Vineyards assessed under a biophysical approach: findings from the biohydrology and TERRAenVISION meetings

During the Biohydrology 2019 (24-27 July 2019, Valencia, Spain) and TERRAenVISION 2019 (2-7 September 2019, Barcelona, Spain) meetings, the scientific sessions joined reputed scientists around the world. Innovative debates during these scientific sessions about vineyards focused on the use of new technologies to assess soil erosion and nutrient losses, benefits or damages generated by tillage, the use of cover crops, and the introduction of organic farming. Among all the high-quality posters and oral presentations in these 2 abovementioned conferences, 3 groups from different countries with an extended list of publications decided to publish their new findings on the special issue: Vineyards Assessed Under a Biophysical Approac

Assessing environmental changes in abandoned German vineyards. Understanding key issues for restoration management plans

Land degradation in vineyards is a big concern which should be considered by farmers, enterprises and policymakers. Due to intense tillage, the use of herbicides and heavy machinery, vine plantations are registering a decrease in soil fertility and, subsequently, in productivity. Recently, farmers have decided to abandon the vineyards, but any restoration planning is being carried out to recover biodiversity or to reduce soil and water losses. Nowadays, there is no information about environmental changes after the abandonment in terms of possible soil property changes and erosion in Central European vineyards such as in Germany. Therefore, the main aims of this preliminary study were to compare: i) soil properties and soil profiles of one cultivated vineyard and an abandoned one; and, ii) to assess the activation of soil erosion processes using a small portable rainfall simulator. Our results showed that the vineyard registered several differences in soil properties among slope positions and soil profile characteristics due to tillage and trampling effects, showing clear marks of compaction and soil detachment in the lower parts. Also, in this cultivated field, higher means and maxima of soil losses (g m-2) and sediment concentration (g l-1) values than in the abandoned plot were quantified, being the main driving factors the vegetation cover and the inclination. On the other hand, in the abandoned vine plantation, a rapid homogenization of soil profiles and soil properties were found along the hillslope, where a deeper organic horizon was consistently developed above a compacted and rocky horizon, which was generated during the cultivation phase. Due to the high compaction due to the machinery cultivation and the difficulties for the roots to make deep into the soil, the infiltration defaulted and the amount of runoff and runoff coefficient were higher in the abandoned plots than in the cultivated ones

Finding Possible Weakness in the Runoff Simulation Experiments to Assess Rill Erosion Changes without Non-Intermittent Surveying Capabilities

The Terrestrial Photogrammetry Scanner (TEPHOS) offers the possibility to precisely monitor linear erosion features using the Structure from Motion (SfM) technique. This is a static, multi-camera array and dynamically moves the digital videoframe camera designed to obtain 3-D models of rills before and after the runoff experiments. The main goals were to (1) obtain better insight into the rills; (2) reduce the technical gaps generated during the runoff experiments using only one camera; (3) enable the visual location of eroded, transported and accumulated material. In this study, we obtained a mean error for all pictures reaching up to 0.00433 pixels and every single one of them was under 0.15 pixel. So, we obtained an error of about 1/10th of the maximum possible resolution. A conservative value for the overall accuracy was one pixel, which means that, in our case, the accuracy was 0.0625 mm. The point density, in our example, reached 29,484,888 pts/m2. It became possible to get a glimpse of the hotspots of sidewall failure and rill-bed incision. We conclude that the combination of both approaches—rill experiment and 3D models—will make easy under laboratory conditions to describe the soil erosion processes accurately in a mathematical–physical way

Combining the stock unearthing method and structure-from-motion photogrammetry for a gapless estimation of soil mobilisation in vineyards

Gyasi-Agyei, Y ORCiD: 0000-0002-2671-1180In vineyards, especially on steep slopes like the Ruwer-Mosel Valley, Germany, soil erosion is a well-known environmental problem. Unfortunately, some enterprises and farmers are not aware of how much soil is being lost and the long-term negative impacts of soil erosion. The non-invasive technique of the stock unearthing method (SUM) can be used for a quick assessment of soil erosion in vineyards. SUM uses the graft union as a reference elevation for soil surface changes since the time of plantation commencement, which is modelled with the help of a geographic information system. A shortcoming of SUM is that the areas between the pair-vine cross sections are not surveyed, hence it is not accurate enough to identify erosion hot-spots. A structure-from-motion (SfM) photogrammetric technique is adopted to complement SUM to fill this data gap. Combining SUM (only measuring the graft unions) and SfM techniques could lead to an improved, easy and low-cost method with a higher accuracy for estimation of soil erosion based on interpolation by projection, and contact and gapless measuring. Thus, the main aim of this paper was to map the current soil surface level and to improve the accuracy of estimation of long-term soil mobilisation rates in vineyards. To achieve this goal, the TEPHOS (TErrestrial PHOtogrammetric Scanner), a static five camera array, was developed on a 20 m 2 plot located in a steeply sloping vineyard of the Ruwer-Mosel Valley, Trier, Germany. A total soil mobilisation of 0.52 m 3 (9.14 Mg ha yr −1 ) with soil surface level differences in excess of 30 cm in the 40 years since plantation commencement were recorded. Further research is, however, needed to reduce the number of photos used for the point cloud without loss of accuracy. This method can be useful for the observation of the impacts of other factors in vineyards, such as tillage erosion, runoff pathway detection or the trampling effect on soil erosion in vineyards. © 2018 by the authors

Design, Synthesis and Biological Evaluation of β-Peptoid-Capped HDAC Inhibitors with Anti-Neuroblastoma and Anti-Glioblastoma Activity

Histone deacetylases (HDACs) have been identified as promising epigenetic drug targets for the treatment of neuroblastomaand glioblastoma. In this work, we have rationally designed a novel type of peptoid‐based histone deacetylase inhibitors(HDACi). A mini library of β‐peptoid‐capped HDACi was synthesized using a four‐step protocol. All compounds were screenedin biochemical assays for its inhibition of HDAC1 and HDAC6 and docking studies were performed to rationalize the observedselectivity profile. The synthesized compounds were further examined for tumor cell‐inhibitory activity against a panel ofneuroblastoma and glioblastoma cell lines. In particular, non‐selective compounds with potent activity against HDAC1 andHDAC6 showed strong antiproliferative effects. The most promising HDACi, compound 6i, displayed submicromolar tumorcell‐inhibitory potential (IC50: 0.21 – 0.67 μM) against all five cancer cell lines investigated and exceeded the activity of theFDA‐approved HDACi vorinostat

Sensitivity towards HDAC inhibition is associated with RTK/MAPK pathway activation in gastric cancer

Gastric cancer ranks the fifth most common and third leading cause of cancer-related deaths worldwide. Alterations in the RTK/MAPK, WNT, cell adhesion, TP53, TGF beta, NOTCH, and NF kappa B signaling pathways could be identified as main oncogenic drivers. A combination of altered pathways can be associated with molecular subtypes of gastric cancer. In order to generate model systems to study the impact of different pathway alterations in a defined genetic background, we generated three murine organoid models: a RAS-activated (Kras(G12D), Tp53(R172H)), a WNT-activated (Apc(fl/fl), Tp53(R172H)), and a diffuse (Cdh1(fl/fl), Apc(fl/fl)) model. These organoid models were morphologically and phenotypically diverse, differed in proteome expression signatures and possessed individual drug sensitivities. A differential vulnerability to RTK/MAPK pathway interference based on the different mitogenic drivers and according to the level of dependence on the pathway could be uncovered. Furthermore, an association between RTK/MAPK pathway activity and susceptibility to HDAC inhibition was observed. This finding was further validated in patient-derived organoids from gastric adenocarcinoma, thus identifying a novel treatment approach for RTK/MAPK pathway altered gastric cancer patients.11Nsciescopu

Integrative multi-omics reveals two biologically distinct groups of pilocytic astrocytoma

© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.Pilocytic astrocytoma (PA), the most common pediatric brain tumor, is driven by aberrant mitogen-activated protein kinase signaling most commonly caused by BRAF gene fusions or activating mutations. While 5-year overall survival rates exceed 95%, tumor recurrence or progression constitutes a major clinical challenge in incompletely resected tumors. Here, we used similarity network fusion (SNF) analysis in an integrative multi-omics approach employing RNA transcriptomic and mass spectrometry-based proteomic profiling to molecularly characterize PA tissue samples from 62 patients. Thereby, we uncovered that PAs segregated into two molecularly distinct groups, namely, Group 1 and Group 2, which were validated in three non-overlapping cohorts. Patients with Group 1 tumors were significantly younger and showed worse progression-free survival compared to patients with group 2 tumors. Ingenuity pathways analysis (IPA) and gene set enrichment analysis (GSEA) revealed that Group 1 tumors were enriched for immune response pathways, such as interferon signaling, while Group 2 tumors showed enrichment for action potential and neurotransmitter signaling pathways. Analysis of immune cell-related gene signatures showed an enrichment of infiltrating T Cells in Group 1 versus Group 2 tumors. Taken together, integrative multi-omics of PA identified biologically distinct and prognostically relevant tumor groups that may improve risk stratification of this single pathway driven tumor type.This project funded in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 418179183—KFO 337, RO 3577/7-1 (A.R.), RE 2857/4-1 (M.R.) and supported by Biomed Valley and Day One Therapeutics (T.M.), Fundação Amélia de Melo (C.C.F.) and Fundação Millennium bcp (C.C.F.)info:eu-repo/semantics/publishedVersio

The long non-coding RNA HOTAIRM1 promotes tumor aggressiveness and radiotherapy resistance in glioblastoma

Glioblastoma is the most common malignant primary brain tumor. To date, clinically relevant biomarkers are restricted to isocitrate dehydrogenase (IDH) gene 1 or 2 mutations and O6-methylguanine DNA methyltransferase (MGMT) promoter methylation. Long non-coding RNAs (lncRNAs) have been shown to contribute to glioblastoma pathogenesis and could potentially serve as novel biomarkers. The clinical significance of HOXA Transcript Antisense RNA, Myeloid-Specific 1 (HOTAIRM1) was determined by analyzing HOTAIRM1 in multiple glioblastoma gene expression data sets for associations with prognosis, as well as, IDH mutation and MGMT promoter methylation status. Finally, the role of HOTAIRM1 in glioblastoma biology and radiotherapy resistance was characterized in vitro and in vivo. We identified HOTAIRM1 as a candidate lncRNA whose up-regulation is significantly associated with shorter survival of glioblastoma patients, independent from IDH mutation and MGMT promoter methylation. Glioblastoma cell line models uniformly showed reduced cell viability, decreased invasive growth and diminished colony formation capacity upon HOTAIRM1 down-regulation. Integrated proteogenomic analyses revealed impaired mitochondrial function and determination of reactive oxygen species (ROS) levels confirmed increased ROS levels upon HOTAIRM1 knock-down. HOTAIRM1 knock-down decreased expression of transglutaminase 2 (TGM2), a candidate protein implicated in mitochondrial function, and knock-down of TGM2 mimicked the phenotype of HOTAIRM1 down-regulation in glioblastoma cells. Moreover, HOTAIRM1 modulates radiosensitivity of glioblastoma cells both in vitro and in vivo. Our data support a role for HOTAIRM1 as a driver of biological aggressiveness, radioresistance and poor outcome in glioblastoma. Targeting HOTAIRM1 may be a promising new therapeutic approach

Natural Compound Library Screening Identifies New Molecules for the Treatment of Cardiac Fibrosis and Diastolic Dysfunction.

High-throughput natural compound library screening identified 15 substances with antiproliferative effects in human cardiac fibroblasts. Using multiple in vitro fibrosis assays and stringent selection algorithms, we identified the steroid bufalin (from Chinese toad venom) and the alkaloid lycorine (from Amaryllidaceae species) to be effective antifibrotic molecules both in vitro and in vivo, leading to improvement in diastolic function in 2 hypertension-dependent rodent models of cardiac fibrosis. Administration at effective doses did not change plasma damage markers or the morphology of kidney and liver, providing the first toxicological safety data. Using next-generation sequencing, we identified the conserved microRNA 671-5p and downstream the antifibrotic selenoprotein P1 as common effectors of the antifibrotic compounds