Cell cycle regulation of the psoriasis associated gene CCHCR1 by transcription factor E2F1.

The coiled-coil alpha-helical rod protein 1 (CCHCR1) was first identified as a candidate gene in psoriasis and has lately been found to be associated with a wide range of clinical conditions including COVID-19. CCHCR1 is located within P-bodies and centrosomes, but its exact role in these two subcellular structures and its transcriptional control remain largely unknown. Here, we showed that CCHCR1 shares a bidirectional promoter with its neighboring gene, TCF19. This bidirectional promoter is activated by the G1/S-regulatory transcription factor E2F1, and both genes are co-induced during the G1/S transition of the cell cycle. A luciferase reporter assay suggests that the short intergenic sequence, only 287 bp in length, is sufficient for the G1/S induction of both genes, but the expression of CCHCR1 is further enhanced by the presence of exon 1 from both TCF19 and CCHCR1. This research uncovers the transcriptional regulation of the CCHCR1 gene, offering new perspectives on its function. These findings contribute to the broader understanding of diseases associated with CCHCR1 and may serve as a foundational benchmark for future research in these vital medical fields.

Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration.

Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well known for their regeneration capacity. However, how non-coding RNAs such as microRNAs (also known as miRNAs) contribute to cnidarian tissue regeneration is poorly understood. Here, we sequenced and assembled the genome of the sea anemone Exaiptasia pallida collected in Hong Kong waters. The assembled genome size of E. pallida is 229.21 Mb with a scaffold N50 of 10.58 Mb and BUSCO completeness of 91.1%, representing a significantly improved genome assembly of this species. The organization of ANTP-class homeobox genes in this anthozoan further supported the previous findings in jellyfishes, where most of these genes are mainly located on three scaffolds. Tentacles of E. pallida were excised, and both mRNA and miRNA were sequenced at 9 time points (0 h, 6 h, 12 h, 18 h, 1 day, 2, 3, 6, and 8 days) from regenerating tentacles. In addition to the Wnt signaling pathway and homeobox genes that are shown to be likely involved in tissue regeneration as in other cnidarians, we have shown that GLWamide neuropeptides, and for the first time sesquiterpenoid pathway genes could potentially be involved in the late phase of cnidarian tissue regeneration. The established sea anemone model will be useful for further investigation of biology and evolution in, and the effect of climate change on this important group of animals.

Toxic effects of octocrylene on zebrafish larvae and liver cell line (ZFL).

Octocrylene (OC) is a broad-spectrum ultraviolet-absorbing chemical used in sunscreen and other personal care products. Its health effects are a concern because it has been detected in water, fish, humans, and food chains. In vivo and in vitro investigations were performed in zebrafish (Danio rerio) larvae and a zebrafish liver cell line (ZFL), respectively, to understand the potential risks and molecular mechanisms of OC toxicity. The 96-h median lethal concentration (LC50) of OC was determined to be 251.8 µM in larvae and 5.5 µM in ZFL cells. Quantitative real-time PCR (qRT-PCR) showed that OC induced the expression of genes for CYPs (CYP1A, CYP3A65), estrogen receptors (ERα, ERß1, GPER), vitellogenin (VTG1), and sex determination (BRCA2, CYP19A, DMRT1, SOX9A), both in vitro and in vivo. A whole-transcriptome sequencing method was used to evaluate the gene expression profile of larvae exposed to OC. OC was found to mediate the biosynthesis of estrogens (such as estriol) and affect the antioxidant pathway (glutathione transferases and peroxisome). These findings clarify the toxic effects and molecular mechanisms of OC and support banning its use in cosmetics.

Promotion of cadmium uptake and cadmium-induced toxicity by the copper transporter CTR1 in HepG2 and ZFL cells.

Cadmium (Cd2+) is considered a human carcinogen as it causes oxidative stress and alters DNA repair responses. However, how Cd2+ is taken up by cells remains unclear. We hypothesized that Cd2+ could be transported into cells via a membrane copper (Cu) transporter, CTR1. CTR1 expression was not affected by Cd2+ exposure at the mRNA or protein level. Stable cell lines overexpressing either hCTR1, in the human liver cell line HepG2, or zCTR1, in the zebrafish liver cell line ZFL, were created to study their responses to Cd2+ insult. It was found that both HepG2 and ZFL cells overexpressing CTR1 had higher Cd2+ uptake and thus became sensitive to Cd2+. In contrast, hCTR1 knockdown in HepG2 cells led to a reduced uptake of Cd2+, making the cells relatively resistant to Cd2+. Localization studies revealed that hCTR1 had a clustered pattern after Cd2+ exposure, possibly in an attempt to reduce both Cd2+ uptake and Cd2+-induced toxicity. These in vitro results indicate that CTR1 can transport Cd2+ into the cell, resulting in Cd2+ toxicity.

Whole-transcriptome sequencing (RNA-seq) study of the ZFL zebrafish liver cell line after acute exposure to Cd2+ ions.

Cadmium (Cd) is a non-essential metal with no known biological function and a broad range of toxic effects in biological systems. We used whole-transcriptome sequencing (RNA-seq) to study the effects of Cd2+ toxicity in zebrafish liver cells, ZFL. The results of an RNA-Seq analysis of ZFL cells exposed to 5, 10 or 20 µM Cd2+ for 4- or 24-h. The differentially expressed genes affected by Cd2+ were analyzed by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to study the regulated pathways. Cd2+ regulated the expression of genes associated with cellular Cu, Zn, and Fe homeostasis, DNA replication leading to cell cycle arrest and apoptosis, and glutathione metabolism. Cd2+ boosted up the amino acid synthesis, possibly to support the glutathione metabolism for tackling the oxidative stress generated from Cd2+. Cd2+ stimulation was similar to heat or xenobiotics, based on the responses from ZFL such as endoplasmic reticulum stress and protein folding. We linked also those finding of gene activations relating to carcinogenesis of Cd. This paper provides a comprehensive analysis of the expression profiles induced by Cd2+ exposure in ZFL cells, as well as useful insights into the specific toxic effects.

Oxidative stress and apoptotic effects of copper and cadmium in the zebrafish liver cell line ZFL.

Copper (Cu) and cadmium (Cd) are widely used in industrial activities, resulting in Cu and Cd contamination in aquatic systems worldwide. Although Cu plays an essential role in many biological functions, an excessive amount of the metal causes cytotoxicity. In contrast, Cd is a non-essential metal that usually co-exists with Cu. Together, they cause oxidative stress in cells, leading to cell damage. These metal ions are also believed to cause cell apoptosis. In this study, we used a zebrafish liver cell line, ZFL, to study combined Cu and Cd cytotoxicity. Although Cd is more toxic than Cu, both were found to regulate the expression of oxidative stress related genes, and neither significantly altered the activity of oxidative stress related enzymes. Co-exposure tests with the antioxidant N-acetyl-l-cysteine and the Cu chelator bathocuproinedisulfonic acid disodium salt demonstrated that Cd toxicity was due to the oxidative stress caused by Cu, and that Cu at a low concentration could in fact exert an antioxidant effect against the oxidative stress in ZFL. Excessive Cu concentration triggered the expression of initiator caspases (caspase 8 and caspase 9) but suppressed that of an executioner caspase (caspase 3), halting apoptosis. Cd could only trigger the expression of initiator caspases; it could not halt apoptosis. However, a low concentration of Cu reduced the mitochondrial superoxide level, suppressing the Cd-induced apoptotic effects in ZFL.

Microplastics from effluents of sewage treatment works and stormwater discharging into the Victoria Harbor, Hong Kong.

Sewage treatment works and stormwater outfalls were identified as sources of microplastics in the Victoria Harbor, Hong Kong. Local treated sewage and stormwater effluents contained up to 10,816 pieces per m3 of microplastics, mainly polyethylene (PE) and polypropylene (PP), being discharged at an average rate of 3.5 mg per capita daily. Bioaccumulation of microplastics in marine fish collected from the vicinity of the effluent discharge outfalls was also studied. The temporal variations of microplastics in terms of abundance, shape and polymer type in fish were found consistent with those in the effluents and surface water. The abundance of microplastics was significantly higher in March 2017 (dry season). Microplastics in fish were predominantly in fiber form and identified as PE and PP. The observed temporal variations suggest uptake of microplastics by fish from the treated sewage and stormwater effluents.

Toxic effects and transcriptome analyses of zebrafish (Danio rerio) larvae exposed to benzophenones.

Sunscreen chemicals, such as benzophenones (BPs), are common environmental contaminants that are posing a growing health concern due to their increasing presence in water, fish, and human systems. Benzoresorcinol (BP1), oxybenzone (BP3), and dioxybenzone (BP8) are the most commonly used BPs for their ability to protect from sunburn by absorbing a broad spectrum of ultraviolet radiation. In this study, zebrafish larvae were used as an in vivo model to investigate the potential risks and molecular mechanisms of the toxic effects of BPs. The effects of these BPs on the gene expression in the aryl hydrocarbon receptor pathway, estrogen receptor pathway, and sex differentiation were detected using quantitative real-time PCR. All BPs were found to function as agonists of the estrogen receptors α and ß1, indicating that these BPs likely undergo similar molecular metabolism in vivo, whereby they can activate cytochrome P450 genes and promote the expression of CYP19A and DMRT1. Furthermore, the gene expression profile of larvae after BP3 exposure was evaluated using a whole transcriptome sequencing approach. BP3 affected estradiol biosynthesis and sex differentiation. It also regulated gonadotropin-releasing hormone, thus interfering with the endocrine system. As a xenobiotic toxicant, BP3 upregulated the expression of cytochrome P450 genes (CYP1A and CYP3A65) and glutathione metabolism-related genes (GSTA, GSTM, and GSTP). It also interfered with the nervous system by regulating the calcium signaling pathway. These findings will be useful for understanding the toxicity mechanisms and metabolism of BPs in aquatic organisms and promote the regulation of these chemicals in the environment.

Seasonal variation and the distribution of endocrine-disrupting chemicals in various matrices affected by algae in the eutrophic water environment of the pearl river delta, China.

The seasonal variation and distribution among different matrices of endocrine-disrupting chemicals (EDCs) were investigated in the eutrophic water ecosystem of the Pearl River Delta, Guangdong, China. The chlorophyll a (Chl a) levels were generally higher in summer than in spring; however, the concentrations of 4-tert-octylphenol (OP), 4-nonylphenol (NP), and bisphenol A (BPA) in surface water were generally higher in spring (oligotrophic) than in summer (eutrophic). The levels of EDCs in SPM were lower in spring than in summer, a pattern seen in the seasonal variation of Chl a and particulate organic carbon (POC). The seasonal variations of EDCs in water bodies with different levels of eutrophication were analyzed in several dimensions including sediment, POC, algae and fish bile. The log Koc for SPM/water was higher in summer than in spring. The log Koc values for NP, OP, and BPA exhibited the following trends between matrices: colloid/water > sediment/water > SPM/water > algae/water, colloid/water > sediment/water > algae/water > SPM/water, and colloid/water > algae/water > sediment/water > SPM/water. The EDCs levels were different in fish tissues with the order bile > liver > muscle, with the concentrations being an order of magnitude higher in bile than in liver and an order of magnitude higher in liver than in muscle. The sequence of the bioconcentration factor (log BCF) for bile/water and liver/water was NP < OP < BPA in eutrophic conditions, but NP > OP > BPA in oligotrophic conditions. The order in eutrophic conditions was the same as the log BCF and log Koc for algae/water, indicating that the accumulation of EDCs in water bodies could be affected by algae, which could be one of the reasons of the seasonal variation of EDCs in water.

Functional analyses of copper transporter genes in the human liver cell line HepG2.

Copper (Cu) is an essential element regulated by four genes (hCTR1, hATOX1, hATP7A, and hATP7B in humans and zctr1, zatox1, zatp7a, and zatp7b in zebrafish) in copper uptake, distribution, and transport in animal cells. Zebrafish (Danio rerio) shows a higher endogenous ratio of zatp7a to zatp7b in the liver, is relatively intolerant to copper ions and has a different zatp7a and zatp7b expression patterns in different organs. As high-affinity copper transporters, both zctr1 and hCTR1 increased copper toxicity, whereas hATOX1 and zatox1 slightly reduced copper toxicity in HepG2 cells after copper administration for 24 h. The transfected zatp7b functioned in HepG2 cells as effectively as hATP7B after both 24-h and 96-h copper exposure, but zatp7a failed to function in HepG2 cells as effectively as hATP7A. Our findings suggest that ATP7A dysfunction would increase cytotoxicity in the liver; the reason for zebrafish's copper intolerance could be the bulk dysfunction and abnormal localization of zATP7A.

Whole-transcriptome sequencing (RNA-seq) analyses of the zebrafish liver cell line, ZFL, after acute exposure to Cu2+ ions.

All cells require Cu as a cofactor, but Cu2+ induces toxicity and oxidative damage. A strict system is thus needed to maintain Cu homeostasis. Using the ZFL zebrafish liver cell line as a model, we studied the cellular responses after exposure to Cu2+, using whole-transcriptome shotgun sequencing (RNA-seq) to screen nearly all transcriptomes in cell samples and identify changes in gene expression. ZFL cells were treated with 100, 200, or 400 µM CuCl2 and harvested after 4 and 24 h. RNA was then extracted and subjected to RNA-Seq and qPCR validation. Exposure to 400 µM CuCl2 for 4 h and 24 h led to the regulation of 5993 and 4235 genes, respectively. In a gene ontology enrichment analysis, Cu2+ exposure enriched the nitrogen compound metabolic process and antioxidant activity but did not significantly affect cellular copper, zinc, iron and calcium ion homeostasis. In a KEGG pathway enrichment analysis, anti-oxidative stress induced the glutathione metabolism pathway. Furthermore, Cu2+ also induced genes related to apoptosis and arrested the cell cycle in the G2 phase. This study was based on the full gene expression profile combined with pathway analysis details, providing a full cellular response picture for Cu.

A crustacean annotated transcriptome (CAT) database.

BACKGROUND: Decapods are an order of crustaceans which includes shrimps, crabs, lobsters and crayfish. They occur worldwide and are of great scientific interest as well as being of ecological and economic importance in fisheries and aquaculture. However, our knowledge of their biology mainly comes from the group which is most closely related to crustaceans - insects. Here we produce a de novo transcriptome database, crustacean annotated transcriptome (CAT) database, spanning multiple tissues and the life stages of seven crustaceans. DESCRIPTION: A total of 71 transcriptome assemblies from six decapod species and a stomatopod species, including the coral shrimp Stenopus hispidus, the cherry shrimp Neocaridina davidi, the redclaw crayfish Cherax quadricarinatus, the spiny lobster Panulirus ornatus, the red king crab Paralithodes camtschaticus, the coconut crab Birgus latro, and the zebra mantis shrimp Lysiosquillina maculata, were generated. Differential gene expression analyses within species were generated as a reference and included in a graphical user interface database at http://cat.sls.cuhk.edu.hk/. Users can carry out gene name searches and also access gene sequences based on a sequence query using the BLAST search function. CONCLUSIONS: The data generated and deposited in this database offers a valuable resource for the further study of these crustaceans, as well as being of use in aquaculture development.

Impact of juvenile hormone analogue insecticides on the water flea Moina macrocopa: Growth, reproduction and transgenerational effect.

The increasing quantities of insecticides that leach into water bodies severely affect the health of the aquatic environment. Juvenile hormone analogue (JHA) insecticides are endocrine disrupters that interfere with hormonal activity in insects by mimicking juvenile hormones (JHs). Because the structure and functions of methyl farnesoate in crustaceans are similar to the insect JHs, exogenous JHA insecticides may cause adverse effects on the growth and reproduction in crustaceans similar to those observed in insects. This study examined the toxic effects of two JHA insecticides, methoprene and fenoxycarb, on the water flea Moina macrocopa. The 24-h and 48-h LC50 values for fenoxycarb and methoprene were 0.53 and 0.32 mg/L and 0.70 and 0.54 mg/L, respectively. Chronic exposure to the two JHAs caused a series of toxic effects in M. macrocopa, including shortening of life expectancy, repression of body growth, reduction in fecundity, and disturbed the expression of genes involved in the JH signaling pathway, in cuticle development, and in the carbohydrate, amino acid, and ATP metabolic processes. Moreover, JHA exposure impaired the growth and reproduction of the offspring of M. macrocopa exposed to JHAs, even when the neonates were not exposed to the chemicals. In addition, changes in the expression of genes related to histone methylation indicate that epigenetic changes may promote transgenerational impairment in M. macrocopa. These results demonstrate the toxic effects of fenoxycarb and methoprene on non-target aquatic organisms. The damages done by these JHA insecticides to the aquatic environment is worthy of our attention and further studies.

Ecdysteroid-mimicking compounds act as both agonists and antagonists to the crustacean ecdysone receptor.

To characterize the potential endocrine-disrupting chemicals (EDCs) in the environment that interact with the crustacean ecdysone receptor (EcR), we established a method involving in silico modeling/molecular docking and in vitro reporter gene assay. Cherry shrimp (Neocaridina davidi) EcR (NdEcR) and retinoid X receptor (NdRxR) were identified and cloned for use in this method. A theoretical 3D model of NdEcR ligand-binding domain (LBD) was built in silico based on sequence homology with the established X-ray structure of insect EcR. The interaction of the NdEcR LBD with ecdysteroids, diacylhydrazine (DAH) pesticides, and other potential EDCs was evaluated using molecular docking programs. The results revealed that the ligand-binding pocket in the NdEcR LBD was flexible and adaptive for accommodating ligands of different shapes. The agonistic and antagonistic activities of the candidate compounds were further assessed by in vitro reporter gene assay using human cell lines transiently transfected with NdEcR and NdRxR expression plasmids and a reporter plasmid containing synthesized ecdysone response element. The assay was validated by the dose-dependent responses of EcR-mediated gene transcription after treating the transfected cell lines with ecdysteroids, 20-hydroxyecdysone, and ponasterone A. Examination of the candidate compounds using the reporter gene assay revealed restricted functional specificity to ecdysteroids and DAHs. Three of the tested DAH pesticides originally targeting the insect EcR were found to be weak agonists and strong antagonists of NdEcR. These results suggest that DAHs are potential EDCs for crustaceans that disrupt their ecdysteroid signals by functioning as EcR agonists or antagonists.

Functional characterization of copper transporters zCtr1, zAtox1, zAtp7a and zAtp7b in zebrafish liver cell line ZFL.

Copper (Cu) is an essential element for all organisms, serving as an enzyme cofactor to maintain cellular activity and vitality. However, Cu homeostasis must be maintained at the physiological and cellular levels as Cu ions can be highly toxic. In mammals, ATP7A is expressed in most tissues, but relatively lower expression is found in the liver, and is responsible for the intestinal uptake of Cu, while ATP7B is highly expressed in the liver, kidneys and placenta, and is responsible for removal of Cu in the liver. CTR1 and ATOX1 are responsible for cellular Cu uptake and intracellular Cu transport, respectively. Here, using a zebrafish liver cell line (ZFL), we studied the cellular functions of four zebrafish Cu transporters. In zebrafish, zAtp7a is expressed mainly in the liver and zAtp7b is expressed mainly in the intestines, different from that of humans which have a high ATP7b level in the liver and high ATP7a level in the intestines. We here found that zctr1 or zatox1 overexpression increased Cu accumulation in ZFL cells. Moreover, zctr1 overexpression made ZFL cells more sensitive to Cu and Zn exposure, and overexpression of zatox1 or zatp7b increased Cu uptake and Cu tolerance in ZFL cells. Overexpression of zatp7a made ZFL cells more sensitive to Zn. Taken together, our findings suggest that zatp7b is responsible for Cu export despite its expression level being much lower than zatp7a in ZFL cells.

Effects of two juvenile hormone analogue insecticides, fenoxycarb and methoprene, on Neocaridina davidi.

Juvenile hormone analogue (JHA) insecticides are endocrine disrupters that interfere with hormonal action in insects by mimicking their juvenile hormones (JH). As the structure and functions of methyl farnesoate in crustaceans are similar to those of JH in insects, exogenous JHA insecticides could have adverse effects on the development and reproduction of crustaceans. This study examined the toxic effects of two JHA insecticides, fenoxycarb and methoprene, on a freshwater shrimp model of cherry shrimp, Neocaridina davidi. Both insecticides had detrimental effects on cherry shrimp, but fenoxycarb was more toxic than methoprene. Chronic exposure to these insecticides reduced the shrimp's body length and molting frequency. Based on transcriptome annotations for N. davidi, we identified important gene homologues that were active in both insect JH biosynthetic and degradative pathways as well as JH and ecdysteroid signaling pathways. Chronic treatments with JHAs had significant effects on these genes in N. davidi. Our transcriptomic analysis showed that genes involved in the pathways related to cuticle development, serine protease activity, and carbohydrate, peptide and lipid metabolic processes were differentially expressed in shrimp exposed to JHAs. These results demonstrate the toxicity of fenoxycarb and methoprene to freshwater crustaceans and indicate the need to monitor the use of JHA insecticides.

Acute toxic effects of polyethylene microplastic on adult zebrafish.

To identify the physical effects, behavioral changes, and gene expression profiles of the phase 1 detoxification-related gene (cyp 1a) and oogenesis-related gene (vtg 1) induced by microplastics, high-density polyethylene microplastics of various sizes were used because of their dominance in coastal areas and effluent samples in Hong Kong. Adult zebrafish were used as the model organism to identify the upper and lower boundaries of microplastics ingestion and were exposed to individual polyethylene microplastics in five size ranges (10-22 µm, 45-53 µm, 90-106 µm, 212-250 µm, and 500-600 µm) at a concentration of 2 mg/L for 96 h. To study behavioral changes and targeted gene expression profiles via real-time PCR (qPCR), a mixture of microplastics in three size ranges at effluent-related (11 particles/L), moderate (110 particles/L), and high concentrations (1,100 particles/L) were applied for 96 h. The zebrafish behavior was recorded by a video camera and by two observers (interrater reliability, >85%). The results implied that the upper and lower size boundaries for microplastic ingestion were 558.4 ±â€¯26.2 µm (yellow) and 19.7 ±â€¯3.1 µm (red), respectively. In addition, 61 ±â€¯10% of fish in medium concentration treatments and 61 ±â€¯10% of fish in high concentration treatments were found with the microplastic ingestion and remaining in their intestine. In addition, 28 ±â€¯10% of fish in high concentration treatments were found with microplastic retaining in their gills (No. of fishes = 18 in each treatment). The presence of microplastics, which occupied 89 ±â€¯6% of intestine area, reduced the voids inside the intestine for feed. The expression of cyp1a in the intestine (medium concentration) and vtg1 in the liver (medium and high concentration) showed significant up-regulation, and abnormal behavior (i.e., seizures and tail bent downward) was observed (medium and high concentration). In summary, the effects on the aryl hydrocarbon receptor (AHR) pathway, disruption of the oogenesis process, and neurotoxicity could be caused by acute exposure of adult zebrafish to microplastics.

Modulations of TCDD-mediated induction of zebrafish cyp1a1 and the AHR pathway by administering Cd2+in vivo.

Trace metal ions such as cadmium (Cd2+) and trace organics typified by 2,3,7,8- tetrachlorodibenzo-p-dioxin (TCDD) are common co-contaminants in the environment and cause toxic effects in aquatic organisms that pose serious health risks. We studied the effects of Cd2+ on the regulation of cytochrome P450 1A1 (cyp1a1) gene-induction by TCDD using zebrafish embryos and larvae and adult zebrafish tissues. Our results showed that TCDD induced the cyp1a1 gene in all developmental stages and tissues of zebrafish, and the induction was higher in females than males. However, for the upstream genes (ahr2 and arnt2b) that mediate cyp1a1 gene induction in the zebrafish liver cell line was not induced by TCDD similar to the pattern of cyp1a1 in all investigated groups. After co-treatment with Cd2+, induction of the aryl hydrocarbon receptor pathway by TCDD was inhibited in the zebrafish larvae and the livers, intestines, kidneys and gills of adult zebrafish, but not in the embryos or brains of adult zebrafish, indicating that the toxicological effects of Cd2+ on TCDD are dependent on the developmental stages and tissue types. The present study confirms that Cd2+ blocks the TCDD-induced cyp1a1 gene in vivo but emphasizes that the effects are specific to the developmental stage, type of tissue and sex. The combined effects of Cd2+ and TCDD must be taken into consideration together with these parameters to accurately predict and assess cadmium and TCDD-induced toxicity in fish and carcinogenesis in animals in general.

A comprehensive web tool for toehold switch design.

Motivation: Toehold switches are a class of RNAs with a hairpin loop that can be unfolded upon binding a trigger RNA, thereby exposing a ribosome binding site (RBS) and permitting translation of the reporter protein. They have been shown very useful in detecting a variety of targets including RNAs from Zika and Ebola viruses. The base complementation between the toehold switch and the trigger RNA also makes it sensitive to sequence variations. Design of toehold switches involves a series of considerations related to their sequence properties, structures and specificities. Results: Here we present the first comprehensive web tool for designing toehold switches. We also propose a score for predicting the efficacy of designed toehold switches based on properties learned from ∼180 experimentally tested switches. Availability and implementation: The toehold switch web tool is available at https://yiplab.cse.cuhk.edu.hk/toehold/.