CLEMSite, a software for automated phenotypic screens using light microscopy and FIB-SEM

This work was supported by EMBL funds and by by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project number 240245660 – SFB 1129 (project Z2).In recent years, Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) has emerged as a flexible method that enables semi-automated volume ultrastructural imaging. We present a toolset for adherent cells that enables tracking and finding cells, previously identified in light microscopy (LM), in the FIB-SEM, along with the automatic acquisition of high-resolution volume datasets. We detect the underlying grid pattern in both modalities (LM and EM), to identify common reference points. A combination of computer vision techniques enables complete automation of the workflow. This includes setting the coincidence point of both ion and electron beams, automated evaluation of the image quality and constantly tracking the sample position with the microscope’s field of view reducing or even eliminating operator supervision. We show the ability to target the regions of interest in EM within 5 µm accuracy while iterating between different targets and implementing unattended data acquisition. Our results demonstrate that executing volume acquisition in multiple locations autonomously is possible in EM.Publisher PDFPeer reviewe

Applying cumulative effects to strategically advance large-scale ecosystem restoration

International efforts to restore degraded ecosystems will continue to expand over the coming decades, yet the factors contributing to the effectiveness of long-term restoration across large areas remain largely unexplored. At large scales, outcomes are more complex and synergistic than the additive impacts of individual restoration projects. Here, we propose a cumulative-effects conceptual framework to inform restoration design and implementation and to comprehensively measure ecological outcomes. To evaluate and illustrate this approach, we reviewed long-term restoration in several large coastal and riverine areas across the US: the greater Florida Everglades; Gulf of Mexico coast; lower Columbia River and estuary; Puget Sound; San Francisco Bay and Sacramento–San Joaquin Delta; Missouri River; and northeastern coastal states. Evidence supported eight modes of cumulative effects of interacting restoration projects, which improved outcomes for species and ecosystems at landscape and regional scales. We conclude that cumulative effects, usually measured for ecosystem degradation, are also measurable for ecosystem restoration. The consideration of evidence-based cumulative effects will help managers of large-scale restoration capitalize on positive feedback and reduce countervailing effects

Groundwater dynamics in coastal gravel barriers backed by freshwater lagoons and the potential for saline intrusion: Two cases from the UK

“NOTICE: this is the author’s version of a work that was accepted for publication in Journal of Marine Systems. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Journal of Marine Systems, [VOL 123, (01.08.13)] DOI 10.1016/j.jmarsys.2013.04.004". The full text is under embargo until 01.08.15

Localized topological changes of the plasma membrane upon exocytosis visualized by polarized TIRFM

Imaging of individual secretory granules reveals how exocytosis curves the membrane

Nanoscale Visualization of Elastic Inhomogeneities at TiN Coatings Using Ultrasonic Force Microscopy

Ultrasonic force microscopy has been applied to the characterization of titanium nitride coatings deposited by physical vapor deposition dc magnetron sputtering on stainless steel substrates. The titanium nitride layers exhibit a rich variety of elastic contrast in the ultrasonic force microscopy images. Nanoscale inhomogeneities in stiffness on the titanium nitride films have been attributed to softer substoichiometric titanium nitride species and/or trapped subsurface gas. The results show that increasing the sputtering power at the Ti cathode increases the elastic homogeneity of the titanium nitride layers on the nanometer scale. Ultrasonic force microscopy elastic mapping on titanium nitride layers demonstrates the capability of the technique to provide information of high value for the engineering of improved coatings

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Selecting teachers and prospective teachers : a meta-analysis

The purpose of this review article was to examine the methods used for the selection of teachers for employment and prospective teachers entering initial teacher education (ITE) programs, and to assess the predictive validity of these methods. We reviewed 32 studies reporting selection methods administered in high-stakes conditions and that included an external (not self-reported) teacher effectiveness outcome measure. The overall effect size was small but significant (r = 0.12, p <.001). Moderator analyses showed that academic and non-academic predictors were both significantly associated with teacher effectiveness measures and that effect sizes were small (but significant) for selection into employment and ITE. We conclude the review by proposing a research agenda that has the potential to enhance educational outcomes by improving the selection of prospective teachers

Consortia of the oleaginous yeast Lipomyces starkeyi and the microalga Chlamydomonas reinhardtii for microbial oil production

Renewable energy is necessary to reduce our dependence on fossil fuels and can help to substantially lower the emission of the greenhouse gas carbon dioxide. A growing effort is being devoted to the use of non-food feedstocks to obtain microbial Single-Cell Oils (SCO) suitable for the production of biodiesel, bioplastics and other products [1]. Lignocellulosic biomass is the most abundant residue of agricultural crops. Various pretreatment methods to hydrolyze the complex fibers produce organic molecules such as glucose, xylose and acetate, which can be used as substrates for oleaginous microorganisms to produce SCO. Yeasts and microalgae have been most often used for the industrial production of SCO [2]. The yeast Lipomyces starkeyi is very efficient in accumulating high levels of lipids [3]. In aerobic conditions it exhibits high growth rates, involving high levels of O2 consumption and CO2 emission. When cultivated in consortium, microalgae can provide O2 to the yeast and consume its CO2 if light is present. This virtuous gas exchange cycle is projected to maximize the yield of biomass and oil production. Questions regarding a yeast-alga system relate to the proper medium and conditions to support growth of the consortium, the growth rates and yields of biomass and lipids, and the extent to which the system is symbiotic/synergistic.In this work, we have developed a system using L. starkeyi and the green alga Chlamydomonas reinhardtii. The yeast can use the sugars found in lignocellulosic hydrolysate, whereas the alga can use only acetate. Due to this specific complementarity, competition for carbon is very low in these consortia, which may imply higher carbon conversion efficiency. To test the consortium in clearly defined conditions, a synthetic medium was developed that integrates necessary elements of known culture media for both organisms, with the use of pH control. Growth series were done in batch, under constant light, agitation and temperature, in closed bottles to monitor gas exchange. In this model system, symbiotic growth was observed of the consortium with synergistic effects on biomass yield. Similar results were obtained in a system using the hydrolysate of acid-treated wheat straw, except for an increase in lag phase due the presence of phenols. Growth even in nitrogen-flushed bottles confirmed the interdependence of the microalga and the oleaginous yeast. The performance of the consortium under different conditions is discussed in terms of growth rate, substrate assimilation, gas exchange, biomass production and lipid content of the biomass

Consortia of the oleaginous yeast Lipomyces starkeyi and the microalga Chlamydomonas reinhardtii for microbial oil production

Renewable energy is necessary to reduce our dependence on fossil fuels and can help to substantially lower the emission of the greenhouse gas carbon dioxide. A growing effort is being devoted to the use of non-food feedstocks to obtain microbial Single-Cell Oils (SCO) suitable for the production of biodiesel, bioplastics and other products [1]. Lignocellulosic biomass is the most abundant residue of agricultural crops. Various pretreatment methods to hydrolyze the complex fibers produce organic molecules such as glucose, xylose and acetate, which can be used as substrates for oleaginous microorganisms to produce SCO. Yeasts and microalgae have been most often used for the industrial production of SCO [2]. The yeast Lipomyces starkeyi is very efficient in accumulating high levels of lipids [3]. In aerobic conditions it exhibits high growth rates, involving high levels of O2 consumption and CO2 emission. When cultivated in consortium, microalgae can provide O2 to the yeast and consume its CO2 if light is present. This virtuous gas exchange cycle is projected to maximize the yield of biomass and oil production. Questions regarding a yeast-alga system relate to the proper medium and conditions to support growth of the consortium, the growth rates and yields of biomass and lipids, and the extent to which the system is symbiotic/synergistic.In this work, we have developed a system using L. starkeyi and the green alga Chlamydomonas reinhardtii. The yeast can use the sugars found in lignocellulosic hydrolysate, whereas the alga can use only acetate. Due to this specific complementarity, competition for carbon is very low in these consortia, which may imply higher carbon conversion efficiency. To test the consortium in clearly defined conditions, a synthetic medium was developed that integrates necessary elements of known culture media for both organisms, with the use of pH control. Growth series were done in batch, under constant light, agitation and temperature, in closed bottles to monitor gas exchange. In this model system, symbiotic growth was observed of the consortium with synergistic effects on biomass yield. Similar results were obtained in a system using the hydrolysate of acid-treated wheat straw, except for an increase in lag phase due the presence of phenols. Growth even in nitrogen-flushed bottles confirmed the interdependence of the microalga and the oleaginous yeast. The performance of the consortium under different conditions is discussed in terms of growth rate, substrate assimilation, gas exchange, biomass production and lipid content of the biomass

Sampling protocols and risk of error significance in molecular detection tests for fruit trees certification.

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