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Abstract Background Studies on innate immunity have benefited from the introduction of zebrafish as a model system. Transgenic fish expressing fluorescent proteins in leukocyte populations allow direct, quantitative visualization of an inflammatory response in vivo. It has been proposed that this animal model can be used for high-throughput screens aimed at the identification of novel immunomodulatory lead compounds. However, current assays require invasive manipulation of fish individually, thus preventing high-content screening. Results Here we show that specific, noninvasive damage to lateral line neuromast cells can induce a robust acute inflammatory response. Exposure of fish larvae to sublethal concentrations of copper sulfate selectively damages the sensory hair cell population inducing infiltration of leukocytes to neuromasts within 20 minutes. Inflammation can be assayed in real time using transgenic fish expressing fluorescent proteins in leukocytes or by histochemical assays in fixed larvae. We demonstrate the usefulness of this method for chemical and genetic screens to detect the effect of immunomodulatory compounds and mutations affecting the leukocyte response. Moreover, we transformed the assay into a high-throughput screening method by using a customized automated imaging and processing system that quantifies the magnitude of the inflammatory reaction. Conclusions This approach allows rapid screening of thousands of compounds or mutagenized zebrafish for effects on inflammation and enables the identification of novel players in the regulation of innate immunity and potential lead compounds toward new immunomodulatory therapies. We have called this method the chemically induced inflammation assay, or ChIn assay. See Commentary article: http://www.biomedcentral.com/1741-7007/8/148.

High incidences of the foodborne pathogen Listeria monocytogenes have been reported on smear cheeses, and despite increased hygiene efforts, this incidence has remained stable in recent years. Applying antilisterial strains may increase the safety of smear cheeses. To find and test antilisterial strains, we inoculated fresh soft cheeses from nine dairies with the surrogate species Listeria innocua and assessed its growth under standardized ripening conditions. Acetic acid at day 23 (r = -0.66), lactose in fresh cheese (r = -0.63), and glucose at day 10 (r = -0.62), as well as seven amplicon sequence variants (ASVs), were negatively correlated with L. innocua growth. Two of these ASVs were assigned to the genus Leuconostoc of Lactobacillaceae (r = -0.82 and -0.71). Isolates from this family, from Aerococcaceae, and Carnobacteriaceae were characterized according to their inhibitory properties, and those showing antilisterial properties were applied as protective cultures in challenge tests. The combined application of strains of Leuconostoc mesenteroides , Aerococcaceae, and Carnobacteriaceae successfully eliminated low levels of L. innocua in the final products. This is likely explained by antimicrobial compounds, including mesentericin Y105 and acetate, and competition for carbon sources and iron. This study shows a promising way to improve the safety of soft smear cheeses by applying defined protective cultures.

How the timing of development is linked to organismal size is a longstanding question. Although numerous studies have reported a correlation of temporal and spatial traits, the developmental or selective constraints underlying this link remain largely unexplored. We address this question by studying the periodic process of embryonic axis segmentation in-vivo in Oryzias fish. Interspecies comparisons reveal that the timing of segmentation correlates to segment, tissue and organismal size. Segment size in turn scales according to tissue and organism size. To probe for underlying causes, we genetically hybridised two closely related species. Quantitative analysis in ~600 phenotypically diverse F2 embryos reveals a decoupling of timing from size control, while spatial scaling is preserved. Using developmental quantitative trait loci (devQTL) mapping we identify distinct genetic loci linked to either the control of segmentation timing or tissue size. This study demonstrates that a developmental constraint mechanism underlies spatial scaling of axis segmentation, while its spatial and temporal control are dissociable modules., (© 2024. The Author(s).)

The dissolution of a nanomaterial (NM) in an in vitro simulant of the oro-gastrointestinal (OGI) tract is an important predictor of its biodurability in vivo . The cascade addition of simulated digestive juices (saliva, stomach and intestine), including inorganic/organic biomacromolecules and digestive enzymes (complete composition, referred to as "Type 1 formulation"), strives for realistic representation of chemical composition of the OGI tract. However, the data robustness requires consideration of analytical feasibility, such as the use of simplified media. Here we present a systematic analysis of the effects exerted by different digestive juice formulations on the dissolution% (or half-life values) of benchmark NMs ( e.g. , zinc oxide, titanium dioxide, barium sulfate, and silicon dioxide). The digestive juices were progressively simplified by removal of components such as organic molecules, enzymes, and inorganic molecules (Type 2, 3 and 4). The results indicate that the "Type 1 formulation" augments the dissolution via sequestration of ions by measurable factors compared to formulations without enzymes ( i.e. , Type 3 and 4). Type 1 formulation is thus regarded as a preferable option for predicting NM biodurability for hazard assessment. However, for grouping purposes, the relative similarity among diverse nanoforms (NFs) of a NM is decisive. Two similarity algorithms were applied, and additional case studies comprising NFs and non NFs of the same substance were included. The results support the grouping decision by simplified formulation (Type 3) as a robust method for screening and grouping purposes., Competing Interests: At the time of the study, JGK and WW were employees of BASF SE, a company producing nanomaterials. The other authors declare that they have no competing interests., (This journal is © The Royal Society of Chemistry.)

The profession of firefighter working on the rescue and emergency care involves many skills and requirements. The Health Sub-Directorate's supervisory division oversees the activities of these agents in partnership with the Operations, Forecasting and Prevention Division. A firefighter nurse is present on the site and watches over the 250 to 350 daily interventions., (Copyright © 2023 Elsevier Masson SAS. All rights reserved.)

Objective: A 2-year sampling campaign was realized on French Mediterranean beach (Palavas-les-Flots Hérault) in order to measure the concentration of UV filters released from the sunscreen used by bathers. Multiple factors suspected of playing determining roles in the UV filter pattern in water were explored, such as the seasonal and daily time evolutions, or the vertical and horizontal distributions, and they were regarded through the UV filter characteristics., Methods: The beach was monitored during periods of high and low tourist attendance, typically before, during and after the summer peak. The beachgoers attendance was counted. Bathing water was sampled distinctly from the bulk column and from the top surface layer, testing different sampling tools. Sediments and mussels were also sampled and analysed as potential UV filter sinks. Three organic UV filters (octocrylene OCR, avobenzone BMDBM and octyl methoxycinnamate OMC) and one mineral (titanium dioxide TiO 2 ) were studied here as representatives of the current cosmetic market., Results: Summer peak attendance on the beach was confirmed associated with peak levels of UV filter concentration in the bathing water, even more pronounced during a heat wave period. This relation was also observed at day scale with an afternoon peak, suggesting a rapid evolution of the UV filter pattern in water. Contrasted fates were measured between the four studied UV filters, that could be mainly explained by their respective characteristics, i.e. particulate or dissolved, hydrophilic or lipophilic, lifetime. Generally, this resulted in a concentration ranking TiO 2  > OCR > OMC > BMDBM, ranging from 0.5 to 500 μg/L. The most lipophilic and recalcitrant OCR was found most vertically differentiated and over concentrated in the top surface layer of water. Finally, a large horizontal heterogeneity was also observed in the UV filter concentration pattern, raising the need for sample replicates that cover a significant area., Conclusion: This work fulfils some knowledge gaps on the issue of UV filter release in coastal environments, not only by providing original field data and methodological recommendations but also importantly in the comparison made of organic and mineral UV filters, which are often considered separately and rarely evaluated at the same time., (© 2023 The Authors. International Journal of Cosmetic Science published by John Wiley & Sons Ltd on behalf of Society of Cosmetic Scientists and Societe Francaise de Cosmetologie.)

The assembly of the embryo's primary axis is a fundamental landmark for the establishment of the vertebrate body plan. Although the morphogenetic movements directing cell convergence towards the midline have been described extensively, little is known on how gastrulating cells interpret mechanical cues. Yap proteins are well-known transcriptional mechanotransducers, yet their role in gastrulation remains elusive. Here we show that the double knockout of yap and its paralog yap1b in medaka results in an axis assembly failure, due to reduced displacement and migratory persistence in mutant cells. Accordingly, we identified genes involved in cytoskeletal organization and cell-ECM adhesion as potentially direct Yap targets. Dynamic analysis of live sensors and downstream targets reveal that Yap is acting in migratory cells, promoting cortical actin and focal adhesions recruitment. Our results indicate that Yap coordinates a mechanoregulatory program to sustain intracellular tension and maintain the directed cell migration for embryo axis development., (© 2023. The Author(s).)

Assessing the integrity of neural functions in coma after cardiac arrest remains an open challenge. Prognostication of coma outcome relies mainly on visual expert scoring of physiological signals, which is prone to subjectivity and leaves a considerable number of patients in a 'grey zone', with uncertain prognosis. Quantitative analysis of EEG responses to auditory stimuli can provide a window into neural functions in coma and information about patients' chances of awakening. However, responses to standardized auditory stimulation are far from being used in a clinical routine due to heterogeneous and cumbersome protocols. Here, we hypothesize that convolutional neural networks can assist in extracting interpretable patterns of EEG responses to auditory stimuli during the first day of coma that are predictive of patients' chances of awakening and survival at 3 months. We used convolutional neural networks (CNNs) to model single-trial EEG responses to auditory stimuli in the first day of coma, under standardized sedation and targeted temperature management, in a multicentre and multiprotocol patient cohort and predict outcome at 3 months. The use of CNNs resulted in a positive predictive power for predicting awakening of 0.83 ± 0.04 and 0.81 ± 0.06 and an area under the curve in predicting outcome of 0.69 ± 0.05 and 0.70 ± 0.05, for patients undergoing therapeutic hypothermia and normothermia, respectively. These results also persisted in a subset of patients that were in a clinical 'grey zone'. The network's confidence in predicting outcome was based on interpretable features: it strongly correlated to the neural synchrony and complexity of EEG responses and was modulated by independent clinical evaluations, such as the EEG reactivity, background burst-suppression or motor responses. Our results highlight the strong potential of interpretable deep learning algorithms in combination with auditory stimulation to improve prognostication of coma outcome., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Guarantors of Brain.)

Morphological left-right brain asymmetries are universal phenomena in animals. These features have been studied for decades, but the functional relevance is often unclear. Studies from the zebrafish dorsal diencephalon on the genetics underlying the establishment and function of brain asymmetries have uncovered genes associated with the development of functional brain asymmetries. To gain further insights, comparative studies help to investigate the emergence of asymmetries and underlying genetics in connection to functional adaptation. Evolutionarily distant isogenic medaka inbred lines, that show divergence of complex traits such as morphology, physiology and behavior, are a valuable resource to investigate intra-species variations in a given trait of interest. For a detailed study of asymmetry in the medaka diencephalon we generated molecular probes of ten medaka genes that are expressed asymmetrically in the zebrafish habenulae and pineal complex. We find expression of eight genes in the corresponding brain areas of medaka with differences in the extent of left-right asymmetry compared to zebrafish. Our marker gene analysis of the diverged medaka inbred strains revealed marked inter-strain size differences of the respective expression domains in the parapineal and the habenulae, which we hypothesize may result from strain-specific gene loss. Thus, our analysis reveals both inter-species differences but also intra-species plasticity of gene expression in the teleost dorsal diencephalon. These findings are a starting point showing the potential to identify the genetics underlying the emergence and modulations of asymmetries. They are also the prerequisite to examine whether variance in habenular gene expression may cause variation of behavioral traits., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Agostini, Bühler, Antico Calderone, Aadepu, Herder, Loosli and Carl.)

Teleosts display the highest level of brain plasticity of all vertebrates. Yet we still know little about how seasonality affects fish behaviour and the underlying cognitive mechanisms since the common neurobehavioral fish models are native to tropical environments where seasonal variation is absent or reduced. The medaka, Oryzias latipes, which inhabits temperate zone habitats, represents a promising model in this context given its large phenotypic changes associated with seasonality and the possibility to induce seasonal plasticity by only manipulating photoperiod. Here, we report the first extended investigation of seasonal plasticity in medaka behaviour and cognition, as well as the potential underlying molecular mechanisms. We compared medaka exposed to summer photoperiod (16 h light:8 h dark) with medaka exposed to winter photoperiod (8 h light:16 h dark), and detected substantial differences. Medaka were more active and less social in summer photoperiod conditions, two effects that emerged in the second half of an open-field and a sociability test, respectively, and might be at least in part related to habituation to the testing apparatus. Moreover, the cognitive phenotype was significantly affected: in the early response to a social stimulus, brain functional lateralisation shifted between the two hemispheres under the two photoperiod conditions, and inhibitory and discrimination learning performance were reduced in summer conditions. Finally, the expression of genes encoding key pituitary hormones, tshß and gh, and of the tshß regulatory transcription factor tef in the brain was increased in summer photoperiod conditions. This work reveals remarkable behavioural and cognitive phenotypic plasticity in response to photoperiod in medaka, and suggests a potential regulatory role for the same hormones involved in seasonal plasticity of other vertebrates., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Nanoforms (NFs) of a substance may be distinguished from one another through differences in their physicochemical properties. When registering nanoforms of a substance for assessment under the EU REACH framework, five basic descriptors are required for their identification: composition, surface chemistry, size, specific surface area and shape. To make the risk assessment of similar NFs efficient, a number of grouping frameworks have been proposed, which often require assessment of similarity on individual physicochemical properties as part of the group justification. Similarity assessment requires an understanding of the achievable accuracy of the available methods. It must be demonstrated that measured differences between NFs are greater than the achievable accuracy of the method, to have confidence that the measured differences are indeed real. To estimate the achievable accuracy of a method, we assess the reproducibility of six analytical techniques routinely used to measure these five basic descriptors of nanoforms: inductively coupled plasma mass spectrometry (ICP-MS), Thermogravimetric analysis (TGA), Electrophoretic light scattering (ELS), Brunauer-Emmett-Teller (BET) specific surface area and transmission and scanning electron microscopy (TEM and SEM). Assessment was performed on representative test materials to evaluate the reproducibility of methods on single NFs of substances. The achievable accuracy was defined as the relative standard deviation of reproducibility (RSD R ) for each method. Well established methods such as ICP-MS quantification of metal impurities, BET measurements of specific surface area, TEM and SEM for size and shape and ELS for surface potential and isoelectric point, all performed well, with low RSD R , generally between 5 and 20%, with maximal fold differences usually <1.5 fold between laboratories. Applications of technologies such as TGA for measuring water content and putative organic impurities, additives or surface treatments (through loss on ignition), which have a lower technology readiness level, demonstrated poorer reproducibility, but still within 5-fold differences. The expected achievable accuracy of ICP-MS may be estimated for untested analytes using established relationships between concentration and reproducibility, but this is not yet the case for TGA measurements of loss on ignition or water content. The results here demonstrate an approach to estimate the achievable accuracy of a method that should be employed when interpreting differences between NFs on individual physicochemical properties., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

The medaka, Oryzias latipes, is rapidly growing in importance as a model in behavioural research. However, our knowledge of its behaviour is still incomplete. In this study, we analysed the performance of medaka in 3 tests for anxiety-like behaviour (open-field test, scototaxis test, and diving test) and in 3 sociability tests (shoaling test with live stimuli, octagonal mirror test, and a modified shoaling test with mirror stimulus). The behavioural response of medaka was qualitatively similar to that observed in other teleosts in the open-field test (thigmotaxis), and in 2 sociability tests, the shoaling test and in the octagonal mirror test (attraction towards the social stimulus). In the remaining tests, medaka did not show typical anxiety (i.e., avoidance of light environments and preference for swimming at the bottom of the aquarium) and social responses (attraction towards the social stimulus). As a reference, we compared the behaviour of the medaka to that of a teleost species with well-studied behaviour, the zebrafish, tested under the same conditions. This interspecies comparison indicates several quantitative and qualitative differences across all tests, providing further evidence that the medaka responds differently to the experimental settings compared to other fish models., (© 2022. The Author(s).)

Background: The teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains. Medaka has a high tolerance to inbreeding from the wild, thus allowing one to establish inbred lines from wild founder individuals., Results: We exploit this feature to create an inbred panel resource: the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. This panel of 80 near-isogenic inbred lines contains a large amount of genetic variation inherited from the original wild population. We use Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allows us to identify a large variety of high-quality structural variants, and we present results and methods using a pan-genome graph representation of 12 individual medaka lines. This graph-based reference MIKK panel genome reveals novel differences between the MIKK panel lines and standard linear reference genomes. We find additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. We are also able to identify and quantify the presence of repeat elements in each of the lines. Finally, we investigate line-specific CpG methylation and performed differential DNA methylation analysis across these 12 lines., Conclusions: We present a detailed analysis of the MIKK panel genomes using long and short read sequence technologies, creating a MIKK panel-specific pan genome reference dataset allowing for investigation of novel variation types that would be elusive using standard approaches., (© 2022. The Author(s).)

Background: Unraveling the relationship between genetic variation and phenotypic traits remains a fundamental challenge in biology. Mapping variants underlying complex traits while controlling for confounding environmental factors is often problematic. To address this, we establish a vertebrate genetic resource specifically to allow for robust genotype-to-phenotype investigations. The teleost medaka (Oryzias latipes) is an established genetic model system with a long history of genetic research and a high tolerance to inbreeding from the wild., Results: Here we present the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel: the first near-isogenic panel of 80 inbred lines in a vertebrate model derived from a wild founder population. Inbred lines provide fixed genomes that are a prerequisite for the replication of studies, studies which vary both the genetics and environment in a controlled manner, and functional testing. The MIKK panel will therefore enable phenotype-to-genotype association studies of complex genetic traits while allowing for careful control of interacting factors, with numerous applications in genetic research, human health, drug development, and fundamental biology., Conclusions: Here we present a detailed characterization of the genetic variation across the MIKK panel, which provides a rich and unique genetic resource to the community by enabling large-scale experiments for mapping complex traits., (© 2022. The Author(s).)

Before placing a new nanoform (NF) on the market, its potential adverse effects must be evaluated. This may e.g. be done via hazard and risk assessment. Grouping and read-across of NFs is a possible strategy to reduce resource consumption, maximising the use of existing data for assessment of NFs. The GRACIOUS project provides a framework in which possible grouping and read-across for NFs is mainly based on an evaluation of their similarity. The impact of NFs on human health and the environment depends strongly on the concentration of the NF and its physicochemical properties, such as chemical composition, size distribution, shape, etc. Hence, knowledge of the most relevant physicochemical properties is essential information for comparing similarity. The presented work aims to refine existing proposals for sets of descriptors (descriptor array) that are needed to describe distinct NFs of a material to identify the most relevant ones for grouping and read-across. The selection criteria for refining this descriptor array are explained and demonstrated. Relevant protocols and methods are proposed for each physicochemical property. The required and achievable measurement accuracies of the refined descriptor array are reviewed, as this information is necessary for similarity assessment of NFs based on individual physicochemical properties., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

Nanoparticles (NPs) can be produced via physical, chemical, or biological approaches. Yet, the impact of the synthesis approaches on the environmental fate and effects of NPs is poorly understood. Here, we synthesized AgNPs through chemical and biological approaches (cit-AgNPs and bio-AgNPs), characterized their properties, and toxicities relative to commercially available Ag nanopowder (np-AgNPs) to the clam Mercenaria mercenaria. The chemical synthesis is based on the reduction of ionic silver using sodium borohydride as a reducing agent and trisodium citrate as a capping agent. The biological synthesis is based on the reduction of ionic silver using biomolecules extracted from an atoxigenic strain of a filamentous fungus Aspergillus parasiticus. The properties of AgNPs were determined using UV-vis, dynamic light scattering, laser Doppler electrophoresis, (single particle)-inductively coupled plasma-mass spectroscopy, transmission electron microscopy, and asymmetric flow-field flow fractionation. Both chemical and biological synthesis approaches generated spherical AgNPs. The chemical synthesis produced AgNPs with narrower size distributions than those generated through biological synthesis. The polydispersity of bio-AgNPs decreased with increases in cell free extract (CFE):Ag ratios. The magnitude of the zeta potential of the cit-AgNPs was higher than those of bio-AgNPs. All AgNPs formed aggregates in the test media i.e., natural seawater. Based on the same total Ag concentrations, all AgNPs were less toxic than AgNO 3 . The toxicity of AgNPs toward the juvenile clam, Mercenaria mercenaria, decreased following the order np-AgNPs > cit-AgNPs > bio-AgNPs. Expressed as a function of dissolved Ag concentrations, the toxicity of Ag decreased following the order cit-AgNPs > bio-AgNPs > AgNO 3 ~ np-AgNPs. Therefore, the toxicity of AgNP suspensions can be attributed to a combined effect of dissolved and particulate Ag forms. These results indicate that AgNP synthesis methods determine their environmental and biological behaviors and should be considered for a more comprehensive environmental risk assessment of AgNPs., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The relationship between genetic variation and phenotypic traits is often poorly understood since specific genotypes do not always easily translate into associated phenotypes, especially for complex disorders. The genetic background has been shown to affect metabolic pathways and thus contribute to variations in the metabolome. Here, we tested the suitability of NMR metabolomics for comparative analysis of fish lines as a first step towards phenotype-genotype association studies. The Japanese rice fish, medaka ( Oryzias latipes ), is a widely used genetic vertebrate model with several isogenic inbred laboratory strains. We used liver extracts of medaka iCab and HO5 strains as a paradigm to test the feasibility of distinguishing the metabolome of two different inbred strains. Fifteen metabolites could be detected in uni- and multivariate analyses that showed strain-specific levels. Differences could be assigned to specific metabolic pathways. Our results show that NMR spectroscopy is a suitable method to detect variance of the metabolome caused by subtle genetic differences. Thus, it has the potential to address genotype-phenotype associations in medaka, providing an additional level of phenotypic analysis.

Behavioral analysis of moving animals relies on a faithful recording and track analysis to extract relevant parameters of movement. To study group behavior and social interactions, often simultaneous analyses of individuals are required. To detect social interactions, for example to identify the leader of a group as opposed to followers, one needs an error-free segmentation of individual tracks throughout time. While automated tracking algorithms exist that are quick and easy to use, inevitable errors will occur during tracking. To solve this problem, we introduce a robust algorithm called epiTracker for segmentation and tracking of multiple animals in two-dimensional (2D) videos along with an easy-to-use correction method that allows one to obtain error-free segmentation. We have implemented two graphical user interfaces to allow user-friendly control of the functions. Using six labeled 2D datasets, the effort to obtain accurate labels is quantified and compared to alternative available software solutions. Both the labeled datasets and the software are publicly available.

Day length in conjunction with seasonal cycles affects many aspects of animal biology. We have studied photoperiod-dependent alterations of complex behavior in the teleost, medaka ( Oryzias latipes ), a photoperiodic breeder, in a learning paradigm whereby fish have to activate a sensor to obtain a food reward. Medaka were tested under a long (14:10 LD) and short (10:14 LD) photoperiod in three different groups: mixed-sex, all-males, and all-females. Under long photoperiod, medaka mixed-sex groups learned rapidly with a stable response. Unexpectedly, males-only groups showed a strong learning deficit, whereas females-only groups performed efficiently. In mixed-sex groups, female individuals drove group learning, whereas males apparently prioritized mating over feeding behavior resulting in strongly reduced learning performance. Under short photoperiod, where medaka do not mate, male performance improved to a level similar to that of females. Thus, photoperiod has sex-specific effects on the learning performance of a seasonal vertebrate., Competing Interests: The authors declare no competing interests., (© 2021 The Authors.)

The use of juvenile and larval fish models has been growing in importance for several fields. Accordingly, the evaluation of behavioural tests that can be applied to larvae and juveniles is becoming increasingly important. We tested medaka at four different ages (1, 10, 30, and 120 dph) in the open field test, one of the most commonly used behavioural assays, to investigate its suitability for larvae and juveniles of this species. We also explored ontogenetic variation in behaviour during this test. On average, adult 120-day-old medaka showed higher locomotor activity in terms of distance moved compared with younger fish. Our analysis suggests that this effect was derived from both quantitative changes in locomotion related to the ontogenetic increase in fish size as well as qualitative changes in two aspects of locomotor behaviour. Specifically, time spent moving was similar between 1- and 10-day-old medaka, but progressively increased with development. In addition, we revealed that adult medaka showed constant levels of activity, whereas younger medaka progressively reduced their activity over the course of the entire experiment. The thigmotaxis behaviour typically used to assess anxiety in the open field test emerged at 120 days post-hatching, even though a difference in the temporal pattern of spatial preference emerged earlier, between 10 and 30 days post-hatching. In conclusion, some measures of the open field test such as total distance moved allow behavioural phenotyping in the medaka of all ages, although with some degree of quantitative and qualitative developmental variation. In contrast, immature medaka appear not to exhibit thigmotactic behaviour.

Stormwater conveys natural and engineered (nano)-particles, like any other pollutants, from urban areas to water resources. Thus, the use of stormwater green infrastructures (SGI), which infiltrate and treat stormwater, can potentially limit the spread of engineered (nano)-particles in the environment. However, the concentration of engineered (nano)-particles in soil or biofilter media used in SGI has not been measured due to difficulties in distinguishing natural vs. engineered (nano)-particles. This study reports, for the first time, the concentration and size distribution of TiO 2 engineered (nano)-particles in soils collected from SGI. The concentrations of TiO 2 engineered (nano)-particles were determined by mass balance calculations based on shifts in elemental concentration ratios, i.e., Ti to Nb, Ti to Ta, and Ti to Al in SGI soils relative to natural background elemental ratios. The concentrations of TiO 2 engineered (nano)-particles in SGI soils varied between 550 ± 13 and 1800 ± 200 mg kg -1 . A small fraction of TiO 2 engineered (nano)-particles could be extracted by ultrapure water (UPW) and Na 4 P 2 O 7 ; however, the concentration of TiO 2 engineered (nano)-particles was higher in the Na 4 P 2 O 7 -extracted suspensions than in UPW-extracted suspensions. The concentration of TiO 2 in the nanosize range increased with the increase in extractant (Na 4 P 2 O 7 ) volume to soil mass ratio due to the increased disaggregation of soil heteroaggregates. The size distribution of TiO 2 engineered (nano)-particles in the < 450 nm Na 4 P 2 O 7 -extracted suspension from one of the SGI soils was determined by asymmetrical flow-field flow fractionation coupled to inductively coupled plasma-mass spectrometer, and was found to vary in the range of 25-200 nm with a modal size of 50 nm. These results demonstrated that the increase in the Ti to natural tracers (e.g., Nb, Ta, and Al) elemental ratios in the SGI soil relative to bulk soil can be used to estimate the concentration of TiO 2 engineered (nano)-particles in SGI., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Quantification of engineered nanomaterials (ENMs) concentrations in surface waters remains one of the key challenges in environmental nanoscience and nanotechnology. A promising approach to estimate metal and metal oxide ENM concentrations in complex environmental samples is based on the increase in the elemental ratios of ENM-contaminated samples relative to the corresponding natural background elemental ratios. This contribution evaluated the detection and quantification of Ag, CeO 2 , and Fe 2 O 3 ENMs spiked in synthetic soft, or in natural river waters using the elemental ratio approach, and evaluated the effect of extractants including sodium hydroxide (NaOH), sodium oxalate (Na 2 C 2 O 4 ) and sodium pyrophosphate (Na 4 P 2 O 7 ) on the recovery of ENMs from the spiked waters. The extracted ENM concentrations were higher in Na 4 P 2 O 7 -extracted suspensions than in NaOH- and Na 2 C 2 O 4 -extracted suspensions due to the higher efficiency of Na 4 P 2 O 7 to break up natural and engineered nanomaterial heteroaggregates. The size distributions of the extracted suspensions were determined by asymmetrical flow-field flow fractionation coupled to inductively coupled plasma-mass spectrometer (AF4-ICP-MS). These size distribution analysis demonstrated that Ag ENMs were extracted from the spiked river water as both primary particles and small (<100 nm) aggregates, whereas CeO 2 ENMs were extracted from the spiked river water as aggregates of particles in the size range 0-200 nm. The number particle size distribution of the extracted suspensions confirmed that Ag ENMs were extracted as a mixture of primary and aggregated Ag ENMs. Small Ag ENMs (i.e. <20 nm) were detected by AF4-ICP-MS, but these particles were not detected by single particle (sp)-ICP-MS due to high size detection limit of sp-ICP-MS. This study illustrates that the elemental ratio approach is a promising approach to detect and quantify ENMs in surface waters. This study also illustrates the need for a multi-method approach, including extraction, filtration, AF4-ICP-MS and sp-ICP-MS, to detect, quantify, and characterize ENMs in surface waters., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Accurate quantification of heartbeats in fish models is an important readout to study cardiovascular biology, disease states and pharmacology. However, dependence on anaesthesia, laborious sample orientation or requirement for fluorescent reporters have hampered the use of high-throughput heartbeat analysis. To overcome these limitations, we established an efficient screening assay employing automated label-free heart rate determination of randomly oriented, non-anesthetized medaka (Oryzias latipes) and zebrafish (Danio rerio) embryos in microtiter plates. Automatically acquired bright-field data feeds into an easy-to-use HeartBeat software with graphical user interface for automated quantification of heart rate and rhythm. Sensitivity of the assay was demonstrated by profiling heart rates during entire embryonic development. Our analysis revealed rapid adaption of heart rates to temperature changes, which has implications for standardization of experimental layout. The assay allows scoring of multiple embryos per well enabling a throughput of >500 embryos per 96-well plate. In a proof of principle screen for compound testing, we captured concentration-dependent effects of nifedipine and terfenadine over time. Our novel assay permits large-scale applications ranging from phenotypic screening, interrogation of gene functions to cardiovascular drug development.

Characterization and understanding of natural nanomaterials (NNMs) properties is essential to differentiate engineered nanomaterials (ENMs) from NNMs. However, NNMs in environmental samples typically occur as heteroaggregates with other particles, e.g., NNMs, ENMs, and larger particles. Therefore, there is a need to isolate NNMs into their primary particles to better characterize their physicochemical properties. Here, we evaluated the efficiency of sodium hydroxide, sodium oxalate, and sodium pyrophosphate to extract NNMs from surface waters. The extracted NNMs were characterized for total metal concentration by inductively coupled plasma-mass spectrometry (ICP-MS) following full digestion; size distribution, elemental composition and ratios by flow-field flow fractionation (AF4)-ICP-MS; and morphology by transmission electron microscopy (TEM). Sodium pyrophosphate extraction resulted in the highest NNM concentration and the smallest NNM size distribution. Sodium hydroxide and sodium oxalate extraction generated heteroaggregates with a broad size distribution. The NNM extraction efficiency increased with extractant (sodium oxalate and sodium pyrophosphate) concentration. The concentration of metals in the sodium pyrophosphate-extracted NNMs compared to the total metal concentration was element-dependent and varied from as high as >80% for Cu, Zn, and Sr to as low as <5% for Al, Ti, and Nb. This study provides a simple protocol for NNM extraction from complex environmental samples and provides a better understanding of NNM physicochemical properties. The presented NNM extraction protocol forms the basis for ENM extraction from natural waters., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Characterization of natural nanomaterial (NNM) physicochemical properties - such as size, size distribution, elemental composition and elemental ratios - is often hindered by lack of methods to disperse NNMs from environmental samples. This study evaluates the effect of extractant composition, pH, and ionic strength on soil NNM extraction in term of recovery and release of primary particles/small aggregate sizes (i.e., <200 nm). The extracted NNMs were characterized for hydrodynamic diameter and zeta potential by dynamic light scattering and laser Doppler electrophoresis, natural organic matter desorption by UV-Vis spectroscopy, element composition by inductively coupled plasma-mass spectroscopy (ICP-MS), size based elemental distribution by field flow fractionation coupled to ICP-MS, and morphology by transmission electron microscopy. The extracted NNM concentrations increased following the order of NaOH ≤ Na 2 CO 3  < Na 2 C 2 O 4  < Na 4 P 2 O 7 . Na 4 P 2 O 7 was the most efficient extractant and results in 2-12 folds higher NNM extraction than other extractants. The Na 4 P 2 O 7 extracted NNMs exhibited narrower size distribution with smaller modal size relative to NaOH, Na 2 CO 3 , Na 2 C 2 O 4 extracted NNMs. Thus, Na 4 P 2 O 7 enhances the extraction of primary NNMs and/or smaller NNM aggregates (i.e., size <200 nm). Na 4 P 2 O 7 promote soil microaggregates breakup and release of NNMs by reducing free multivalent cation concentration in soil pore water by forming metal-phosphate complexes and by enhancing NNM surface charge via phosphate sorption on NNM surfaces. Additionally, the extracted NNM concentrations increased with the increase in extractant concentration and pH, except at 100 mM where the high ionic strength might have induced NNM aggregation. The improved NNM-extraction will improve the overall understanding of the physicochemical properties of NNMs in environmental systems. This study presents the key properties of NNMs that can be used as background information to differentiate engineered nanomaterials (ENMs) from NNMs in complex environmental media., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Fish species such as medaka or zebrafish are widely used as animal models to study physiology, disease development, and treatment efficacy. They are also used to study the rapidly growing field of behavior research, such as social interactions, anxiety, and the influence of environmental factors. Here we describe an automated experimental setup allowing the recording of general locomotor activity in combination with a food-on-demand system. It can simply be built with some basic electronic knowledge. Our setup enables the recording of locomotor and feeding activity of several fish for long-term studies, excluding disturbing external influences. A description of the automated recording system is given, as well as examples of recordings to illustrate its applicability for the study of fish behavior. The construction manual and operation instructions can be downloaded for free.

Sanitary sewer overflows (SSOs) are a common problem across the United States. An estimated 23,000-75,000 SSOs occurred annually in 2004 discharging between 11 and 38 billion liters of untreated wastewater to receiving waters. SSOs release many contaminants, including engineered nanomaterials (ENMs), to receiving water bodies. Measuring ENM concentrations in environmental samples remains a key challenge in environmental nanotechnology and requires the distinction between natural and engineered particles. This distinction between natural and engineered particles is often hampered by the similarities in the intrinsic properties of natural and engineered particles such as particle size, composition, density, surface chemistry, and by the limitations of the available nanometrology tools. To overcome these challenges, we applied a multi-method approach to measure the concentrations and properties of TiO 2 engineered particles ( e.g., ENMs and pigments) including 1) multi-element single particle-inductively coupled plasma-mass spectrometry (ME-SP-ICP-MS) to identify elemental associations and to determine elemental ratios in natural particles, 2) total elemental concentrations and ratios calculated from total metal concentrations measured following total sample digestion to estimate engineered particle concentrations, and 3) transmission electron microscopy (TEM) to characterize engineered particle size and morphology. ME-SP-ICP-MS analysis revealed that natural TiO 2 particles are often associated with at least one of the following elements Al, Fe, Ce, Si, La, Zr, Nb, Pb, Ba, Th, Ta, W and U, and that elemental ratios of Ti to these elements is typical of riverine particulates and the average crustal ratios, except for Pb likely due to anthropogenic Pb contamination. High TiO 2 engineered particle concentrations up to 100 μg L -1 were found in SSOs-impacted surface waters. TEM analysis demonstrated the presence of regular-shape TiO 2 particles in SSOs-impacted surface waters. This study provides a comprehensive approach for measuring TiO 2 engineered particle concentrations in surface waters. The quantitative data produced in this work can be used as input for modeling studies and pave the road toward routine monitoring of ENMs in environmental systems, validation of ENM fate models, and more accurate ENM exposure and risk assessment.

Vertebrate models provide indispensable paradigms to study development and disease. Their analysis requires a quantitative morphometric study of the body, organs and tissues. This is often impeded by pigmentation and sample size. X-ray micro-computed tomography (micro-CT) allows high-resolution volumetric tissue analysis, largely independent of sample size and transparency to visual light. Importantly, micro-CT data are inherently quantitative. We report a complete pipeline of high-throughput 3D data acquisition and image analysis, including tissue preparation and contrast enhancement for micro-CT imaging down to cellular resolution, automated data processing and organ or tissue segmentation that is applicable to comparative 3D morphometrics of small vertebrates. Applied to medaka fish, we first create an annotated anatomical atlas of the entire body, including inner organs as a quantitative morphological description of an adult individual. This atlas serves as a reference model for comparative studies. Using isogenic medaka strains we show that comparative 3D morphometrics of individuals permits identification of quantitative strain-specific traits. Thus, our pipeline enables high resolution morphological analysis as a basis for genotype-phenotype association studies of complex genetic traits in vertebrates.

The field of macro-imaging has grown considerably with the appearance of innovative clearing methods and confocal microscopes with lasers capable of penetrating increasing tissue depths. The ability to visualize and model the growth of whole organs as they develop from birth, or with manipulation, disease or injury, provides new ways of thinking about development, tissue-wide signaling, and cell-to-cell interactions. The zebrafish ( Danio rerio ) has ascended from a predominantly developmental model to a leading adult model of tissue regeneration. The unmatched neurogenic and regenerative capacity of the mature central nervous system, in particular, has received much attention, however tools to interrogate the adult brain are sparse. At present there exists no straightforward methods of visualizing changes in the whole adult brain in 3-dimensions (3-D) to examine systemic patterns of cell proliferation or cell populations of interest under physiological, injury, or diseased conditions. The method presented here is the first of its kind to offer an efficient step-by-step pipeline from intraperitoneal injections of the proliferative marker, 5-ethynyl-2'-deoxyuridine (EdU), to whole brain labeling, to a final embedded and cleared brain sample suitable for 3-D imaging using optical projection tomography (OPT). Moreover, this method allows potential for imaging GFP-reporter lines and cell-specific antibodies in the presence or absence of EdU. The small size of the adult zebrafish brain, the highly consistent degree of EdU labeling, and the use of basic clearing agents, benzyl benzoate, and benzyl alcohol, makes this method highly tractable for most laboratories interested in understanding the vertebrate central nervous system in health and disease. Post-processing of OPT-imaged adult zebrafish brains injected with EdU illustrate that proliferative patterns in EdU can readily be observed and analyzed using IMARIS and/or FIJI/IMAGEJ software. This protocol will be a valuable tool to unlock new ways of understanding systemic patterns in cell proliferation in the healthy and injured brain, brain-wide cellular interactions, stem cell niche development, and changes in brain morphology.

Background: Comparative studies beyond the traditional model organisms have been instrumental in enhancing our understanding of the conserved and derived features of gastrulation, a fundamental process in which the germ layers are specified and shaped to form the body axis. Here, we analyzed gastrulation in a vertebrate group with an extreme mode of early development, the annual killifish., Results: Gastrulation in annual killifish of the genus Austrolebias takes place after the initially dispersed deep blastomeres congregate to form the so-called reaggregate. Cells from the early reaggregate do not appear to form part of any recognizable axial embryonic structure and are possibly extraembryonic. In contrast, later reaggregate cells become engaged in morphogenetic transformations indicative of a process of gastrulation and axis formation. The expression of brachyury and goosecoid suggests that gastrulation takes place in a compressed blastopore-like structure with an organizer region displaced to one end. No collective cell internalization proper of blastopore architecture is observed, though, and it appears that gastrulation primarily involves the reorganization of individual cells., Conclusions: The unique mode of gastrulation in annual killifish demonstrates that a process so ancient and fundamental to ontogenesis can have striking morphogenetic variations nonpredicted from the sole examination of model species. Developmental Dynamics 246:812-826, 2017. © 2017 Wiley Periodicals, Inc., (© 2017 Wiley Periodicals, Inc.)