A Course-Based Research Experience Using the Allen Brain Map: From Research Question to Poster Session.

San Francisco, CA A major challenge in implementing course-based undergraduate research experiences (CUREs) is for students to collect enough data for a robust analysis given the time and equipment available. One approach to mitigating this constraint in a CURE is to use massive open datasets such as those from the Allen Brain Map, produced by the Allen Institute for Brain Science. We describe a multi-week CURE module in which students generate a research question that can be addressed using at least two datasets of the Allen Brain Map, perform their analysis, and produce a conference-style poster detailing their findings. This article includes an adaptable CURE assignment, tutorials introducing students to selected datasets from the Allen Brain Map, and a summary of student outcomes.

Perspectives on Relevancy Assessment for Non-Standard Ecotoxicity Data in Environment Quality Standard derivation: Examples for Diclofenac.

A key step in deriving an Environmental Quality Standard (EQS) is assessing the reliability and relevance of the underpinning ecotoxicity data. While the assessment of data reliability is relatively well established, the detailed evaluation of data relevancy is a more recent development. We applied broadly accepted relevancy criteria to a series of non-standard ecotoxicity studies on diclofenac, focusing on some aspects that should be accounted for in studies used in EQS derivation. Specific relevancy issues include potential experimental bias, claimed 'significant effects' that are indistinguishable from controls, or within the range of normal, and lack of environmental applicability. We highlight that rigorous, comprehensive and, where necessary, specialist assessment of data relevancy for studies potentially applicable for EQS setting is critical if studies are to be appropriately used regulatory decision-making. We provide recommendations for researchers and environmental practitioners to ensure robust accounting of relevancy in non-standard studies is undertaken.

Overexpression of antibiotic resistance genes in hospital effluents over time.

Objectives: Effluents contain a diverse abundance of antibiotic resistance genes that augment the resistome of receiving aquatic environments. However, uncertainty remains regarding their temporal persistence, transcription and response to anthropogenic factors, such as antibiotic usage. We present a spatiotemporal study within a river catchment (River Cam, UK) that aims to determine the contribution of antibiotic resistance gene-containing effluents originating from sites of varying antibiotic usage to the receiving environment. Methods: Gene abundance in effluents (municipal hospital and dairy farm) was compared against background samples of the receiving aquatic environment (i.e. the catchment source) to determine the resistome contribution of effluents. We used metagenomics and metatranscriptomics to correlate DNA and RNA abundance and identified differentially regulated gene transcripts. Results: We found that mean antibiotic resistance gene and transcript abundances were correlated for both hospital ( ρ = 0.9, two-tailed P <0.0001) and farm ( ρ = 0.5, two-tailed P <0.0001) effluents and that two ß-lactam resistance genes ( bla GES and bla OXA ) were overexpressed in all hospital effluent samples. High ß-lactam resistance gene transcript abundance was related to hospital antibiotic usage over time and hospital effluents contained antibiotic residues. Conclusions: We conclude that effluents contribute high levels of antibiotic resistance genes to the aquatic environment; these genes are expressed at significant levels and are possibly related to the level of antibiotic usage at the effluent source.

Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment.

The aquatic environment has been implicated as a reservoir for antimicrobial resistance genes (ARGs). In order to identify sources that are contributing to these gene reservoirs, it is crucial to assess effluents that are entering the aquatic environment. Here we describe a metagenomic assessment for two types of effluent entering a river catchment. We investigated the diversity and abundance of resistance genes, mobile genetic elements (MGEs) and pathogenic bacteria. Findings were normalised to a background sample of river source water. Our results show that effluent contributed an array of genes to the river catchment, the most abundant being tetracycline resistance genes tetC and tetW from farm effluents and the sulfonamide resistance gene sul2 from wastewater treatment plant (WWTP) effluents. In nine separate samples taken across 3 years, we found 53 different genes conferring resistance to seven classes of antimicrobial. Compared to the background sample taken up river from effluent entry, the average abundance of genes was three times greater in the farm effluent and two times greater in the WWTP effluent. We conclude that effluents disperse ARGs, MGEs and pathogenic bacteria within a river catchment, thereby contributing to environmental reservoirs of ARGs.

Does Uptake of Pharmaceuticals Vary Across Earthworm Species?

This study compared the uptake and depuration of four commonly used pharmaceuticals (carbamazepine, diclofenac, fluoxetine and orlistat) in two earthworm species (Lumbricus terrestris and Eisenia fetida). L. terrestris are a larger species and often found in deep burrows whereas E. fetida prefer to reside near the soil surface. Species burrowing habits and sizes may alter uptake by earthworms. All four pharmaceuticals were taken up into both L. terrestris and E. fetida tissue after 21 days exposure to spiked soil. Bioconcentration factors (BCFs) ranged between 1.72 and 29.83 for L. terrestris and 1.14 and 63.03 for E. fetida. For carbamazepine and diclofenac, BCFs were similar whereas for fluoxetine and orlistat, BCFs in E. fetida were more than double those seen in L. terrestris. Results indicate that uptake into earthworms cannot be generalised between species and that the influence of species traits can vary depending on the nature of the study chemical.

Minimised bioconcentration tests: a useful tool for assessing chemical uptake into terrestrial and aquatic invertebrates?

Current guidelines for determining bioconcentration factors (BCF) and uptake and depuration rate constants require labor intensive studies with large numbers of organisms. A minimized approach has recently been proposed for fish BCF studies but its applicability to other taxonomic groups is unknown. In this study, we therefore evaluate the use of the minimized approach for estimating BCF and uptake and depuration rate constants for chemicals in aquatic and terrestrial invertebrates. Data from a range of previous BCF studies were resampled to calculate BCFs and rate constants using the minimized method. The resulting values were then compared to values obtained using full study designs. Results demonstrated a good correlation for uptake rate constants, a poor correlation for depuration rate constants and a very good correlation between the BCFs obtained using the traditional and minimized approach for a variety of organic compounds. The minimized approach therefore has merit in deriving bioconcentration factors and uptake rate constants but may not be appropriate for deriving depuration rate constants for use in, for example, toxico-kinetic toxico-dynamic modeling. The approach uses up to 70% fewer organisms, requires less labor and has lower analytical costs. The minimized design therefore could be a valuable approach for running large multifactorial studies to assess bioconcentration of the plethora of chemicals that occur in the environment into the many taxonomic groups that occur in the environment. The approach should therefore help in accelerating the development of our understanding of factors and processes affecting uptake of chemicals into organisms in the environment.

Design of greener drugs: aligning parameters in pharmaceutical R&D and drivers for environmental impact.

Active pharmaceutical ingredients (APIs) in the environment, primarily resulting from patient excretion, are of concern because of potential risks to wildlife. This has led to more restrictive regulatory policies. Here, we discuss the 'benign-by-design' approach, which encourages the development of environmentally friendly APIs that are also safe and efficacious for patients. We explore the challenges and opportunities associated with identifying chemical properties that influence the environmental impact of APIs. Although a straightforward application of greener properties could hinder the development of new drugs, more nuanced approaches could lead to drugs that benefit both patients and the environment. We advocate for an enhanced dialogue between research and development (R&D) and environmental scientists and development of a toolbox to incorporate environmental sustainability in drug development.

Cross-cultural validity and reliability of the BRIEF-P at age 2 and 4.5 years in children born at risk of neonatal hypoglycemia.

Executive function (EF) encompasses several neurocognitive processes that are important in self-regulation of behavior and the attainment of social and cognitive competencies. While much progress has been made in developing valid measures for adult and adolescent EF, there is a dearth of valid measures for preschool children. Given the steep trajectory of neuropsychological development among this age group and the importance of EF, a valid measure for clinical assessment and research is needed that can capture EF in the everyday context of early childhood. The Behavior Rating Inventory of Executive Function Preschool Version (BRIEF-P) measures parent and teacher observations of children's everyday self-regulatory behaviors. The BRIEF-P has been validated in a range of normative and non-normative samples, but further validation is needed across cultures. This study aimed to evaluate the cross-cultural validity and reliability of the BRIEF-P when used by New Zealand Maori (n = 131) and European (n = 193) parents of children born with risk factors of neonatal hypoglycemia. Parents of children who participated in the prospective, longitudinal Children with Hypoglycemia and their Later Development (CHYLD) study completed the BRIEF-P when the child was 2 years ±4 weeks and 4.5 years ±8 weeks old. Results showed that the BRIEF-P is a highly reliable and valid instrument. Comparisons between Maori and New Zealand European samples revealed biases, which could be a source of further work to improve the construct validity of this measure, such as the development of norms and item validation for non-European and non-Western samples.

Default predicted no-effect target concentrations for antibiotics in the absence of data for the protection against antibiotic resistance and environmental toxicity.

The pharmaceutical manufacturing industry, via the AMR Industry Alliance, has developed and implemented steps to help minimize the potential impact of pharmaceutical manufacturing on the spread of antimicrobial resistance (AMR). One of these steps was to publish predicted no-effect concentrations (PNECs) to serve as targets for antibiotic manufacturing wastewater effluent risk assessments aimed to help protect environmental receptors and to mitigate against the spread of antibiotic resistance. Concentrations below which adverse effects in the environment are not expected to occur (PNECs) were first published in 2018 and are updated annually. The current list now stands at 125 antibiotics; however, it is recognized that this list does not encompass all manufactured antibiotics. Therefore, a statistical evaluation of currently available data was conducted and a default PNEC of 0.05 µg/L for antibiotics in the absence of other data was derived. Integr Environ Assess Manag 2022;18:863-867. © 2022 Merck, Sanofi, Johnson & Johnson Services, Inc, F.Hoffmann-La Roche Ltd, Teva Pharmaceuticals, GlaxoSmithKline, Novartis Pharma AG, and Pfizer lnc. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

GREENER Pharmaceuticals for More Sustainable Healthcare.

Medicines are essential to human health but can also impact the aquatic and terrestrial environment after use by patients and release via excreta into wastewater. We highlight the need for a GREENER approach to identify and meet important environmental criteria, which will help reduce the impact of medicinal residues on the environment. These criteria include effect reduction by avoiding nontarget effects or undesirable moieties, exposure reduction via lower emissions or environmental (bio)degradability, no PBT (persistent, bioaccumulative, and toxic) substances, and risk mitigation. With all of these criteria, however, patient health is of primary importance as medicines are required to be safe and efficacious for treating diseases. We discuss the feasibility of including these criteria for green by design active pharmaceutical ingredients in the process of drug discovery and development and which tools or assays are needed to accomplish this. The integrated GREENER approach can be used to accelerate discussions about future innovations in drug discovery and development.

Putting pharmacogenetics into practice.

Genetics is slowly explaining variations in drug response, but applying this knowledge depends on implementation of a host of policies that provide long-term support to the field, from translational research and regulation to professional education.

Uptake and Effects of the Beta-Adrenergic Agonist Salbutamol in Fish: Supporting Evidence for the Fish Plasma Model.

The fish plasma model (FPM) predicts the fish blood plasma concentration of a pharmaceutical from the water concentration to which the fish is exposed and compares it with the human therapeutic plasma concentration (Hther PC) with the postulate that no adverse toxic effects occur below the Hther PC. The present study provides several lines of evidence supporting the FPM for the beta-adrenergic agonist salbutamol, a small cationic molecule at ambient pH. Salbutamol exhibited very low acute toxicity to early and adult life stages of fish. Biomass reduction in fish early life stages was the most sensitive apical endpoint, with no-observed-effect concentrations (NOECs) in the low mg/L range after continuous exposure for up to 120 d. Given that predicted and measured environmental concentrations are at least 1000-fold lower, the risk of salbutamol in freshwater is deemed very low. Increase in heart beat rate and decrease in total triglyceride content in fish also occurred at the low mg/L range and resembled effects known from humans. This finding supports the FPM assumption of conserved targets in fish with similar functionality. Plasma concentrations measured in adult and juvenile fish exposed to water concentrations at approximately the NOECs exceeded Hther PC and even approached plasma concentrations toxic to humans. This result confirms for salbutamol the FPM hypothesis that no adverse (i.e., population-relevant) toxic effects occur in fish below the Hther PC. Environ Toxicol Chem 2019;38:2509-2519. © 2019 SETAC.

Science-based Targets for Antibiotics in Receiving Waters from Pharmaceutical Manufacturing Operations.

In 2016, the United Nations declared the need for urgent action to combat the global threat of antimicrobial resistance (AMR). In support of this effort, the pharmaceutical industry has committed to measures aimed at improving the stewardship of antibiotics both within and outside the clinic. Notably, a group of companies collaborated to specifically address concerns related to antibiotic residues being discharged from manufacturing sites. In addition to developing a framework of minimum environmental expectations for antibiotic manufacturers, science-based receiving water targets were established for antibiotics discharged from manufacturing operations. This paper summarizes the holistic approach taken to derive these targets and includes previously unpublished, company-generated, environmental toxicity data.

Effects of soil properties on the uptake of pharmaceuticals into earthworms.

Pharmaceuticals can enter the soil environment when animal slurries and sewage sludge are applied to land as a fertiliser or during irrigation with contaminated water. These pharmaceuticals may then be taken up by soil organisms possibly resulting in toxic effects and/or exposure of organisms higher up the food chain. This study investigated the influence of soil properties on the uptake and depuration of pharmaceuticals (carbamazepine, diclofenac, fluoxetine and orlistat) in the earthworm Eisenia fetida. The uptake and accumulation of pharmaceuticals into E. fetida changed depending on soil type. Orlistat exhibited the highest pore water based bioconcentration factors (BCFs) and displayed the largest differences between soil types with BCFs ranging between 30.5 and 115.9. For carbamazepine, diclofenac and fluoxetine BCFs ranged between 1.1 and 1.6, 7.0 and 69.6 and 14.1 and 20.4 respectively. Additional analysis demonstrated that in certain treatments the presence of these chemicals in the soil matrices changed the soil pH over time, with a statistically significant pH difference to control samples. The internal pH of E. fetida also changed as a result of incubation in pharmaceutically spiked soil, in comparison to the control earthworms. These results demonstrate that a combination of soil properties and pharmaceutical physico-chemical properties are important in terms of predicting pharmaceutical uptake in terrestrial systems and that pharmaceuticals can modify soil and internal earthworm chemistry which may hold wider implications for risk assessment.

Use of acute and chronic ecotoxicity data in environmental risk assessment of pharmaceuticals.

For many older pharmaceuticals, chronic aquatic toxicity data are limited. To assess risk during development, scale-up, and manufacturing processes, acute data and physicochemical properties need to be leveraged to reduce potential long-term impacts to the environment. Aquatic toxicity data were pooled from daphnid, fish, and algae studies for 102 active pharmaceutical ingredients (APIs) to evaluate the relationship between predicted no-effect concentrations (PNECs) derived from acute and chronic tests. The relationships between acute and chronic aquatic toxicity and the n-octanol/water distribution coefficient (D(OW)) were also characterized. Statistically significant but weak correlations were observed between toxicity and log D(OW), indicating that D(OW) is not the only contributor to toxicity. Both acute and chronic PNEC values could be calculated for 60 of the 102 APIs. For most compounds, PNECs derived from acute data were lower than PNECs derived from chronic data, with the exception of steroid estrogens. Seven percent of the PNECs derived from acute data were below the European Union action limit of 0.01 µg/L and all were anti-infectives affecting algal species. Eight percent of available PNECs derived from chronic data were below the European Union action limit, and fish were the most sensitive species for all but 1 API. These analyses suggest that the use of acute data may be acceptable if chronic data are unavailable, unless specific mode of action concerns suggest otherwise.

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.

BACKGROUND: Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring. RESULTS: Here we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR's application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei. CONCLUSIONS: We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR is effective in detecting antimicrobial resistance genes in metagenomic and isolate sequencing data from both environmental metagenomes and sequencing data from clinical isolates.

Experiences with the OECD 308 transformation test: a human pharmaceutical perspective.

The Organisation for Economic Co-operation and Development (OECD) 308 water-sediment transformation test has been routinely conducted in Phase II Tier A testing of the environmental risk assessment (ERA) for all human pharmaceutical marketing authorization applications in Europe, since finalization of Environmental Medicines Agency (EMA) ERA guidance in June 2006. In addition to the "Ready Biodegradation" test, it is the only transformation test for the aquatic/sediment compartment that supports the classification of the drug substance for its potential persistence in the environment and characterizes the fate of the test material in a water-sediment environment. Presented is an overview of 31 OECD 308 studies conducted by 4 companies with a focus on how pharmaceuticals behave in these water-sediment systems. The geometric mean (gm) parent total system half-life for the 31 pharmaceuticals was 30 days with 10th/90th percentile (10/90%ile) of 14.0/121.6 d respectively, with cationic substances having a half-life approximately 2 times that of neutral and anionic substances. The formation of nonextractable residues (NER) was considerable, with gm (10/90%ile) of 38% (20.5/81.4) of the applied radioactivity: cationic substances 50.8% (27.7/87.6), neutral substances 31.9% (15.3/52.3), and anionic substances 16.7% (9.5/30.6). In general, cationic substances had fewer transformation products and more unchanged parent remaining at day 100 of the study. A review of whether a simplified 1-point analysis could reasonably estimate the parent total system half-life showed that the total amount of parent remaining in the water and sediment extracts at day 100 followed first-order kinetics and that the theoretical half-life and the measured total system half-life values agreed to within a factor of 1.68. Recommendations from this 4-company collaboration addressed: 1) the need to develop a more relevant water-sediment transformation test reflecting the conditions of the discharge scenario more representative of human pharmaceuticals, 2) potential use of a 1-point estimate of parent total system half-life in the EMA ERA screening phase of testing, 3) the need for a more consistent and transparent interpretation of the results from the transformation study; consistent use of terminology such as dissipation, transformation, depletion, and degradation in describing their respective processes in the ERA, 4) use of the parent total system dissipation half-life in hazard classification schemes and in revising predicted environmental concentration in ERA, and 5) further research into cationic pharmaceuticals to assess whether their classification as such serves as a structural alert to high levels of NER; and whether this results in reduced bioavailability of those residues.