Dose-Response Analysis Using R

Comparative transcriptomics provides insights into molecular mechanisms of zinc tolerance in the ectomycorrhizal fungus Suillus luteus

Zinc (Zn) is a major soil contaminant and high Zn levels can disrupt growth, survival, and reproduction of fungi. Some fungal species evolved Zn tolerance through cell processes mitigating Zn toxicity, although the genes and detailed mechanisms underlying mycorrhizal fungal Zn tolerance remain unexplored. To fill this gap in knowledge, we investigated the gene expression of Zn tolerance in the ectomycorrhizal fungus Suillus luteus. We found that Zn tolerance in this species is mainly a constitutive trait that can also be environmentally dependent. Zinc tolerance in S. luteus is associated with differences in the expression of genes involved in metal exclusion and immobilization, as well as recognition and mitigation of metal-induced oxidative stress. Differentially expressed genes were predicted to be involved in transmembrane transport, metal chelation, oxidoreductase activity, and signal transduction. Some of these genes were previously reported as candidates for S. luteus Zn tolerance, while others are reported here for the first time. Our results contribute to understanding the mechanisms of fungal metal tolerance and pave the way for further research on the role of fungal metal tolerance in mycorrhizal associations.

Evaluation of Germicidal UV-C Light for Suppression of Grape Powdery Mildew and Botrytis Bunch Rot in Western Oregon

Germicidal UV light (UV-C) has been shown to effectively suppress several plant pathogens as well as some arthropod pests. Recent reports describe the efficacy of nighttime applications of UV-C at doses from 100 to 200 J/m2 in vineyards to reduce grape powdery mildew (Erysiphe necator). Our in vitro studies confirmed the efficacy of UV-C to inhibit germination of E. necator and Botrytis cinerea conidia, demonstrated a range of tolerances to UV-C within a collection of E. necator isolates, and showed growth stage-specific effects of UV-C on B. cinerea. Nighttime use of UV-C was evaluated at 48 to 96 J/m2 in small plot trials (<1,000 vines) from 2020 to 2023. Once- or twice-weekly UV-C applications significantly reduced the incidence of foliar powdery mildew compared with non-UV-C-treated controls (P < 0.02). Suppression of powdery mildew on fruit was less consistent, where once or twice weekly UV-C exposure reduced powdery mildew disease severity in 2020 (P = 0.04), 2021 (P = 0.02), and 2023 (P = 0.003) but less so in 2022 (P = 0.07). Bunch rot severity was not significantly reduced with UV-C treatment in any year of the study. Application of UV-C until the onset of fruit color change (veraison) also had a minimal effect on the fruit-soluble solids, pH, anthocyanins, or phenolics in harvested fruit at any UV-C dose or frequency (P > 0.10). Suppression of powdery mildew by nighttime application of UV-C at lower doses in small plots suggests that such treatments merit further evaluation in larger-scale studies in Western Oregon.

Sensitivity of Alabama Freshwater Gastropod Species to Nickel Exposure

Snails are effective bioindicators due to their prolific distribution, high level of endemism, and capacity to accumulate contaminants. Freshwater snails have unique ecological niches which are imperiled by land-use change and the introduction of hazardous chemicals. To assess how environmental alterations affect gastropods, lab-based studies are needed to characterize the toxicity of specific stressors. This can help guide policy decisions and remediation efforts. The aim of this research was to characterize acute toxicity of nickel (Ni) on endemic snails (Somatogyrus georgianus [Walker, 1904], Elimia cahawbensis [Lea, 1861], and Elimia spp.) and measure the accumulation of Ni and mineral elements including calcium (Ca), magnesium, potassium, and sodium (Na). Snails were exposed to six concentrations (25-800 µg/L) of Ni for 96 h. Among the studied snail species, E. cahawbensis was the most sensitive to Ni, with the lowest lethal concentration where 50% of the organisms died (LC50) at 88.88 µg/L Ni after 96 h. The LC50 at 96 h for S. georgianus was 167.78 µg/L Ni, and 393.13 μg/L Ni for Elimia spp. Except for Elimia spp., mortality of the other two snail species corresponded to the whole-body uptake of Ni. Nickel exposure also influenced Ca and Na uptake for Elimia spp. All three endemic species are potential candidate species for evaluating localized effects of human activities, and the present study provides a first step in characterizing how snails would be affected by environmental alterations. More research could further characterize potential effects of other human stressors on these endemic snail species. Future research into subindividual responses and routes of exposure can further elucidate variations in species sensitivity. Environ Toxicol Chem 2024;00:1-11. © 2024 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Resistance to acetyl-CoA carboxylase (ACCase)-inhibiting herbicides in Lolium multiflorum Lam. populations of Argentina

BACKGROUND

Italian ryegrass (Lolium multiflorum Lam.) is one of the most troublesome grass weeds in Argentina. The extensive and repetitive use of acetyl-CoA carboxylase (ACCase)-inhibiting herbicides has induced resistance in this weed species. The objectives of this study were to quantify the resistance levels to ACCase-inhibiting herbicides in two resistant populations and to identify the target-site mutations associated with their resistance.

RESULTS

Two resistant Italian ryegrass populations, Roldán and H2, were studied. Roldán was a suspected haloxyfop-resistant population, located in a wheat field from Santa Fe province with a history of ACCase-inhibiting herbicide use. The H2 population was obtained from the susceptible Hernandarias population (H0) after two cycles of selection with the herbicide quizalofop-ethyl. Whole-plant dose-response assays revealed that the resistant populations exhibited a high resistance to haloxyfop, with resistance factors (RF) exceeding 97-fold. Additionally, both populations showed a moderate resistance to pinoxaden (RF > 7), while maintaining susceptibility to clethodim. Partial chloroplastic ACCase sequences revealed isoleucine-to-asparagine substitution at position 2041 (Ile-2041-Asn) in both resistant populations.

CONCLUSION

This work provides a better understanding of cross-resistance to ACCase-inhibiting herbicides in L. multiflorum populations and represents the first report of the target-site mutation Ile-2041-Asn conferring resistance in populations from Argentina. © 2024 Society of Chemical Industry.

Global impact of unproductive splicing on human gene expression

Alternative splicing (AS) in human genes is widely viewed as a mechanism for enhancing proteomic diversity. AS can also impact gene expression levels without increasing protein diversity by producing 'unproductive' transcripts that are targeted for rapid degradation by nonsense-mediated decay (NMD). However, the relative importance of this regulatory mechanism remains underexplored. To better understand the impact of AS-NMD relative to other regulatory mechanisms, we analyzed population-scale genomic data across eight molecular assays, covering various stages from transcription to cytoplasmic decay. We report threefold more unproductive splicing compared with prior estimates using steady-state RNA. This unproductive splicing compounds across multi-intronic genes, resulting in 15% of transcript molecules from protein-coding genes being unproductive. Leveraging genetic variation across cell lines, we find that GWAS trait-associated loci explained by AS are as often associated with NMD-induced expression level differences as with differences in protein isoform usage. Our findings suggest that much of the impact of AS is mediated by NMD-induced changes in gene expression rather than diversification of the proteome.

Rapid identification of reproductive toxicants among environmental chemicals using an in vivo evaluation of gametogenesis in budding yeast Saccharomyces cerevisiae

Infertility affects ∼12 % of couples, with environmental chemical exposure as a potential contributor. Of the chemicals that are actively manufactured, very few are assessed for reproductive health effects. Rodents are commonly used to evaluate reproductive effects, which is both costly and time consuming. Thus, there is a pressing need for rapid methods to test a broader range of chemicals. Here, we developed a strategy to evaluate large numbers of chemicals for reproductive toxicity via a yeast, S. cerevisiae high-throughput assay to assess gametogenesis as a potential new approach method (NAM). By simultaneously assessing chemicals for growth effects, we can distinguish if a chemical affects gametogenesis only, proliferative growth only or both. We identified a well-known mammalian reproductive toxicant, bisphenol A (BPA) and ranked 19 BPA analogs for reproductive harm. By testing mixtures of BPA and its analogs, we found that BPE and 17 β-estradiol each together with BPA showed synergistic effects that worsened reproductive outcome. We examined an additional 179 environmental chemicals including phthalates, pesticides, quaternary ammonium compounds and per- and polyfluoroalkyl substances and found 57 with reproductive effects. Many of the chemicals were found to be strong reproductive toxicants that have yet to be tested in mammals. Chemicals having affect before meiosis I division vs. meiosis II division were identified for 16 gametogenesis-specific chemicals. Finally, we demonstrate that in general yeast reproductive toxicity correlates well with published reproductive toxicity in mammals illustrating the promise of this NAM to quickly assess chemicals to prioritize the evaluation for human reproductive harm.

Effect of Insecticide Exposure Across Multiple Generations of the Earthworm Eisenia andrei

The toxicity of neonicotinoids and many of their replacement insecticides to nontarget soil invertebrates such as earthworms has previously been established. However, the long-term effects of these substances on these organisms are largely unknown. In the field of soil ecotoxicology, lumbricid earthworms such as Eisenia andrei are used extensively due to the availability of standardized test methods and their adaptability to laboratory culture and testing. Multigenerational studies have gained popularity and attention in recent years, with a shift toward the use of long-term assays and lower concentrations of test chemicals. The use of exposure concentrations that include those measured in a monitoring program carried out by the Government of Ontario presents a realistic exposure scenario that may not show significant effects in contemporary, shorter term studies. We used current standardized test methods as a basis for the development of multigenerational studies on E. andrei. The effects of exposure to a single application of the insecticides thiamethoxam and cyantraniliprole on the survival and reproduction of E. andrei were observed over three (thiamethoxam) or two (cyantraniliprole) generations using consecutive reproduction tests. No significant impacts on adult survival were reported in any generation for either insecticide, whereas reproduction decreased between the first and second generations in the thiamethoxam test, with median effective concentration (EC50) values of 0.022 mg/kg dry weight reported for the first generation compared with 0.002 mg/kg dry weight in the second generation. For cyantraniliprole, an EC50 of 0.064 was determined for the first generation compared with 0.016 mg/kg dry weight in the second generation. A third generation was completed for the thiamethoxam test, and a significant decrease in reproduction was observed in all treatments and controls compared with previous generations. No significant difference between thiamethoxam treatments and the control treatment was reported for the third generation. Collectively, these data indicate that exposure of oligochaetes to these two insecticides at concentrations representative of field conditions may result in long-term stresses. Environ Toxicol Chem 2024;43:2058-2070. © 2024 The Author(s). Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Environmental factors modify silver nanoparticles ecotoxicity in Chydorus eurynotus (Cladocera)

Silver nanoparticles (AgNPs) are among the most produced nanomaterials in the world and are incorporated into several products due to their biocide and physicochemical properties. Since freshwater bodies are AgNPs main final sink, several consequences for biota are expected to occur. With the hypothesis that AgNPs can interact with environmental factors, we analyzed their ecotoxicity in combination with humic acids and algae. In addition to the specific AgNPs behavior in the media, we analyzed the mortality, growth, and phototactic behavior of Chydorus eurynotus (Cladocera) as response variables. While algae promoted Ag+ release, humic acids reduced it by adsorption, and their combination resulted in an intermediated Ag+ release. AgNPs affected C. eurynotus survival and growth, but algae and humic acids reduced AgNPs lethality, especially when combined. The humic acids mitigated AgNP effects in C. eurynotus growth, and both factors improved its phototactic behavior. It is essential to deepen the study of the isolated and combined influences of environmental factors on the ecotoxicity of nanoparticles to achieve accurate predictions under realistic exposure scenarios.

ClonoScreen3D - A Novel 3-Dimensional Clonogenic Screening Platform for Identification of Radiosensitizers for Glioblastoma

PURPOSE

Glioblastoma (GBM) is a lethal brain tumor. Standard-of-care treatment comprising surgery, radiation, and chemotherapy results in median survival rates of 12 to 15 months. Molecular-targeted agents identified using conventional 2-dimensional (2D) in vitro models of GBM have failed to improve outcome in patients, rendering such models inadequate for therapeutic target identification. A previously developed 3D GBM in vitro model that recapitulates key GBM clinical features and responses to molecular therapies was investigated for utility for screening novel radiation-drug combinations using gold-standard clonogenic survival as readout.

METHODS AND MATERIALS

Patient-derived GBM cell lines were optimized for inclusion in a 96-well plate 3D clonogenic screening platform, ClonoScreen3D. Radiation responses of GBM cells in this system were highly reproducible and comparable to those observed in low-throughout 3D assays. The screen methodology provided quantification of candidate drug single agent activity (half maximal effective concentration or EC50) and the interaction between drug and radiation (radiation interaction ratio).

RESULTS

The poly(ADP-ribose) polymerase inhibitors talazoparib, rucaparib, and olaparib each showed a significant interaction with radiation by ClonoScreen3D and were subsequently confirmed as true radiosensitizers by full clonogenic assay. Screening a panel of DNA damage response inhibitors revealed the expected propensity of these compounds to interact significantly with radiation (13/15 compounds). A second screen assessed a panel of compounds targeting pathways identified by transcriptomic analysis and demonstrated single agent activity and a previously unreported interaction with radiation of dinaciclib and cytarabine (radiation interaction ratio 1.28 and 1.90, respectively). These compounds were validated as radiosensitizers in full clonogenic assays (sensitizer enhancement ratio 1.47 and 1.35, respectively).

CONCLUSIONS

The ClonoScreen3D platform was demonstrated to be a robust method to screen for single agent and radiation-drug combination activity. Using gold-standard clonogenicity, this assay is a tool for identification of radiosensitizers. We anticipate this technology will accelerate identification of novel radiation-drug combinations with genuine translational value.

High-level tumour methylation of BRCA1 and RAD51C is required for homologous recombination deficiency in solid cancers

In ovarian and breast cancer, promoter methylation of BRCA1 or RAD51C is a promising biomarker for PARP inhibitor response, as high levels lead to homologous recombination deficiency (HRD). Yet the extent and role of such methylation in other cancers is not clear. This study comprehensively investigated promoter methylation of eight homologous recombination repair genes across 23 solid cancer types. Here, we showed that BRCA1 methylated cancers were associated with reduced gene expression, loss of heterozygosity (LOH), TP53 mutations and genomic features of HRD. We identified BRCA1 methylation in 3% of the copy-number high subtype of endometrial cancer, and as a rare event in six other cancer types, including lung squamous cell, pancreatic, bladder and stomach cancer. RAD51C promoter methylation was widespread across multiple cancer types, but HRD features were only observed for cases which contained high-level tumour methylation and LOH of RAD51C. While RAD51C methylation was frequent in stomach adenocarcinoma (6%) and low-grade glioma (2.5%), it was mostly detected at a low tumour level, suggestive of heterozygous methylation, and was associated with CpG island methylator phenotype. Our findings indicate that high-level tumour methylation of BRCA1 and RAD51C should be explored as a PARP inhibitor biomarker across multiple cancers.

New substituted benzoxazine derivatives as potent inducers of membrane permeability and cell death

The search for new agents targeting different forms of cell death is an important research focus for developing new and potent antitumor therapies. As a contribution to this endeavor, we have designed and synthesized a series of new substituted 3,4-dihydro-2H-1,4-benzoxazine derivatives. These compounds have been evaluated for their efficacy against MCF-7 breast cancer and HCT-116 colon cancer cell lines. Overall, substituting this heterocycle led to improved antiproliferative activity compared to the unsubstituted derivative 1. The most active compounds, 2b and 4b, showed IC50 values of 2.27 and 3.26 μM against MCF-7 cells and 4.44 and 7.63 μM against HCT-116 cells, respectively. To investigate the mechanism of action of the target compounds, the inhibition profile of 8 kinases involved in cell signaling was studied highlighting residual activity on HER2 and JNK1 kinases. 2b and 4b showed a consistent binding mode to both receptor kinases, establishing significant interactions with known and catalytically important domains and residues. Compounds 2b and 4b exhibit potent cytotoxic activity by disrupting cell membrane permeability, likely triggering both inflammatory and non-inflammatory cell death mechanisms. This dual capability increases their versatility in the treatment of different stages or types of tumors, providing greater flexibility in clinical applications.

Synergy of retinoic acid and BH3 mimetics in MYC(N)-driven embryonal nervous system tumours

BACKGROUND

Certain paediatric nervous system malignancies have dismal prognoses. Retinoic acid (RA) is used in neuroblastoma treatment, and preclinical data indicate potential benefit in selected paediatric brain tumour entities. However, limited single-agent efficacy necessitates combination treatment approaches.

METHODS

We performed drug sensitivity profiling of 76 clinically relevant drugs in combination with RA in 16 models (including patient-derived tumouroids) of the most common paediatric nervous system tumours. Drug responses were assessed by viability assays, high-content imaging, and apoptosis assays and RA relevant pathways by RNAseq from treated models and patient samples obtained through the precision oncology programme INFORM (n = 2288). Immunoprecipitation detected BCL-2 family interactions, and zebrafish embryo xenografts were used for in vivo efficacy testing.

RESULTS

Group 3 medulloblastoma (MBG3) and neuroblastoma models were highly sensitive to RA treatment. RA induced differentiation and regulated apoptotic genes. RNAseq analysis revealed high expression of BCL2L1 in MBG3 and BCL2 in neuroblastomas. Co-treatments with RA and BCL-2/XL inhibitor navitoclax synergistically decreased viability at clinically achievable concentrations. The combination of RA with navitoclax disrupted the binding of BIM to BCL-XL in MBG3 and to BCL-2 in neuroblastoma, inducing apoptosis in vitro and in vivo.

CONCLUSIONS

RA treatment primes MBG3 and NB cells for apoptosis, triggered by navitoclax cotreatment.

Unraveling the reasons for failure to control Amaranthus albus: insights into herbicide application at different growth stages, temperature effect, and herbicide resistance on a regional scale

BACKGROUND

This study investigates factors contributing Amaranthus albus control failure in processing tomato fields in northern Israel. The study region is characterized by a significant climate gradient from east to west, providing the opportunity to investigate the effect of critical elements of the agricultural environment, e.g., temperature. Eight populations were collected from commercial fields in this region. Post-emergence herbicide efficacy of metribuzin, a photosystem II inhibitor, and rimsulfuron, an acetolactate synthase (ALS) inhibitor, was assessed through dose-response analyses at various growth stages. Temperature effects on control efficacy and resistance mechanisms were also explored.

RESULTS

Standard metribuzin dose (X) was ineffective on A. albus plants with more than six true-leaves, whereas 2X dose proved effective. Rimsulfuron at 16X dose was ineffective on plants with more than four true-leaves. We report here the first case of target site resistance to ALS inhibitors in A. albus, due to point mutation in the ALS gene (Pro197 to Leu). Furthermore, our findings suggest potential involvement of CYT P450 enzymes in enhanced metabolizing of rimsulfuron. An overall decrease in dry weight was observed in response to both herbicides at 16/22 °C (P < 0.0001). Rimsulfuron was effective against only one population when applied at 28/34 °C. A possible fitness cost associated with target site-resistant biotypes was observed under low temperature conditions, leading to effective control.

CONCLUSION

This regional-scale study highlights the challenges faced by growers, emphasizes the need for adapting management practices to the local climatic conditions and lays the groundwork for implementing location-specific weed management strategies in commercial fields. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Long-term, landscape-level assessment of aquatic pesticide exposure to identify amphibian ontological traits affecting vulnerability

Amphibians worldwide are threatened by habitat loss, some of which is driven by a changing climate, as well as exposure to pesticides, among other causes. The timing and duration of the larval development phase vary between species, thereby influencing the relative impacts of stochastic hydroregime conditions as well as potential aquatic pesticide exposure. We describe the stages of breeding through metamorphosis for eight amphibian species, based on optimal hydroregime conditions, and use a model of pesticide fate and exposure representative of central Florida citrus groves to simulate hydrodynamics based on observed weather data over a 54-year period. Using the Pesticide in Water Calculator and Plant Assessment Tool, we estimated daily wetland depth and pyraclostrobin exposure, with label-recommended application quantities. Species' timing and duration of larval development determined the number of years of suitable hydroregime for breeding and the likelihood of exposure to peak aquatic concentrations of pyraclostrobin. Although the timing of pesticide application determined the number of surviving larvae, density-dependent constraints of wetland hydroregime also affected larval survival across species and seasons. Further defining categorical amphibian life history types and habitat requirements supports the development of screening-level assessments by incorporating environmental stochasticity at the appropriate temporal resolution. Subsequent refinement of these screening-level risk assessment strategies to include spatially explicit landscape data along with terrestrial exposure estimates would offer additional insights into species vulnerability to pesticide exposure throughout the life cycle. Computational simulation of ecologically relevant exposure scenarios, such as these, offers a more realistic interpretation of differential agrichemical risk among species based on their phenology and habits and provides a more situation-specific risk assessment perspective for threatened species. Integr Environ Assess Manag 2024;20:1667-1676. Published 2024. This article is a U.S. Government work and is in the public domain in the USA.

The perspective of the logarithmic field sprayer technology

A logarithmic sprayer was suggested about 70 years ago, but it has not yet been seriously used in research and development, and subsequent registration of plant protection products. Logarithmic sprayers have resorted to mere demonstration experiments to show end users and others how plant protection products work. Fitting dose-response curves in field experiments, however, generates much essential information, e.g., extraction of various effective field rate levels (e.g., ED20, ED50, and ED80). One of the reasons for it rarely being used in the registration of plant protection products is that the dose-response curve regression was hitherto difficult to fit; the registration requirement solely focuses on analyses of variance. Another alleged obstacle is that the logarithmic plots have systematically, not randomly distributed field rates. This paper goes through some of the problems of how to non-randomly analyze field rates by taking autocorrelation into account to make the logarithmic sprayer palatable as registration documentation by assessing efficacy, selectivity, environmental side effects, general toxicity of plant protection products, and cost-effectiveness. The development in precision agriculture, drone technology, and automation of data capture and subsequent analysis could make the logarithmic sprayer a cost-effective alternative to numerous ANOVA experiments with very few fixed field rates to aid the precision spraying of pesticides and thus reduce unnecessary environmental side effects. © 2024 Society of Chemical Industry.

Effects of water quality on palladium-induced olfactory toxicity and bioaccumulation in rainbow trout (Oncorhynchus mykiss)

Through emission processes, palladium (Pd) particulates from industrial sources are introduced into a range of ecosystems including freshwater environments. Despite this, research on Pd-induced bioaccumulation, uptake, and toxicity is limited for freshwater fishes. Unlike other metals, there are currently no regulations or protective guidelines to limit Pd release into aquatic systems, indicating a global absence of measures addressing its environmental impact. To assess the olfactory toxicity potential of Pd, the present study aimed to explore Pd accumulation in olfactory tissues, olfactory disruption, and oxidative stress in rainbow trout (Oncorhynchus mykiss) following waterborne Pd exposure. Olfactory sensitivity, measured by electro-olfactography, demonstrated that Pd inhibits multiple pathways of the olfactory system following 96 h of Pd exposure. In this study, the concentrations of Pd for inhibition of olfactory function by 20% (2.5 μg/L; IC20) and 50% (19 μg/L; IC50) were established. Rainbow trout were then exposed to IC20 and IC50 Pd concentrations in combination with varying exposure conditions, as changes in water quality alter the toxicity of metals. Independent to Pd, increased water hardness resulted in decreased olfactory perception owing to ion competition at the olfactory epithelium. No other environmental parameter in this study significantly influenced Pd-induced olfactory toxicity. Membrane-associated Pd was measured at the olfactory rosette and gill following exposure; however, this accumulation did not translate to oxidative stress as measured by the production of malondialdehyde. Our data suggest that Pd is toxic to rainbow trout via waterborne contamination near field-measured levels. This study further demonstrated Pd bioavailability and uptake at water-adjacent tissues, adding to our collective understanding of the toxicological profile of Pd. Taken together, our results provide novel insights into the olfactory toxicity in fish following Pd exposure. Integr Environ Assess Manag 2024;20:1407-1419. © 2024 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

YBX1 as a therapeutic target to suppress the LRP1-β-catenin-RRM1 axis and overcome gemcitabine resistance in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is highly malignant and has a poor prognosis, without effective therapeutic targets in common gene mutations. Gemcitabine, a first-line chemotherapeutic for PDAC, confers <10% 5-year survival rate because of drug resistance. Y-box binding protein 1 (YBX1), associated with multidrug-resistance gene activation, remains unelucidated in PDAC gemcitabine resistance. In vivo and in vitro, we verified YBX1's promotional effects, especially gemcitabine resistance, in pancreatic cancer cells. YBX1-induced LRP1 transcription by binding to the LRP1 promoter region significantly altered the concentration and distribution of β-catenin in pancreatic cancer cells. Through TCF3, β-catenin bound to the promoter region of RRM1, a key gene for gemcitabine resistance, that promotes RRM1 expression. Combination therapy with the YBX1 inhibitor SU056 and gemcitabine effectively reduced gemcitabine resistance in in vivo and in vitro experiments. High YBX1 expression promoted pathogenesis and gemcitabine resistance in pancreatic cancer through the YBX1-LRP1-β-catenin-RRM1 axis. Combining YBX1 inhibitors with gemcitabine may provide a new direction for combination chemotherapy to overcome gemcitabine resistance, which frequently occurs during chemotherapy for pancreatic cancer.

Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast

Auxins are crucial signaling molecules that regulate the growth, metabolism, and behavior of various organisms, most notably plants but also bacteria, fungi, and animals. Many microbes synthesize and perceive auxins, primarily indole-3-acetic acid (IAA, referred to as auxin herein), the most prevalent natural auxin, which influences their ability to colonize plants and animals. Understanding auxin biosynthesis and signaling in fungi may allow us to better control interkingdom relationships and microbiomes from agricultural soils to the human gut. Despite this importance, a biological tool for measuring auxin with high spatial and temporal resolution has not been engineered in fungi. In this study, we present a suite of genetically encoded, ratiometric, protein-based auxin biosensors designed for the model yeast Saccharomyces cerevisiae. Inspired by auxin signaling in plants, the ratiometric nature of these biosensors enhances the precision of auxin concentration measurements by minimizing clonal and growth phase variation. We used these biosensors to measure auxin production across diverse growth conditions and phases in yeast cultures and calibrated their responses to physiologically relevant levels of auxin. Future work will aim to improve the fold change and reversibility of these biosensors. These genetically encoded auxin biosensors are valuable tools for investigating auxin biosynthesis and signaling in S. cerevisiae and potentially other yeast and fungi and will also advance quantitative functional studies of the plant auxin perception machinery, from which they are built.

Automated Image-Based Fluorescence Screening of Mitochondrial Membrane Potential in Daphnia magna: An Advanced Ecotoxicological Testing Tool

This study demonstrated the strengths of in vivo molecular staining coupled with automated imaging analysis in Daphnia magna. A multiwell plate protocol was developed to assess mitochondrial membrane potential using the JC-1 dye. The suitability of five common anesthetics was initially tested, and 5% ethanol performed best in terms of anesthetic effects and healthy recovery. The staining conditions were optimized to 30 min staining with 2 μM JC-1 for best J-aggregate formation. The protocol was validated with the model compound carbonyl cyanide 3-chlorophenylhydrazone (CCCP) and used to measure the effect of four environmental contaminants, 2,4-dinitrophenol, triclosan, n-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD), and ibuprofen, on mitochondrial health. Test organisms were imaged using an automated confocal microscope, and fluorescence intensities were automatically quantified. The effect concentrations for CCCP were lower by a factor of 30 compared with the traditional OECD 202 acute toxicity test. Mitochondrial effects were also detected at lower concentrations for all tested environmental contaminants compared to the OCED 202 test. For 2,4-dinitrophenol, mitochondria effects were detectable after 2 h exposure to environmentally relevant concentrations and predicted organism death was observed after 24 h. The high sensitivity and time efficiency of this novel automated imaging method make it a valuable tool for advancing ecotoxicological testing.

Chronic Toxicity of Per- and Polyfluoroalkyl Substance-Free Firefighting Foams to Aquatic Organisms

Amid global concern regarding the health and environmental impacts of per- and polyfluoroalkyl substances (PFAS), there is an urgent need to develop and implement alternative products without PFAS. Consequently, PFAS-free firefighting foams used for fire suppression have been developed for use in military and residential settings. To facilitate the selection of lower-risk PFAS-free foams, the present study focused on the chronic toxicity of seven PFAS-free and one PFAS-containing foam to six aquatic species. Target species included two cladocerans, Daphnia magna and Ceriodaphnia dubia; the chironomid Chironomus dilutus; the mysid Americamysis bahia; and two fish species, Pimephales promelas and Cyprinodon variegatus, with endpoints including growth, development, reproduction, and survival. To facilitate comparison and product toxicity rankings, effective concentrations (20%, 50%) and no- and lowest-observed-effect concentrations (NOECs and LOECs, respectively) were calculated. Effective concentrations, NOECs, and LOECs varied by over an order of magnitude among foams and species, with several of the PFAS-free formulations ranked as highly toxic based on US Environmental Protection Agency alternatives assessment hazard criteria. Overall, the PFAS-free foams were found to exhibit either similar or greater toxicity compared to the PFAS-containing reference foam across several species and endpoints. Nonmonotonic and hormetic dose responses were observed in D. magna for several of the tested foams, with increased reproduction and growth at intermediate exposures. Generally, tested foam toxicity rankings were consistent with a related acute toxicity study using the same species and formulations, and other research using soil invertebrates. Combined with related efforts for other taxa including mammals, birds, and plants, the present research will facilitate the selection of appropriate PFAS-free firefighting foams that minimize harm to the environment. Environ Toxicol Chem 2024;00:1-19. © 2024 SETAC.

Transcriptome analysis of Drosophila suzukii reveals molecular mechanisms conferring pyrethroid and spinosad resistance

Drosophila suzukii lay eggs in soft-skinned, ripening fruits, making this insect a serious threat to berry production. Since its 2008 introduction into North America, growers have used insecticides, such as pyrethroids and spinosads, as the primary approach for D. suzukii management, resulting in development of insecticide resistance in this pest. This study sought to identify the molecular mechanisms conferring insecticide resistance in these populations. We sequenced the transcriptomes of two pyrethroid- and two spinosad-resistant isofemale lines. In both pyrethroid-resistant lines and one spinosad-resistant line, we identified overexpression of metabolic genes that are implicated in resistance in other insect pests. In the other spinosad-resistant line, we observed an overexpression of cuticular genes that have been linked to resistance. Our findings enabled the development of molecular diagnostics that we used to confirm persistence of insecticide resistance in California, U.S.A. To validate these findings, we leveraged D. melanogaster mutants with reduced expression of metabolic or cuticular genes that were found to be upregulated in resistant D. suzukii to demonstrate that these genes are involved in promoting resistance. This study is the first to characterize the molecular mechanisms of insecticide resistance in D. suzukii and provides insights into how current management practices can be optimized.

Lethal effects and sex-specific tolerance of copper and cadmium in the buff-tailed bumble bee

Exposure to environmental pollutants, including trace metals, is a major driver of bee decline worldwide. While pesticides undergo standardised risk assessments (i.e., LD50) and the implementation of online databases, no such approaches exist for trace metals. Here, using acute oral exposure, we determined the LC50, LD50, and mass-standardised LD50 of copper and cadmium, essential and non-essential metals, respectively, in workers and males of the buff-tailed bumble bee. We also evaluated gut damage and sucrose consumption in workers post-exposure. Cadmium was more toxic than copper for workers at same doses, although both metals induced severe gut melanisation and reduced sucrose consumption at high concentrations. Males displayed higher tolerance to cadmium, but it was correlated to their higher body mass, emphasising the necessity for reporting mass-standardised LD50 for genuine sex comparisons in risk assessments. Our findings advocate for the establishment of databases focusing on metal-induced lethal effects on model bee species.

Computational Modeling of Drug Response Identifies Mutant-Specific Constraints for Dosing panRAF and MEK Inhibitors in Melanoma

PURPOSE

This study explores the potential of pre-clinical in vitro cell line response data and computational modeling in identifying the optimal dosage requirements of pan-RAF (Belvarafenib) and MEK (Cobimetinib) inhibitors in melanoma treatment. Our research is motivated by the critical role of drug combinations in enhancing anti-cancer responses and the need to close the knowledge gap around selecting effective dosing strategies to maximize their potential.

RESULTS

In a drug combination screen of 43 melanoma cell lines, we identified specific dosage landscapes of panRAF and MEK inhibitors for NRAS vs. BRAF mutant melanomas. Both experienced benefits, but with a notably more synergistic and narrow dosage range for NRAS mutant melanoma (mean Bliss score of 0.27 in NRAS vs. 0.1 in BRAF mutants). Computational modeling and follow-up molecular experiments attributed the difference to a mechanism of adaptive resistance by negative feedback. We validated the in vivo translatability of in vitro dose-response maps by predicting tumor growth in xenografts with high accuracy in capturing cytostatic and cytotoxic responses. We analyzed the pharmacokinetic and tumor growth data from Phase 1 clinical trials of Belvarafenib with Cobimetinib to show that the synergy requirement imposes stricter precision dose constraints in NRAS mutant melanoma patients.

CONCLUSION

Leveraging pre-clinical data and computational modeling, our approach proposes dosage strategies that can optimize synergy in drug combinations, while also bringing forth the real-world challenges of staying within a precise dose range. Overall, this work presents a framework to aid dose selection in drug combinations.

A broadly cross-reactive i-body to AMA1 potently inhibits blood and liver stages of Plasmodium parasites

Apical membrane antigen-1 (AMA1) is a conserved malarial vaccine candidate essential for the formation of tight junctions with the rhoptry neck protein (RON) complex, enabling Plasmodium parasites to invade human erythrocytes, hepatocytes, and mosquito salivary glands. Despite its critical role, extensive surface polymorphisms in AMA1 have led to strain-specific protection, limiting the success of AMA1-based interventions beyond initial clinical trials. Here, we identify an i-body, a humanised single-domain antibody-like molecule that recognises a conserved pan-species conformational epitope in AMA1 with low nanomolar affinity and inhibits the binding of the RON2 ligand to AMA1. Structural characterisation indicates that the WD34 i-body epitope spans the centre of the conserved hydrophobic cleft in AMA1, where interacting residues are highly conserved among all Plasmodium species. Furthermore, we show that WD34 inhibits merozoite invasion of erythrocytes by multiple Plasmodium species and hepatocyte invasion by P. falciparum sporozoites. Despite a short half-life in mouse serum, we demonstrate that WD34 transiently suppressed P. berghei infections in female BALB/c mice. Our work describes the first pan-species AMA1 biologic with inhibitory activity against multiple life-cycle stages of Plasmodium. With improved pharmacokinetic characteristics, WD34 could be a potential immunotherapy against multiple species of Plasmodium.

Short-Term Chronic Toxicity of Copper to Hyalella azteca: Contrast in Terms of Equilibrating Diet, Diet Type, and Organic Matter Source

The most up-to-date regulatory guidelines for establishing acute and chronic numeric limits for copper in freshwaters are based on a biotic ligand model for various species, but the model for Cu lacks data on dietary uptake. In addition, some common macroinvertebrate toxicity assay parameters are less representative of the ecosystem. We investigated the effects of diet and its type in the experimental setup and as an exposure pathway to an established amphipod (crustacean) Hyalella azteca (H. azteca) for Cu toxicity assays. We also investigated another overlooked aspect, the organic matter (OM) source. Our experiments compared the toxicity of pre-equilibrated and unequilibrated natural diets and a laboratory-favored diet in effluent and stormwater sources of organic matter adjusted to standard water characteristics. The experiments indicated a more toxic effect of the pre-equilibrated diet and natural dietary sources, and less toxic effects in the presence of effluent OM compared with stormwater OM, shifting LC50 or EC20 values by as much as 67% compared with the controls. The use of a pre-equilibrated natural diet in toxicity assays provides the advantage of producing toxicity data more representative of field conditions. Considering organic matter type, especially in dietary exposures, will better predict toxicity, accounting for copper complexation with OM from different sources and partitioning to the food supply. Adapting these ecologically relevant parameters in whole effluent toxicity testing or other assays will also provide safer regulatory oversite of discharges to surface waters.

Acute and chronic toxicity of rare earth elements-enriched sediments from a prospective mining area: Effects on life history traits, behavioural and physiological responses of Gammarus fossarum (Crustacea Amphipoda)

Rare earth elements (REE) have an essential role and growing importance in the world's economy. They are attracting interest from society, policymakers, and scientists. The rapidly growing global demand for REE in several strategic industrial and agricultural sectors led many countries to consider the (re)-opening of mining activities for REE extraction. Hence, their increasing use led to the disruption of their biogeochemical cycles with anthropic abnormalities already observed in aquatic ecosystems. Nonetheless, REE remain less studied, and their mechanisms of toxicity actions are not fully understood. As amphipods, Gammarus fossarum represent an important part of the aquatic macroinvertebrate assemblage and are generally used in ecotoxicological studies for their high ecological relevance. However, their use for the study of REE effects has been rather limited so far. The current study aims to assess the potential effects of two naturally REE-enriched sediments (N2 and B4) on G. fossarum. Effects on life history traits, behavioural and physiological responses have been evaluated. Exposing G. fossarum males for 72h to sediments N2 and B4 led to a decrease in haemolymph osmolality and locomotion while an increase in ventilatory activity was observed. Exposing G. fossarum pre-copula pairs with females at the same reproductive stage to the naturally REE-enriched sediments, for one moult cycle duration (∼30 days) showed that sediment B4 led to i) a significant uptake of REE, ii) a significant decrease in the proportion of females with oocytes and iii) a significant reduction in the total number of juveniles. The physicochemical analyses of sediments showed that B4 contains the highest amount of REE with a higher proportion of light REE. The present study gives the first insights into the potential toxicity of REE on G. fossarum as they may have deleterious effects on G. fossarum population's dynamics, which may alter the functioning of aquatic ecosystems.

Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor Design

The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem, which could enable many practical applications of protein biosensors. In this work, we analyzed two engineered biosensors, derived from the plant hormone sensor PYR1, to recognize either the agrochemical mandipropamid or the synthetic cannabinoid WIN55,212-2. Using a combination of quantitative deep mutational scanning experiments and molecular dynamics simulations, we demonstrated that mutations at common positions can promote protein-ligand shape complementarity and revealed prominent differences in the electrostatic networks needed to complement diverse ligands. MD simulations indicate that both PYR1 protein-ligand complexes bind a single conformer of their target ligand that is close to the lowest free-energy conformer. Computational design using a fixed conformer and rigid body orientation led to new WIN55,212-2 sensors with nanomolar limits of detection. This work reveals mechanisms by which the versatile PYR1 biosensor scaffold can bind diverse ligands. This work also provides computational methods to sample realistic ligand conformers and rigid body alignments that simplify the computational design of biosensors for novel ligands of interest.

Rational design of base, sugar and backbone modifications improves ADAR-mediated RNA editing

AIMers are short, chemically modified oligonucleotides that induce A-to-I RNA editing through interaction with endogenous adenosine deaminases acting on RNA (ADAR) enzymes. Here, we describe the development of new AIMer designs with base, sugar and backbone modifications that improve RNA editing efficiency over our previous design. AIMers incorporating a novel pattern of backbone and 2' sugar modifications support enhanced editing efficiency across multiple sequences. Further efficiency gains were achieved through incorporation of an N-3-uridine (N3U), in place of cytidine (C), in the 'orphan base' position opposite the edit site. Molecular modeling suggests that N3U might enhance ADAR catalytic activity by stabilizing the AIMer-ADAR interaction and potentially reducing the energy required to flip the target base into the active site. Supporting this hypothesis, AIMers containing N3U consistently enhanced RNA editing over those containing C across multiple target sequences and multiple nearest neighbor sequence combinations. AIMers combining N3U and the novel pattern of 2' sugar chemistry and backbone modifications improved RNA editing both in vitro and in vivo. We provide detailed N3U synthesis methods and, for the first time, explore the impact of N3U and its analogs on ADAR-mediated RNA editing efficiency and targetable sequence space.

Expression Patterns of MOTS-c in Adrenal Tumors: Results from a Preliminary Study

Adrenal tumors, such as adrenocortical carcinoma (ACC), adrenocortical adenoma (ACA), and pheochromocytoma (PCC) are complex diseases with unclear causes and treatments. Mitochondria and mitochondrial-derived peptides (MDPs) are crucial for cancer cell survival. The primary aim of this study was to analyze samples from different adrenal diseases, adrenocortical carcinoma, adrenocortical adenoma, and pheochromocytoma, and compare them with normal adrenal tissue to determine whether the expression levels of the mitochondrial open reading frame of the 12S rRNA type-c (MOTS-c) gene and protein vary between different types of adrenal tumors compared to healthy controls using qPCR, ELISA, and IHC methods. Results showed decreased MOTS-c mRNA expression in all adrenal tumors compared to controls, while serum MOTS-c protein levels increased in ACA and PCC but not in ACC. The local distribution of MOTS-c protein in adrenal tissue was reduced in all tumors. Notably, MOTS-c protein expression declined with ACC progression (stages III and IV) but was unrelated to patient age or sex. Tumor size and testosterone levels positively correlated with MOTS-c mRNA but negatively with serum MOTS-c protein. Additionally, serum MOTS-c protein correlated positively with glucose, total cholesterol, HDL, LDL, and SHGB levels. These findings suggest disrupted expression of MOTS-c in the spectrum of adrenal diseases, which might be caused by mechanisms involving increased mitochondrial dysfunction and structural changes in the tissue associated with disease progression. This study provides a detailed examination of MOTS-c mRNA and protein in adrenal tumors, indicating the potential role of MDPs in tumor biology and progression.

How do outside-hosts-overwintering parasitoids, at the adult stage, cope with cold?

INTRODUCTION

When overwintering, most endoparasitoids are protected from the cold inside their hosts. However, some endoparasitoids, along with ectoparasitoids, fall into the category called outside-hosts-overwintering parasitoids (OHOP) at immature or adult stages. We compared the cold-hardiness capacity and strategy between adult OHOP and their hosts (HOST) by examining their supercooling points (SCP), with acclimation periods and acclimation temperatures, and their lower lethal temperatures at 50% mortality (LLT50). We hypothesized that OHOP are more cold-hardy than their HOST, with lower SCP and LLT50.

MATERIALS AND METHODS

Throughout the summers of 2020, 2021, and 2022, adult cabbage seedpod weevils (HOST) were sampled with a sweep net at the canola pod stage, and thousands of pods were collected and placed in emergence boxes to retrieve the adult OHOP Trichomalus perfectus. Regarding SCP measures, OHOP and HOST were separated according to various treatments. Each treatment considered a target exposure temperature (5, 10, or 20 °C) or a target exposure period (5, 15 or 25 days) at 5 °C. Regarding LLT measures, OHOP and HOST were categorized into five treatments, each corresponding to a specific exposure temperature (-5, -10, -15, -20 or -25 °C).

RESULTS AND CONCLUSION

Acclimations to a lower temperature (5 °C) and a longer period (25 days) led to a significantly lower SCP of OHOP than HOST. Regarding OHOP, the average SCP was -19.71 °C when the acclimation temperature was 20 °C and significantly decreased to -23.20 °C when it was 5 °C. The average SCP was -18.82 °C when the acclimation period was five days and significantly decreased to -23.20 °C when it was 25 days. Conversely, the average SCP for HOST was never below -20 °C. At 20 °C acclimation temperature, HOST exhibited a significantly higher SCP of -14.64 °C compared to acclimations at 5 °C (-19.19 °C) and 10 °C (-20.00 °C), but there were no significant differences between 5 and 10 °C nor between acclimation periods. Therefore, the adult OHOP is more cold-hardy than its HOST. OHOP also exhibited a lower LLT50 than HOST, with -19.20 °C versus -17.59 °C. Finally, OHOP and HOST employ the same freeze-avoidance strategy, as evidenced by their SCP values (-19.57 °C versus -16.80 °C) which closely align with their respective LLT50. Adult OHOP better survive winter than their HOST in cold environments.

Pan-cancer proteogenomics expands the landscape of therapeutic targets

Fewer than 200 proteins are targeted by cancer drugs approved by the Food and Drug Administration (FDA). We integrate Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteogenomics data from 1,043 patients across 10 cancer types with additional public datasets to identify potential therapeutic targets. Pan-cancer analysis of 2,863 druggable proteins reveals a wide abundance range and identifies biological factors that affect mRNA-protein correlation. Integration of proteomic data from tumors and genetic screen data from cell lines identifies protein overexpression- or hyperactivation-driven druggable dependencies, enabling accurate predictions of effective drug targets. Proteogenomic identification of synthetic lethality provides a strategy to target tumor suppressor gene loss. Combining proteogenomic analysis and MHC binding prediction prioritizes mutant KRAS peptides as promising public neoantigens. Computational identification of shared tumor-associated antigens followed by experimental confirmation nominates peptides as immunotherapy targets. These analyses, summarized at https://targets.linkedomics.org, form a comprehensive landscape of protein and peptide targets for companion diagnostics, drug repurposing, and therapy development.

Rational selection of morphological phenotypic traits to extract essential similarities in chemical perturbation in the ergosterol pathway

Terbinafine, fluconazole, and amorolfine inhibit fungal ergosterol synthesis by acting on their target enzymes at different steps in the synthetic pathway, causing the accumulation of various intermediates. We found that the effects of these three in- hibitors on yeast morphology were different. The number of morphological parameters commonly altered by these drugs was only approximately 6% of the total. Using a rational strategy to find commonly changed parameters,we focused on hidden essential similarities in the phenotypes possibly due to decreased ergosterol levels. This resulted in higher apparent morphological similarity. Improvements in morphological similarity were observed even when canonical correlation analysis was used to select biologically meaningful morphological parameters related to gene function. In addition to changes in cell morphology, we also observed differences in the synergistic effects among the three inhibitors and in their fungicidal effects against pathogenic fungi possibly due to the accumulation of different intermediates. This study provided a comprehensive understanding of the properties of inhibitors acting in the same biosynthetic pathway.

Computational modeling of drug response identifies mutant-specific constraints for dosing panRAF and MEK inhibitors in melanoma

Purpose

This study explores the potential of preclinical in vitro cell line response data and computational modeling in identifying optimal dosage requirements of pan-RAF (Belvarafenib) and MEK (Cobimetinib) inhibitors in melanoma treatment. Our research is motivated by the critical role of drug combinations in enhancing anti-cancer responses and the need to close the knowledge gap around selecting effective dosing strategies to maximize their potential.

Results

In a drug combination screen of 43 melanoma cell lines, we identified unique dosage landscapes of panRAF and MEK inhibitors for NRAS vs BRAF mutant melanomas. Both experienced benefits, but with a notably more synergistic and narrow dosage range for NRAS mutant melanoma. Computational modeling and molecular experiments attributed the difference to a mechanism of adaptive resistance by negative feedback. We validated in vivo translatability of in vitro dose-response maps by accurately predicting tumor growth in xenografts. Then, we analyzed pharmacokinetic and tumor growth data from Phase 1 clinical trials of Belvarafenib with Cobimetinib to show that the synergy requirement imposes stricter precision dose constraints in NRAS mutant melanoma patients.

Conclusion

Leveraging pre-clinical data and computational modeling, our approach proposes dosage strategies that can optimize synergy in drug combinations, while also bringing forth the real-world challenges of staying within a precise dose range.

Developing a Passive Dosing Method for Acute Aquatic Toxicity Tests of Cationic Surfactant Benzalkoniums (BACs)

Benzalkonium chlorides (BACs) have been of environmental concern due to their widespread use and potential harm. However, challenges arise in defining and controlling the exposure concentration (Cw) in aquatic toxicity tests involving BACs with a long alkyl chain (i.e., #C > 14). To address this, a novel passive dosing method was introduced in the 48 h-acute ecotoxicity test on Daphnia magna and compared to the conventional solvent-spiking method in terms of Cw stability and toxicity results. Among 13 sorbent materials tested for their sorption capacity, poly(ether sulfone) (PES) membrane was an optimal passive dosing reservoir, with equilibrium desorption of BACs to water achieved within 24 h. The Cw of BACs remained constant in both applied dosing methods during the test period. However, the Cw in solvent-spiking tests was lower than the nominal concentration for long-chain BACs, particularly at low exposure concentrations. Notably, the solvent-spiking tests indicated that the toxicity of BACs increased with alkyl chain length from C6 to 14, followed by a decline in toxicity from C14 to 18. In contrast, the passive dosing method displayed similar or slightly increasing toxicity levels of BACs from C14 to C18, indicating higher toxicity of C16 and C18-BACs than that inferred by the solvent spiking test. These findings emphasize the potential of applying this innovative passive dosing approach in aquatic toxicity tests to generate reliable and accurate toxicity data and support a comprehensive risk assessment of cationic surfactants.

Resistance to protoporphyrinogen oxidase inhibitors in giant ragweed (Ambrosia trifida)

BACKGROUND

Giant ragweed (Ambrosia trifida L.) is one of the most troublesome weed species in corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] cropping systems. Following numerous reports in 2018 of suspected herbicide resistance in several Ambrosia trifida populations from Wisconsin, our objective was to characterize the response of these accessions to acetolactate synthase (ALS), enolpyruvyl shikimate phosphate synthase (EPSPS), and protoporphyrinogen oxidase (PPO) inhibitors applied POST.

RESULTS

Four accessions (AT1, AT4, AT6, and AT10) exhibited ≥ 50% plant survival after exposure to the cloransulam 3× rate. Two accessions (AT8 and AT10) and one accession (AT2) exhibited ≥ 50% plant survival after exposure to glyphosate and fomesafen 1× rates, respectively. The AT10 accession exhibited multiple resistance to cloransulam and glyphosate. The AT12 accession was 28.8-fold resistant to fomesafen and 3.7-fold resistant to lactofen. A codon change in PPX2 conferring a R98L substitution was identified as the most likely mechanism conferring PPO-inhibitor resistance.

CONCLUSION

To our knowledge, this is the first confirmed case of PPO-inhibitor resistance in Ambrosia trifida globally and we identified the genetic mutation likely conferring resistance. Proactive and diversified integrated weed management strategies are of paramount importance for sustainable long-term Ambrosia trifida management. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Insights into the synergistic toxicity mechanisms caused by nano- and microplastics with triclosan using a dose-dependent functional genomics approach in Saccharomyces cerevisiae

The emergence of polystyrene (PS) nano- and microplastics (NMPs) and triclosan (TCS) as environmental contaminants has raised concerns about their combined toxicities to organisms, but the complex toxicity arising from their interactions and the underlying molecular mechanisms remain obscure to us. In this study, we comprehensively detected the combined toxicity of PS-NMPs and TCS via the dose-dependent yeast functional genomics profiling. Firstly, our findings demonstrated that the combined exposure to PS-NMPs and TCS elicited a synergistic toxic effect in which the toxicity depended on the size of the PS-NMPs. Secondly, we found that TCS exposure, either alone or in combination with PS-NMPs, influenced lipid biosynthetic processes and ATP export pathways, while the unique responsive genes triggered by combined exposure to TCS and PS-NMPs are significantly enriched in mitochondrial translation, ribosomal small subunit assembly, and tRNA wobble uridine modification. Thirdly, our results demonstrated that point of departure (POD) at the pathway level was positively correlated with IC50, and POD was a more sensitive predictor of toxicity than the apical toxicity endpoints. More importantly, our findings suggested that the combined exposure of PS-NMPs in a size-dependent manner not only alleviated the harmful effects of TCS on glycerophospholipid metabolism, but also exacerbated its negative impact on oxidative phosphorylation. Collectively, our study not only provides new insights into the intricate molecular mechanisms that control the combined toxicity of PS-NMPs and TCS, but also confirms the effectiveness of the dose-dependent functional genomics approach in elucidating the molecular mechanisms of the combined toxicity of pollutants.

Phenotypic adaptation of Chironomus riparius to chronic Bti exposure: effects on emergence time and nutrient content

Insects with aquatic larval and terrestrial adult life stages are a key component of coupled aquatic-terrestrial ecosystems. Thus, stressors applied to water bodies adversely affecting those larvae have the potential to influence the riparian zone through altered emergence, with differences in prey availability, timing, or nutrition. In this study, the common model organism Chironomus riparius, a species of Chironomidae (Diptera), was used. This selection was further motivated by its wide distribution in European freshwaters and its importance as prey for terrestrial predators. A stressor of high importance in this context is the globally used mosquito control agent Bacillus thuringiensis var. israelensis (Bti) which has been shown to affect Chironomidae. Here, we investigated the ability of chironomid populations to adapt to a regularly applied stressor, leading to a reduced impact of Bti. Therefore, the initial sensitivity of laboratory populations of C. riparius was investigated under the influence of field-relevant Bti treatments (three doses × two application days) and different food sources (high-quality TetraMin vs. low-quality Spirulina). Following a chronic exposure to Bti over six months, the sensitivity of pre-exposed and naïve populations was re-evaluated. Food quality had a strong impact on emergence timing and nutrient content. In addition, alterations in emergence time as well as protein and lipid contents of chronically exposed populations indicated a selection for individuals of advantageous energetics, potentially leading to a more efficient development while combating Bti. Signs of adaptation could be confirmed in five out of 36 tested scenarios suggesting adaptation to Bti at the population level. Adaptive responses of one or several species could theoretically (via eco-evolutionary dynamics) result in a community shift, favouring the prevalence of Bti-tolerant species. (In)direct effects of Bti and the adaptive responses at both population and community levels could affect higher trophic levels and may determine the fate of meta-ecosystems.

First evidence of lithium toxicity in the cryptic species complex of the estuarine copepod Eurytemora affinis

The development of renewable and low-carbon energy sources means that strategic elements such as lithium (Li) are increasingly being used. The data available on the effects of Li on aquatic organisms are relatively scarce. The copepod Eurytemora affinis, widely distributed in the brackish estuarine waters of the northern hemisphere, is a species of choice in ecotoxicology but in fact constitutes a cryptic species complex, composed of at least six cryptic species. Cryptic diversity can lead to misinterpretation and alter the reproducibility of routine ecotoxicological tests. In the present study, two cryptic species of the E. affinis complex from the Seine (European clade) and the St. Lawrence (North-Atlantic clade) estuaries were used to assess Li toxicity and to compare their differential sensitivity. Larvae were exposed to different concentrations of Li (0.4, 4.39, 35.36 and 80.83 mg L-1) under semi-static conditions for 96 h. Larval development stages were determined and log-logistic functions were fitted to evaluate mortality (LC50) and growth (EC50) parameters. After 96 h of exposure, the results showed that the European and North-Atlantic clades had LC50 values of 55.33 and 67.81 mg L-1 and EC50 values of 28.94 and 41.45 mg L-1, respectively. A moderate difference in sensitivity to Li between the European and North-Atlantic clades of the E. affinis complex was observed. Thus, the cryptic species diversity should be considered using E. affinis to avoid bias in the interpretation of the data. Despite environmental concentrations of Li are expected to increase over the next years, EC50 and LC50 found for E. affinis cryptic species are largely higher than Li environmental concentrations to provoke extreme effects.

Dissolved nitrogen uptake versus nitrogen fixation: Mode of nitrogen acquisition affects stable isotope signatures of a diazotrophic cyanobacterium and its grazer

Field studies suggest that changes in the stable isotope ratios of phytoplankton communities can be used to track changes in the utilization of different nitrogen sources, i.e., to detect shifts from dissolved inorganic nitrogen (DIN) uptake to atmospheric nitrogen (N2) fixation by diazotrophic cyanobacteria as an indication of nitrogen limitation. We explored changes in the stable isotope signature of the diazotrophic cyanobacterium Trichormus variabilis in response to increasing nitrate (NO3-) concentrations (0 to 170 mg L-1) under controlled laboratory conditions. In addition, we explored the influence of nitrogen utilization at the primary producer level on trophic fractionation by studying potential changes in isotope ratios in the freshwater model Daphnia magna feeding on the differently grown cyanobacteria. We show that δ 15N values of the cyanobacterium increase asymptotically with DIN availability, from -0.7 ‰ in the absence of DIN (suggesting N2 fixation) to 2.9 ‰ at the highest DIN concentration (exclusive DIN uptake). In contrast, δ 13C values of the cyanobacterium did not show a clear relationship with DIN availability. The stable isotope ratios of the consumer reflected those of the differently grown cyanobacteria but also revealed significant trophic fractionation in response to nitrogen utilization at the primary producer level. Nitrogen isotope turnover rates of Daphnia were highest in the absence of DIN as a consequence of N2 fixation and resulting depletion in 15N at the primary producer level. Our results highlight the potential of stable isotopes to assess nitrogen limitation and to explore diazotrophy in aquatic food webs.

Confirmation and characterization of the first case of acetolactate synthase (ALS)-inhibitor resistance in Japanese brome (Bromus japonicus) in the US

BACKGROUND

Japanese brome (Bromus japonicus Thumb.) is one of the problematic annual weeds in winter wheat (Triticum aestivum L.) and is generally controlled by acetolactate synthase (ALS) inhibitors. Repeated use of the ALS inhibitor propoxycarbazone-Na resulted in the evolution of resistance to this herbicide in three B. japonicus populations, i.e., R1, R2, and R3 in Kansas (KS). However, the level of resistance and mechanism conferring resistance in these populations is unknown. The objectives of this research were to (i) evaluate the level of resistance to propoxycarbazone-Na in R1, R2, and R3 in comparison with a known susceptible population (S1), (ii) investigate the mechanism of resistance involved in conferring ALS-inhibitor resistance, and (iii) investigate the cross-resistance to other ALS inhibitors.

RESULTS

Dose-response (0 to 16x; x = 44 g ai ha-1 of propoxycarbazone-Na) assay indicated 167, 125, and 667-fold resistance in R1, R2 and R3 populations, respectively, compared to S1 population. ALS gene sequencing confirmed the mutations resulting in amino acid substitutions, i.e., Pro-197-Thr (R3, R1)/Ser (R2, R1) bestowing resistance to these ALS inhibitors. Such amino acid substitutions also showed differential cross-resistance to sulfosulfuron, mesosulfuron-methyl, pyroxsulam, and imazamox among resistant populations. Pretreatment with malathion (a cytochrome P450 enzyme-inhibitor) followed by imazamox treatment suggested cross-resistance to this herbicide possibly via metabolism only in R3 population.

CONCLUSION

Overall, these results confirm the first case of target-site based resistance to ALS inhibitors in B. japonicus in the US, highlighting the need for exploring herbicides with alternative modes of action to enhance weed control in winter wheat. © 2024 Society of Chemical Industry.

Insights into the nature of ichthyotoxins from the Chrysochromulina leadbeateri blooms in Northern Norwegian fjords

In May-June 2019, the microalga Chrysochromulina leadbeateri caused a massive fish-killing event in several fjords in Northern Norway, resulting in the largest direct impact ever on aquaculture in northern Europe due to toxic algae. Motivated by the fact that no algal toxins have previously been described from C. leadbeateri, we set out to investigate the chemical nature and toxicity of secondary metabolites in extracts of two strains (UIO 393, UIO 394) isolated from the 2019 bloom, as well as one older strain (UIO 035) isolated during a bloom in Northern Norway in 1991. Initial LC-DAD-MS/MS-based molecular networking analysis of the crude MeOH extracts of the cultivated strains showed that their profiles of small organic molecules, including a large number of known lipids, were very similar, suggesting that the same class of toxin(s) were likely the causative agents of the two harmful algal bloom (HAB) events. Next, bioassay-guided fractionation using the RTgill-W1 cell line and metabolomics analysis pointed to a major compound affording [M + H]+ ions at m/z 1399.8333 as a possible toxin, corresponding to a compound with the formula C67H127ClO27. Moreover, our study unveiled a series of minor analogues exhibiting distinct patterns of chlorination and sulfation, together defining a new family of compounds, which we propose to name leadbeaterins. Remarkably, these suspected toxins were detected in situ in samples collected during the 2019 bloom close to Tromsø, thereby consistent with a role in fish kills. The elemental compositions of the putative C. leadbeateri ichthyotoxins strongly indicate them to be long linear polyhydroxylated polyketides, structurally similar to sterolysins reported from a number of dinoflagellates.

Improvement of anti-prion efficacy with stearoxy conjugation of hydroxypropyl methylcellulose in prion-infected mice

Prion diseases are fatal transmissible neurodegenerative disorders. Among known anti-prions, hydroxypropyl methylcellulose compounds (HPMCs) are unique in their chemical structure and action. They have several excellent anti-prion properties but the effectiveness depends on the prion-infected mouse model. In the present study, we investigated the effects of stearoxy-modified HPMCs on prion-infected cells and mice. Stearoxy modification improved the anti-prion efficacy of HPMCs in prion-infected cells and significantly prolonged the incubation period in a lower HPMC-responding mouse model. However, stearoxy modification showed no improvement over nonmodified HPMCs in an HPMC-responding mouse model. These results offer a new line of inquiry for use with prion-infected mice that do not respond well to HPMCs.

Characterization of Springtail (Arrhopalites caecus) for Use in Soil Ecotoxicity Testing

Springtails (subclass: Collembola) represent one of the most extensively studied invertebrate groups in soil ecotoxicology. This is because of their ease of laboratory culture, significant ecological role, and sensitivity to environmental contaminants. Folsomia candida (family: Isotomidae) is a globally widespread parthenogenetic species that is prevalent in laboratory toxicity testing with springtails. Conversely, Arrhopalites caecus (family: Arrhopalitidae), a parthenogenic globular springtail species, remains untested in soil ecotoxicology. This species is found in diverse habitats, including cave systems and forest leaf litter, and has a global distribution. The sensitivity of A. caecus to environmental contaminants, such as neonicotinoid insecticides, as well as its life history and optimal culturing conditions, are largely unknown. The present study describes the establishment of a pure A. caecus laboratory culture and characterization of its life cycle and culturing conditions. We assessed the sensitivity of A. caecus to various insecticides, including exposures to the neonicotinoid thiamethoxam in soil and through a novel feeding assay as well as to clothianidin and cyantraniliprole in spiked soil exposures. In 7- and 14-day exposures to thiamethoxam in agricultural soil, the 50% lethal concentration (LC50) values were determined to be 0.129 mg/kg dry weight and 0.010 mg/kg dry weight, respectively. The 14-day LC50 for exposure to thiamethoxam via spiked food was determined to be 0.307 mg/kg dry weight. In addition, the 28-day 50% effect concentration for inhibition of juvenile production from cyantraniliprole exposure in the same soil type was 0.055 mg/kg dry weight. Challenges encountered in using this species included susceptibility to mite infestation and low adult survival rates in the 28-day cyantraniliprole test. Environ Toxicol Chem 2024;43:1820-1835. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Collective effects of rising average temperatures and heat events on oviparous embryos

Survival of the immobile embryo in response to rising temperature is important to determine a species' vulnerability to climate change. However, the collective effects of 2 key thermal characteristics associated with climate change (i.e., rising average temperature and acute heat events) on embryonic survival remain largely unexplored. We used empirical measurements and niche modeling to investigate how chronic and acute heat stress independently and collectively influence the embryonic survival of lizards across latitudes. We collected and bred lizards from 5 latitudes and incubated their eggs across a range of temperatures to quantify population-specific responses to chronic and acute heat stress. Using an embryonic development model parameterized with measured embryonic heat tolerances, we further identified a collective impact of embryonic chronic and acute heat tolerances on embryonic survival. We also incorporated embryonic chronic and acute heat tolerance in hybrid species distribution models to determine species' range shifts under climate change. Embryos' tolerance of chronic heat (T-chronic) remained consistent across latitudes, whereas their tolerance of acute heat (T-acute) was higher at high latitudes than at low latitudes. Tolerance of acute heat exerted a more pronounced influence than tolerance of chronic heat. In species distribution models, climate change led to the most significant habitat loss for each population and species in its low-latitude distribution. Consequently, habitat for populations across all latitudes will shift toward high latitudes. Our study also highlights the importance of considering embryonic survival under chronic and acute heat stresses to predict species' vulnerability to climate change.

Colony environment and absence of brood enhance tolerance to a neonicotinoid in winter honey bee workers, Apis mellifera

In eusocial insects, worker longevity is essential to ensure colony survival in brood-free periods. Trade-offs between longevity and other traits may render long-living workers in brood-free periods more susceptible to pesticides compared to short-lived ones. Further, colony environment (e.g., adequate nutrition) may enable workers to better cope with pesticides, yet data comparing long vs. short-living workers and the role of the colony environment for pesticide tolerance are scarce. Here, we show that long-living honey bee workers, Apis mellifera, are less susceptible to the neonicotinoid thiamethoxam than short-lived workers, and that susceptibility was further reduced when workers were acclimatized under colony compared to laboratory conditions. Following an OECD protocol, freshly-emerged workers were exposed to thiamethoxam in summer and winter and either acclimatized within their colony or in the laboratory. Mortality and sucrose consumption were measured daily and revealed that winter workers were significantly less susceptible than summer workers, despite being exposed to higher thiamethoxam dosages due to increased food consumption. Disparencies in fat body activity, which is key for detoxification, may explain why winter bees were less susceptible. Furthermore, colony acclimatization significantly reduced susceptibility towards thiamethoxam in winter workers likely due to enhanced protein nutrition. Brood absence and colony environment seem to govern workers' ability to cope with pesticides, which should be considered in risk assessments. Since honey bee colony losses occur mostly over winter, long-term studies assessing the effects of pesticide exposure on winter bees are required to better understand the underlying mechanisms.

Water relations and photosystem II efficiency of the intertidal macroalga Fucus virsoides

Intertidal macroalgae are sessile poikilohydric organisms exposed to desiccation stress during emersion. Water relations parameters are useful tools to evaluate an organism's capacity to withstand water scarcity conditions, but such information on marine intertidal macroalgae is scarce. We assessed the water relations of the intertidal relict Fucus virsoides, the unique Fucus species endemic to the Mediterranean. We combined measurements of water potential (Ψ) parameters derived from pressure-volume curves and chlorophyll a fluorescence (Fv/Fm) in juvenile and adult thalli sampled in three different dates between March and April 2023. F. virsoides exhibited remarkable water stress tolerance, as evidenced by the low water potential at turgor loss point (Ψtlp, -7.0 MPa on average), and the maintenance of high Fv/Fm at low water potentials indicating a prolonged maintenance of healthy physiological status. While no differences were observed between growth stages, Ψtlp, capacitance (C) and the bulk modulus of elasticity (ε) varied significantly according to the sampling dates, whereas the osmotic potential at full turgor did not significantly change. Ψ measured on thalli collected after a typical prolonged emersion period was markedly lower (-12.3 MPa on average) than the estimated Ψtlp, suggesting that the population is frequently undergoing turgor loss. Further investigations are required to determine environmental tolerance ranges based on water status characteristics to enhance our understanding of F. virsoides responses and vulnerability to climate change, thus providing insight into the possible causes of its widespread decline.

Risk Assessment of Displaced Sediment by an Extreme Event Cyclone in a Peri-Urban Zone Using Bioassays and Analytical Chemistry

Hawke's Bay in New Zealand was impacted by Cyclone Gabrielle in 2023, experiencing intense weather conditions and rainfall. Rivers and streams surged beyond their banks, displacing large amounts of sediment. The sewage treatment plant and industries in the Waitangi catchment, south of the city of Napier, were heavily impacted, making them potential sources of contaminants. The aim of this study was to investigate the risk of displaced sediments deposited south of Napier City, using bioassays and chemical analysis methods. Sediment samples were collected across a gradient between the coastline and the Waitangi Stream. The toxicity of chemically extracted or elutriate samples was assessed by Microtox®, mussel embryo-larval development, and aryl hydrocarbon and constitutive androstane receptor yeast two-hybrid assays. Targeted chemical analysis and automated identification and quantification system (AIQS-GC) methods were used to identify contaminants. The elutriates showed low toxicity and the yeast assays showed levels of activity like those previously reported. Chemical methods confirmed historical contamination by DDT and its metabolites DDE and DDD, as well as by plant sterols. Overall, the toxicity and chemicals detected are what would be expected from a typical agricultural soil. The risk posed by the displaced sediment in the Waitangi catchment can be considered low. Combining chemical and bioanalytical methods was an effective approach to investigate the potential risks of post-disaster contamination.

The SRC family kinase inhibitor NXP900 demonstrates potent antitumor activity in squamous cell carcinomas

NXP900 is a selective and potent SRC family kinase (SFK) inhibitor, currently being dosed in a phase 1 clinical trial, that locks SRC in the "closed" conformation, thereby inhibiting both kinase-dependent catalytic activity and kinase-independent functions. In contrast, several multi-targeted kinase inhibitors that inhibit SRC, including dasatinib and bosutinib, bind their target in the active "open" conformation, allowing SRC and other SFKs to act as a scaffold to promote tumorigenesis through non-catalytic functions. NXP900 exhibits a unique target selectivity profile with sub-nanomolar activity against SFK members over other kinases. This results in highly potent and specific SFK pathway inhibition. Here, we demonstrate that esophageal squamous cell carcinomas and head and neck squamous cell carcinomas are exquisitely sensitive to NXP900 treatment in cell culture and in vivo, and we identify a patient population that could benefit from treatment with NXP900.

Exploring SDHI fungicide resistance in Botrytis cinerea through genetic transformation system and AlphaFold model-based molecular docking

BACKGROUND

Gray mold caused by Botrytis cinerea is one of the most serious diseases affecting strawberry. Succinate dehydrogenase inhibitor (SDHI) fungicides have been used for more than a decade to control the disease. Monitoring resistance and improving in-depth understanding of resistance mechanisms are essential for the control of B. cinerea.

RESULTS

In this study, resistance monitoring of a SDHI fungicide boscalid was conducted on B. cinerea isolated from strawberries in Korea during 2020 and 2021, with resistance rates of 76.92% and 72.25%, respectively. In resistant strains, mutations P225F/H and H272R were found in SdhB, with P225F representing the dominant mutation type. Simultaneous mutations G85A, I93V, M158V, and V168I in SdhC were detected in 54.84% of sensitive strains. Sensitivity profiles of different Sdh genotypes of B. cinerea strains to six SDHIs were determined in vitro and in vivo. In addition, the mutation(s) were genetically validated through in situ SdhB (SdhC) expression. Docking assays between SDHIs and AlphaFold model-based Sdh complexes revealed generally consistent patterns with their in vitro phenotypes.

CONCLUSION

Resistance of B. cinerea to SDHI fungicide on strawberry was systematically investigated in this study. Deciphering of SDHI resistance through the genetic transformation system and AlphaFold model-based molecular docking will provide valuable insights into other target site-based fungicide resistance in fungal pathogens. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Scalable assessment of genome editing off-targets associated with genetic variants

Genome editing with RNA-guided DNA binding factors carries risk of off-target editing at homologous sequences. Genetic variants may introduce sequence changes that increase homology to a genome editing target, thereby increasing risk of off-target editing. Conventional methods to verify candidate off-targets rely on access to cells with genomic DNA carrying these sequences. However, for candidate off-targets associated with genetic variants, appropriate cells for experimental verification may not be available. Here we develop a method, Assessment By Stand-in Off-target LentiViral Ensemble with sequencing (ABSOLVE-seq), to integrate a set of candidate off-target sequences along with unique molecular identifiers (UMIs) in genomes of primary cells followed by clinically relevant gene editor delivery. Gene editing of dozens of candidate off-target sequences may be evaluated in a single experiment with high sensitivity, precision, and power. We provide an open-source pipeline to analyze sequencing data. This approach enables experimental assessment of the influence of human genetic diversity on specificity evaluation during gene editing therapy development.