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The outstanding work performed by standardization organizations for guidelines to assess hazards, e.g., OECD (Organisation for Economic Co-operation and Development), is clearly visible by the currently available number and broad coverage, from aquatic to terrestrial organisms dealing with environmental relevant issues. Nevertheless, novel materials challenge the adequateness and fit-for-purpose of such standards, as the standards were developed to assess hazards of “conventional” chemical substances and not advanced materials (e.g. materials that may deliberately change behaviour). While standardization is a well-known process that requires extended time before reaching implementation stage, there is strong support from regulatory bodies for the development of New Approach Methodologies (NAMs) (e.g., updating of current guidelines, development of novel omics-, in vitro-, and in silico- tests including modelling and read-across) that meet regulatory preparedness (i.e. have considered issues important for regulatory testing). There are currently several NAMs available, complying with high quality standards and relevancy, which should be adopted. In the current review, we collected the available literature on NAMs to assess hazards of Nanomaterials (NMs), focusing on the terrestrial environment, and critically discuss the advantages, challenges and gaps. Tests were grouped into 1) Standard tests (OECD/ISO), 2) Standard tests (OECD/ISO) extensions: time course or prolonged exposures and/or multigenerational, and 3) Alternative tests, beyond current OECD/ISO: omics, biomarkers, in vitro, in silico and modelling. The goal is to provide guidance on the best practices and test designs focusing on the specificities of testing NMs, outlining recommendations and way forward.
Susana I.L. Gomes; Janeck J. Scott-Fordsmand; Monica J.B. Amorim. Alternative test methods for (nano)materials hazards assessment: Challenges and recommendations for regulatory preparedness. Nano Today 2021, 40, 101242 .
AMA StyleSusana I.L. Gomes, Janeck J. Scott-Fordsmand, Monica J.B. Amorim. Alternative test methods for (nano)materials hazards assessment: Challenges and recommendations for regulatory preparedness. Nano Today. 2021; 40 ():101242.
Chicago/Turabian StyleSusana I.L. Gomes; Janeck J. Scott-Fordsmand; Monica J.B. Amorim. 2021. "Alternative test methods for (nano)materials hazards assessment: Challenges and recommendations for regulatory preparedness." Nano Today 40, no. : 101242.
The commercial formulation of atrazine (Gesaprim) was the least toxic to E. crypticus, followed by nano_ATZ and ATZ (a.i.).
Susana I. L. Gomes; Janeck J. Scott-Fordsmand; Estefânia V. R. Campos; Renato Grillo; Leonardo F. Fraceto; Mónica J. B. Amorim. On the safety of nanoformulations to non-target soil invertebrates – an atrazine case study. Environmental Science: Nano 2019, 6, 1950 -1958.
AMA StyleSusana I. L. Gomes, Janeck J. Scott-Fordsmand, Estefânia V. R. Campos, Renato Grillo, Leonardo F. Fraceto, Mónica J. B. Amorim. On the safety of nanoformulations to non-target soil invertebrates – an atrazine case study. Environmental Science: Nano. 2019; 6 (6):1950-1958.
Chicago/Turabian StyleSusana I. L. Gomes; Janeck J. Scott-Fordsmand; Estefânia V. R. Campos; Renato Grillo; Leonardo F. Fraceto; Mónica J. B. Amorim. 2019. "On the safety of nanoformulations to non-target soil invertebrates – an atrazine case study." Environmental Science: Nano 6, no. 6: 1950-1958.
Nickel nanoparticles (NiNPs) have an estimated production of ca. 20 tons per year in the US. Nickel has been risk-assessed for long in Europe, but not NiNPs, hence the concern for the environment. In the present study, we focused on investigating the mechanisms of toxicity of NiNPs and the comparison to NiNO3. The high-throughput microarray for the soil ecotox model Enchytraeus crypticus (Oligochaeta) was used. To anchor gene to phenotype effect level, organisms were exposed to reproduction effect concentrations EC20 and EC50, for 3 and 7 days. Results showed commonly affected pathways between NiNPs and NiNO3, including increase in proteolysis, apoptosis and inflammatory response, and interference with the nervous system. Mechanisms unique to NiNO3 were also observed (e.g. glutathione synthesis). No specific mechanisms for NiNPs were found, which could indicate that longer exposure period (>7 days) is required to capture the peak response to NiNPs. A mechanisms scheme is assembled, showing both common and unique mechanisms to NiNO3 and NiNPs, providing an important framework for further, more targeted, studies.
Susana I.L. Gomes; Carlos P. Roca; Janeck J. Scott-Fordsmand; Mónica J.B. Amorim. High-throughput transcriptomics: Insights into the pathways involved in (nano) nickel toxicity in a key invertebrate test species. Environmental Pollution 2018, 245, 131 -140.
AMA StyleSusana I.L. Gomes, Carlos P. Roca, Janeck J. Scott-Fordsmand, Mónica J.B. Amorim. High-throughput transcriptomics: Insights into the pathways involved in (nano) nickel toxicity in a key invertebrate test species. Environmental Pollution. 2018; 245 ():131-140.
Chicago/Turabian StyleSusana I.L. Gomes; Carlos P. Roca; Janeck J. Scott-Fordsmand; Mónica J.B. Amorim. 2018. "High-throughput transcriptomics: Insights into the pathways involved in (nano) nickel toxicity in a key invertebrate test species." Environmental Pollution 245, no. : 131-140.
The photoactivity of TiO2 plays a major role in TiO2 toxicity, triggering specific mechanisms of response.
Susana I. L. Gomes; Carlos P. Roca; Frank von der Kammer; Janeck James Scott-Fordsmand; Mónica J. B. Amorim. Mechanisms of (photo)toxicity of TiO2 nanomaterials (NM103, NM104, NM105): using high-throughput gene expression in Enchytraeus crypticus. Nanoscale 2018, 10, 21960 -21970.
AMA StyleSusana I. L. Gomes, Carlos P. Roca, Frank von der Kammer, Janeck James Scott-Fordsmand, Mónica J. B. Amorim. Mechanisms of (photo)toxicity of TiO2 nanomaterials (NM103, NM104, NM105): using high-throughput gene expression in Enchytraeus crypticus. Nanoscale. 2018; 10 (46):21960-21970.
Chicago/Turabian StyleSusana I. L. Gomes; Carlos P. Roca; Frank von der Kammer; Janeck James Scott-Fordsmand; Mónica J. B. Amorim. 2018. "Mechanisms of (photo)toxicity of TiO2 nanomaterials (NM103, NM104, NM105): using high-throughput gene expression in Enchytraeus crypticus." Nanoscale 10, no. 46: 21960-21970.
Gene expression can vary with the organisms' life stage. It is known that embryos can be more sensitive to toxicant exposure, as previously demonstrated for Enchytraeus crypticus (Oligochaeta) exposed to cadmium (Cd), known to cause embryotoxicity and hatching delay. It was shown that Ca enters embryos via the L-type Ca channels in the cocoon membrane, this being affected in Cd exposed embryos (Cd-Ca competition is well-known). In the present study, the embryotoxic mechanisms of Cd were studied via high-throughput gene expression for E. crypticus. Cocoons (1–2 days old), instead of the adult organism, were exposed in Cd spiked LUFA 2.2 soil during 1 day. Results showed that Cd affected Ca homeostasis which is implicated in several other molecular processes. Several of the major modulators of Cd toxicity (e.g., impaired gene expression, cell cycle arrest, DNA and mitochondrial damage) were identified in the embryos showing its relevancy as a model in ecotoxicogenomics. The draft Adverse Outcome Pathway was improved. Previously was hypothesized that gene regulation mechanisms were activated to synthesize more Ca channel proteins – this was confirmed here. Further, novel evidences were that, besides the extracellular competition, Cd competes intracellularly which causes a reduction in Ca efflux, and potentiates Cd embryotoxicity.
Susana I.L. Gomes; Micael F.M. Gonçalves; Rita C. Bicho; Carlos P. Roca; Amadeu M.V.M. Soares; Janeck J. Scott-Fordsmand; Mónica J.B. Amorim. High-throughput gene expression in soil invertebrate embryos – Mechanisms of Cd toxicity in Enchytraeus crypticus. Chemosphere 2018, 212, 87 -94.
AMA StyleSusana I.L. Gomes, Micael F.M. Gonçalves, Rita C. Bicho, Carlos P. Roca, Amadeu M.V.M. Soares, Janeck J. Scott-Fordsmand, Mónica J.B. Amorim. High-throughput gene expression in soil invertebrate embryos – Mechanisms of Cd toxicity in Enchytraeus crypticus. Chemosphere. 2018; 212 ():87-94.
Chicago/Turabian StyleSusana I.L. Gomes; Micael F.M. Gonçalves; Rita C. Bicho; Carlos P. Roca; Amadeu M.V.M. Soares; Janeck J. Scott-Fordsmand; Mónica J.B. Amorim. 2018. "High-throughput gene expression in soil invertebrate embryos – Mechanisms of Cd toxicity in Enchytraeus crypticus." Chemosphere 212, no. : 87-94.
Studies have been showing how changes in ultraviolet (UV) affect the terrestrial system, mostly focusing on higher plants and indirect effects, e.g. UV changed food quality/decomposition. Much less attention has been given to direct effect on terrestrial species, although the negative effects have been recognized for some earthworms. Further, the actual mechanisms of UV toxicity to soil invertebrates are even less understood. We here studied the effect of UV on the soil oligochaete Enchytraeus crypticus, and attempted to identify the possible mechanisms of toxicity using high-throughput gene expression. Applying a UV dose equivalent to UV during the winter months in northern Europe we observed an 80% decrease in reproduction. For these organisms, approximately 5% of the genes were differentially expressed. Among the observations was an activation of the DNA repair mechanisms, nucleotide excision repair, which correlated with survival of the organisms. An observed repressing of apoptosis seems to have deleterious effects (e.g. because it may lead to the accumulation of aberrant cells) leading to a decline in reproduction. The mechanisms activated by UV were similar to those mechanisms activated in humans, showing conservation across species.
Susana I. L. Gomes; Carlos P. Roca; Janeck J. Scott-Fordsmand; Mónica J. B. Amorim. Identifying conserved UV exposure genes and mechanisms. Scientific Reports 2018, 8, 8605 .
AMA StyleSusana I. L. Gomes, Carlos P. Roca, Janeck J. Scott-Fordsmand, Mónica J. B. Amorim. Identifying conserved UV exposure genes and mechanisms. Scientific Reports. 2018; 8 (1):8605.
Chicago/Turabian StyleSusana I. L. Gomes; Carlos P. Roca; Janeck J. Scott-Fordsmand; Mónica J. B. Amorim. 2018. "Identifying conserved UV exposure genes and mechanisms." Scientific Reports 8, no. 1: 8605.
The current testing of nanomaterials (NMs) via standard toxicity tests does not cover many of the NMs specificities. One of the recommendations lays on understanding the mechanisms of action, as these can help predicting long-term effects and safe-by-design production. In the present study, we used the high-throughput gene expression tool, developed for Enchytraeus crypticus (4 × 44k Agilent microarray), to study the effects of exposure to several copper (Cu) forms. The Cu treatments included two NMs (spherical and wires) and two copper-salt treatments (CuNO3 spiked and Cu salt field historical contamination). To relate gene expression with higher effect level, testing was done with reproduction effect concentrations (EC20, EC50), using 3 and 7 days as exposure periods. Results showed that time plays a major role in the transcriptomic response, most of it occurring after 3 days. Analysis of gene expression profiles showed that Cu-salt-aged and Cu-nanowires (Nwires) differed from CuNO3 and Cu-nanoparticles (NPs). Functional analysis revealed specific mechanisms: Cu-NPs uniquely affected senescence and cuticle pattern formation, which can result from the contact of the NPs with the worms' tegument. Cu-Nwires affected reproduction via male gamete generation and hermaphrodite genitalia development. CuNO3 affected neurotransmission and locomotory behavior, both of which can be related with avoidance response. Cu salt-aged uniquely affected phagocytosis and reproductive system development (via different mechanisms than Cu-Nwires). For the first time for Cu (nano)materials, the adverse outcome pathways (AOPs) drafted here provide an overview for common and unique effects per material and linkage with apical effects.
Susana I. L. Gomes; Carlos P. Roca; Natália Pegoraro; Tito Trindade; Janeck J. Scott-Fordsmand; Mónica J. B. Amorim. High-throughput tool to discriminate effects of NMs (Cu-NPs, Cu-nanowires, CuNO3, and Cu salt aged): transcriptomics in Enchytraeus crypticus. Nanotoxicology 2018, 12, 325 -340.
AMA StyleSusana I. L. Gomes, Carlos P. Roca, Natália Pegoraro, Tito Trindade, Janeck J. Scott-Fordsmand, Mónica J. B. Amorim. High-throughput tool to discriminate effects of NMs (Cu-NPs, Cu-nanowires, CuNO3, and Cu salt aged): transcriptomics in Enchytraeus crypticus. Nanotoxicology. 2018; 12 (4):325-340.
Chicago/Turabian StyleSusana I. L. Gomes; Carlos P. Roca; Natália Pegoraro; Tito Trindade; Janeck J. Scott-Fordsmand; Mónica J. B. Amorim. 2018. "High-throughput tool to discriminate effects of NMs (Cu-NPs, Cu-nanowires, CuNO3, and Cu salt aged): transcriptomics in Enchytraeus crypticus." Nanotoxicology 12, no. 4: 325-340.
This corrects the article DOI: 10.1038/srep42460.
Carlos P. Roca; Susana Gomes; Mónica J. B. Amorim; Janeck J. Scott-Fordsmand. Erratum: Corrigendum: Variation-preserving normalization unveils blind spots in gene expression profiling. Scientific Reports 2018, 8, 46941 .
AMA StyleCarlos P. Roca, Susana Gomes, Mónica J. B. Amorim, Janeck J. Scott-Fordsmand. Erratum: Corrigendum: Variation-preserving normalization unveils blind spots in gene expression profiling. Scientific Reports. 2018; 8 (1):46941.
Chicago/Turabian StyleCarlos P. Roca; Susana Gomes; Mónica J. B. Amorim; Janeck J. Scott-Fordsmand. 2018. "Erratum: Corrigendum: Variation-preserving normalization unveils blind spots in gene expression profiling." Scientific Reports 8, no. 1: 46941.
Nanoparticles (NPs) such as nickel (Ni) are widely used in several applications. Nevertheless, the environmental effects of Ni NPs are still poorly understood. In the present study, the toxicity of Ni NPs and nickel nitrate (NiNO3) was assessed using the standard test species in soil ecotoxicology, Enchytraeus crypticus (Oligochaeta), in a full life cycle test, adding the endpoints hatching, growth, and time to reach maturity, besides survival and reproduction as in the standard Organisation for Economic Co‐operation and Development Guideline 220 and/or International Organization for Standardization 16387. For Ni NPs, the Ni in soil and in soil solution was concentration‐ and time‐dependent, with a relatively higher soil solution content in the lower and shorter exposure concentrations and times. Overall, NiNO3 was more toxic than Ni NPs, and toxicity seemed to occur via different mechanisms. The former caused reduced hatching (50% effect concentration [EC50] = 39 mg Ni/kg soil), and the negative effects remained throughout the life cycle, in all measured endpoints (growth, maturation, survival, and reproduction). For Ni NPs, hatching was the most sensitive endpoint (EC50 = 870 mg Ni/kg soil), although the organisms recovered; that is, additional endpoints across the life cycle showed that this effect corresponded to a delay in hatching because organisms survived and reproduced at concentrations up to 1800 mg Ni/kg soil. On the other hand, the lowest tested concentration of Ni NPs (100 mg Ni/kg soil) caused reproduction effects similar to those at higher concentrations (1000 and 1800 mg Ni/kg soil). The present results show that the potential implications of a nonmonotonic dose response should be considered when assessing the risks of Ni NP exposure in soil. Environ Toxicol Chem 2017;36:2934–2941. © 2017 SETAC
Fátima Santos; Susana I.L. Gomes; Janeck Scott-Fordsmand; Mónica Amorim. Hazard assessment of nickel nanoparticles in soil-The use of a full life cycle test with Enchytraeus crypticus. Environmental Toxicology and Chemistry 2017, 36, 2934 -2941.
AMA StyleFátima Santos, Susana I.L. Gomes, Janeck Scott-Fordsmand, Mónica Amorim. Hazard assessment of nickel nanoparticles in soil-The use of a full life cycle test with Enchytraeus crypticus. Environmental Toxicology and Chemistry. 2017; 36 (11):2934-2941.
Chicago/Turabian StyleFátima Santos; Susana I.L. Gomes; Janeck Scott-Fordsmand; Mónica Amorim. 2017. "Hazard assessment of nickel nanoparticles in soil-The use of a full life cycle test with Enchytraeus crypticus." Environmental Toxicology and Chemistry 36, no. 11: 2934-2941.
Toxicity tests that last the all life duration of the organisms are not common, instead, long-term tests usually include one reproductive cycle. In the present study we optimized and propose a lifespan (all life) term test using Enchytraeus crypticus (Oligochaeta). The effect of copper oxide nanoparticles (CuO-NPs) was assessed in this lifespan test and compared to copper salt (CuCl2), using the same effect concentrations on reproduction (EC50). Monitored endpoints included survival and reproduction over-time (202 days). Results from survival showed that CuO-NPs caused shorter life of the adults compared to CuCl2 (control LT50: 218 days > CuCl2 LT50: 175 days > CuO-NPs LT50: 145 days). The effect was even more amplified in terms of reproduction (control ET50: 158 days > CuCl2 ET50: 138 days > CuO-NPs ET50: 92 days). Results suggest that CuO-NPs may cause a higher Cu effect via a trojan horse mechanism. The use of lifespan tests brings a novel concept in soil ecotoxicity, the longevity. This is a particularly important aspect when the subject is nanomaterials toxicity, where longer term exposure time is expected to reveal unpredicted effects via the current short/long-term tests. The present study confirms this higher effect for CuO-NPs.
Micael F. M. Gonçalves; Susana I. L. Gomes; Janeck J. Scott-Fordsmand; Mónica J. B. Amorim. Shorter lifetime of a soil invertebrate species when exposed to copper oxide nanoparticles in a full lifespan exposure test. Scientific Reports 2017, 7, 1355 .
AMA StyleMicael F. M. Gonçalves, Susana I. L. Gomes, Janeck J. Scott-Fordsmand, Mónica J. B. Amorim. Shorter lifetime of a soil invertebrate species when exposed to copper oxide nanoparticles in a full lifespan exposure test. Scientific Reports. 2017; 7 (1):1355.
Chicago/Turabian StyleMicael F. M. Gonçalves; Susana I. L. Gomes; Janeck J. Scott-Fordsmand; Mónica J. B. Amorim. 2017. "Shorter lifetime of a soil invertebrate species when exposed to copper oxide nanoparticles in a full lifespan exposure test." Scientific Reports 7, no. 1: 1355.
RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following the implicit assumption that most genes are not differentially expressed. Here, we present a mathematical approach to normalization that makes no assumption of this sort. We have found that variation in gene expression is much larger than currently believed, and that it can be measured with available assays. Our results also explain, at least partially, the reproducibility problems encountered in transcriptomics studies. We expect that this improvement in detection will help efforts to realize the full potential of gene expression profiling, especially in analyses of cellular processes involving complex modulations of gene expression.
Carlos P. Roca; Susana Gomes; Mónica Amorim; Janeck Scott-Fordsmand. Variation-preserving normalization unveils blind spots in gene expression profiling. Scientific Reports 2017, 7, srep42460 .
AMA StyleCarlos P. Roca, Susana Gomes, Mónica Amorim, Janeck Scott-Fordsmand. Variation-preserving normalization unveils blind spots in gene expression profiling. Scientific Reports. 2017; 7 (1):srep42460.
Chicago/Turabian StyleCarlos P. Roca; Susana Gomes; Mónica Amorim; Janeck Scott-Fordsmand. 2017. "Variation-preserving normalization unveils blind spots in gene expression profiling." Scientific Reports 7, no. 1: srep42460.
Understanding the mode of action of nanomaterials (NMs) aids in improving predictions and environmental risk assessment. In the present study, a high-throughput (HTP) microarray was used to study Enchytraeus crypticus gene expression. Four Ag materials (Ag NM300K, PVP-coated AgNPs, AgNPs, and AgNO3) were tested at reproduction effect concentrations, EC20 and EC50, to anchor gene expression responses to higher effect level. The results showed that while PVP-AgNPs and AgNPs had similar responses, Ag NM300K caused effects via a differentiated transcriptomic profile, with uniquely affected processes (e.g. transcytosis). For the AgNPs, the EC50 negatively affected apoptosis, which can lead to accumulation of abnormal cells and cause apical damage (reproduction). Mechanisms which are known to be related to Ag toxicity and which were observed here for the various Ag forms included apoptosis regulation, cell redox homeostasis, impairment of energy production and response to DNA damage. This HTP genomic tool enabled discrimination between Ag materials, which is not possible via standard tests (i.e. survival and reproduction endpoints). Moreover, gene expression analysis provided information regarding the mechanisms of toxicity of NMs and the pathways uniquely affected by NMs. An adverse outcome pathway (AOP) was drafted for the first time for Ag NMs; this AOP can and should be used as a basis for further research.
Susana I. L. Gomes; Carlos P. Roca; Janeck J. Scott-Fordsmand; Mónica J. B. Amorim. High-throughput transcriptomics reveals uniquely affected pathways: AgNPs, PVP-coated AgNPs and Ag NM300K case studies. Environmental Science: Nano 2017, 4, 929 -937.
AMA StyleSusana I. L. Gomes, Carlos P. Roca, Janeck J. Scott-Fordsmand, Mónica J. B. Amorim. High-throughput transcriptomics reveals uniquely affected pathways: AgNPs, PVP-coated AgNPs and Ag NM300K case studies. Environmental Science: Nano. 2017; 4 (4):929-937.
Chicago/Turabian StyleSusana I. L. Gomes; Carlos P. Roca; Janeck J. Scott-Fordsmand; Mónica J. B. Amorim. 2017. "High-throughput transcriptomics reveals uniquely affected pathways: AgNPs, PVP-coated AgNPs and Ag NM300K case studies." Environmental Science: Nano 4, no. 4: 929-937.
Organisms’ density can influence physiological processes related with fitness. In the present study we assessed the influence of organisms’ density on the life-history parameters in two consecutive generations in Enchytraeus crypticus (Oligochaeta), a standard model in soil ecotoxicology. The densities tested were 1 (N1) and 20 (N20) organisms per replicate and 10 vs. 20 g of soil (for the 2nd generation test only). Results showed that reproductive output was affected by density, with organisms in N1 producing three times more juveniles per adult than when at N20. Organisms’ length was affected by both density and space, i.e., organisms were smaller when less space available. Further, the density of parental generation (F0) had no influence on the endpoints reproduction and length assessed in F1, hence there was no transference of effects. These findings have potential implications in the standard Enchytraeid Reproduction Test, i.e. early mortality of the adults during toxicant exposure can affect the number and size of the offspring and the final results will also reflect the density related changes in reproduction.
Micael Gonçalves; Susana I. L. Gomes; Amadeu Soares; Janeck Scott-Fordsmand; Mónica Amorim. Enchytraeus crypticus fitness: effect of density on a two-generation study. Ecotoxicology 2017, 26, 570 -575.
AMA StyleMicael Gonçalves, Susana I. L. Gomes, Amadeu Soares, Janeck Scott-Fordsmand, Mónica Amorim. Enchytraeus crypticus fitness: effect of density on a two-generation study. Ecotoxicology. 2017; 26 (4):570-575.
Chicago/Turabian StyleMicael Gonçalves; Susana I. L. Gomes; Amadeu Soares; Janeck Scott-Fordsmand; Mónica Amorim. 2017. "Enchytraeus crypticus fitness: effect of density on a two-generation study." Ecotoxicology 26, no. 4: 570-575.
Effects of nickel and copper on Enchytraeus albidus (Oligochaeta) were investigated using the cellular energy allocation approach. This methodology is used to evaluate the energetic status of an organism and is indicative of its overall condition. Enchytraeids were exposed to the reproduction Effect Concentrations (EC50 and EC90), and the parameters measured were the total energy reserves available (protein, carbohydrate and lipid budgets) and the energy consumption [based on electron transport system activity] which were further integrated to obtain the cellular energy allocation over different periods of exposure (0–2, 2–4 and 4–8 days). Carbohydrates (in comparison to lipids and proteins) were the only energy source mobilized in the case of nickel within 8 days of exposure. For copper exposure, protein budgets were also strongly reduced. Energy consumption increased in a time and dose-dependent way for copper and in the longer exposure period (4–8 days) at the EC90 for Ni exposure, indicating that this is a good biomarker for effects of short-time metal exposure, while cellular energy allocation was only significantly reduced for the EC90 of copper (4–8 days) and EC50 of nickel (2–4 days). The effects of nickel at concentrations causing 50 and 90 % decrease in reproduction were likely not due to the changes in cellular energy allocation within 8 days of exposure.
Susana I.L. Gomes; Amadeu M.V.M. Soares; Mónica J.B. Amorim. Effect of Cu and Ni on cellular energy allocation in Enchytraeus albidus. Ecotoxicology 2016, 25, 1523 -1530.
AMA StyleSusana I.L. Gomes, Amadeu M.V.M. Soares, Mónica J.B. Amorim. Effect of Cu and Ni on cellular energy allocation in Enchytraeus albidus. Ecotoxicology. 2016; 25 (8):1523-1530.
Chicago/Turabian StyleSusana I.L. Gomes; Amadeu M.V.M. Soares; Mónica J.B. Amorim. 2016. "Effect of Cu and Ni on cellular energy allocation in Enchytraeus albidus." Ecotoxicology 25, no. 8: 1523-1530.
Energy budget studies offer important information in terms of organisms' fitness and this has become an increasingly common stress marker. The method is well developed but the issue of food supply (addition or not) during exposure is not consensual. Moreover, chemicals such as cadmium (Cd) are known to affect food uptake, e.g. via feeding inhibition, hence energy budget results could be because of decreased uptake and not direct toxicity. On the other hand, food deprivation can be a stressor itself and bias results. In the present study we compared exposure with (F) and without food (NF) along time (2, 4 and 8 days). The Cellular Energy Allocation (CEA) method was used to study the effects of Cd in the soil standard species Enchytraeus albidus (Oligochaeta). In control conditions (un-spiked soil), carbohydrate and lipid budgets were mobilized in NF. When testing Cd, variations in carbohydrates and lipid budgets depend on the presence of food and time of exposure. The main hypothesized mechanisms triggered by Cd exposure were similar (i.e. induction of protein synthesis and increase in energy consumption). Differences between F and NF over time indicate that the process of mobilization/preservation of energy reserves depends on the food/energy intake (e.g. in Cd exposed organisms, mobilization of proteins occurred within 2 days when food was present, while in the absence of food carbohydrate and protein budgets were mobilized from 2 to 4 days). Comparisons between F-NF studies should not be done directly. Moreover, we recommend exposure without food because it allows a better discrimination of effects (in particular within periods of exposure).
Susana.I.L. Gomes; Amadeu M.V.M. Soares; Mónica J.B. Amorim. Energy reserves and cellular energy allocation studies: Should food supply be provided? Geoderma 2016, 284, 51 -56.
AMA StyleSusana.I.L. Gomes, Amadeu M.V.M. Soares, Mónica J.B. Amorim. Energy reserves and cellular energy allocation studies: Should food supply be provided? Geoderma. 2016; 284 ():51-56.
Chicago/Turabian StyleSusana.I.L. Gomes; Amadeu M.V.M. Soares; Mónica J.B. Amorim. 2016. "Energy reserves and cellular energy allocation studies: Should food supply be provided?" Geoderma 284, no. : 51-56.
Certain invertebrates (and vertebrates) are able to regenerate lost body parts. In the present study we investigated if Enchytraeus crypticus (Oligocheata), a species used for standard ecotoxicological testing, shows regeneration ability. Artificial amputation was induced. The results showed that regeneration occurs for this species, this being promoted by the presence of a mass of undifferentiated cells (blastema) in the wound site. This only occurred in the anterior fragment resulting in the posterior regeneration (formation of the tail), i.e. the posterior fragment does not regenerate the head and degenerates. The regenerated organisms were tested for fertility, which was confirmed. This is an important knowledge and ecological feature, E. crypticus has an additional survival strategy. Further, given this is an ecotoxicological model species and the possible implications thereof – E. crypticus can fragment and regenerate hence survival results may include this occurrence.
Micael F.M. Gonçalves; Susana I.L. Gomes; Amadeu M.V.M. Soares; Mónica J.B. Amorim. Enchytraeus crypticus (Oligochaeta) is able to regenerate—Considerations for a standard ecotoxicological species. Applied Soil Ecology 2016, 107, 320 -323.
AMA StyleMicael F.M. Gonçalves, Susana I.L. Gomes, Amadeu M.V.M. Soares, Mónica J.B. Amorim. Enchytraeus crypticus (Oligochaeta) is able to regenerate—Considerations for a standard ecotoxicological species. Applied Soil Ecology. 2016; 107 ():320-323.
Chicago/Turabian StyleMicael F.M. Gonçalves; Susana I.L. Gomes; Amadeu M.V.M. Soares; Mónica J.B. Amorim. 2016. "Enchytraeus crypticus (Oligochaeta) is able to regenerate—Considerations for a standard ecotoxicological species." Applied Soil Ecology 107, no. : 320-323.
The nano-form of copper (Cu-NPs) is already extensively used. In this paper the toxic effect of Cu in the worm Enchytraeus crypticus (Oligochaeta: Enchytraeidae) was assessed following exposure to (1) Cu-salt: freshly spiked soil with copper-nitrate, (2) Cu-NPs: freshly spiked soil with Cu nanoparticles (80 nm), and (3) Cu-field: historically Cu contaminated soil (80 years ago). Our main aims were to compare the three different exposure regimes and respective toxicity, and to determine how the oxidation state of the Cu and dissolution state of the particles differed. Characterization of in situ-exposure included identification of oxidation states with synchrotron generated X-ray absorption near-edge spectroscopy (XANES) analysis, activity of free Cu$^{2+}$ in soil-solution (Ion Selective Electrode), and the relative distribution of the labile Cu-fractions (Sequential Extraction). Freshly spiked Cu-salt was the most toxic for reproductive output of the worms, followed by Cu-NPs and then Cu-field. XANES indicated only one oxidation state (II) in Cu-salt and Cu-field soil, whereas in Cu-NPs soil it was present in all oxidation states (0, I and II). The partial oxidation of the Cu-NPs (in soil) was evident and with limited dissolution
Susana I.L. Gomes; Michael Murphy; Margrethe T. Nielsen; Søren Kristiansen; Mónica Amorim; Janeck Scott-Fordsmand. Cu-nanoparticles ecotoxicity – Explored and explained? Chemosphere 2015, 139, 240 -245.
AMA StyleSusana I.L. Gomes, Michael Murphy, Margrethe T. Nielsen, Søren Kristiansen, Mónica Amorim, Janeck Scott-Fordsmand. Cu-nanoparticles ecotoxicity – Explored and explained? Chemosphere. 2015; 139 ():240-245.
Chicago/Turabian StyleSusana I.L. Gomes; Michael Murphy; Margrethe T. Nielsen; Søren Kristiansen; Mónica Amorim; Janeck Scott-Fordsmand. 2015. "Cu-nanoparticles ecotoxicity – Explored and explained?" Chemosphere 139, no. : 240-245.
RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following an implicit assumption that most genes are not differentially expressed. Here, we present a mathematical approach to normalization that makes no assumption of this sort. We have found that variation in gene expression is much greater than currently believed, and that it can be measured with available technologies. Our results also explain, at least partially, the problems encountered in transcriptomics studies. We expect this improvement in detection to help efforts to realize the full potential of gene expression profiling, especially in analyses of cellular processes involving complex modulations of gene expression.
Carlos P. Roca; Susana I. L. Gomes; Mónica J. B. Amorim; Janeck J. Scott-Fordsmand. Variation-preserving normalization unveils blind spots in gene expression profiling. 2015, 021212 .
AMA StyleCarlos P. Roca, Susana I. L. Gomes, Mónica J. B. Amorim, Janeck J. Scott-Fordsmand. Variation-preserving normalization unveils blind spots in gene expression profiling. . 2015; ():021212.
Chicago/Turabian StyleCarlos P. Roca; Susana I. L. Gomes; Mónica J. B. Amorim; Janeck J. Scott-Fordsmand. 2015. "Variation-preserving normalization unveils blind spots in gene expression profiling." , no. : 021212.
The effects of several copper (Cu) and silver (Ag) nanomaterials were assessed using the cellular energy allocation (CEA), a methodology used to evaluate the energetic status and which relates with organisms’ overall condition and response to toxic stress. Enchytraeus crypticus (Oligochatea), was exposed to the reproduction effect concentrations EC20/50 of several Cu and Ag materials (CuNO3, Cu-Field, Cu-Nwires and Cu-NPs; AgNO3, Ag NM300K, Ag-NPs Non-coated and Ag-NPs PVP-coated) for 7 days (0-3-7d). The parameters measured were the total energy reserves available (protein, carbohydrate and lipid budgets) and the energy consumption (Ec) integrated to obtain the CEA. Results showed that these parameters allowed a clear discrimination between Cu and Ag, but less clearly within each of the various materials. For Cu there was an increase in Ec and protein budget, while for Ag a decrease was observed. The results corroborate known mechanisms, e.g., with Cu causing an increase in metabolic rate whereas Ag induces mitochondrial damage. The various Cu forms seem to activate different mechanisms with size and shape (e.g., Cu-NPs versus Cu-Nwires), causing clearly different effects. For Ag, results are in line with a slower oxidation rate of Ag-NMs in comparison with Ag-salt and hence delayed effects.
Susana I. L. Gomes; Janeck J. Scott-Fordsmand; Mónica J. B. Amorim. Cellular Energy Allocation to Assess the Impact of Nanomaterials on Soil Invertebrates (Enchytraeids): The Effect of Cu and Ag. International Journal of Environmental Research and Public Health 2015, 12, 6858 -6878.
AMA StyleSusana I. L. Gomes, Janeck J. Scott-Fordsmand, Mónica J. B. Amorim. Cellular Energy Allocation to Assess the Impact of Nanomaterials on Soil Invertebrates (Enchytraeids): The Effect of Cu and Ag. International Journal of Environmental Research and Public Health. 2015; 12 (6):6858-6878.
Chicago/Turabian StyleSusana I. L. Gomes; Janeck J. Scott-Fordsmand; Mónica J. B. Amorim. 2015. "Cellular Energy Allocation to Assess the Impact of Nanomaterials on Soil Invertebrates (Enchytraeids): The Effect of Cu and Ag." International Journal of Environmental Research and Public Health 12, no. 6: 6858-6878.
Nearly 80% of all the nano‐powders produced worldwide are metal oxides, and among these materials titanium dioxide (TiO2) is one of the most produced. Titanium dioxide's toxicity is estimated as low to soil organisms, but some studies have shown that TiO2 nanoparticles can cause oxidative stress. Additionally, it is known that TiO2 is activated by ultraviolet (UV) radiation, which can promote photocatalytic generation of reactive oxygen species, which is seldom taken into account in toxicity testing. In the present study, the authors investigated the effects of different TiO2 and zirconium materials on the soil oligochaete Enchytraeus crypticus, using exposure via soil, water, and soil:water extracts, and studied the effects combined with UV radiation. The results showed that zirconium dioxide (bulk and nano) was not toxic, whereas zirconium tetrachloride reduced enchytraeid reproduction in soil (50% effect concentration = 502 mg/kg). The TiO2 materials were also not toxic via soil exposure or under UV radiation. However, pre‐exposure to TiO2 and UV radiation via aqueous media caused a lower reproductive output post‐exposure in clean soil (20–50% less but only observed at the lowest concentration tested, 1 mg/L); that is, the effect of TiO2 in water was potentiated by the UV radiation and measurable as a decrease in reproduction in soil media. Environ Toxicol Chem 2015;34:2409–2416. © 2015 SETAC
Susana I. L. Gomes; Gianvito Caputo; Nicola Pinna; Janeck Scott-Fordsmand; Mónica Amorim. Effect of 10 different TiO2and ZrO2(nano)materials on the soil invertebrateEnchytraeus crypticus. Environmental Toxicology and Chemistry 2015, 34, 2409 -2416.
AMA StyleSusana I. L. Gomes, Gianvito Caputo, Nicola Pinna, Janeck Scott-Fordsmand, Mónica Amorim. Effect of 10 different TiO2and ZrO2(nano)materials on the soil invertebrateEnchytraeus crypticus. Environmental Toxicology and Chemistry. 2015; 34 (10):2409-2416.
Chicago/Turabian StyleSusana I. L. Gomes; Gianvito Caputo; Nicola Pinna; Janeck Scott-Fordsmand; Mónica Amorim. 2015. "Effect of 10 different TiO2and ZrO2(nano)materials on the soil invertebrateEnchytraeus crypticus." Environmental Toxicology and Chemistry 34, no. 10: 2409-2416.