Reflections on Several Landmark Advances in Circadian Biology

Circadian Biology intersects with diverse scientific domains, intricately woven into the fabric of organismal physiology and behavior. The rhythmic orchestration of life by the circadian clock serves as a focal point for researchers across disciplines. This retrospective examination delves into several of the scientific milestones that have fundamentally shaped our contemporary understanding of circadian rhythms. From deciphering the complexities of clock genes at a cellular level to exploring the nuances of coupled oscillators in whole organism responses to stimuli. The field has undergone significant evolution lately guided by genetics approaches. Our exploration here considers key moments in the circadian-research landscape, elucidating the trajectory of this discipline with a keen eye on scientific advancements and paradigm shifts.

Integration of HiBiT into enteroviruses: A universal tool for advancing enterovirus virology research

The utilization of enteroviruses engineered with reporter genes serves as a valuable tool for advancing our understanding of enterovirus biology and its applications, enabling the development of effective therapeutic and preventive strategies. In this study, our initial attempts to introduce a NanoLuc luciferase (NLuc) reporter gene into recombinant enteroviruses were unsuccessful in rescuing viable progenies. We hypothesized that the size of the inserted tag might be a determining factor in the rescue of the virus. Therefore, we inserted the 11-amino-acid HiBiT tag into the genomes of enterovirus A71 (EV-A71), coxsackievirus A10 (CVA10), coxsackievirus A7 (CVA7), coxsackievirus A16 (CVA16), namely EV-A71-HiBiT, CVA16-HiBiT, CVA10-HiBiT, CVA7-HiBiT, and observed that the HiBiT-tagged viruses exhibited remarkably high rescue efficiency. Notably, the HiBiT-tagged enteroviruses displayed comparable characteristics to the wild-type viruses. A direct comparison between CVA16-NLuc and CVA16-HiBiT recombinant viruses revealed that the tiny HiBiT insertion had minimal impact on virus infectivity and replication kinetics. Moreover, these HiBiT-tagged enteroviruses demonstrated high genetic stability in different cell lines over multiple passages. In addition, the HiBiT-tagged viruses were successfully tested in antiviral drug assays, and the sensitivity of the viruses to drugs was not affected by the HiBiT tag. Ultimately, our findings provide definitive evidence that the integration of HiBiT into enteroviruses presents a universal, convenient, and invaluable method for advancing research in the realm of enterovirus virology. Furthermore, HiBiT-tagged enteroviruses exhibit great potential for diverse applications, including the development of antivirals and the elucidation of viral infection mechanisms.

A comparative study of structural and catalytic activity alterations in firefly luciferase induced by carbon quantum dots containing amine and carboxyl functional groups

Despite of growing interest in use of carbon-based nanomaterials as carriers of functional proteins, less attention has been paid to the effects of these nanomaterials on the structure and function of the proteins. In this study, with the aim of shedding light on the mechanisms of interaction between carbon-based nanomaterials and proteins, the interactions of carbon quantum dots (CQDs) containing amine (CQD-NH2) or carboxyl groups (CQD-COOH) with Photinus pyralis firefly luciferase enzyme were investigated by experimental and computational approaches. The structural changes and reduction in activity of the luciferase upon treatment with CQDs were experimentally proved. CQD-NH2 induced more reduction in enzyme activity (15 %) compared to CQD-COOH (7.4 %). The interactions CQD-NH2 with luciferase led to higher affinity of the enzyme for its substrate. It was found by molecular dynamic simulations that CQD-NH2 binds to multiple regions on the surface of luciferase. Secondary structure analysis showed that CQD-NH2 had more profound effects on the active site amino acids, the adjacent amino acids to the active site and the residues involved in ATP binding site. In addition, CQD-NH2 interactions with luciferase were suggested to be stronger than CQD-COOH based on the number of hydrogen bonds and the binding energies.

Novel BRET combination for detection of rapamycin-induced protein dimerization using luciferase from fungus Neonothopanusnambi

Bioluminescence resonance energy transfer (BRET) is one of the most promising approaches used for noninvasive imaging of protein-protein interactions in vivo. Recently, our team has discovered a genetically encodable bioluminescent system from the fungus Neonothopanus nambi and identified a novel luciferase that represents an imaging tool orthogonal to other luciferin-luciferase systems. We demonstrated the possibility of using the fungal luciferase as a new BRET donor by creating fused pairs with acceptor red fluorescent proteins, of which tdTomato provided the highest BRET efficiency. Using this new BRET system, we also designed a mTOR pathway specific rapamycin biosensor by integrating the FRB and FKBP12 protein dimerization system. We demonstrated the specificity and efficacy of the new fungal luciferase-based BRET combination for application in mammalian cell culture that will provide the unique opportunity to perform multiplexed BRET assessment in the future.

Sensing chemical-induced DNA damage using CRISPR/Cas9-mediated gene-deletion yeast-reporter strains

Microorganism-based genotoxicity assessments are vital for evaluating potential chemical-induced DNA damage. In this study, we developed both chromosomally integrated and single-copy plasmid-based reporter assays in budding yeast using a RNR3 promoter-driven luciferase gene. These assays were designed to compare the response to genotoxic chemicals with a pre-established multicopy plasmid-based assay. Despite exhibiting the lowest luciferase activity, the chromosomally integrated reporter assay showed the highest fold induction (i.e., the ratio of luciferase activity in the presence and absence of the chemical) compared with the established plasmid-based assay. Using CRISPR/Cas9 technology, we generated mutants with single- or double-gene deletions, affecting major DNA repair pathways or cell permeability. This enabled us to evaluate reporter gene responses to genotoxicants in a single-copy plasmid-based assay. Elevated background activities were observed in several mutants, such as mag1Δ cells, even without exposure to chemicals. However, substantial luciferase induction was detected in single-deletion mutants following exposure to specific chemicals, including mag1Δ, mms2Δ, and rad59Δ cells treated with methyl methanesulfonate; rad59Δ cells exposed to camptothecin; and mms2Δ and rad10Δ cells treated with mitomycin C (MMC) and cisplatin (CDDP). Notably, mms2Δ/rad10Δ cells treated with MMC or CDDP exhibited significantly enhanced luciferase induction compared with the parent single-deletion mutants, suggesting that postreplication and for nucleotide excision repair processes predominantly contribute to repairing DNA crosslinks. Overall, our findings demonstrate the utility of yeast-based reporter assays employing strains with multiple-deletion mutations in DNA repair genes. These assays serve as valuable tools for investigating DNA repair mechanisms and assessing chemical-induced DNA damage. KEY POINTS: • Responses to genotoxic chemicals were investigated in three types of reporter yeast. • Yeast strains with single- and double-deletions of DNA repair genes were tested. • Two DNA repair pathways predominantly contributed to DNA crosslink repair in yeast.

In Vivo Bioluminescence and Fluorescence Imaging: Optical Tool for Cancer Research

In vivo whole-body imaging, using optical tools based on bioluminescence and fluorescence detection, offers tremendous opportunities to specifically determine the spatiotemporal resolution of cancer cells within the tested animals. This enables the study of many aspects of cancer biology, including cell proliferation, trafficking, and invasions. The antitumor therapeutic properties of various tested compounds (e.g., CD19 CAR-T cells, used for cancer immunotherapy) can be monitored within the same animal at different time points, significantly reducing the number of animals used in the study as indicated in this method.

LuBiA (Luciferase-Based Binding Assay): Glowing Peptides as Sensitive Probes to Study Ligand-Receptor Interactions

The quantitative and qualitative biochemical description of molecular interactions is fundamental to the study of ligand/receptor pairs and their structure/function relationships. Bioactive peptides often are active at (sub-)nanomolar concentrations, indicating they have a high affinity for their sites of action, notably binding sites on receptors. Since such receptor proteins are commonly of low abundance, highly sensitive detection methods are required to study these ligand/receptor interactions. We present a protocol for an inexpensive luminescence-based detection setup in which the peptide ligand of interest is extended with the 11-amino acid HiBiT tag. This tag can be quantified easily down to fmol amounts by its ability to reconstitute the enzymatic activity of LgBiT, a truncated version of the Oplophorus gracilirostris luciferase.

Oxomer- and Reporter Gene-Based Analysis of FIH Activity in Cells

Cellular and tissue adaptations to oxygen deprivation (hypoxia) are necessary for both normal physiology and disease. Responses to hypoxia are initiated by the cellular oxygen sensors prolyl-4-hydroxylase domain (PHD) proteins 1-3 and factor inhibiting HIF (FIH). These enzymes regulate the transcription factor hypoxia-inducible factor (HIF) in a hypoxia-sensitive manner. FIH also regulates proteins outside the HIF pathway, including the deubiquitinase OTUB1. Numerous preclinical analyses have demonstrated that treatment with HIF hydroxylase inhibitors is beneficial and protective in many hypoxia-associated diseases. However, clinically available HIF hydroxylase inhibitors increase erythropoietin (EPO) gene expression and red blood cell production, which can be detrimental in hypoxia-associated conditions, such as ischemia/reperfusion injury of the heart or chronic inflammation. Our understanding of the relevance of FIH in (patho)physiology is only in its infancy, but FIH activity does not govern erythropoietin expression. Therefore, it is of prime interest to assess the relevance of FIH activity in (patho)physiology in detail, as it may contribute to developing novel therapeutic options for treating hypoxia-associated diseases that do not affect Epo regulation. Here, we describe specific protocols for two different methods to assess FIH enzymatic activity within cells, using a HIF-dependent firefly luciferase-reporter gene and an oxomer-dependent assay. Oxomers are oxygen-dependent stable protein oligomers formed by FIH, for example, with the deubiquitinase OTUB1. Oxomer formation directly depends on FIH activity, providing a suitable cellular readout for an easy-to-use analysis of FIH enzymatic activity in cellulo. These techniques permit an analysis of FIH activity toward HIF and outside the HIF pathway, allowing the investigation of FIH activity under different (patho)physiological conditions and assessment of novel (putative) inhibitors.

The Split-Luciferase Complementation Assay to Detect and Quantify Protein-Protein Interactions in Planta

Protein-protein interactions play a critical role in plant viral infection and defense responses against pathogens. This protocol provides a detailed and reliable methodology for investigating protein-protein interactions using a luciferase-based complementation assay that includes easy luminescence-based normalization within a single plate. The protocol includes step-by-step procedures, reagent lists, and considerations for data interpretation, ensuring robust and reproducible results. By following this protocol, researchers can advance on understanding of the crucial role of protein-protein interactions in plant viral infection and defense responses to other pathogen attacks.

Biochemical Reconstitution of Ca2+-Dependent Exosome Secretion in Permeabilized Mammalian Cells

Exosomes are a subpopulation of the heterogenous pool of extracellular vesicles that are secreted to the extracellular space. Exosomes have been purported to play a role in intercellular communication and have demonstrated utility as biomarkers for a variety of diseases. Despite broad interest in exosome biology, the conditions that regulate their secretion are incompletely understood. The goal of this procedure is to biochemically reconstitute exosome secretion in Streptolysin O (SLO)-permeabilized mammalian cells. This protocol describes the reconstitution of lyophilized SLO, preparation of cytosol and SLO-permeabilized cells, assembly of the biochemical reconstitution reaction, and quantification of exosome secretion using a sensitive luminescence-based assay. This biochemical reconstitution reaction can be utilized to characterize the molecular mechanisms by which different gene products regulate exosome secretion. Key features This protocol establishes a functional in vitro system to reconstitute exosome secretion in permeabilized mammalian cells upon addition of cytosol, ATP, GTP, and calcium (Ca2+).

A Non-Coding Variant in SLC15A4 Modulates Enhancer Activity and Lysosomal Deacidification Linked to Lupus Susceptibility

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near the SLC15A4 gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer of SLC15A4. Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters of SLC15A4, GLTLD1, and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.

Bioluminescent immunoassay for serine/threonine protein kinase activity using an aequorin-labeled monoclonal antibody and a synthetic peptide as a substrate

A bioluminescent immunoassay system was developed to determine serine/threonine protein kinase activity using an aequorin-labeled monoclonal antibody and a synthetic peptide as the substrate. A monoclonal antibody against the synthetic phosphorylated serine peptide (K9P peptide) of histone H3 (19 amino acid residues), referred to as the H3S10P antibody, was chemically conjugated to maleimide-activated aequorin to prepare aequorin-labeled H3S10P (AQ-S-H3S10P). For the serine/threonine kinase assay, a non-phosphorylated serine peptide (K9C peptide) coated on a microplate was incubated with serine/threonine protein kinase in the presence of ATP and Mg2+. The resulting phosphorylated K9C peptides (K9P peptide) were identified using AQ-S-H3S10P. Thus, after the removal of unbound AQ-S-H3S10P though washing, the serine/threonine kinase activity was determined by the luminescence activity of aequorin from AQ-S-H3S10P bound to the K9P peptide. This assay system, in combination with the K9C peptide and AQ-S-H3S10P, could be used to screen inhibitors of various serine/threonine protein kinases in general.

Optimization of Strategy for Modified mRNA Inducing Cardiac-Specific Expression in Mice

Lipid nanoparticle (LNP)-coated-modified RNA(modRNA) has been developed for enhancing the stability of modRNA, but it tends to accumulate in liver. The current study aimed to optimize strategy for increasing cardiac expression efficiency of modRNA. We synthesized Luciferase (Luc)-modRNA, and also developed 122Luc modRNA, a liver silencing Luc modRNA. Intramyocardial injection of naked Luc modRNA induced high bioluminescence signal in heart, but very low in other organs including liver. Luc modRNA-LNP injection showed the signal was increased by 5 folds in the heart and by 15,000 folds in the liver, compared to naked Luc modRNA group. In comparison with Luc modRNA-LNP group, the liver signal was decreased to 0.17%, while cardiac signal showed a slight drop by intramyocardial injection of 122Luc-modRNA-LNP. Our data revealed that intramyocardial injection of naked modRNA could effectively induced cardiac-specific expression. For cardiac delivery of Luc modRNA-LNP, 122modRNA-LNP enhances specificity of cardiac expression by abolishing liver signal.

Identification of Cyclocybe erebia metabolites that affect the circadian rhythm of Eluc expression under control of Bmal1 promoter in mouse fibroblast cells

Pharmacological intervention of circadian rhythms is a potentially useful approach for ameliorating various health problems caused by disturbed circadian rhythms including sleep disorder and metabolic diseases. To find compounds that affect circadian rhythms, we screened mushroom extracts using mouse cells expressing the luciferase gene under the control of the mouse Bmal1 promoter. The culture filtrate extract from the basidiomycete Cyclocybe erebia enhanced the oscillation of bioluminescence caused by the expression of the luciferase gene and prolonged the period of bioluminescence. Bioassay-guided fractionation of the extract resulted in purification of compounds 1 and 2. Spectroscopic analyses along with single-crystal X-ray diffraction analysis, revealed that these compounds were diterpenoids with a unique skeleton and a fused ring system comprising 3-, 7-, and 5-membered rings. Compounds 1 and 2 were named cyclocircadins A and B, respectively. These findings suggested that natural diterpenoids could be a source of compounds with the activity affecting circadian rhythms.

Mesenchymal stem cell-derived extracellular vesicles prevent the formation of pulmonary arterial hypertension through a microRNA-200b-dependent mechanism

BACKGROUND

Bone marrow mesenchymal stem cell-derived extracellular vesicles (BMSC-EVs) have been highly studied with their critical roles as carriers of therapeutic targets such as microRNAs (miRNAs) in the treatment of human diseases, including pulmonary arterial hypertension (PAH). Herein, we tried to study the potential of BMSC-EVs to deliver miR-200b for the regulation of macrophage polarization in PAH.

METHODS

Rat models of PAH were induced with monocrotaline treatment, followed by miR-200b expression detection in lung tissues, pulmonary artery smooth muscle cells (PASMCs) and macrophages. miR-200b-containing BMSCs or miR-200b-deficient BMSCs were selected to extract EVs. Then, we assessed the changes in rats with PAH-associated disorders as well as in vitro macrophage polarization and the functions of PASMCs after treatment with BMSC-EVs. Moreover, the interaction between miR-200b, phosphodiesterase 1 A (PDE1A) was identified with a luciferase assay, followed by an exploration of the downstream pathway, cAMP-dependent protein kinase (PKA).

RESULTS

miR-200b was reduced in lung tissues, PASMCs and macrophages of rats with PAH-like pathology. BMSC-EVs transferred miR-200b into macrophages, and subsequently accelerated their switch to the M2 phenotype and reversed the PAH-associated disorders. Furthermore, miR-200b carried by BMSC-EVs induced PKA phosphorylation by targeting PDE1A, thereby expediting macrophage polarization.

CONCLUSION

Our current study highlighted the inhibitory role of BMSC-EV-miR-200b in PAH formation.

The crucial role of Y109 and R162 as catalytic residues of nanoKAZ: insights from molecular docking, molecular dynamics simulation, and quantum chemical investigations

CONTEXT

nanoKAZ is a compact luciferase that exhibits intense blue light emission when it catalyzes the substrate Furimazine (FMZ) as a luciferin, making it an excellent candidate as a reporter protein. However, the specific catalytic residues and mechanism of nanoKAZ have not been revealed. Recently, the structure of nanoKAZ was determined, and it was observed that the luminescent properties changed when FMZ analogs with naphthalene replacing benzene were used. It is speculated that the substituted naphthalene may influence the interaction between the catalytic residues and luciferins, thereby affecting the energy of the emitted light signal.

METHOD

Therefore, the primary objective of this study is to analyze and compare the molecular recognition between nanoKAZ and FMZ along with its four activity-altered naphthalene analogs, with aiming to identify the catalytic residues. Molecular docking was employed to construct all nanoKAZ-luciferin models, followed by a 500 ns molecular dynamics simulation. The simulation trajectory was subjected to MM/PBSA analysis to identify crucial residues that contribute significantly to luciferin binding. In the result, two polar residues Y109, and R162 were identified as active residues as their notable contributions to the binding energy. Subsequently, an oxygen molecule was introduced into the local region of the nanoKAZ-FMZ complex and followed with quantum chemical calculations (semiempirical and DFT methods were used) to investigate the catalysis details. The results illustrated the involvement of Y109 and R162 in the oxygenation of FMZ, leading to the formation of dioxetanone, which has been suggested as an important intermediate in the oxidation process among various luciferins sharing the same functional group as FMZ.

Construction of coxsackievirus B5 viruses with luciferase reporters and their applications in vitro and in vivo

Coxsackievirus belongs to the Picornaviridae family and is one of the major pathogens that cause hand, foot and mouth disease (HFMD) in infants and children with potential serious complications and even deaths. The pathogenesis of this virus is not fully elucidated and no vaccine or antiviral drug has been approved. In this study, a full-length infectious cDNA clone of coxsackievirus B5 virus was assembled and the recombinant virus displayed similar growth kinetics and ability to cause cytopathic effects as the parental virus. Luciferase reporter was then incorporated to generate both full-length and subgenomic replicon (SGR) reporter viruses. The full-length reporter virus is suitable for high-throughput antiviral screening, while the SGR is a useful tool to study viral-host interactions. More importantly, the full-length reporter virus has also been shown to infect the suckling mouse model and the reporter gene could be detected using an in vivo imaging system, thus providing a powerful tool to track viruses in vivo. In summary, we have generated coxsackievirus B5 reporter viruses and provided unique tools for studying virus-host interactions in vitro and in vivo as well as for high-throughput screenings (HTS) to identify novel antivirals.

Long-Read Genome Sequencing of Abscondita cerata (Coleoptera: Lampyridae), the Endemic Firefly of Taiwan

Abscondita cerata is the most abundant and widely distributed endemic firefly species in Taiwan and is considered a key environmental and ecological indicator organism. In this study, we report the first long-read genome sequencing of Abs. cerata sequenced by Nanopore technology. The draft genome size, 967 Mb, was measured through a hybrid approach that consisted of assembling using 11.25-Gb Nanopore long reads and polishing using 9.47-Gb BGI PE100 short reads. The drafted genome was assembled into 4,855 contigs, with the N50 reaching 325.269 kb length. The assembled genome was predicted to possess 55,206 protein-coding genes, of which 20,862 (37.78%) were functionally annotated with public databases. 47.11% of the genome sequences consisted of repeat elements; among them DNA transposons accounted for the largest proportion (26.79%). A BUSCO (Benchmarking Universal Single Copy Orthologs) evaluation demonstrated that the genome and gene completeness were 84.8% and 79%, respectively. The phylogeny constructed using 1,792 single copy genes was consistent with previous studies. The comparative transcriptome between adult male head and lantern tissues revealed (1) the vision of Abs. cerata is primarily UV-sensitive to environmental twilight, which determines when it begins its nocturnal activity, (2) the major expressed OR56d receptor may be correlated to suitable humidity sensing, and (3) Luc1-type luciferase is responsible for Abs. cerata's luminescent spectrum.

Hybridization-based CpG methylation level detection using methyl-CpG-binding domain-fused luciferase

Hypermethylation of tumor-suppressor genes and global hypomethylation, which is related to methylation level at the retroelement, have been recognized as features of the cancer genome. In this study, we developed a hybridization-based CpG methylation level detection method using methyl-CpG-binding domain-fused firefly luciferase (MBD-Fluc). In this method, methylated probe oligonucleotides were used to capture target oligonucleotides. Fully methylated and hemimethylated double-stranded DNA (dsDNA) was formed by hybridization of the methylated captured oligonucleotides with methylated or unmethylated target oligonucleotides, respectively. MBD-Fluc specifically binds to fully methylated dsDNA but not to hemimethylated dsDNA; therefore, methylated target oligonucleotides can be detected by measuring the luciferase activity of the bound MBD-Fluc. Using the corresponding methylated probe oligonucleotides, the CpG methylation levels of SEPT9, BRCA1, and long interspersed nuclear element-1 (LINE-1) oligonucleotides were quantified. Moreover, we demonstrated that the emission detection signal was not affected by the methylation state of the overhang region of the target oligonucleotide, which was not hybridized to the probe oligonucleotide, indicating that methylated CpG of the target region could be accurately detected. Unmethylated-CpG-binding domain-fused luciferases and 5-hydroxymethyl-CpG-binding domain-fused luciferases have been constructed, suggesting that other modified bases can be detected by the same platform.

A 1-kb human CDCA8 promoter directs the spermatogonia-specific luciferase expression in adult testis

Cell division cycle associated 8 (CDCA8) is a component of the chromosomal passenger complex and plays an essential role in mitosis, meiosis, cancer growth, and undifferentiated state of embryonic stem cells. However, its expression and role in adult tissues remain largely uncharacterized. Here, we studied the CDCA8 transcription in adult tissues by generating a transgenic mouse model, in which the luciferase was driven by a 1-kb human CDCA8 promoter. Our previous study showed that this 1-kb promoter was active enough to dictate reporter expression faithfully reflecting endogenous CDCA8 expression. Two founder mice carrying the transgene were identified. In vivo imaging and luciferase assays in tissue lysates revealed that CDCA8 promoter was highly activated and drove robust luciferase expression in testes. Subsequently, immunohistochemical and immunofluorescent staining showed that in adult transgenic testes, the expression of luciferase was restricted to a subset of spermatogonia that were located along the basement membrane and positive for the expression of GFRA1, a consensus marker for early undifferentiated spermatogonia. These findings for the first time indicate that the CDCA8 was transcriptionally activated in testis and thus may play a role in adult spermatogenesis. Moreover, the 1-kb CDCA8 promoter could be used for spermatogonia-specific gene expression in vivo and the transgenic lines constructed here could also be used for recovery of spermatogonia from adult testes.

Assembly and operation of an imaging system for long-term monitoring of bioluminescent and fluorescent reporters in plants

BACKGROUND

Non-invasive reporter systems are powerful tools to query physiological and transcriptional responses in organisms. For example, fluorescent and bioluminescent reporters have revolutionized cellular and organismal assays and have been used to study plant responses to abiotic and biotic stressors. Integrated, cooled charge-coupled device (CCD) camera systems have been developed to image bioluminescent and fluorescent signals in a variety of organisms; however, these integrated long-term imaging systems are expensive.

RESULTS

We have developed self-assembled systems for both growing and monitoring plant fluorescence and bioluminescence for long-term experiments under controlled environmental conditions. This system combines environmental growth chambers with high-sensitivity CCD cameras, multi-wavelength LEDs, open-source software, and several options for coordinating lights with imaging. This easy-to-assemble system can be used for short and long-term imaging of bioluminescent reporters, acute light-response, circadian rhythms, delayed fluorescence, and fluorescent-protein-based assays in vivo.

CONCLUSIONS

We have developed two self-assembled imaging systems that will be useful to researchers interested in continuously monitoring in vivo reporter systems in various plant species.

A Fluorescence-Based Reporter Gene Assay to Characterize Nuclear Receptor Modulators

Reporter gene assays are critical tools of nuclear receptor research for characterizing the effects of ligands on nuclear receptor activity. Common luciferase-based techniques require expensive substrates and are typically performed in endpoint format. Here, we describe a versatile reporter gene assay to observe nuclear receptor activity with fluorescent proteins as reporters. This setting is highly cost-efficient and enables observation of nuclear receptor activity over time with multiple measurements from one plate.

Detecting Protein-Protein Interactions Using Bimolecular Fluorescence Complementation (BiFC) and Luciferase Complementation Assays (LCA)

In multicellular organisms, establishing the full body plane involves cell-cell signaling where protein associations are important for the diverse cellular functions within the cells. For the study of protein-protein interactions (PPI), bimolecular fluorescence complementation (BiFC) and luciferase complementation assays (LCA) have proven to be reliable tools that can be used to confirm the physical association of two proteins in a semi-in vivo environment. This chapter provides a detailed description of these two techniques using Nicotiana benthamiana as a semi-in vivo transient expression system. As an example, we will use the interaction of the two well-described transcription factors SHORT-ROOT (SHR) and SCARECROW (SCR), which are known as regulators of asymmetric cell division and stem cell specification in the root meristem of the model plant Arabidopsis thaliana. While the BiFC assay provides subcellular information by displaying a fluorescence signal, nuclear in this case, resulting from the reconstituted fluorophore, the LCA generates a quantitative readout of the SCR-SHR interaction. The combination of both assays provides information on the localization and strength of the PPI.

Convenient site-selective protein coupling from bacterial raw lysates to coenzyme A-modified tobacco mosaic virus (TMV) by Bacillus subtilis Sfp phosphopantetheinyl transferase

A facile enzyme-mediated strategy enables site-specific covalent one-step coupling of genetically tagged luciferase molecules to coenzyme A-modified tobacco mosaic virus (TMV-CoA) both in solution and on solid supports. Bacillus subtilis surfactin phosphopantetheinyl transferase Sfp produced in E. coli mediated the conjugation of firefly luciferase N-terminally extended by eleven amino acids forming a 'ybbR tag' as Sfp-selective substrate, which even worked in bacterial raw lysates. The enzymes displayed on the protein coat of the TMV nanocarriers exhibited high activity. As TMV has proven a beneficial high surface-area adapter template stabilizing enzymes in different biosensing layouts in recent years, the use of TMV-CoA for fishing ybbR-tagged proteins from complex mixtures might become an advantageous concept for the versatile equipment of miniaturized devices with biologically active proteins. It comes along with new opportunities for immobilizing multiple functionalities on TMV adapter coatings, as desired, e.g., in handheld systems for point-of-care detection.

Two Complementary Strategies to Quantitate Extracellular Vesicle Uptake Using Bioluminescence and Non-Lipidic Dyes

The study of the molecular mechanisms controlling extracellular vesicle uptake by a target cell is an aspect of great interest within the EV community due to EV relevance in intercellular communication for tissue homeostasis or different disease progressions such as cancer or Alzheimer's. Since the EV field is relatively young, standardization of techniques for even basic aspects such as their isolation and characterization is still under development and debate. So it is for the study of EV uptake, where the currently most used strategies have critical limitations. Newly designed techniques should try to discern the uptake events from the surface EV binding or to improve the sensitivity and fidelity of the assays. Here, we describe two different complementary methods to measure and quantify EV uptake that we believe, help to overcome certain limitations of the currently used techniques. One is based on a mEGFP-Tspn-Rluc construct, to sort these two reporters into EVs. The use of bioluminescence signal to measure EV uptake allows for a better sensitivity, discerns EV binding from uptake, and allows kinetics measurement in alive cells, being compatible with a high-throughput screen format. The second one is a flow cytometry assay based in EV staining with a maleimide conjugated with a fluorophore, a chemical compound that covalently binds to proteins within sulfhydryl residues, being a good alternative to lipidic dyes and compatible with flow cytometry sorting of cell populations that have captured the labeled EVs.

In Embryo Gene Reporter Assays for Evaluation of Cis-Regulatory Regions

Gene expression reporter assays measure the relevance of cis-regulatory elements and DNA-binding proteins in modulating transcriptional activity. Commonly, they are performed in cell lines. However, regulation of transcriptional activity during development is complex and dynamic, and not many cell lines reproduce the embryonic conditions. Thus, conclusions derived from cell line data provide limited information about embryonic development. On the other hand, one of the major hurdles for embryonic assays is delivering reporter plasmids in a tissue-specific manner. In this sense, the chick embryo is a good model system to perform these assays. Electroporation of chick embryos provides temporal and spatially controlled plasmid delivery. Further, it is a well-established, easy, and an economical procedure. Here, we describe in detail how to measure in the chick neural tube (1) enhancer activity with GFP, (2) enhancer activity with luciferase, and (3) 3'UTR activity with luciferase.

Characterization of SARS-CoV-2 Glycoprotein Using a Quantitative Cell-Cell Fusion System

Coronaviruses (CoVs) infect host cells through the fusion of viral and cellular membrane and may also spread to the neighboring uninfected cells from infected cells through cell-cell fusion. The viral spike (S) glycoproteins play an essential role in mediating membrane fusion. Here, we present a luciferase-based quantitative assay to measure the efficiency of cell-cell fusion mediated by the S protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This method applies to S proteins of the other coronaviruses and can be adapted to fusion proteins of other enveloped viruses.

Constitutive glucose dehydrogenase elevates intracellular NADPH levels and luciferase luminescence in Bacillus subtilis

BACKGROUND

Genetic modifications in Bacillus subtilis have allowed the conversion of myo-inositol into scyllo-inositol, which is proposed as a therapeutic agent for Alzheimer's disease. This conversion comprises two reactions catalyzed by two distinct inositol dehydrogenases, IolG and IolW. The IolW-mediated reaction requires the intracellular regeneration of NADPH, and there appears to be a limit to the endogenous supply of NADPH, which may be one of the rate-determining factors for the conversion of inositol. The primary mechanism of NADPH regeneration in this bacterium remains unclear.

RESULTS

The gdh gene of B. subtilis encodes a sporulation-specific glucose dehydrogenase that can use NADP⁺ as a cofactor. When gdh was modified to be constitutively expressed, the intracellular NADPH level was elevated, increasing the conversion of inositol. In addition, the bacterial luciferase derived from Photorhabdus luminescens became more luminescent in cells in liquid culture and colonies on culture plates.

CONCLUSION

The results indicated that the luminescence of luciferase was representative of intracellular NADPH levels. Luciferase can therefore be employed to screen for mutations in genes involved in NADPH regeneration in B. subtilis, and artificial manipulation to enhance NADPH regeneration can promote the production of substances such as scyllo-inositol.

Robustness of NanoBiT luciferase complementation technology in the presence of widely used kinase inhibitors

Bioluminescence assays using luciferase enzymes are widely used in research to monitor gene expression and an array of other cell properties, and split luciferase enzymes can be used to measure protein interactions in biochemical assays and in living cells. When these methods are employed in chemical library screening efforts, it is vital that the activity of the luciferase enzyme itself is not strongly influenced by library components. Here, we developed a NanoBiT split luciferase assay to measure phosphorylation of Histone H3 peptides and used it to test the robustness of split luciferase to interference from two libraries of commonly used kinase inhibitors, including the Kinase Chemogenomic Set (KCGS). We found that NanoBiT luciferase is not significantly affected by the great majority of kinase inhibitors tested. However, the weak inhibition observed for a small minority of kinase inhibitors encourages the inclusion of suitable controls in NanoBiT (or NanoLuc) assays.

Novel fluorescent and secreted transcriptional reporters for quantifying activity of the xenobiotic sensor aryl hydrocarbon receptor (AHR)

Aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that plays a critical role in diverse biological processes, including xenobiotic metabolism, carcinogenesis, and physiological functions such as regulation of the immune system and cell differentiation. To improve studies of AHR activity, we constructed two new reporter genes: a fluorescent GFP-tagged histone 2B (XRE-H2B-eGFP) and a secreted nanoluciferase (XRE-pNL1.3[secNluc]). Here, we demonstrate how these reporters can be used to monitor AHR activity in different types of cells, including human primary trophoblasts and cell lines, following incubation with a strong AHR ligand, benzo[a]pyrene (B[a]P), or an AHR inhibitor (CH223191). Compared to vehicle control cells, a significant increase in AHR activity was observed in cells treated with 0.5 and/or 2 µM B[a]P and a significant decrease was detected in response to treatment with 3 µM CH223191. These new plasmids have great potential for use in a variety of applications, such as screening for endogenous or exogenous ligands of AHR.

Monitoring autochthonous lung tumors induced by somatic CRISPR gene editing in mice using a secreted luciferase

Background

In vivo gene editing of somatic cells with CRISPR nucleases has facilitated the generation of autochthonous mouse tumors, which are initiated by genetic alterations relevant to the human disease and progress along a natural timeline as in patients. However, the long and variable, orthotopic tumor growth in inner organs requires sophisticated, time-consuming and resource-intensive imaging for longitudinal disease monitoring and impedes the use of autochthonous tumor models for preclinical studies.

Methods

To facilitate a more widespread use, we have generated a reporter mouse that expresses a Cre-inducible luciferase from Gaussia princeps (GLuc), which is secreted by cells in an energy-consuming process and can be measured quantitatively in the blood as a marker for the viable tumor load. In addition, we have developed a flexible, complementary toolkit to rapidly assemble recombinant adenoviruses (AVs) for delivering Cre recombinase together with CRISPR nucleases targeting cancer driver genes.

Results

We demonstrate that intratracheal infection of GLuc reporter mice with CRISPR-AVs efficiently induces lung tumors driven by mutations in the targeted cancer genes and simultaneously activates the GLuc transgene, resulting in GLuc secretion into the blood by the growing tumor. GLuc blood levels are easily and robustly quantified in small-volume blood samples with inexpensive equipment, enable tumor detection already several months before the humane study endpoint and precisely mirror the kinetics of tumor development specified by the inducing gene combination.

Conclusions

Our study establishes blood-based GLuc monitoring as an inexpensive, rapid, high-throughput and animal-friendly method to longitudinally monitor autochthonous tumor growth in preclinical studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12943-022-01661-2.

Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p13.1

Genome-wide association studies have identified 2p13.1 as a prominent susceptibility locus for systemic lupus erythematosus (SLE)—a complex, multisystem autoimmune disease. However, the identity of underlying causal variant (s) and molecular mechanisms for increasing disease susceptibility are poorly understood. Using meta-analysis (cases = 10,252, controls = 21,604) followed by conditional analysis, bioinformatic annotation, and eQTL and 3D-chromatin interaction analyses, we computationally prioritized potential functional variants and subsequently experimentally validated their effects. Ethnicity-specific meta-analysis revealed striking allele frequency differences between Asian and European ancestries, but with similar odds ratios. We identified 20 genome-wide significant (p < 5 × 10−8) variants, and conditional analysis pinpointed two potential functional variants, rs6705628 and rs2272165, likely to explain the association. The two SNPs are near DGUOK, mitochondrial deoxyguanosine kinase, and its associated antisense RNA DGUOK-AS1. Using luciferase reporter gene assays, we found significant cell type- and allele-specific promoter activity at rs6705628 and enhancer activity at rs2272165. This is supported by ChIP-qPCR showing allele-specific binding with three histone marks (H3K27ac, H3K4me3, and H3K4me1), RNA polymerase II (Pol II), transcriptional coactivator p300, CCCTC-binding factor (CTCF), and transcription factor ARID3A. Transcriptome data across 28 immune cell types from Asians showed both SNPs are cell-type-specific but only in B-cells. Splicing QTLs showed strong regulation of DGUOK-AS1. Genotype-specific DGOUK protein levels are supported by Western blots. Promoter capture Hi-C data revealed long-range chromatin interactions between rs2272165 and several nearby promoters, including DGUOK. Taken together, we provide mechanistic insights into how two noncoding variants underlie SLE risk at the 2p13.1 locus.

In Vivo Bioluminescence Analyses of Circadian Rhythms in Arabidopsis thaliana Using a Microplate Luminometer

Our understanding of the circadian clock function in plants has been markedly assisted by studies with the model species Arabidopsis thaliana. Molecular and genetics approaches have delivered a comprehensive view of the transcriptional regulatory networks underlying the Arabidopsis circadian system. The use of the luciferase as a reporter allowed the precise in vivo determination of circadian periods, phases, and amplitudes of clock promoter activities with unprecedented temporal resolution. An increasing repertoire of fine-tuned luciferases together with additional applications such as translational fusions or bioluminescence molecular complementation assays have considerably expanded our view of circadian protein expression and activity, far beyond transcriptional regulation. Further applications have focused on the in vivo simultaneous examination of rhythms in different parts of the plant. The use of intact versus excised plant organs has also provided a glimpse on both the organ-specific and autonomy of the clocks and the importance of long distance communication for circadian function. This chapter provides a basic protocol for in vivo high-throughput monitoring of circadian rhythms in Arabidopsis seedlings using bioluminescent reporters and a microplate luminometer.

Restoration of the Indicator Properties of Whole-cell Luminescent Biosensors

Whole-cell biosensors are widely used to produce medical diagnostic tests, but in the long term, they tend to lose their indicator properties. Consequently, it is crucial to find ways to restore these properties and prolong the shelf life of the tests. Here, we propose to use electromagnetic radiation with optimally selected parameters of frequency, power, and exposure time. The impact of radiation parameters on biosensor luminescence was studied as well as the effects of different types of radiation coming from laser sources (λ = 875 nm), a LED source (λ = 850 ÷ 890 nm), and microwave units (at frequencies 42.22, 53.53, 61.18 и 34 ÷ 38 GHz). IR treatment resulted in dose-dependent suppression of biosensor luminescence. The luminescence level when exposed to microwave radiation depends on the radiation time and frequency. Also, it has been found that optimal selection of the main radiation parameters enables to restore indicator properties partially lost by biosensors during storage. We explain the mechanism responsible for the sensitizing effect of radiation, which implies the polarization of solvent dipoles and changes in mobility of acceptor molecules. This, in turn, leads to a shift in the chemical equilibrium states and triggers a cascade of biochemical reactions that lead to restoration of the lost indicator properties of biosensors. The study of antagonistic activity has revealed that restored biosensors provide reliable test results after the expiration of their warranty period.

Cloning and molecular properties of a novel luciferase from the Brazilian Bicellonycha lividipennis (Lampyridae: Photurinae) firefly: comparison with other firefly luciferases

Several firefly luciferases eliciting light emission in the yellow-green range of the spectrum and with distinct kinetic properties have been already cloned, sequenced, and characterized. Some of them are currently being applied as analytical reagents and reporter genes for bioimaging and biosensors, and more recently as potential color tuning indicators of intracellular pH and toxic metals. They were cloned from the subfamilies Lampyrinae (Photinini: Photinus pyralis, Macrolampis sp2; Cratomorphini: Cratomorphus distinctus), Photurinae (Photuris pennsylvanica), Luciolinae (Luciola cruciata, L. lateralis, L. mingrelica, L. italica, Hotaria parvula), and Amydetinae (Amydetes vivianii) occurring in different parts of the world. The largest number has been cloned from fireflies occurring in Brazilian biomes. Taking advantage of the large biodiversity of fireflies occurring in the Brazilian Atlantic rainforest, here we report the cloning and characterization of a novel luciferase cDNA from the Photurinae subfamily, Bicellonycha lividipennis, which is a very common firefly in marshlands in Brazil. As expected, multialignements and phylogenetic analysis show that this luciferase clusters with Photuris pennsylvanica adult isozyme, and with other adult lantern firefly luciferases, in reasonable agreement with traditional phylogenetic analysis. The luciferase elicits light emission in the yellow-green region, has kinetics properties similar to other adult lantern firefly luciferases, including pH- and metal sensitivities, but displays a lower sensitivity to nickel, which is suggested to be caused by the natural substitution of H310Y.

Establishment of a luciferase-based method for measuring cancer cell adhesion and proliferation

BACKGROUND

Methods measuring cell proliferation and adhesion are widely used but each hold limitations. We, therefore, introduce novel methods for measuring cell proliferation and adhesion based on CRISPR-modified cancer cell lines secreting luciferase to the growth media.

MATERIALS AND METHODS

Using CRISPR genome editing, we generated stable luciferase-secreting LS174T, HCT 116, Caco-2, and PANC-1 cell lines. The modified cells were seeded, and luciferase activity was measured in the media and compared to Coulter counter cell counts and iCELLigence impedance assay to evaluate the value of the secreted luciferase activities as a measurement for adhesion and proliferation.

RESULTS

Our results demonstrate that luciferase secreted into the media can be used quantifying cell proliferation and adhesion. The adhesion luciferase assay and the iCELLigence impedance assay showed similar results with increased significant difference observed in the luciferase assays. The luciferase proliferation assay showed increased growth following increased serum concentrations in all cell lines vs. only two cell lines in the iCELLigence impedance assay.

CONCLUSIONS

Our results show that the luciferase adhesion and proliferation assays are reliable methods for measuring adhesion and proliferation. The luciferase assays have advantages over existing assays as they are highly sensitive, easy to perform, non-invasive and suitable as high-throughput measurements.

Luciferin Synthesis and Pesticide Detection by Luminescence Enzymatic Cascades

D-Luciferin (D-LH₂ ), a substrate of firefly luciferase (Fluc), is important for a wide range of bioluminescence applications. This work reports a new and green method using enzymatic reactions (HELP, HadA Enzyme for Luciferin Preparation) to convert 19 phenolic derivatives to 8 D-LH₂ analogues with ≈51 % yield. The method can synthesize the novel 5'-methyl-D-LH₂ and 4',5'-dimethyl-D-LH₂ , which have never been synthesized or found in nature. 5'-Methyl-D-LH₂ emits brighter and longer wavelength light than the D-LH₂ . Using HELP, we further developed LUMOS (Luminescence Measurement of Organophosphate and Derivatives) technology for in situ detection of organophosphate pesticides (OPs) including parathion, methyl parathion, EPN, profenofos, and fenitrothion by coupling the reactions of OPs hydrolase and Fluc. The LUMOS technology can detect these OPs at parts per trillion (ppt) levels. The method can directly detect OPs in food and biological samples without requiring sample pretreatment.

Fuchs Endothelial Corneal Dystrophy associated risk variant, rs3768617 in LAMC1 shows allele specific binding of GFI1B

AIMS

To investigate the genetic and functional association of an intronic variant of LAMC1, rs3768617 with Fuchs endothelial corneal dystrophy (FECD) in the Indian population.

METHODS

Blood samples were collected from age and sex matched 356 controls and 120 FECD patients after a detailed assessment via specular microscopy. Genomic DNA was extracted and genotyping was done by fluorescence based capillary electrophoresis. The genetic association of rs3768617 polymorphisms was computed by the chi-square (χ²) test. Bioinformatics studies were performed to find the allele specific binding of different transcription factors in the region of rs3768617 and functional evaluation assessed by luciferase assay followed by Electrophoretic Mobility Shift Assay (EMSA) and Chromatin Immunoprecipitation assay (ChIP). Immunofluorescence assay was carried out to check for any differential expression of GFI1B between control and FECD endothelium samples.

RESULTS

SNP rs3768617 {chr1:183123365 (GRCh38.p13)} was found to be genetically associated with FECD in Indian population (p = 2.646 × 10^-8). Luciferase assay suggested that the rs3768617 locus has a regulatory role. In silico analysis showed that the transcription factor, GFI1B binds to the risk allele 'G' of rs3768617, but not to the protective allele 'A' which was also experimentally validated by EMSA. High enrichment of DNA flanking the surrounding region of rs3768617 was also found in presence of GFI1B specific antibody in ChIP assay. There was a 0.63 fold decrease in GFI1B expression in FECD affected corneal endothelium compared to control endothelium.

CONCLUSIONS

The genetic association of rs3768617 in LAMC1 with FECD pathogenesis is mediated by GFI1B, thus finding the functional role of LAMC1 in FECD pathogenesis.

CYP19A1 Promoters Activity in Human Granulosa Cells: A Comparison between PCOS and Normal Subjects

Objective

Estrogen, a female hormone maintaining several critical functions in women's physiology, e.g., folliculogenesis and fertility, is predominantly produced by ovarian granulosa cells where aromatase enzyme converts androgen to estrogen. The principal enzyme responsible for this catalytic reaction is encoded by the CYP19A1 gene, with a long regulatory region. Abnormalities in this process cause metabolic disorders in women, one of the most common of which is polycystic ovary syndrome (PCOS). The main purpose of this research was to determine the effect of the promoters on aromatase expression in cells with normal and PCOS characteristics.

Materials and Methods

In this experimental study, four promoters of the CYP19A1 gene, including PII, I.3, I.4, and PII/ I .3 promoter fragments, were cloned upstream of the luciferase gene and transfected into normal and PCOS granulosa cells. Subsequently, the effect of follicle-stimulating hormone (FSH) on the activity of these regulatory regions was examined in the presence and absence of FSH. Western blotting was used to confirm aromatase expression in all groups. Data analysis was performed using ANOVA and paired sample t test, compared by post-hoc least significant difference (LSD) test.

Results

Luciferase results confirmed the intense activity of PII promoter in the presence of FSH. Moreover, the study demonstrated reduced activity of PII promoter in normal granulosa cells, possibly due to the regulatory region of I.3 next to PII.

Conclusion

FSH stimulates transcription of aromatase enzyme by affecting PII promoter, a process regulated by the inhibitory role of the I.3 region in PII activity in granulosa cells. Given the distinct role of these promoters in normal and PCOS granulosa cells, the importance of nuclear factors residing in these regions can be discerned.

Method for quantification of porcine type I interferon activity using luminescence, by direct and indirect means

BACKGROUND

Type I interferons are widely used in research applications and as biotherapeutics. Current assays used to measure interferon concentrations, such as plaque reduction assays and ELISA, are expensive, technically challenging, and may take days to provide results. We sought to develop a robust and rapid assay to determine interferon concentrations produced from transiently transfected cell cultures.

METHOD

Indirect quantification of recombinant interferon was evaluated using a novel bi-cistronic construct encoding the Foot-and-mouth disease virus 2A translational interrupter sequence to yield equimolar expression of Gaussia princeps luciferase and porcine interferon α. Direct quantification was evaluated by expression of a novel fusion protein comprised of Gaussia princeps luciferase and porcine type I interferon. Plasmids encoding constructs are transiently transfected into cell cultures and supernatant harvested for testing of luminescence, ELISA determined concentration, and anti-viral activity against vesicular stomatitis virus.

RESULTS

Bi-cistronic constructs, utilized for indirect quantification, demonstrate both luciferase activity and anti-viral activity. Fusion proteins, utilized for direct quantification, retained secretion and luminescence however only the interferon α fusion protein had antiviral activity comparable to wildtype porcine interferon α. A strong linear correlation was observed between dilution and luminescence for all compounds over a dynamic range of concentrations.

CONCLUSION

The correlation of antiviral and luciferase activities demonstrated the utility of this approach, both direct and indirect, to rapidly determine recombinant interferon concentrations. Concentration can be determined over a more dynamic concentration range than available ELISA based assays using this methodology.

Real-time monitoring of immediate drug response and adaptation upon repeated treatment in a microfluidic chip system

Microfluidic tissue culture and organ-on-a-chip models provide efficient tools for drug testing in vivo and are considered to become the basis of in vitro test systems to analyze drug response, drug interactions and toxicity to complement and reduce animal testing. A major limitation is the efficient recording of drug action. Here we present an efficient experimental setup that allows long-term cultivation of cells in a microfluidic system in combination with continuous recording of luciferase reporter gene expression. The system combines a sensitive cooled luminescence camera system in combination with a custom build miniaturized incubation chamber. The setup allows to monitor time-dependent activation, but also the end of drug response. Repeated activation and recovery as well as varying durations of drug treatment periods can be monitored, and different modes of drug activity can be visualized.

Split-luciferase complementary assay of NLRP3 PYD-PYD interaction indicates inflammasome formation during inflammation

The NLRP3 inflammasome is a key macromolecular complex of the innate immune system that activates the inflammatory signalling cascade in response to a wide range of stimuli. Structural studies have shown that the intracellular cytosolic receptor NLRP3 oligomerizes upon stimulation and serves as a scaffold to form the ASC filaments necessary for procaspase-1 activation. Despite the abundant structural evidences on NLRP3 inflammasome, the interactions of the NLRP3 Pyrin domain and its functional relevance are poorly understood. In this study, the split luciferase complementation assay is used as an alternative approach to investigate NLRP3^PYD-NLRP3^PYD interactions during inflammasome formation. Since the homotypic NLRP3 interaction is mainly based on electrostatic interactions, a phosphomimetic residue (S5) at the interface of the NLRP3^PYDs interactions has been mutated to show a disruptive effect on luciferase activity. According to the results presented, the designed biosensor was able to monitor the NLRP3^PYD-NLRP3^PYD interaction in vitro. The current reporter assay not only provides a specific NLRP3^PYD-NLRP3^PYD assay to study the PYD-PYD interaction in vitro, but also provides a suitable system for screening chemicals and drugs to identify activators and inhibitors of NLRP3.

A biochemiluminescent assay for rapid diagnosis of influenza

A biochemiluminescent assay of influenza diagnosis is presented. The assay diagnoses influenza based on detection of the influenza viral neuraminidase activity. An instrument designed for the assay is also reported. This assay solves the problem that current influenza virus diagnosis assays are susceptible to virus mutation. A luciferase-based complex is synthesized as biochemiluminescent substrate. The substrate is cleaved to free luciferin with presence of influenza neuraminidase in specimen. Luciferase is oxidized to oxyluciferin with luciferin as catalyzer resulting in luminescence, which is proportional to the neuraminidase activity and measured by instrument. The instrument uses a photomultiplier tube as sensor, with 24 test channels. Fine optical arrangements enable the instrument with high sensitivity and accuracy. A total of 389 clinical specimens were collected to evaluate the performance of the assay in clinical settings. This assay had a sensitivity and specificity of 95.92% (95% confidence interval 91.38-98.12%) and 97.93% (95% confidence interval 95.26-99.11%), respectively, compared to the colloidal gold assay. As a biochemiluminscence assay, this assay is advantageous in sensitivity and specificity. It does not require any washing or separation steps, which makes the instrument simple in design and easy to operate or maintenance. The assay is suitable for the rapid diagnosis of influenza virus in point-of-care settings.

Dopamine D2L receptor density influences the recruitment of β-arrestin2 and Gi1 induced by antiparkinsonian drugs

INTRODUCTION

Brain imaging studies have highlighted that the density of dopamine D₂ receptors markedly fluctuates across the stages of Parkinson's disease and in response to pharmacological treatment. Moreover, receptor density constitutes a molecular determinant for the signaling profile of D₂ receptor ligands. We therefore hypothesized that variations in receptor expression could influence D₂ receptor response to antiparkinsonian drugs, most notably with respect to the recruitment bias between G_i1 and β-arrestin2.

METHODS

The recruitment bias of dopamine, pramipexole, ropinirole, and rotigotine was examined using a nanoluciferase-based biosensor for probing the interactions of the D_2L receptor with either G_i1 or β-arrestin2. The characterization of the functional selectivity of these D₂ receptor agonists was performed at two distinct D_2L receptor densities by taking advantage of a cell model carrying an inducible system that enables the overexpression of the D_2L receptor when exposed to doxycycline.

RESULTS

A high receptor density oriented the balanced signaling profile of dopamine towards a preferential recruitment of G_i1. It also moderated the marked G_i1 and β-arrestin2 biases of pramipexole and rotigotine, respectively. At variance, the G_i1 bias of ropinirole appeared as not being influenced by D_2L receptor density.

CONCLUSIONS

Taken together, these observations highlight receptor density as a key driver of the signaling transducer recruitment triggered by antiparkinsonian agents. Moreover, given the putative beneficial properties of β-arrestin2 in promoting locomotion, this study provides molecular insights that position the arrestin-biased ligand rotigotine as a putatively more beneficial D₂ receptor agonist for the treatment of early and late Parkinson's disease.

High Spatial Resolution Luciferase Imaging of the Arabidopsis thaliana Circadian Clock

The A. thaliana circadian clock is an example of a gene network that generates rich temporal and spatial dynamics. Bioluminescent imaging has proven a powerful method to help dissect the genetic mechanisms that generate oscillations of gene expression over the course of the day. However, its use for the study of spatial regulation is often limited by resolution. Here, we describe a modified luciferase imaging method for the study of the Arabidopsis circadian clock across the plant at sub-tissue-level resolution.

Use of BRET to Measure β-Arrestin Recruitment at Oxytocin and Vasopressin Receptors

Bioluminescence resonance energy transfer (BRET) is a cutting-edge biophysical technique used for exploring G protein-coupled receptor (GPCR) pharmacology. BRET relies on the nonradiative energy transfer from a luciferase energy donor to an acceptor fluorophore after oxidation of a luciferase substrate. This energy transfer occurs only if the donor and acceptor are within close proximity. Over the past few years, BRET has been successfully applied to study GPCR oligomerization as well as interactions of receptors with G proteins, G protein-coupled receptor kinases (GRKs), or β-arrestins. Herein, we describe how BRET can be applied to study signaling at the oxytocin receptor (OTR) and vasopressin receptors, thereby enabling the identification of (biased) ligands and molecular probes for investigating receptor functionality.

Time-Lapse Bioluminescence Imaging of Hes7 Expression In Vitro and Ex Vivo

Somites are formed sequentially by the segmentation of the anterior parts of the presomitic mesoderm (PSM), and such periodical somite formation is crucial to ensure the proper vertebrae. In the mouse embryo, Hes7, a segmentation clock gene, controls this periodic event with new somites forming every 2 h. Hes7 oscillations are synchronized between neighboring PSM cells and propagate from the posterior to the anterior PSM in the form of traveling waves. However, the exact mechanisms that generate these oscillatory dynamics and control synchronization are still unclear. Given that the half-life of Hes7 is too short to be monitored with most fluorescent proteins, time-lapse bioluminescence imaging (BLI) is a suitable tool to monitor the chronological Hes7 expression dynamics. In this chapter, we introduce a ubiquitinated luciferase reporter which enables the visualization of Hes7 expression dynamics with high temporal and spatial resolution in living cells and tissues.

Identifying CAR Modulators Utilizing a Reporter Gene Assay

The constitutive androstane receptor (CAR, NR1I3) controls the transcription of numerous hepatic drug metabolizing enzymes and transporters. There are two possible methods of activation for CAR, direct ligand binding and a ligand-independent method, which makes this a unique nuclear receptor. Both mechanisms require the translocation of CAR from the cytoplasm into the nucleus. Interestingly, CAR is constitutively active and spontaneously localized in the nucleus of most immortalized cell lines. This creates an important challenge in most in vitro assay models because immortalized cells cannot be used without inhibiting the high basal activity. In this book chapter, we go into detail of how to perform quantitative high-throughput screens to identify human CAR modulators through the employment of a double stable cell line. Using this line, we can identify activators, as well as deactivators, of the challenging nuclear receptor, CAR.

Bioluminescent Tracking of Human Induced Pluripotent Stem Cells In Vitro and In Vivo

The discovery and development of induced pluripotent stem cells (iPSCs) opened a novel venue for disease modeling, drug discovery, and personalized medicine. Additionally, iPSCs have been utilized for a wide variety of research and clinical applications without immunological and ethical concerns that arise from using embryonic stem cells. Understanding the in vivo behavior of iPSCs, as well as their derivatives, requires the monitoring of their localization, proliferation, and viability after transplantation. Bioluminescence imaging (BLI) gives investigators a non-invasive and sensitive means for spatio-temporal tracking in vivo. For scientists working within the field of iPSCs, this protocol provides a walk-through on how to conduct in vitro and in vivo experiments with an iPSCs constitutively expressing luciferase.

A Simple and Rapid Bioluminescence-Based Functional Assay of Organic Anion Transporter 1 as a D-Luciferin Transporter

Organic anion transporter 1 (SLC22A6/OAT1) plays a key role in renal tubular excretion of endo- and exogenous anionic substances including drugs. Since the inhibition of OAT1 function by a concomitant drug may cause pharmacokinetic drug-drug interactions (DDIs) in clinical practice, an in vitro uptake study to evaluate the inhibition potency of OAT1 is useful for the prediction and avoidance of DDIs and recommended for drug candidates in drug development. In this chapter, we describe a rapid and highly sensitive functional assay of OAT1 based on bioluminescence (BL) detection using D-luciferin as a substrate in living cells. The principle of measurement simply relies on the biochemical feature of D-luciferin to be recognized as a substrate of OAT1, and the BL intensity depending on intracellular D-luciferin level and luciferase activity, thereby allowing the quantitative analysis of OAT1-mediated D-luciferin transport. The BL measurement can be completed within 1 min without experimental procedures for removing extracellular uptake solution and washing cells, both of which involve in the conventional uptake studies using isotope-labeled or fluorescent compounds. The present method is applicable to high-throughput screening to identify and avoid potential OAT1 inhibitors in drug development.