ecological Society of America, 2015. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecological Applications 25 (2015): 1725-1838, doi:10.1890/14-1740.1.Deforestation and fragmentation influence the microclimate, vegetation structure, and composition of remaining patches of tropical forest. In the southern Amazon, at the frontier of cropland expansion, forests are converted and fragmented in a pattern that leaves standing riparian forests whose dimensions are mandated by the Brazilian National Forest Code. These altered riparian forests share many characteristics of well-studied upland forest fragments, but differ because they remain connected to larger areas of forest downstream, and because they may experience wetter soil conditions because reduction of forest cover in the surrounding watershed raises groundwater levels and increases stream runoff. We compared forest regeneration, structure, composition, and diversity in four areas of intact riparian forest and four areas each of narrow, medium, and wide altered riparian forests that have been surrounded by agriculture since the early 1980s. We found that seedling abundance was reduced by as much as 64% and sapling abundance was reduced by as much as 67% in altered compared to intact riparian forests. The most pronounced differences between altered and intact forest occurred near forest edges and within the narrowest sections of altered riparian forests. Woody plant species composition differed and diversity was reduced in altered forests compared to intact riparian forests. However, despite being fragmented for several decades, large woody plant biomass and carbon storage, the number of live or dead large woody plants, mortality rates, and the size distribution of woody plants did not differ significantly between altered and intact riparian forests. Thus, even in these relatively narrow forests with high edge : area ratios, we saw no evidence of the increases in mortality and declines in biomass that have been found in other tropical forest fragment studies. However, because of the changes in both species community and reduced regeneration, it is unclear how long this relative lack of change will be sustained. Additionally, Brazil recently passed a law in their National Forest Code allowing narrower riparian buffers than those studied here in restored areas, which could affect their long-term sustainability.This research has been supported by a grant from the U.S. Environmental Protection Agency's Science to Achieve Results (STAR) program (Award #: FP-91749001-0). Additional support was provided by NSF Award # DEB 0949370 and the São Paulo Research Foundation (FAPESP)

Decorin protein core affects the global gene expression profile of the tumor microenvironment in a triple-negative orthotopic breast carcinoma xenograft model

Decorin, a member of the small leucine-rich proteoglycan gene family, exists and functions wholly within the tumor microenvironment to suppress tumorigenesis by directly targeting and antagonizing multiple receptor tyrosine kinases, such as the EGFR and Met. This leads to potent and sustained signal attenuation, growth arrest, and angiostasis. We thus sought to evaluate the tumoricidal benefits of systemic decorin on a triple-negative orthotopic breast carcinoma xenograft model. To this end, we employed a novel high-density mixed expression array capable of differentiating and simultaneously measuring gene signatures of both Mus musculus (stromal) and Homo sapiens (epithelial) tissue origins. We found that decorin protein core modulated the differential expression of 374 genes within the stromal compartment of the tumor xenograft. Further, our top gene ontology classes strongly suggests an unexpected and preferential role for decorin protein core to inhibit genes necessary for immunomodulatory responses while simultaneously inducing expression of those possessing cellular adhesion and tumor suppressive gene properties. Rigorous verification of the top scoring candidates led to the discovery of three genes heretofore unlinked to malignant breast cancer that were reproducibly found to be induced in several models of tumor stroma. Collectively, our data provide highly novel and unexpected stromal gene signatures as a direct function of systemic administration of decorin protein core and reveals a fundamental basis of action for decorin to modulate the tumor stroma as a biological mechanism for the ascribed anti-tumorigenic properties

Solute and sediment export from Amazon forest and soybean headwater streams

Author Posting. © Ecological Society of America, 2016. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecological Applications 27 (2017): 193–207, doi:10.1002/eap.1428.Intensive cropland agriculture commonly increases streamwater solute concentrations and export from small watersheds. In recent decades, the lowland tropics have become the world's largest and most important region of cropland expansion. Although the effects of intensive cropland agriculture on streamwater chemistry and watershed export have been widely studied in temperate regions, their effects in tropical regions are poorly understood. We sampled seven headwater streams draining watersheds in forest (n = 3) or soybeans (n = 4) to examine the effects of soybean cropping on stream solute concentrations and watershed export in a region of rapid soybean expansion in the Brazilian state of Mato Grosso. We measured stream flows and concentrations of NO3−, PO43−, SO42−, Cl−, NH4+, Ca2+, Mg2+, Na+, K+, Al3+, Fe3+, and dissolved organic carbon (DOC) biweekly to monthly to determine solute export. We also measured stormflows and stormflow solute concentrations in a subset of watersheds (two forest, two soybean) during two/three storms, and solutes and δ18O in groundwater, rainwater, and throughfall to characterize watershed flowpaths. Concentrations of all solutes except K+ varied seasonally in streamwater, but only Fe3+ concentrations differed between land uses. The highest streamwater and rainwater solute concentrations occurred during the peak season of wildfires in Mato Grosso, suggesting that regional changes in atmospheric composition and deposition influence seasonal stream solute concentrations. Despite no concentration differences between forest and soybean land uses, annual export of NH4+, PO43−, Ca2+, Fe3+, Na+, SO42−, DOC, and TSS were significantly higher from soybean than forest watersheds (5.6-fold mean increase). This increase largely reflected a 4.3-fold increase in water export from soybean watersheds. Despite this increase, total solute export per unit watershed area (i.e., yield) remained low for all watersheds (<1 kg NO3− N·ha−1·yr−1, <2.1 kg NH4+-N·ha−1·yr−1, <0.2 kg PO43−-P·ha−1·yr−1, <1.5 kg Ca2+·ha−1·yr−1). Responses of both streamflows and solute concentrations to crop agriculture appear to be controlled by high soil hydraulic conductivity, groundwater-dominated hydrologic flowpaths on deep soils, and the absence of nitrogen fertilization. To date, these factors have buffered streams from the large increases in solute concentrations that often accompany intensive croplands in other locations.NSF Grant Numbers: DEB-0640661, DEB-0949370; Fundação de Amparo á Pesquisa do Estado de São Paulo Grant Number: FAPESP 03/13172-2; Watson Graduate Student Fellowship; Center for Latin American and Caribbean Studies at Brown Universit

Restoring mucosal barrier function and modifying macrophage phenotype with an extracellular matrix hydrogel: potential therapy for ulcerative colitis

Background & Aims: Despite advances in therapeutic options, more than half of all patients with ulcerative colitis (UC) do not achieve long-term remission, many require colectomy, and the disease still has a marked negative impact on quality of life. Extracellular matrix (ECM) bioscaffolds facilitate the functional repair of many soft tissues by mechanisms that include mitigation of pro-inflammatory macrophage phenotype and mobilization of endogenous stem/progenitor cells. The aim of the present study was to determine if an ECM hydrogel therapy could influence outcomes in an inducible rodent model of UC. Methods: The dextran sodium sulfate (DSS)-colitis model was used in male Sprague Dawley rats. Animals were treated via enema with an ECM hydrogel and the severity of colitis was determined by clinical and histologic criteria. Lamina propria cells were isolated and the production of inflammatory mediators was quantified. Mucosal permeability was assessed in-vivo by administering TRITC-dextran and in-vitro using transepithelial electrical resistance (TEER). Results: ECM hydrogel therapy accelerated healing and improved outcome. The hydrogel was adhesive to colonic tissue, which allowed for targeted delivery of the therapy, and resulted in a reduction in clinical and histologic signs of disease. ECM hydrogel facilitated functional improvement of colonic epithelial barrier function and the resolution of the pro-inflammatory state of tissue macrophages. Conclusions: The present study shows that a nonsurgical and nonpharmacologic ECM-based therapy can abate DSS-colitis not by immunosuppression but by promoting phenotypic change in local macrophage phenotype and rapid replacement of the colonic mucosal barrie

THE B LYMPHOCYTE DIFFERENTIATION FACTOR (BAFF) IS EXPRESSED IN THE AIRWAYS OF CHILDREN WITH CF AND IN LUNGS OF MICE INFECTED WITH PSEUDOMONAS AERUGINOSA

Background Chronic lung infection with Pseudomonas aeruginosa remains a major cause of mortality and morbidity among individuals with CF. Expression of mediators promoting recruitment and differentiation of B cells, or supporting antibody production is poorly understood yet could be key to controlling infection. Methods BAFF was measured in BAL from children with CF, both with and without P. aeruginosa, and controls. Mice were intra-nasally infected with P. aeruginosa strain LESB65 for up to 7 days. Cellular infiltration and expression of B cell chemoattractants and B cell differentiation factor, BAFF were measured in lung tissue. Results BAFF expression was elevated in both P. aeruginosa negative and positive CF patients and in P. aeruginosa infected mice post infection. Expression of the B cell chemoattractants CXCL13, CCL19 and CCL21 increased progressively post infection. Conclusions In a mouse model, infection with P. aeruginosa was associated with elevated expression of BAFF and other B cell chemoattractants suggesting a role for airway B cell recruitment and differentiation in the local adaptive immune response to P. aeruginosa. The paediatric CF airway, irrespective of pseudomonal infection, was found to be associated with an elevated level of BAFF implying that BAFF expression is not specific to pseudomonas infection and may be a feature of the CF airway. Despite the observed presence of a potent B cell activator, chronic colonisation is common suggesting that this response is ineffective