webchem: An R Package to Retrieve Chemical Information from the Web

A wide range of chemical information is freely available online, including identifiers, experimental and predicted chemical properties. However, these data are scattered over various data sources and not easily accessible to researchers. Manual searching and downloading of such data is time-consuming and error-prone. We developed the open-source R package webchem that allows users to automatically query chemical data from currently 14 web sources. These cover a broad spectrum of information. The data are automatically imported into an R object and can directly be used in subsequent analyses. webchem enables easy, structured and reproducible data retrieval and usage from publicly available web sources. In addition, it facilitates data cleaning, identification and reporting of substances. Consequently, it reduces the time researchers need to spend on chemical data compilation

Consensus Paper: Radiological Biomarkers of Cerebellar Diseases

Hereditary and sporadic cerebellar ataxias represent a vast and still growing group of diseases whose diagnosis and differentiation cannot only rely on clinical evaluation. Brain imaging including magnetic resonance (MR) and nuclear medicine techniques allows for characterization of structural and functional abnormalities underlying symptomatic ataxias. These methods thus constitute a potential source of radiological biomarkers, which could be used to identify these diseases and differentiate subgroups of them, and to assess their severity and their evolution. Such biomarkers mainly comprise qualitative and quantitative data obtained from MR including proton spectroscopy, diffusion imaging, tractography, voxel-based morphometry, functional imaging during task execution or in a resting state, and from SPETC and PET with several radiotracers. In the current article, we aim to illustrate briefly some applications of these neuroimaging tools to evaluation of cerebellar disorders such as inherited cerebellar ataxia, fetal developmental malformations, and immune-mediated cerebellar diseases and of neurodegenerative or early-developing diseases, such as dementia and autism in which cerebellar involvement is an emerging feature. Although these radiological biomarkers appear promising and helpful to better understand ataxia-related anatomical and physiological impairments, to date, very few of them have turned out to be specific for a given ataxia with atrophy of the cerebellar system being the main and the most usual alteration being observed. Consequently, much remains to be done to establish sensitivity, specificity, and reproducibility of available MR and nuclear medicine features as diagnostic, progression and surrogate biomarkers in clinical routine

Intraspecific variability in aquatic plant response to chemical contaminants

Im Zuge dieser Studie wurden Labortests zur Untersuchung des Einflusses von intraspezifischer Variabilität der beiden Makrophyten Lemna minor L. und Ceratophyllum demersum L. in Bezug auf Kontaminierung mit den Schadstoffen Atrazin und Kupfer durchgeführt. In einem ersten Dosis-Wirkungs-Experiment wurden L. minor Individuen verschieden hohe Atrazin (0, 3.75, 7.5, 15, 30, 60, 100, 120, 240, 480, 960gL-1) und Kupfer (0, 0.025, 0.05, 0.1, 0.25, 0.5, 0.75, 1, 2, 5, 10, 15mgL-1) Konzentrationen ausgesetzt um den negativen Einfluss der Schadstoffe unter stabilen Umweltbedingungen zu bestimmen, und um EC50 Werte für die darauffolgenden Tests zur erhalten. Für Atrazin wurden 122,1g L-1 und für Kupfer 0.69mg L-1 als EC50-Werte bestimmt. In einem zweiten Experiment zur Genetischen Variation wurden L. minor und C. demersum Individuen von geographisch voneinander getrennten Sub-Einzugsgebieten (Dordogne, Garonne, Tarn) im Süd-Westen von Frankreich auf deren Reaktion auf Atrazin und Kupfer getestet um mögliche Unterschiede auf Grund von genetischer Variation zu finden. Unterschiedliche Genotypen wurden aufgrund von räumlicher Distanz angenommen. Nur C. demersum Individuen aus dem Sub-Einzugsgebiet Tarn zeigten unterschiedliche Reaktionen gegenüber den Schadstoffen. Zuletzt wurde ein Experiment zur Bestimmung phänotypischer Unterschiede von L. minor in Bezug auf Schadstoffe und wechselnden Umweltfaktoren durchgeführt. Individuen aus dem Einzugsgebiet der Garonne, welche unter sterilen Bedingungen kultiviert wurden, wurden acht unterschiedlichen Umweltgruppen in einer 14 Tage andauernden PRE-CONTAMINATION Phase ausgesetzt. In einem zweiten Schritt, der CONTAMINATION-EXPOSURE Phase wurden diese Individuen unter dem Abzug in Gefäße mit gleichen bzw. geänderten Umweltfaktoren übertragen. Das Resultat zeigte, dass unterschiedliche Nährstoff-Konzentrationen unterschiedliche Reaktionen auf Schadstoffe auslösen. Daraus wird gefolgert, dass phänotypische Unterschiede eine wichtige Rolle bei der Anpassung an neu auftretende Umweltbedingungen spielen. In Bezug auf Klimawandel und steigenden Schadstoffbelastungen ist eine erhöhte ökologische Toleranz für Organismen von Vorteil.Intra-specific variability in the response of Lemna minor and Ceratophyllum demersum, two aquatic macrophyte species towards chemical contamination was tested in a laboratory environment. In a first Dose-Response experiment L. minor individuals were exposed to atrazine (0, 3.75, 7.5, 15, 30, 60, 100, 120, 240, 480, 960gL-1) and copper (0, 0.025, 0.05, 0.1, 0.25, 0.5, 0.75, 1, 2, 5, 10, 15mgL-1) concentrations in order to evaluate the effect of the contaminants under stable environmental conditions and to determine EC50 values which were intended to be used for subsequent tests. For atrazine 122.1g L-1 and for copper 0.69mg L-1 had been determined as EC50 values. In a second Genetic Variability experiment L. minor and C. demersum individuals from geographically distinct sampling sites within the three subcatchments Dordogne, Garonne and Tarn in the south-west of France in order to determine possible differences in the response to the contaminants atrazine (100g L-1) and copper (1.5mg L-1). Only C. demersum individuals of the Tarn region responded differently, indicating such pattern. Lastly a Phenotypic plasticity experiment testing the environmental influence on L. minor individuals was conducted. Therefore plants of the Garonne catchment, which were kept under axenic conditions, were exposed to eight different environmental groups in a PRE-CONTAMINATION (14 days). They were then in a second step, the CONTAMINTATION-EXPOSURE phase transferred under a fume hood to flasks with the same, and to flasks with different environmental conditions. Additionally a control and an increased exposure group (1.5mg L-1 Cu) were established. The result showed that a change in nutrients conditions influences the contamination response. It is therefore concluded that phenotypic plasticity plays an important role in acclimatization to newly occurring environmental conditions. Especially in consideration of climate change and pollution scenarios that will occur in the near future, plastic organisms may benefit from the advantage of being able to live up to changing environments more easily. However further research is required to quantify and elucidate these mechanisms and to rework experimental designs.Andreas ScharmüllerMit deutscher ZusammenfassungUniversität für Bodenkultur Wien, Masterarbeit, 2016(VLID)193560

Standartox: Standardizing Toxicity Data

An increasing number of chemicals such as pharmaceuticals, pesticides and synthetic hormones are in daily use all over the world. In the environment, chemicals can adversely affect populations and communities and in turn related ecosystem functions. To evaluate the risks from chemicals for ecosystems, data on their toxicity, which are typically produced in standardized ecotoxicological laboratory tests, is required. The results from ecotoxicological tests are compiled in (meta-)databases such as the United States Environmental Protection Agency (EPA) ECOTOXicology Knowledgebase (ECOTOX). However, for many chemicals, multiple ecotoxicity data are available for the same test organism. These can vary strongly, thereby causing uncertainty of related analyses. Given that most current databases lack aggregation steps or are confined to specific chemicals, we developed Standartox, a tool and database that continuously incorporates the ever-growing number of test results in an automated process workflow that ultimately leads to a single aggregated data point for a specific chemical-organism test combination, representing the toxicity of a chemical. Standartox can be accessed through a web application and an R package

Fungicides: An Overlooked Pesticide Class?

Fungicides are indispensable to global food security and their use is forecasted to intensify. Fungicides can reach aquatic ecosystems and occur in surface water bodies in agricultural catchments throughout the entire growing season due to their frequent, prophylactic application. However, in comparison to herbicides and insecticides, the exposure to and effects of fungicides have received less attention. We provide an overview of the risk of fungicides to aquatic ecosystems covering fungicide exposure (i.e., environmental fate, exposure modeling, and mitigation measures) as well as direct and indirect effects of fungicides on microorganisms, macrophytes, invertebrates, and vertebrates. We show that fungicides occur widely in aquatic systems, that the accuracy of predicted environmental concentrations is debatable, and that fungicide exposure can be effectively mitigated. We additionally demonstrate that fungicides can be highly toxic to a broad range of organisms and can pose a risk to aquatic biota. Finally, we outline central research gaps that currently challenge our ability to predict fungicide exposure and effects, promising research avenues, and shortcomings of the current environmental risk assessment for fungicides.</p