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1.
Physiol Rep ; 11(19): e15829, 2023 10.
Artículo en Inglés | MEDLINE | ID: mdl-37771106

RESUMEN

The JAK/STAT pathway plays a crucial role in the pathogenesis of rheumatoid arthritis (RA) and JAK inhibitors have emerged as a new group of effective drugs for RA treatment. Recently, high STAT3 levels have been associated with the upregulation of the scaffold protein NEDD9, which is a regulator of T-cell trafficking and promotes collagen-induced arthritis (CIA). In this study, we aimed to reveal how treatment with JAK inhibitors affects NEDD9 in CD4+ T cells from RA patients. We analyzed NEDD9 expression in CD4+ T cells from 50 patients treated with either baricitinib, tofacitinib, or upadacitinib and performed cell migration assays to assess the potential influence of JAK inhibitor treatment on CD4+ T-cell migration. We observed that treatment with baricitinib and upadacitinib is associated with reduced NEDD9 expression in CD4+ T cells. In contrast, NEDD9 levels were not altered during treatment with tofacitinib. Moreover, treatment with baricitinib was associated with a significantly reduced migratory capacity of effector CD4+ T cells but not with impaired migration of Treg cells. This study reveals previously unknown associations between JAK inhibitor treatment and NEDD9 expression and indicates that JAK inhibitors could reduce effector T-cell migration.


Asunto(s)
Artritis Reumatoide , Inhibidores de las Cinasas Janus , Humanos , Inhibidores de las Cinasas Janus/farmacología , Inhibidores de las Cinasas Janus/uso terapéutico , Quinasas Janus , Linfocitos T CD4-Positivos/patología , Transducción de Señal , Factores de Transcripción STAT , Artritis Reumatoide/tratamiento farmacológico , Artritis Reumatoide/patología , Proteínas Adaptadoras Transductoras de Señales
2.
Nat Ecol Evol ; 7(2): 236-249, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-36376602

RESUMEN

The impact of local biodiversity loss on ecosystem functioning is well established, but the role of larger-scale biodiversity dynamics in the delivery of ecosystem services remains poorly understood. Here we address this gap using a comprehensive dataset describing the supply of 16 cultural, regulating and provisioning ecosystem services in 150 European agricultural grassland plots, and detailed multi-scale data on land use and plant diversity. After controlling for land-use and abiotic factors, we show that both plot-level and surrounding plant diversity play an important role in the supply of cultural and aboveground regulating ecosystem services. In contrast, provisioning and belowground regulating ecosystem services are more strongly driven by field-level management and abiotic factors. Structural equation models revealed that surrounding plant diversity promotes ecosystem services both directly, probably by fostering the spill-over of ecosystem service providers from surrounding areas, and indirectly, by maintaining plot-level diversity. By influencing the ecosystem services that local stakeholders prioritized, biodiversity at different scales was also shown to positively influence a wide range of stakeholder groups. These results provide a comprehensive picture of which ecosystem services rely most strongly on biodiversity, and the respective scales of biodiversity that drive these services. This key information is required for the upscaling of biodiversity-ecosystem service relationships, and the informed management of biodiversity within agricultural landscapes.


Asunto(s)
Biodiversidad , Ecosistema , Agricultura/métodos , Plantas
4.
RMD Open ; 8(2)2022 10.
Artículo en Inglés | MEDLINE | ID: mdl-36216409

RESUMEN

BACKGROUND: Several health authorities recommend a third (booster) vaccination to protect patients with rheumatic and musculoskeletal diseases from severe COVID-19. Methotrexate has been shown to reduce the efficacy of the first and second dose of SARS-CoV-2 mRNA vaccines. So far, it remains unknown how concomitant methotrexate affects the efficacy of a COVID-19 booster vaccination. METHODS: We compared the humoral immune response to SARS-CoV-2 vaccination in 136 patients with rheumatoid arthritis (RA) treated with methotrexate and/or biological or targeted synthetic (b/tsDMARDs). IgG targeting the receptor binding domain (RBD) of SARS-CoV-2 spike protein was measured at a median of 52.5 (range 2-147) days after a third dose of the SARS-CoV-2 mRNA vaccines BNT162b2 or mRNA-1273. RESULTS: Anti-RBD IgG was significantly reduced in elderly patients receiving concomitant treatment with methotrexate as compared with elderly patients receiving monotherapy with b/tsDMARDs or methotrexate (64.8 (20.8, 600.3) binding antibody units per mL (BAU/mL) vs 1106.0 (526.3, 4965.2) BAU/mL vs 1743.8 (734.5, 6779.6) BAU/mL, median (IQR), p<0.001, Kruskal-Wallis test). In younger patients (< 64.5 years), concomitant methotrexate had no significant impact on the humoral immune response. CONCLUSIONS: Concomitant methotrexate increases the risk of an insufficient humoral immune response to SARS-CoV-2 vaccination in elderly patients with RA. Pausing methotrexate during the third vaccination period may be considered for this group of patients.


Asunto(s)
Artritis Reumatoide , Vacunas contra la COVID-19 , COVID-19 , Inmunidad Humoral , Metotrexato , Anciano , Anticuerpos Antivirales , Artritis Reumatoide/tratamiento farmacológico , Vacuna BNT162 , COVID-19/prevención & control , Vacunas contra la COVID-19/inmunología , Humanos , Inmunoglobulina G , Metotrexato/uso terapéutico , SARS-CoV-2 , Glicoproteína de la Espiga del Coronavirus
5.
Lupus Sci Med ; 9(1)2022 08.
Artículo en Inglés | MEDLINE | ID: mdl-35940821

RESUMEN

OBJECTIVE: SLE is an autoimmune disease with a complex pathogenesis. T-cell infiltration into organs contributes to inflammation and organ damage in SLE. Recently, G-protein signalling modulator 2 (GPSM2) has been shown to be implicated in T-cell migration. METHODS: We analysed the expression levels of GPSM2 and of a truncated isoform of GPSM2 containing the GoLoco motif region in CD4+ T cells from patients with SLE and from healthy individuals by western blot. In a next step, we studied the role of the truncated GPSM2 isoform using a CD4+ T-cell migration assay. RESULTS: Our experiments revealed comparable levels of GPSM2 in CD4+ T cells from patients with SLE and healthy controls. In contrast, the truncated 35 kDa isoform of GPSM2 was significantly more highly expressed in CD4+ T cells from patients with SLE as compared with healthy subjects. Antibody-mediated blockade of the 35 kDa GPSM2 isoform reduced the in vitro capacity of CD4+ T cells to migrate towards the chemokine CCL20. CONCLUSIONS: A truncated GPSM2 isoform containing the GoLoco motif region is upregulated in CD4+ T cells from patients with SLE and promotes CD4+ T-cell migration. Targeting this isoform with specific antibodies might be a promising approach to reduce CD4+ T-cell infiltration into inflamed tissues and to prevent organ damage in SLE.


Asunto(s)
Lupus Eritematoso Sistémico , Linfocitos T CD4-Positivos/metabolismo , Movimiento Celular , Humanos , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Isoformas de Proteínas/metabolismo , Linfocitos T
6.
Nano Lett ; 22(15): 6454-6461, 2022 08 10.
Artículo en Inglés | MEDLINE | ID: mdl-35792810

RESUMEN

A recent addition to the toolbox of super-resolution microscopy methods is fluorescence-lifetime single-molecule localization microscopy (FL-SMLM). The synergy of SMLM and fluorescence-lifetime imaging microscopy (FLIM) combines superior image resolution with lifetime information and can be realized using two complementary experimental approaches: confocal-laser scanning microscopy (CLSM) or wide-field microscopy. Here, we systematically and comprehensively compare these two novel FL-SMLM approaches in different spectral regions. For wide-field FL-SMLM, we use a commercial lifetime camera, and for CLSM-based FL-SMLM we employ a home-built system equipped with a rapid scan unit and a single-photon detector. We characterize the performances of the two systems in localizing single emitters in 3D by combining FL-SMLM with metal-induced energy transfer (MIET) for localization along the third dimension and in the lifetime-based multiplexed bioimaging using DNA-PAINT. Finally, we discuss advantages and disadvantages of wide-field and confocal FL-SMLM and provide practical advice on rational FL-SMLM experiment design.


Asunto(s)
ADN , Imagen Individual de Molécula , Microscopía Confocal/métodos , Microscopía Fluorescente/métodos , Nanotecnología , Imagen Individual de Molécula/métodos
7.
Sci Adv ; 8(23): eabo2506, 2022 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-35675401

RESUMEN

Over the past two decades, super-resolution microscopy has seen a tremendous development in speed and resolution, but for most of its methods, there exists a remarkable gap between lateral and axial resolution, which is by a factor of 2 to 3 worse. One recently developed method to close this gap is metal-induced energy transfer (MIET) imaging, which achieves an axial resolution down to nanometers. It exploits the distance-dependent quenching of fluorescence when a fluorescent molecule is brought close to a metal surface. In the present manuscript, we combine the extreme axial resolution of MIET imaging with the extraordinary lateral resolution of single-molecule localization microscopy, in particular with direct stochastic optical reconstruction microscopy (dSTORM). This combination allows us to achieve isotropic three-dimensional super-resolution imaging of subcellular structures. Moreover, we used spectral demixing for implementing dual-color MIET-dSTORM that allows us to image and colocalize, in three dimensions, two different cellular structures simultaneously.

8.
Clin Immunol ; 238: 109025, 2022 05.
Artículo en Inglés | MEDLINE | ID: mdl-35487454

RESUMEN

BACKGROUND: The cell surface molecule CD6 is a modulator of T cell receptor (TCR) signaling. Recently, it has been reported that CD6 is downregulated on CD4+ T cells following T cell activation. This mechanism could limit the efficacy of anti-CD6 therapeutical antibodies. METHODS: We analyzed CD6 expression on activated and non-activated Th1 cells and Th17 cells by flow cytometry. RESULTS: Our experiments confirmed a significant downregulation of CD6 on IFNγ- and IL17-negative CD4+ T cells from healthy individuals and from patients with rheumatoid arthritis following T cell activation with anti-CD3 and anti-CD28 antibodies. In contrast, CD6 expression remained stable on activated Th17 cells and Th1 cells. CONCLUSIONS: Th1 and Th17 cells are resistant towards T cell activation-induced downregulation of CD6. These findings are relevant for the future development of CD6 targeting therapies and show that CD6 expression is differentially regulated in CD4+ T cell subsets.


Asunto(s)
Antígenos CD , Antígenos de Diferenciación de Linfocitos T , Regulación hacia Abajo , Activación de Linfocitos , Células TH1 , Células Th17 , Antígenos CD28/metabolismo , Humanos
9.
Commun Biol ; 5(1): 38, 2022 01 11.
Artículo en Inglés | MEDLINE | ID: mdl-35017652

RESUMEN

DNA point accumulation for imaging in nanoscale topography (DNA-PAINT) is a powerful super-resolution technique highly suitable for multi-target (multiplexing) bio-imaging. However, multiplexed imaging of cells is still challenging due to the dense and sticky environment inside a cell. Here, we combine fluorescence lifetime imaging microscopy (FLIM) with DNA-PAINT and use the lifetime information as a multiplexing parameter for targets identification. In contrast to Exchange-PAINT, fluorescence lifetime PAINT (FL-PAINT) can image multiple targets simultaneously and does not require any fluid exchange, thus leaving the sample undisturbed and making the use of flow chambers/microfluidic systems unnecessary. We demonstrate the potential of FL-PAINT by simultaneous imaging of up to three targets in a cell using both wide-field FLIM and 3D time-resolved confocal laser scanning microscopy (CLSM). FL-PAINT can be readily combined with other existing techniques of multiplexed imaging and is therefore a perfect candidate for high-throughput multi-target bio-imaging.


Asunto(s)
ADN/química , Microscopía Fluorescente/métodos , Imagen Molecular/métodos , Nanotecnología/métodos , ADN/análisis , Colorantes Fluorescentes/química , Células HeLa , Humanos , Microscopía Confocal
10.
Biodivers Data J ; 10: e83523, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36761658

RESUMEN

Background: The decline of pollinating insects in agricultural landscapes proceeds due to intensive land use and the associated loss of habitat and food sources. The feeding of those insects depends on the spatial and temporal distribution of nectar and pollen as food resource. Hence, to protect insect biodiversity, a spatio-temporal assessment of food quantity of their habitats is necessary. Therefore, sufficient data on traits of floral resources are required. New information: As floral resources' traits of plants are important to quantify food availability, we present two databases, the FloRes Database (Floral Resources Database) and the raw database, from where FloRes was derived. Both databases contain the plant traits: (1) flowering period, (2) floral-unit density per day, (3) nectar volume per floral unit per day, (4) sugar content per floral unit, (5) sugar concentration in nectar, (6) pollen mass or volume per floral unit and per day, (7) protein content of pollen and (8) corolla depth. All traits were sampled from literature and online databases. The raw database consists of 702 specified plant species, 138 unspecified species 37 species (spec., sp), 22 species pluralis (spp) and, for 79, only the genus was identified) and two species complexes (agg.). Those 842 taxa belong to 488 genera and 102 families. Finally, only 27 taxa have a complete set of traits, too few for a sufficient assessment of spatio-temporal availability of floral food-resources.As information on floral resources is scattered throughout many publications with different units, we also present our multistep workflow implemented in five consecutive R-scripts. The multistep workflow standardises the trait units of the raw database to comparable entities with identical units and aggregates them on a reasonable taxonomic level into the second application database, the FloRes Database. Finally, the FloRes Database contains aggregated information of traits for 42 taxa and, when corolla depth is excluded, for 72 taxa.This is the first attempt to gather these eight traits from different literature sources into one database with a multistep workflow. The publication of the multistep workflow enables the users to extend the FloRes Database on their own demands with other literature data or newly-gathered data to improve quantification of food resources. Especially, the combination of pollen, nectar and the open flowers per square metre is, as far as we know, a novelty.The FloRes Database can be used to evaluate the quantity of food-resource habitats available for pollinators, for example, to compare seed mixtures of agri-environmental measures, such as flower strips, considering flower phenology on a daily basis.

11.
Cell Mol Life Sci ; 79(1): 3, 2021 Dec 16.
Artículo en Inglés | MEDLINE | ID: mdl-34913099

RESUMEN

Autoimmune arthritis is characterized by impaired regulatory T (Treg) cell migration into inflamed joint tissue and by dysregulation of the balance between Treg cells and Th17 cells. Interleukin-6 (IL-6) is known to contribute to this dysregulation, but the molecular mechanisms behind impaired Treg cell migration remain largely unknown. In this study, we assessed dynamic changes in membrane-bound IL-6 receptor (IL6R) expression levels on Th17 cells by flow cytometry during the development of collagen-induced arthritis (CIA). In a next step, bioinformatics analysis based on proteomics was performed to evaluate potential pathways affected by altered IL-6R signaling in autoimmune arthritis. Our analysis shows that membrane-bound IL-6R is upregulated on Th17 cells and is inversely correlated with IL-6 serum levels in experimental autoimmune arthritis. Moreover, IL-6R expression is significantly increased on Th17 cells from untreated patients with rheumatoid arthritis (RA). Interestingly, CD4+ T cells from CIA mice and RA patients show reduced phosphorylation of vasodilator-stimulated phosphoprotein (VASP). Bioinformatics analysis based on proteomics of CD4+ T cells with low or high phosphorylation levels of VASP revealed that integrin signaling and related pathways are significantly enriched in cells with low phosphorylation of VASP. Specific inhibition of p-VASP reduces the migratory function of Treg cells but has no influence on effector CD4+ T cells. Importantly, IL-6R blockade restores the phosphorylation level of VASP, thereby improving the migratory function of Treg cells from RA patients. Thus, our results establish a link between IL6R signaling and phosphorylation of VASP, which controls Treg cell migration in autoimmune arthritis.


Asunto(s)
Artritis Reumatoide/patología , Moléculas de Adhesión Celular/metabolismo , Proteínas de Microfilamentos/metabolismo , Fosfoproteínas/metabolismo , Receptores de Interleucina-6/metabolismo , Linfocitos T Reguladores/metabolismo , Células Th17/metabolismo , Animales , Artritis Experimental/inducido químicamente , Artritis Experimental/metabolismo , Artritis Experimental/patología , Artritis Reumatoide/metabolismo , Linfocitos T CD8-positivos/citología , Linfocitos T CD8-positivos/inmunología , Linfocitos T CD8-positivos/metabolismo , Movimiento Celular , Humanos , Interleucina-6/sangre , Ratones , Ratones Endogámicos DBA , Fosforilación , Linfocitos T Reguladores/citología , Células Th17/citología , Regulación hacia Arriba
12.
Nat Commun ; 12(1): 3918, 2021 06 24.
Artículo en Inglés | MEDLINE | ID: mdl-34168127

RESUMEN

Land-use intensification is a major driver of biodiversity loss. However, understanding how different components of land use drive biodiversity loss requires the investigation of multiple trophic levels across spatial scales. Using data from 150 agricultural grasslands in central Europe, we assess the influence of multiple components of local- and landscape-level land use on more than 4,000 above- and belowground taxa, spanning 20 trophic groups. Plot-level land-use intensity is strongly and negatively associated with aboveground trophic groups, but positively or not associated with belowground trophic groups. Meanwhile, both above- and belowground trophic groups respond to landscape-level land use, but to different drivers: aboveground diversity of grasslands is promoted by diverse surrounding land-cover, while belowground diversity is positively related to a high permanent forest cover in the surrounding landscape. These results highlight a role of landscape-level land use in shaping belowground communities, and suggest that revised agroecosystem management strategies are needed to conserve whole-ecosystem biodiversity.


Asunto(s)
Biodiversidad , Ecosistema , Plantas , Microbiología del Suelo , Agricultura , Animales , Europa (Continente) , Cadena Alimentaria , Bosques , Pradera , Herbivoria , Insectos
13.
Front Bioinform ; 1: 740281, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-36303750

RESUMEN

Fluorescence-lifetime single molecule localization microscopy (FL-SMLM) adds the lifetime dimension to the spatial super-resolution provided by SMLM. Independent of intensity and spectrum, this lifetime information can be used, for example, to quantify the energy transfer efficiency in Förster Resonance Energy Transfer (FRET) imaging, to probe the local environment with dyes that change their lifetime in an environment-sensitive manner, or to achieve image multiplexing by using dyes with different lifetimes. We present a thorough theoretical analysis of fluorescence-lifetime determination in the context of FL-SMLM and compare different lifetime-fitting approaches. In particular, we investigate the impact of background and noise, and give clear guidelines for procedures that are optimized for FL-SMLM. We do also present and discuss our public-domain software package "Fluorescence-Lifetime TrackNTrace," which converts recorded fluorescence microscopy movies into super-resolved FL-SMLM images.

14.
ACS Nano ; 14(10): 14190-14200, 2020 10 27.
Artículo en Inglés | MEDLINE | ID: mdl-33035050

RESUMEN

Fluorescence lifetime imaging microscopy is an important technique that adds another dimension to intensity and color acquired by conventional microscopy. In particular, it allows for multiplexing fluorescent labels that have otherwise similar spectral properties. Currently, the only super-resolution technique that is capable of recording super-resolved images with lifetime information is stimulated emission depletion microscopy. In contrast, all single-molecule localization microscopy (SMLM) techniques that employ wide-field cameras completely lack the lifetime dimension. Here, we combine fluorescence-lifetime confocal laser-scanning microscopy with SMLM for realizing single-molecule localization-based fluorescence-lifetime super-resolution imaging. Besides yielding images with a spatial resolution much beyond the diffraction limit, it determines the fluorescence lifetime of all localized molecules. We validate our technique by applying it to direct stochastic optical reconstruction microscopy and points accumulation for imaging in nanoscale topography imaging of fixed cells, and we demonstrate its multiplexing capability on samples with two different labels that differ only by fluorescence lifetime but not by their spectral properties.

15.
Front Oncol ; 10: 668, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32435617

RESUMEN

Introduction: Resection of anorectal malignancies may result in extensive perineal/pelvic defects that require an interdisciplinary surgical approach involving reconstructive surgery. The myocutaneous gracilis flap (MGF) and the gluteal fold flap (GFF) are common options for defect coverage in this area. Here we report our experience with the MGF/GFF and compare the outcome regarding clinical key parameters. Methods: In a retrospective chart review, we collected data from the Department of Plastic Surgery of the University of Freiburg from December 2008-18 focusing on epidemiological, oncological, and therapy-related data including comorbidities (ASA Classification) and peri-/postoperative complications (Clavien-Dindo-System). Results: Twenty-nine patients were included with a mean follow-up of 17 months. Of the cases, 19 (65.5%) presented with recurrent disease, 21 (72.4%) received radiochemotherapy preoperatively, 2 (6.9%) received chemotherapy alone. Microscopic tumor free margins were achieved in 25 cases (86.2%). 17 patients (7 men, 10 women, rectal adenocarcinoma n = 11; anal squamous cell carcinoma n = 6; mean age 58.5 ± 10.68, mean BMI 23.1, mean ASA score 2.8) received a MGF (unilateral n = 10; bilateral n = 7). Twelve patients (7 men, 5 women, rectal adenocarcinoma n = 7; anal squamous cell carcinoma n = 4, proctodeal gland carcinoma n = 1, mean age 66.2 ± 9.2, mean BMI 23.6, mean ASA score 2.6) received coverage with a GFF (unilateral n = 4; bilateral n = 8). Mean operation time of coverage was 105 ± 9 min for unilateral and 163 ± 11 for bilateral MGFs, 70 ± 13 min for unilateral and 107 ± 14 for bilateral GFFs. Complications affected 62%. There was no significant difference in the complication rate between the MGF- and GFF-group. Complications were mainly wound healing disorders that did not extend the hospital stay. No flap loss and no complication that lead to long-lasting disability was documented (both groups). Pain-free sitting took more time in the GFF-group due to the location of the donor site. Conclusion: MG-flaps and GF-flaps prove to be reliable and robust techniques for perineal/pelvic reconstruction. Though flap elevation is significantly faster for GF-flaps, preoperative planning and intraoperative Doppler confirmation are advisable. With comparable complication rates, we suggest a decision-making based on distribution of adipose tissue for dead space obliteration, intraoperative patient positioning, and perforator vessel quality/distribution.

16.
J Phys Chem A ; 124(17): 3494-3500, 2020 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-32255633

RESUMEN

Fluorescence lifetime imaging (FLIM) has become an important microscopy technique in bioimaging. The two most important of its applications are lifetime-multiplexing for imaging many different structures in parallel, and lifetime-based measurements of Förster resonance energy transfer. There are two principal FLIM techniques, one based on confocal-laser scanning microscopy (CLSM) and time-correlated single-photon counting (TCSPC) and the other based on wide-field microscopy and phase fluorometry. Although the first approach (CLSM-TCSPC) assures high sensitivity and allows one to detect single molecules, it is slow and has a small photon yield. The second allows, in principal, high frame rates (by 2-3 orders of magnitude faster than CLSM), but it suffers from low sensitivity, which precludes its application for single-molecule imaging. Here, we demonstrate that a novel wide-field TCSPC camera (LINCam25, Photonscore GmbH) can be successfully used for single-molecule FLIM, although its quantum yield of detection in the red spectral region is only ∼5%. This is due to the virtually absent background and readout noise of the camera, assuring high signal-to-noise ratio even at low detection efficiency. We performed single-molecule FLIM of different red fluorophores, and we use the lifetime information for successfully distinguishing between different molecular species. Finally, we demonstrate single-molecule metal-induced energy transfer (MIET) imaging which is a first step for three-dimensional single-molecule localization microscopy (SMLM) with nanometer resolution.


Asunto(s)
Imagen Óptica/métodos , Imagen Individual de Molécula/métodos , Relación Señal-Ruido
17.
F1000Res ; 9: 295, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33552475

RESUMEN

Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.


Asunto(s)
Conocimiento , Investigadores , Programas Informáticos , Predicción , Alemania , Humanos
18.
Biodivers Data J ; 7: e36387, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31598068

RESUMEN

BACKGROUND: The 150 grassland plots were located in three study regions in Germany, 50 in each region. The dataset describes the yearly grassland management for each grassland plot using 116 variables.General information includes plot identifier, study region and survey year. Additionally, grassland plot characteristics describe the presence and starting year of drainage and whether arable farming had taken place 25 years before our assessment, i.e. between 1981 and 2006. In each year, the size of the management unit is given which, in some cases, changed slightly across years.Mowing, grazing and fertilisation were systematically surveyed: Mowing is characterised by mowing frequency (i.e. number of cuts per year), dates of cutting and different technical variables, such as type of machine used or usage of conditioner.For grazing , the livestock species and age (e.g. cattle, horse, sheep), the number of animals, stocking density per hectare and total duration of grazing were recorded. As a derived variable, the mean grazing intensity was then calculated by multiplying the livestock units with the duration of grazing per hectare [LSU days/ha]. Different grazing periods during a year, partly involving different herds, were summed up to an annual grazing intensity for each grassland.For fertilisation , information on the type and amount of different types of fertilisers was recorded separately for mineral and organic fertilisers, such as solid farmland manure, slurry and mash from a bioethanol factory. Our fertilisation measures neglect dung dropped by livestock during grazing. For each type of fertiliser, we calculated its total nitrogen content, derived from chemical analyses by the producer or agricultural guidelines (Table 3).All three management types, mowing, fertilisation and grazing, were used to calculate a combined land use intensity index (LUI) which is frequently used to define a measure for the land use intensity. Here, fertilisation is expressed as total nitrogen per hectare [kg N/ha], but does not consider potassium and phosphorus.Information on additional management practices in grasslands was also recorded including levelling, to tear-up matted grass covers, rolling, to remove surface irregularities, seed addition, to close gaps in the sward. NEW INFORMATION: Investigating the relationship between human land use and biodiversity is important to understand if and how humans affect it through the way they manage the land and to develop sustainable land use strategies. Quantifying land use (the 'X' in such graphs) can be difficult as humans manage land using a multitude of actions, all of which may affect biodiversity, yet most studies use rather simple measures of land use, for example, by creating land use categories such as conventional vs. organic agriculture. Here, we provide detailed data on grassland management to allow for detailed analyses and the development of land use theory. The raw data have already been used for > 100 papers on the effect of management on biodiversity (e.g. Manning et al. 2015).

20.
PLoS One ; 13(7): e0199980, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29995916

RESUMEN

In agricultural landscapes, semi-natural habitats are scarce and remaining habitat patches are largely isolated. However, linear landscape elements might facilitate dispersal of plant species through the agricultural landscape matrix. We investigated the following research questions: 1. are open linear landscape elements (LLE) effective corridors for dispersal of vascular plant species? 2. Which plant species, with respect to phytosociological group and dispersal-distance class, do use LLE as corridors? 3. To which extent is floristic similarity of communities influenced by dispersal through corridors? Field work was carried out in agricultural landscapes of Northwest Germany. We sampled 50 vegetation relevés on open linear landscape elements i.e. field margins (incl. road verges) and ditches, in eight 1-km2 study areas. Then, we calculated Jaccard similarities of all plot pairs within study areas using either all species or only species of certain phytosociological groups or dispersal-distance classes. We assessed the isolation of the plots from each other using both Euclidean distance and resistance distance along LLE. Resistance distance reflected the degree of connectivity of the LLE network between the plots. A stronger effect on Jaccard similarity of resistance distance compared to Euclidean distance would indicate corridor dispersal of plants through LLE. Relationships between Jaccard similarity and the two isolation measures were analysed with Generalised Linear Mixed Models. Resistance distance of LLE had a stronger negative effect on Jaccard similarity than Euclidean distance in field margins, but not in ditches. This was found for species of 'meadows and pastures' and short to medium dispersal distance. In plot pairs that were highly connected by LLE, the models suggested that roughly 20% of all species occurred in both plots due to dispersal through LLE. Other species groups did not respond more strongly to resistance distance than to Euclidean distance. We conclude that linear landscape elements in agricultural landscapes are effective corridors for dispersal of plant species that are confined to semi-natural habitats, such as traditional grasslands, and lack mechanisms of long-distance dispersal.


Asunto(s)
Agricultura , Dispersión de las Plantas , Ecosistema , Modelos Estadísticos
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