The transcription factors, STOP1 and TCP20, are required for root system architecture alterations in response to nitrate deficiency

Nitrate distribution in soils is often heterogeneous. Plants have adapted to this by modifying their root system architecture (RSA). Previous studies showed that NITRATE-TRANSPORTER1.1 (NRT1.1), which also transports auxin, helps inhibit lateral root primordia (LRP) emergence in nitrate-poor patches, by preferentially transporting auxin away from the LRP. In this study, we identified the regulatory system for this response involving the transcription factor (TF), SENSITIVE-TO-PROTON-RHIZOTOXICITY1 (STOP1), which is accumulated in the nuclei of LRP cells under nitrate deficiency and directly regulates Arabidopsis NRT1.1 expression. Mutations in STOP1 mimic the root phenotype of the loss-of-function NRT1.1 mutant under nitrate deficiency, compared to wild-type plants, including increased LR growth and higher DR5promoter activity (i.e., higher LRP auxin signaling/activity). Nitrate deficiency-induced LR growth inhibition was almost completely reversed when STOP1 and the TF, TEOSINTE-BRANCHED1,-CYCLOIDEA,-PCF-DOMAIN-FAMILY-PROTEIN20 (TCP20), a known activator of NRT1.1 expression, were both mutated. Thus, the STOP1-TCP20 system is required for activation of NRT1.1 expression under nitrate deficiency, leading to reduced LR growth in nitrate-poor regions. We found this STOP1-mediated system is more active as growth media becomes more acidic, which correlates with reductions in soil nitrate as the soil pH becomes more acidic. STOP1 has been shown to be involved in RSA modifications in response to phosphate deficiency and increased potassium uptake, hence, our findings indicate that root growth regulation in response to low availability of the major fertilizer nutrients, nitrogen, phosphorus and potassium, all involve STOP1, which may allow plants to maintain appropriate root growth under the complex and varying soil distribution of nutrients.

Comparative analysis of transcriptomic points-of-departure (tPODs) and apical responses in embryo-larval fathead minnows exposed to fluoxetine

Current approaches in chemical hazard assessment face significant challenges because they rely on live animal testing, which is time-consuming, expensive, and ethically questionable. These concerns serve as an impetus to develop new approach methodologies (NAMs) that do not rely on live animal tests. This study explored a molecular benchmark dose (BMD) approach using a 7-day embryo-larval fathead minnow (FHM) assay to derive transcriptomic points-of-departure (tPODs) to predict apical BMDs of fluoxetine (FLX), a highly prescribed and potent selective serotonin reuptake inhibitor frequently detected in surface waters. Fertilized FHM embryos were exposed to graded concentrations of FLX (confirmed at < LOD, 0.19, 0.74, 3.38, 10.2, 47.5 μg/L) for 32 days. Subsets of fish were subjected to omics and locomotor analyses at 7 days post-fertilization (dpf) and to histological and biometric measurements at 32 dpf. Enrichment analyses of transcriptomics and proteomics data revealed significant perturbations in gene sets associated with serotonergic and axonal functions. BMD analysis resulted in tPOD values of 0.56 μg/L (median of the 20 most sensitive gene-level BMDs), 5.0 μg/L (tenth percentile of all gene-level BMDs), 7.51 μg/L (mode of the first peak of all gene-level BMDs), and 5.66 μg/L (pathway-level BMD). These tPODs were protective of locomotor and reduced body weight effects (LOEC of 10.2 μg/L) observed in this study and were reflective of chronic apical BMDs of FLX reported in the literature. Furthermore, the distribution of gene-level BMDs followed a bimodal pattern, revealing disruption of sensitive neurotoxic pathways at low concentrations and metabolic pathway perturbations at higher concentrations. This is one of the first studies to derive protective tPODs for FLX using a short-term embryo assay at a life stage not considered to be a live animal under current legislations.

Assessing the Toxicity of 17α-Ethinylestradiol in Rainbow Trout Using a 4-Day Transcriptomics Benchmark Dose (BMD) Embryo Assay

There is an urgent demand for more efficient and ethical approaches in ecological risk assessment. Using 17α-ethinylestradiol (EE2) as a model compound, this study established an embryo benchmark dose (BMD) assay for rainbow trout (RBT; Oncorhynchus mykiss) to derive transcriptomic points-of-departure (tPODs) as an alternative to live-animal tests. Embryos were exposed to graded concentrations of EE2 (measured: 0, 1.13, 1.57, 6.22, 16.3, 55.1, and 169 ng/L) from hatch to 4 and up to 60 days post-hatch (dph) to assess molecular and apical responses, respectively. Whole proteome analyses of alevins did not show clear estrogenic effects. In contrast, transcriptomics revealed responses that were in agreement with apical effects, including excessive accumulation of intravascular and hepatic proteinaceous fluid and significant increases in mortality at 55.1 and 169 ng/L EE2 at later time points. Transcriptomic BMD analysis estimated the median of the 20th lowest geneBMD to be 0.18 ng/L, the most sensitive tPOD. Other estimates (0.78, 3.64, and 1.63 ng/L for the 10th percentile geneBMD, first peak geneBMD distribution, and median geneBMD of the most sensitive over-represented pathway, respectively) were within the same order of magnitude as empirically derived apical PODs for EE2 in the literature. This 4-day alternative RBT embryonic assay was effective in deriving tPODs that are protective of chronic effects of EE2.

Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (Pimephales promelas)

There is increasing pressure to develop alternative ecotoxicological risk assessment approaches that do not rely on expensive, time-consuming, and ethically questionable live animal testing. This study aimed to develop a comprehensive early life stage toxicity pathway model for the exposure of fish to estrogenic chemicals that is rooted in mechanistic toxicology. Embryo-larval fathead minnows (FHM; Pimephales promelas) were exposed to graded concentrations of 17α-ethinylestradiol (water control, 0.01% DMSO, 4, 20, and 100 ng/L) for 32 days. Fish were assessed for transcriptomic and proteomic responses at 4 days post-hatch (dph), and for histological and apical end points at 28 dph. Molecular analyses revealed core responses that were indicative of observed apical outcomes, including biological processes resulting in overproduction of vitellogenin and impairment of visual development. Histological observations indicated accumulation of proteinaceous fluid in liver and kidney tissues, energy depletion, and delayed or suppressed gonad development. Additionally, fish in the 100 ng/L treatment group were smaller than controls. Integration of omics data improved the interpretation of perturbations in early life stage FHM, providing evidence of conservation of toxicity pathways across levels of biological organization. Overall, the mechanism-based embryo-larval FHM model showed promise as a replacement for standard adult live animal tests.

The Genomics of Cannabis and Its Close Relatives

Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myriad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of pooled published genomics data, andwe present a comprehensive literature review on the evolutionary history of Cannabis and Humulus, including medicinal and industrial applications. We demonstrate that current Cannabis genome assemblies are incomplete, with ∼10% missing, 10-25% unmapped, and 45S and 5S ribosomal DNA clusters as well as centromeres/satellite sequences not represented. These assemblies are also ordered at a low resolution, and their consensus quality clouds the accurate annotation of complete, partial, and pseudogenized gene copies. Considering the importance of genomics in the development of any crop, this analysis underlines the need for a coordinated effort to quantify the genetic and biochemical diversity of this species.

ODIN: Adaptation of an HTML 5-Compatible DICOM Viewer for MIRC-TFS, Enhancing the Incorporation of Clinical Images into the Health Science Curriculum

INTRODUCTION

The use of diagnostic radiology images while teaching has been proven to enhance student learning. The incorporation of images in the Digital Imaging and Communications in Medicine (DICOM) format has been hindered by the lack of integrated, DICOM image-compatible, viewing software.

BACKGROUND

A project was developed to facilitate the migration of clinical diagnostic radiology images, in their native DICOM format into the curriculum at the undergraduate level, including the Medical School, while anonymizing the images and presenting them in a way that simulates a clinical Picture Archive and Communication System (PACS). These images can be directly incorporated into Blackboard Learn or into other applications using embedded URLs.

DISCUSSION

A teaching file server was deployed using the Medical Imaging Resource Community-Teaching File System (MIRC-TFS) platform. An HTML5, DICOM image viewing server was developed and deployed. Plugins were created to integrate the anonymized images in the MIRC-TFS server with the HTML5 DICOM viewer and Blackboard Learn. The solution was deployed at an undergraduate level.

CONCLUSION

This project has resulted in the successful development and deployment of a variety of solutions, including an HTML 5 DICOM viewer, that has allowed for the incorporation of anonymized DICOM images from a clinical imaging repository into the undergraduate curriculum.

Multidimensional daily diary of fatigue-fibromyalgia-17 items (MDF-fibro-17): part 2 psychometric evaluation in fibromyalgia patients

Background

The Multidimensional Daily Diary of Fatigue-Fibromyalgia-17 instrument (MDF-Fibro-17) has been developed for use in fibromyalgia (FM) clinical studies and includes 5 domains: Global Fatigue Experience, Cognitive Fatigue, Physical Fatigue, Motivation, and Impact on Function. Psychometric properties of the MDF-Fibro-17 needed to demonstrate the appropriateness of using this instrument in clinical studies are presented.

Methods

Psychometric analyses were conducted to evaluate the factor structure, reliability, validity, and responsiveness of the MDF-Fibro-17 using data from a Phase 2 clinical study of FM patients (N = 381). Confirmatory factor analyses (CFA) were performed to ensure understanding of the multidimensional domain structure, and a secondary factor analysis of the domains examined the appropriateness of calculating a total score in addition to domain scores. Longitudinal psychometric analyses (test-retest reliability and responder analysis) were also conducted on the data from Baseline to Week 6.

Results

The CFA supported the 17-item, 5 domain structure of this instrument as the best fit of the data: comparative fit index (CFI) and non-normed fit index (NNFI) were 0.997 and 0.992 respectively, standardized root mean square residual (SRMR) was 0.010 and the root mean square error of approximation (RMSEA) was 0.06. In addition, total score (CFI and NNFI both 0.95) met required standards. For the total and 5 domain scores, reliability and validity data were acceptable: test-retest and internal consistency were above 0.9; correlations were as expected with the Global Fatigue Index (GFI) (0.62-0.75), Fibromyalgia Impact Questionnaire (FIQ) Total (0.59–0.71), and 36-Item Short Form Health Survey (SF-36) vitality (VT) (0.43–0.53); and discrimination was shown using quintile scores for the GFI, FIQ Total, and Pain Numeric Rating Scale (NRS) quartiles. In addition, sensitivity to change was demonstrated with an overall mean responder score of -2.59 using anchor-based methods.

Conclusion

The MDF-Fibro-17 reliably measures 5 domains of FM-related fatigue and psychometric evaluation confirms that this measure meets or exceeds each of the predefined acceptable thresholds for evidence of reliability, validity, and responsiveness to changes in clinical status. This suggests that the MDF-Fibro-17 is an appropriate and responsive measure of FM-related fatigue in clinical studies.