Extending the application range of optical nanoscopy

Diekmann R. Extending the application range of optical nanoscopy. Bielefeld: Universität Bielefeld; 2017

Nanoscopy of bacterial cells immobilized by holographic optical tweezers

Diekmann R, Wolfson D, Spahn C, Heilemann M, Schüttpelz M, Huser T. Nanoscopy of bacterial cells immobilized by holographic optical tweezers. Nature Communications. 2016;7(1): 13711

Publisher Correction: Breaking the speed limit with multimode fast scanning of DNA by Endonuclease V.

Ahmadi A, Rosnes I, Blicher P, et al. Publisher Correction: Breaking the speed limit with multimode fast scanning of DNA by Endonuclease V. Nature communications. 2019;10(1): 1991.The original version of this Article was updated shortly after publication to add a link to the Peer Review file, which was inadvertently omitted. The Peer Review file is available to download as a Supplementary File from the HTML version of the Article

Characterization of an industry-grade CMOS camera well suited for single molecule localization microscopy – high performance super-resolution at low cost

Diekmann R, Till K, Müller M, Simonis M, Schüttpelz M, Huser T. Characterization of an industry-grade CMOS camera well suited for single molecule localization microscopy – high performance super-resolution at low cost. Scientific Reports. 2017;7(1): 14425.Many commercial as well as custom-built fluorescence microscopes use scientific-grade cameras that represent a substantial share of the instrument’s cost. This holds particularly true for super-resolution localization microscopy where high demands are placed especially on the detector with respect to sensitivity, noise, and also image acquisition speed. Here, we present and carefully characterize an industry-grade CMOS camera as a cost-efficient alternative to commonly used scientific cameras. Direct experimental comparison of these two detector types shows widely similar performance for imaging by single molecule localization microscopy (SMLM). Furthermore, high image acquisition speeds are demonstrated for the CMOS detector by ultra-fast SMLM imaging

Cost-efficient nanoscopy reveals nanoscale architecture of liver cells and platelets

Single-molecule localization microscopy (SMLM) provides a powerful toolkit to specifically resolve intracellular structures on the nanometer scale, even approaching resolution classically reserved for electron microscopy (EM). Although instruments for SMLM are technically simple to implement, researchers tend to stick to commercial microscopes for SMLM implementations. Here we report the construction and use of a “custom-built” multi-color channel SMLM system to study liver sinusoidal endothelial cells (LSECs) and platelets, which costs significantly less than a commercial system. This microscope allows the introduction of highly affordable and low-maintenance SMLM hardware and methods to laboratories that, for example, lack access to core facilities housing high-end commercial microscopes for SMLM and EM. Using our custom-built microscope and freely available software from image acquisition to analysis, we image LSECs and platelets with lateral resolution down to about 50 nm. Furthermore, we use this microscope to examine the effect of drugs and toxins on cellular morphology

Life strategies of cephalopod paralarvae in a coastal upwelling system (NW Iberian Peninsula): Insights from zooplankton community and spatio-temporal analyses

18 páginas, 6 figuras, 6 tablasThe early life stages of cephalopods - octopods, squids, sepiolids and ommastrephids -, are uncommon in zooplankton samples and little is known about their life strategies. Accordingly, cephalopod paralarvae were examined in the upwelling ecosystem of the Ría de Vigo (NW Spain) at night from 2008 to 2010. Multivariate analyses and generalized linear models (GLMs) were used to explore relationships between cephalopod paralarvae and the zooplankton communities that they inhabited in 2008. In addition, the foraging strategy and prey preferences of Octopus vulgaris paralarvae within these communities were determined. Multivariate and GLM results showed a strong association of cephalopod paralarvae with coastal and frontal zooplankton communities. Octopus paralarvae were shown to be specialist predators with a strong preference for decapod zoeae in each of the communities examined. Using the three years of sampling, GLM analyses of paralarval spatio-temporal variations in relation with the upwelling strength showed a positive relationship with upwelling intensity for O. vulgaris and sepiolids, as well as contrasting temporal, horizontal and vertical distributions for the different paralarvae analysed. Under strong upwelling events, Octopus paralarvae were more abundant in surface waters, whereas the abundance of loliginids and sepiolids was higher in the water column. This vertical behaviour in conjunction with the physical conditions of the Western Iberian Upwelling ecosystem suggests the coexistence of two different life strategies: a coastal strategy displayed by loliginid and sepiolid paralarvae that are retained over the shelf, and an oceanic strategy displayed by O. vulgaris paralarvae that are dispersed far from the shelfThis study was supported by the projects CAIBEX (Spanish Ministry of Innovation and Science CTM2007-66408-C02), LARECO (CTM2011-25929) and FEDER Funds. The first author was supported by a JAE-Predoc fellowship during the sampling, and a ‘Fundacion Barrie de la Maza’ postdoctoral fellowship and RFA funds (La Trobe University, Melbourne) during the writing of the manuscript. J.O. acknowledges the support by a ‘Junta para la Ampliacion de Estudios’ Fellowship (JAE-Doc programme 2011) from the CSIC and ESFPeer reviewe

GrassPlot - a database of multi-scale plant diversity in Palaearctic grasslands

GrassPlot is a collaborative vegetation-plot database organised by the Eurasian Dry Grassland Group (EDGG) and listed in the Global Index of Vegetation-Plot Databases (GIVD ID EU-00-003). GrassPlot collects plot records (releves) from grasslands and other open habitats of the Palaearctic biogeographic realm. It focuses on precisely delimited plots of eight standard grain sizes (0.0001; 0.001;... 1,000 m(2)) and on nested-plot series with at least four different grain sizes. The usage of GrassPlot is regulated through Bylaws that intend to balance the interests of data contributors and data users. The current version (v. 1.00) contains data for approximately 170,000 plots of different sizes and 2,800 nested-plot series. The key components are richness data and metadata. However, most included datasets also encompass compositional data. About 14,000 plots have near-complete records of terricolous bryophytes and lichens in addition to vascular plants. At present, GrassPlot contains data from 36 countries throughout the Palaearctic, spread across elevational gradients and major grassland types. GrassPlot with its multi-scale and multi-taxon focus complements the larger international vegetationplot databases, such as the European Vegetation Archive (EVA) and the global database " sPlot". Its main aim is to facilitate studies on the scale-and taxon-dependency of biodiversity patterns and drivers along macroecological gradients. GrassPlot is a dynamic database and will expand through new data collection coordinated by the elected Governing Board. We invite researchers with suitable data to join GrassPlot. Researchers with project ideas addressable with GrassPlot data are welcome to submit proposals to the Governing Board

<scp>ReSurveyEurope</scp>: A database of resurveyed vegetation plots in Europe

AbstractAimsWe introduce ReSurveyEurope — a new data source of resurveyed vegetation plots in Europe, compiled by a collaborative network of vegetation scientists. We describe the scope of this initiative, provide an overview of currently available data, governance, data contribution rules, and accessibility. In addition, we outline further steps, including potential research questions.ResultsReSurveyEurope includes resurveyed vegetation plots from all habitats. Version 1.0 of ReSurveyEurope contains 283,135 observations (i.e., individual surveys of each plot) from 79,190 plots sampled in 449 independent resurvey projects. Of these, 62,139 (78%) are permanent plots, that is, marked in situ, or located with GPS, which allow for high spatial accuracy in resurvey. The remaining 17,051 (22%) plots are from studies in which plots from the initial survey could not be exactly relocated. Four data sets, which together account for 28,470 (36%) plots, provide only presence/absence information on plant species, while the remaining 50,720 (64%) plots contain abundance information (e.g., percentage cover or cover–abundance classes such as variants of the Braun‐Blanquet scale). The oldest plots were sampled in 1911 in the Swiss Alps, while most plots were sampled between 1950 and 2020.ConclusionsReSurveyEurope is a new resource to address a wide range of research questions on fine‐scale changes in European vegetation. The initiative is devoted to an inclusive and transparent governance and data usage approach, based on slightly adapted rules of the well‐established European Vegetation Archive (EVA). ReSurveyEurope data are ready for use, and proposals for analyses of the data set can be submitted at any time to the coordinators. Still, further data contributions are highly welcome.</jats:sec

Nanoscopy of bacterial cells immobilized by holographic optical tweezers

Imaging non-adherent cells by super-resolution far-field fluorescence microscopy is currently not possible because of their rapid movement while in suspension. Holographic optical tweezers (HOTs) enable the ability to freely control the number and position of optical traps, thus facilitating the unrestricted manipulation of cells in a volume around the focal plane. Here we show that immobilizing non-adherent cells by optical tweezers is sufficient to achieve optical resolution well below the diffraction limit using localization microscopy. Individual cells can be oriented arbitrarily but preferably either horizontally or vertically relative to the microscope’s image plane, enabling access to sample sections that are impossible to achieve with conventional sample preparation and immobilization. This opens up new opportunities to super-resolve the nanoscale organization of chromosomal DNA in individual bacterial cells