Centrifugal microfluidic system for colorimetric sample-to-answer detection of viral pathogens.

We describe a microfluidic system for conducting thermal lysis, polymerase chain reaction (PCR) amplification, hybridization, and colorimetric detection of foodborne viral organisms in a sample-to-answer format. The on-chip protocol entails 24 steps which are conducted by a centrifugal platform that allows for actuating liquids pneumatically during rotation and so facilitates automation of the workflow. The microfluidic cartridge is fabricated from transparent thermoplastic polymers and accommodates assay components along with an embedded micropillar array for detection and read-out. A panel of oligonucleotide primers and probes has been developed to perform PCR and hybridization assays that allows for identification of five different viruses, including pathogens such as norovirus and hepatitis A virus (HAV) in a multiplexed format using digoxigenin-labelled amplicons and immunoenzymatic conversion of a chromogenic substrate. Using endpoint detection, we demonstrate that the system can accurately and repetitively (n = 3) discriminate positive and negative signals for HAV at 350 genome copies per µL. As part of the characterization and optimization process, we show that the implementation of multiple (e.g., seven) micropillar arrays in a narrow fluidic pathway can lead to variation (up to 50% or more) in the distribution of colorimetric signal deriving from the assay. Numerical modeling of flow behaviour was used to substantiate these findings. The technology-by virtue of automation-can provide a pathway toward rapid detection of viral pathogens, shortening response time in food safety surveillance, compliance, and enforcement as well as outbreak investigations.

Automated centrifugal microfluidic system for the preparation of adaptor-ligated sequencing libraries.

The intensive workload associated with the preparation of high-quality DNA libraries remains a key obstacle toward widespread deployment of sequencing technologies in remote and resource-limited areas. We describe the development of single-use microfluidic devices driven by an advanced pneumatic centrifugal microfluidic platform, the PowerBlade, to automate the preparation of Illumina-compatible libraries based on adaptor ligation methodology. The developed on-chip workflow includes enzymatic DNA fragmentation coupled to end-repair, adaptor ligation, first DNA cleanup, PCR amplification, and second DNA cleanup. This complex workflow was successfully integrated into simple thermoplastic microfluidic devices that are amenable to mass production with injection molding. The system was validated by preparing, on chip, libraries from a mixture of genomic DNA extracted from three common foodborne pathogens (Listeria monocytogenes, Escherichia coli and Salmonella enterica serovar Typhimurium) and comparing them with libraries made via a manual procedure. The two types of libraries were found to exhibit similar quality control metrics (including genome coverage, assembly, and relative abundances) and led to nearly uniform coverage independent of GC content. This microfluidic technology offers a time-saving and cost-effective alternative to manual procedures and robotic-based automation, making it suitable for deployment in remote environments where technical expertise and resources might be scarce. Specifically, it facilitates field practices that involve mid- to low-throughput sequencing, such as tasks related to foodborne pathogen detection, characterization, and microbial profiling.

Application of the Cytokinesis-Block Micronucleus Assay for High-Dose Exposures Using Imaging Flow Cytometry.

The cytokinesis-block micronucleus assay is a well-established method to assess radiation-induced genetic damage in human cells. This assay has been adapted to imaging flow cytometry (IFC), allowing automated analysis of many cells, and eliminating the need to create microscope slides. Furthermore, to improve the efficiency of assay performance, a small-volume method previously developed was employed. Irradiated human blood samples were cultured, stained, and analyzed by IFC to produce images of the cells. Samples were run using both manual and 96-well plate automated acquisition. Multiple parameter-based image features were collected for each sample, and the results were compared to confirm that these acquisition methods are functionally identical. This paper details the multi-parametric analysis developed and the resulting calibration curves up to 10 Gy. The calibration curves were created using a quadratic random coefficient model with Poisson errors, as well as a logistic discriminant function. The curves were then validated with blinded, irradiated samples, using relative bias and relative mean square error. Overall, the accuracy of the dose estimates was adequate for triage dosimetry (within 1 Gy of the true dose) over 90% of the time for lower doses and about half the time for higher doses, with the lowest success rate between 5 and 6 Gy where the calibration curve reached its peak and there was the smallest change in MN/BNC with dose. This work describes the application of a novel multi-parametric analysis that fits the calibration curves and allows dose estimates up to 10 Gy, which were previously limited to 4 Gy. Furthermore, it demonstrates that the results from samples acquired manually and with the autosampler are functionally similar.

Deploying elements of scoping review methods for adverse outcome pathway development: a space travel case example.

PURPOSE: Health protection agencies require scientific information for evidence-based decision-making and guideline development. However, vetting and collating large quantities of published research to identify relevant high-quality studies is a challenge. One approach to address this issue is the use of adverse outcome pathways (AOPs) that provide a framework to assemble toxicological knowledge into causally linked chains of key events (KEs) across levels of biological organization to culminate in an adverse health outcome of significance to regulatory decision-making. Traditionally, AOPs have been constructed using a narrative review approach where the collection of evidence that supports each pathway is based on prior knowledge of influential studies that can also be supplemented by individually selecting and reviewing relevant references. OBJECTIVES: We aimed to create a protocol for AOP weight of evidence gathering that harnesses elements of both scoping review methods and artificial intelligence (AI) tools to increase transparency while reducing bias and workload of human screeners. METHODS: To develop this protocol, an existing space-health AOP in the workplan of the Organisation for Economic Co-operation and Development (OECD) AOP Programme was used as a case example. To balance the benefits of both scoping review tools and narrative approaches, a study protocol outlining a screening and search strategy was developed, and three reference collection workflows were tested to identify the most efficient method to inform weight of evidence. The workflows differed in their literature search strategies, and combinations of software tools used. RESULTS: Across the three tested workflows, over 59 literature searches were completed, retrieving over 34,000 references of which over 3300 were human reviewed. The most effective of the three methods used a search strategy with searches across each component of the AOP network, SWIFT Review as a pre-filtering software, and DistillerSR to create structured screening and data extraction forms. This methodology effectively retrieved relevant studies while balancing efficiency in data retrieval without compromising transparency, leading to a well-synthesized evidence base to support the AOP. CONCLUSIONS: The workflow is still exploratory in the context of AOP development, and we anticipate adaptations to the protocol with further experience. To further the systematicity, future iterations of the workflow could include structured quality assessment and risk of bias analysis. Overall, the workflow provides a transparent and documented approach to support AOP development, which in turn will support the need for rigorous methods to identify relevant scientific evidence while being practical to allow uptake by the broader community.

Benchmark dose modeling of transcriptional data: a systematic approach to identify best practices for study designs used in radiation research.

PURPOSE: Benchmark dose (BMD) modeling is a method commonly used in chemical toxicology to identify the point of departure (POD) from a dose-response curve linked to a health-related outcome. Recently, its application in the analysis of transcriptional data for quantitative adverse outcome pathway (AOP) development is being explored. As AOPs are informed by diverse data types, it is important to understand the impact of study parameters such as dose selection, the number of replicates and dose range on BMD outputs for radiation-induced genes and pathways. MATERIALS AND METHODS: Data were selected from the Gene Expression Omnibus (GSE52403) that featured gene expression profiles of peripheral blood samples from C57BL/6 mice 6 hours post-exposure to 137Cs gamma-radiation at 0, 1, 2, 3, 4.5, 6, 8 and 10.5 Gy. The dataset comprised a broad dose range over multiple dose points with consistent dose spacing and multiple biological replicates. This dataset was ideal for systematically transforming across three categories: (1) dose range, (2) dose-spacing and (3) number of controls/replicates. Across these categories, 29 transformed datasets were compared to the original dataset to determine the impact of each transformation on the BMD outputs. RESULTS: Most of the experimental changes did not impact the BMD outputs. The transformed datasets were largely consistent with the original dataset in terms of the number of reproduced genes modeled and absolute BMD values for genes and pathways. Variations in dose selection identified the importance of the absolute value of the lowest and second dose. It was determined that dose selection should include at least two doses <1 Gy and two >5 Gy to achieve meaningful BMD outputs. Changes to the number of biological replicates in the control and non-zero dose groups impacted the overall accuracy and precision of the BMD outputs as well as the ability to fit dose-response models consistent with the original dataset. CONCLUSION: Successful application of transcriptomic BMD modeling for radiation datasets requires considerations of the exposure dose and the number of biological replicates. Most important is the selection of the lowest doses and dose spacing. Reflections on these parameters in experimental design will provide meaningful BMD outputs that could correlate well to apical endpoints of relevance to radiation exposure assessment.

Evaluating the influences of confounding variables on benchmark dose using a case study in the field of ionizing radiation.

PURPOSE: A vast amount of data regarding the effects of radiation stressors on transcriptional changes has been produced over the past few decades. These data have shown remarkable consistency across platforms and experimental design, enabling increased understanding of early molecular effects of radiation exposure. However, the value of transcriptomic data in the context of risk assessment is not clear and represents a gap that is worthy of further consideration. Recently, benchmark dose (BMD) modeling has shown promise in correlating a transcriptional point of departure (POD) to that derived using phenotypic outcomes relevant to human health risk assessment. Although frequently applied in chemical toxicity evaluation, our group has recently demonstrated application within the field of radiation research. This approach allows the possibility to quantitatively compare radiation-induced gene and pathway alterations across various datasets using BMD values and derive meaningful biological effects. However, before BMD modeling can confidently be used, an understanding of the impact of confounding variables on BMD outputs is needed. METHODS: To this end, BMD modeling was applied to a publicly available microarray dataset (Gene Expression Omnibus #GSE23515) that used peripheral blood ex-vivo gamma-irradiated at 0.82 Gy/min, at doses of 0, 0.1, 0.5 or 2 Gy, and assessed 6 hours post-exposure. The dataset comprised six female smokers (F-S), six female nonsmokers (F-NS), six male smokers (M-S), and six male nonsmokers (M-NS). RESULTS: A combined total of 412 genes were fit to models and the BMD distribution was noted to be bi-modal across the four groups. A total of 74, 41, 62 and 62 genes were unique to the F-NS, M-NS, F-S and M-S groups. Sixty-two BMD modeled genes and nine pathways were common across all four groups. There were no differential sensitivity of BMD responses in the robust common genes and pathways. CONCLUSION: For radiation-responsive genes and pathways common across the study groups, the BMD distribution of transcriptional activity was unaltered by sex and smoking status. Although further validation of the data is needed, these initial findings suggest BMD values for radiation relevant genes and pathways are robust and could be explored further in future studies.

Expert consultation is vital for adverse outcome pathway development: a case example of cardiovascular effects of ionizing radiation.

BACKGROUND: The circulatory system distributes nutrients, signaling molecules, and immune cells to vital organs and soft tissues. Epidemiological, animal, and in vitro cellular mechanistic studies have highlighted that exposure to ionizing radiation (IR) can induce molecular changes in cellular and subcellular milieus leading to long-term health impacts, particularly on the circulatory system. Although the mechanisms for the pathologies are not fully elucidated, endothelial dysfunction is proven to be a critical event via radiation-induced oxidative stress mediators. To delineate connectivities of events specifically to cardiovascular disease (CVD) initiation and progression, the adverse outcome pathway (AOP) approach was used with consultation from field experts. AOPs are a means to organize information around a disease of interest to a regulatory question. An AOP begins with a molecular initiating event and ends in an adverse outcome via sequential linkages of key event relationships that are supported by evidence in the form of the modified Bradford-Hill criteria. Detailed guidelines on building AOPs are provided by the Organisation for Economic Cooperation and Development (OECD) AOP program. Here, we report on the questions and discussions needed to develop an AOP for CVD resulting from IR exposure. A recent workshop jointly organized by the MELODI (Multidisciplinary European Low Dose Initiative) and the ALLIANCE (European Radioecology Alliance) associations brought together experts from the OECD to present the AOP approach and tools with examples from the toxicology field. As part of this workshop, four working groups were formed to discuss the identification of adverse outcomes relevant to radiation exposures and development of potential AOPs, one of which was focused on IR-induced cardiovascular effects. Each working group comprised subject matter experts and radiation researchers interested in the specific disease area and included an AOP coach. CONCLUSION: The CVD working group identified the critical questions of interest for AOP development, including the exposure scenario that would inform the evidence, the mechanisms of toxicity, the initiating event, intermediate key events/relationships, and the type of data currently available. This commentary describes the four-day discussion of the CVD working group, its outcomes, and demonstrates how collaboration and expert consultation is vital to informing AOP construction.

Meta-analysis of transcriptomic datasets using benchmark dose modeling shows value in supporting radiation risk assessment.

PURPOSE: Benchmark dose (BMD) modeling is used to determine the dose of a stressor at which a predefined increase in any biological effect above background occurs (e.g. 10% increase from control values). BMD analytical tools have the capacity to model transcriptional dose-response data to derive BMDs for genes, pathways and gene ontologies. We recently demonstrated the value of this approach to support various areas of radiation research using predominately 'in-house' generated datasets. MATERIALS AND METHODS: As a continuation of this work, transcriptomic studies of relevance to ionizing radiation were retrieved through the Gene Expression Omnibus (GEO). The datasets were compiled and filtered, then analyzed using BMDExpress. The objective was to determine the reproducibility of BMD values in relation to pathways and genes across different exposure scenarios and compare to those derived using cytogenetic endpoints. A number of graphic visualization approaches were used to determine if BMD outputs could be correlated to parameters such as dose-rate, radiation quality and cell type. RESULTS: Curated studies were diverse and derived from experiments with varied design and intent. Despite this, common genes and pathways were identified with low and high dose thresholds. The higher BMD values were associated with immune response and cell death, while transcripts with lower BMD values were generally related to the classic DNA damage response/repair processes, centered on TP53 signaling. Analysis of datasets with relatively similar dose-ranges under comparable experimental conditions showed a bi-modal distribution with a high degree of consistency in BMD values across shared genes and pathways, particularly for those below the 25th percentile of total distribution by dose. The median BMD values were noted to be approximately 0.5 Gy for genes/pathways that comprised mode 1. Furthermore, transcriptional BMD values derived from a subset of genes using in vivo and in vitro datasets were in accord to those using cytogenetic endpoints. CONCLUSION: Overall, the results from this work highlight the value of the BMD methodology to derive meaningful outputs that are consistent across different models, provided the studies are conducted using a similar dose-range.

Identification of therapeutics that target eEF1A2 and upregulate utrophin A translation in dystrophic muscles.

Up-regulation of utrophin in muscles represents a promising therapeutic strategy for the treatment of Duchenne Muscular Dystrophy. We previously demonstrated that eEF1A2 associates with the 5'UTR of utrophin A to promote IRES-dependent translation. Here, we examine whether eEF1A2 directly regulates utrophin A expression and identify via an ELISA-based high-throughput screen, FDA-approved drugs that upregulate both eEF1A2 and utrophin A. Our results show that transient overexpression of eEF1A2 in mouse muscles causes an increase in IRES-mediated translation of utrophin A. Through the assessment of our screen, we reveal 7 classes of FDA-approved drugs that increase eEF1A2 and utrophin A protein levels. Treatment of mdx mice with the 2 top leads results in multiple improvements of the dystrophic phenotype. Here, we report that IRES-mediated translation of utrophin A via eEF1A2 is a critical mechanism of regulating utrophin A expression and reveal the potential of repurposed drugs for treating DMD via this pathway.

Celecoxib treatment improves muscle function in mdx mice and increases utrophin A expression.

Duchenne muscular dystrophy (DMD) is a genetic and progressive neuromuscular disorder caused by mutations and deletions in the dystrophin gene. Although there is currently no cure, one promising treatment for DMD is aimed at increasing endogenous levels of utrophin A to compensate functionally for the lack of dystrophin. Recent studies from our laboratory revealed that heparin treatment of mdx mice activates p38 MAPK, leading to an upregulation of utrophin A expression and improvements in the dystrophic phenotype. Based on these findings, we sought to determine the effects of other potent p38 activators, including the cyclooxygenase (COX)-2 inhibitor celecoxib. In this study, we treated 6-wk-old mdx mice for 4 wk with celecoxib. Immunofluorescence analysis of celecoxib-treated mdx muscles revealed a fiber type switch from a fast to a slower phenotype along with beneficial effects on muscle fiber integrity. In agreement, celecoxib-treated mdx mice showed improved muscle strength. Celecoxib treatment also induced increases in utrophin A expression ranging from ∼1.5- to 2-fold in tibialis anterior diaphragm and heart muscles. Overall, these results highlight that activation of p38 in muscles can indeed lead to an attenuation of the dystrophic phenotype and reveal the potential role of celecoxib as a novel therapeutic agent for the treatment of DMD.-Péladeau, C., Adam, N. J., Jasmin, B. J. Celecoxib treatment improves muscle function in mdx mice and increases utrophin A expression.

Purification and Characterization of Lactate Dehydrogenase in the Foot Muscle and Hepatopancreas of Otala lactea.

Lactate dehydrogenase (LDH) has a crucial role in maintaining ATP production as the terminal enzyme in anaerobic glycolysis. This study will determine the effect of posttranslational modifications (PTMs) on the activity of LDH in the foot muscle and hepatopancreas of an estivating snail, Otala lactea. LDH in foot muscle of O. lactea was purified to homogeneity and partially purified in hepatopancreas in a two-step and three-step process, respectively. The kinetic properties and stability of these isoforms were determined where there was a significant difference in Km and I50 values with pyruvate and urea separately in foot muscle; however, hepatopancreas exhibited significant differences in Km and I50 in salt between control and stress. Interestingly, hepatopancreas has a higher affinity for pyruvate in the control state whereas foot muscle has a higher affinity for its substrate in the estivated state. PTMs of each isoform were identified using immunoblotting and dot blots, which prove to be significantly higher in the control state. Overall, foot muscle LDH enters a low phosphorylation state during estivation allowing more efficiency in consuming pyruvate with higher thermal stability but less structural stability. Hepatopancreas LDH becomes dephosphorylated in the estivating snail that decreases the efficiency of the enzyme in the forward direction; however, the snail has an increased tolerance to the presence of salt when water becomes scarce. Such tissue-specific regulations indicate the organism's ability to reduce energy consumption when undergoing metabolic depression.

Role of the TWEAK-Fn14-cIAP1-NF-κB Signaling Axis in the Regulation of Myogenesis and Muscle Homeostasis.

Mammalian skeletal muscle maintains a robust regenerative capacity throughout life, largely due to the presence of a stem cell population known as "satellite cells" in the muscle milieu. In normal conditions, these cells remain quiescent; they are activated upon injury to become myoblasts, which proliferate extensively and eventually differentiate and fuse to form new multinucleated muscle fibers. Recent findings have identified some of the factors, including the cytokine TNFα-like weak inducer of apoptosis (TWEAK), which govern these cells' decisions to proliferate, differentiate, or fuse. In this review, we will address the functions of TWEAK, its receptor Fn14, and the associated signal transduction molecule, the cellular inhibitor of apoptosis 1 (cIAP1), in the regulation of myogenesis. TWEAK signaling can activate the canonical NF-κB signaling pathway, which promotes myoblast proliferation and inhibits myogenesis. In addition, TWEAK activates the non-canonical NF-κB pathway, which, in contrast, promotes myogenesis by increasing myoblast fusion. Both pathways are regulated by cIAP1, which is an essential component of downstream signaling mediated by TWEAK and similar cytokines. This review will focus on the seemingly contradictory roles played by TWEAK during muscle regeneration, by highlighting the interplay between the two NF-κB pathways under physiological and pathological conditions. We will also discuss how myogenesis is negatively affected by chronic conditions, which affect homeostasis of the skeletal muscle environment.