Assessing the reliability of point mutation as data augmentation for deep learning with genomic data.

BACKGROUND: Deep neural networks (DNNs) have the potential to revolutionize our understanding and treatment of genetic diseases. An inherent limitation of deep neural networks, however, is their high demand for data during training. To overcome this challenge, other fields, such as computer vision, use various data augmentation techniques to artificially increase the available training data for DNNs. Unfortunately, most data augmentation techniques used in other domains do not transfer well to genomic data. RESULTS: Most genomic data possesses peculiar properties and data augmentations may significantly alter the intrinsic properties of the data. In this work, we propose a novel data augmentation technique for genomic data inspired by biology: point mutations. By employing point mutations as substitutes for codons, we demonstrate that our newly proposed data augmentation technique enhances the performance of DNNs across various genomic tasks that involve coding regions, such as translation initiation and splice site detection. CONCLUSION: Silent and missense mutations are found to positively influence effectiveness, while nonsense mutations and random mutations in non-coding regions generally lead to degradation. Overall, point mutation-based augmentations in genomic datasets present valuable opportunities for improving the accuracy and reliability of predictive models for DNA sequences.

Interactive Effects of Blue Light and Water Turbulence on the Growth of the Green Macroalga Ulva australis (Chlorophyta).

Macroalgal growth and yield are key to sustainable aquaculture. Although light and water turbulence are two important factors that affect algal productivity, research on their interaction is limited. Therefore, in this study, we investigated the effects of different wavelengths of light and the presence or absence of water turbulence on the growth of the green macroalga Ulva australis. Water turbulence was found to enhance the growth of U. australis irrespective of photosynthetic performance, but only in blue light cultures. The quantum dose of blue light required to induce 50% growth promotion was 1.02 mol m-2, which is comparable to the reported values for cryptochrome-mediated effects in other macroalgae. The combined effect of blue light and water turbulence led to the accumulation of photosynthesis-related proteins that support plastid differentiation and facilitate efficient photosynthesis and growth. Our findings thus highlight the potential of harnessing blue light and water turbulence to maximise macroalgal cultivation for sustainable and profitable algal aquaculture.

Giant Duckweed (Spirodela polyrhiza) Root Growth as a Simple and Sensitive Indicator of Copper and Chromium Contamination.

Aquatic environment are often contaminated with heavy metals from various industrial sources. However, physicochemical techniques for pollutant detection are limited, thus prompting the need for additional bioassays. We investigated the use of greater duckweed (Spirodela polyrhiza) as a bioindicator of metal pollution. We exposed S. polyrhiza to four pollutants (namely, silver, cadmium, copper, and chromium) and assessed metal toxicity by measuring its frond area and the length of its regrown roots. The plant displayed significant differences in both frond size and root growth in response to the four metals. Silver was the most toxic (EC50 = 23 µg L-1) while copper the least (EC50 = 365-607 µg L-1). Direct comparisons of metal sensitivity and the reliability of the two endpoint assays showed that root growth was more sensitive (lower in terms of 50% effective concentration) to chromium, cadmium, and copper, and was more reliable (lower in terms of coefficient of variation) than those for frond area. Compared to conventional Lemna-based tests, the S. polyrhiza test is easier to perform (requiring only one 24-well plate, 3 mL of medium and a 72-h exposure). Moreover, it does not require livestock cultivation/maintenance, making it more suitable for repeated measurements. Measurements of S. polyrhiza root length may be suitable for assessment when copper and chromium in municipal and industrial wastewater exceed the environmentally permissible levels.

Metal Toxicity across Different Thallus Sections of the Green Macroalga, Ulva australis.

We aimed to identify functional differences between different sections of the thallus of Ulva australis and develop tissue-endpoint combinations to assess the toxicity of six metals (i.e., Ag, As, Cd, Cr, Cu, and Ni). EC50 values for these metals in three sections of the thallus of Ulva were obtained for multiple endpoints: relative growth rate (RGR), chlorophyll a fluorescence, pigment contents, and the expression of the photosynthesis-related gene, rbcL. The responses of the endpoints varied across the respective thallus sections; overall, the most toxic metals were Ag and Cu. These endpoints were the best for evaluating metal toxicity: ETRmax of the middle thallus sections for Ag toxicity; RGR of the middle thallus section for As and Cd; ETRmax of the marginal thallus section for Cr; Chl b contents of the marginal thallus section for Cu; RGR of the basal thallus section for Ni. The EC50 values for the inhibition of ETRmax in middle (0.06 mg∙L-1) and Chl b in the marginal thallus sections (0.06 mg∙L-1) were all lower than those of the quality standard for wastewater discharge values of Ag and Cu in Republic of Korea and the US, pointing to the suitability of U. australis-based endpoints for risk assessment.

How to make sense of 3D representations for plant phenotyping: a compendium of processing and analysis techniques.

Computer vision technology is moving more and more towards a three-dimensional approach, and plant phenotyping is following this trend. However, despite its potential, the complexity of the analysis of 3D representations has been the main bottleneck hindering the wider deployment of 3D plant phenotyping. In this review we provide an overview of typical steps for the processing and analysis of 3D representations of plants, to offer potential users of 3D phenotyping a first gateway into its application, and to stimulate its further development. We focus on plant phenotyping applications where the goal is to measure characteristics of single plants or crop canopies on a small scale in research settings, as opposed to large scale crop monitoring in the field.

Mutate and observe: utilizing deep neural networks to investigate the impact of mutations on translation initiation.

MOTIVATION: The primary regulatory step for protein synthesis is translation initiation, which makes it one of the fundamental steps in the central dogma of molecular biology. In recent years, a number of approaches relying on deep neural networks (DNNs) have demonstrated superb results for predicting translation initiation sites. These state-of-the art results indicate that DNNs are indeed capable of learning complex features that are relevant to the process of translation. Unfortunately, most of those research efforts that employ DNNs only provide shallow insights into the decision-making processes of the trained models and lack highly sought-after novel biologically relevant observations. RESULTS: By improving upon the state-of-the-art DNNs and large-scale human genomic datasets in the area of translation initiation, we propose an innovative computational methodology to get neural networks to explain what was learned from data. Our methodology, which relies on in silico point mutations, reveals that DNNs trained for translation initiation site detection correctly identify well-established biological signals relevant to translation, including (i) the importance of the Kozak sequence, (ii) the damaging consequences of ATG mutations in the 5'-untranslated region, (iii) the detrimental effect of premature stop codons in the coding region, and (iv) the relative insignificance of cytosine mutations for translation. Furthermore, we delve deeper into the Beta-globin gene and investigate various mutations that lead to the Beta thalassemia disorder. Finally, we conclude our work by laying out a number of novel observations regarding mutations and translation initiation. AVAILABILITY AND IMPLEMENTATION: For data, models, and code, visit github.com/utkuozbulak/mutate-and-observe.

Evaluating ecotoxicological assays for comprehensive risk assessment of toxic metals present in industrial wastewaters in the Republic of Korea.

Toxicity tests represent a rapid, user-friendly and cost-effective means to assess the impact of wastewater quality on aquatic ecosystems. There are not many cases where wastewater management standards are set based on various bio-based ecotoxicity values. Here, we tested a novel multitaxon approach to compare standard water quality indices to toxicity metrics obtained from ecotoxicity tests, conducted using aquatic organisms representing several trophic levels (Aliivibrio, Ulva, Daphnia, and Lemna), for 99 industrial wastewater samples from South Korea. For five wastewater samples, the concentrations of Se, Zn, or Ni exceeded the permissible limits (1, 5, and 3 mg L-1, respectively). All the four physiochemical water quality indices tested were positively correlated with Se and Pb concentrations. The toxicity unit (TU) scores indicated a declining sensitivity to pollutants, in the order Lemna (2.87) >Daphnia (2.24) >Aliivibrio (1.78) >Ulva (1.42). Significant correlations were observed between (1) Cd and Ni, and Aliivibrio, (2) Cu and Daphnia, (3) Cd, Cu, Zn, and Cr and Lemna, and (4) Cu, Zn, and Ni and Ulva. Daphnia-Lemna and Lemna-Ulva were found to be good indicators of ecologically harmful Se and Ni contents in wastewater, respectively. We suggest that regulatory thresholds based on these bioassays should be set at TU = 1 for all the species or at TU = 1 for Aliivibrio and Ulva and TU = 2 for Daphnia and Lemna, if the number of companies whose wastewater discharge exceeds the allowable TU levels is <1 % or 5 % of the total number of industries, respectively. Taken together, these findings could help in establishing a rapid, ecologically relevant wastewater quality assessment system that would be useful for developing strategies to protect aquatic ecosystems.

IMPLANT: a new technique for transgene copy number estimation in plants using a single end-point PCR reaction.

BACKGROUND: Copy number determination is one of the first steps in the characterization of transgenic plant lines. The classical approach to this, Southern blotting, is time-consuming, expensive and requires massive amounts of high-quality genomic DNA. Other PCR-based techniques are either inaccurate, laborious, or expensive. RESULTS: Here, we propose a new technique, IMPLANT (Insertion of competitive PCR calibrator for copy number estimation), a competitive PCR-based technique in which the competitor (based on an endogenous gene) is also incorporated in the T-DNA, which then gets integrated in the genome together with the gene of interest. As the number of integrated competitor molecules directly corresponds to the number of transgene copies, the transgene copy number can be determined by a single PCR reaction. We demonstrate that the results of this technique closely correspond with those obtained by segregation analysis in Arabidopsis and digital PCR In rice, indicating that it is a powerful alternative for other techniques for copy number determination. CONCLUSIONS: We show that this technique is not only reliable, but is also faster, easier, and cheaper as compared with other techniques. Accurate results are obtained in both Arabidopsis and rice, but this technique can be easily extended to other organisms and as such can be widely adopted in the field of biotechnology.

Opposing effects of trans- and cis-cinnamic acid during rice coleoptile elongation.

The phenylpropanoid cinnamic acid (CA) is a plant metabolite that can occur under a trans- or cis-form. In contrast to the proven bioactivity of the cis-form (c-CA), the activity of trans-CA (t-CA) is still a matter of debate. We tested both compounds using a submerged rice coleoptile assay and demonstrated that they have opposite effects on cell elongation. Notably, in the tip of rice coleoptile t-CA showed an inhibiting and c-CA a stimulating activity. By combining transcriptomics and (untargeted) metabolomics with activity assays and genetic and pharmacological experiments, we aimed to explain the underlying mechanistic processes. We propose a model in which c-CA treatment activates proton pumps and stimulates acidification of the apoplast, which in turn leads to the loosening of the cell wall, necessary for elongation. We hypothesize that c-CA also inactivates auxin efflux transporters, which might cause a local auxin accumulation in the tip of the coleoptile. For t-CA, the phenotype can partially be explained by a stimulation of cell wall polysaccharide feruloylation, leading to a more rigid cell wall. Metabolite profiling also demonstrated that salicylic acid (SA) derivatives are increased upon t-CA treatment. As SA is a known antagonist of auxin, the shift in SA homeostasis provides an additional explanation of the observed t-CA-mediated restriction on cell growth.

A Ten-Minute Bioassay to Test Metal Toxicity with the Freshwater Flagellate Euglena agilis.

A chemical analysis of water quality cannot detect some toxicants due to time constraints, high costs, and limited interactions for detection. Bioassays would offer a complementary means to assess pollution levels in water. Euglena is a flagellate green alga and an excellent system for toxicity testing thanks to its ease of culture, rapid growth, and quick response to environmental stresses. Herein, we examined the sensitivity of E. agilis to seven heavy metals by analyzing six end-point parameters: motility, velocity, cell compactness, upward swimming, r-value, and alignment. Notably, the velocity of E. agilis was most sensitive to cadmium (96.28 mg·L-1), copper (6.51 mg·L-1), manganese (103.28 mg·L-1), lead (78.04 mg·L-1), and zinc (101.90 mg·L-1), while r-values were most sensitive to arsenic (12.84 mg·L-1) and mercury (4.26 mg·L-1). In this study, velocity and r-values are presented as useful biomarkers for the assessment of metal toxicity in Euglena. The metals As, Cd, Cu, and Pb were suitable for this test. The advantages of the ecotoxicity test are its rapidity: It takes 10 min to obtain results, as opposed to the typical 3-4 d of exposure time with intensive labor. Moreover, this test can be performed at room temperature under dark conditions.

MAX2-dependent competence for callus formation and shoot regeneration from Arabidopsis thaliana root explants.

Although the division of the pericycle cells initiates both lateral root development and root-derived callus formation, these developmental processes are affected differently in the strigolactone and karrikin/KARRIKIN INSENSITIVE 2 (KAI2) ligand signalling mutant more axillary growth 2 (max2). Whereas max2 produces more lateral roots than the wild type, it is defective in the regeneration of shoots from root explants. We suggest that the decreased shoot regeneration of max2 originates from delayed formation of callus primordium, yielding less callus material to regenerate shoots. Indeed, when incubated on callus-inducing medium, the pericycle cell division was reduced in max2 and the early gene expression varied when compared with the wild type, as determined by a transcriptomics analysis. Furthermore, the expression of the LATERAL ORGAN BOUNDARIES DOMAIN genes and of callus-induction genes was modified in correlation with the max2 phenotype, suggesting a role for MAX2 in the regulation of the interplay between cytokinin, auxin, and light signalling in callus initiation. Additionally, we found that the in vitro shoot regeneration phenotype of max2 might be caused by a defect in KAI2, rather than in DWARF14, signalling. Nevertheless, the shoot regeneration assays revealed that the strigolactone biosynthesis mutants max3 and max4 also play a minor role.

Commercial Potential of the Cyanobacterium Arthrospira maxima: Physiological and Biochemical Traits and the Purification of Phycocyanin.

Arthrospira maxima is a natural source of fine chemicals for multiple biotechnological applications. We determined the optimal environmental conditions for A. maxima by measuring its relative growth rate (RGR), pigment yield, and photosynthetic performance under different pH and temperature conditions. RGR was highest at pH 7-9 and 30 °C. Chlorophyll a, phycocyanin, maximal quantum yield (Fv/Fm), relative maximal electron transport rate (rETRmax), and effective quantum yield (ΦPSII) were highest at pH 7-8 and 25 °C. Interestingly, phycoerythrin and allophycocyanin content was highest at 15 °C, which may be the lowest optimum temperature reported for phycobiliprotein production in the Arthrospira species. A threestep purification of phycocyanin (PC) by ultrafiltration, ion-exchange chromatography, and gel filtration resulted in a 97.6% purity of PC.

Assessment of Various Toxicity Endpoints in Duckweed (Lemna minor) at the Physiological, Biochemical, and Molecular Levels as a Measure of Diuron Stress.

The common, broad-spectrum herbicide diuron poses some risks to the environment due to its long persistence and high toxicity. Therefore, the effective monitoring of diuron residues will inform efforts to assess its impacts on ecosystems. In this study, we evaluated the toxicity targets of diuron in the model aquatic macrophyte Lemna minor at the physiological (growth and photosynthetic efficiency), biochemical (pigment biosynthesis and reactive oxygen species (ROS) levels), and molecular (rbcL transcript) levels. The toxicity of diuron was detectable after 48 h of exposure and the order of sensitivity of toxicity endpoints was gene transcription > maximum electron transport rate (ETRmax) > non-photochemical quenching (NPQ) > maximum quantum yield (Fv/Fm) > ROS > fresh weight > chlorophyll b > chlorophyll a > total frond area > carotenoids. Under diuron stress, pigment, ROS, and gene transcript levels increased while frond area, fresh weight, and photosynthesis (Fv/Fm and ETRmax) gradually decreased with the increasing duration of exposure. Notably, ROS levels, Fv/Fm, frond area, and fresh weight were highly correlated with diuron concentration. The growth endpoints (frond area and fresh weight) showed a strong negative correlation with ROS levels and a positive correlation with Fv/Fm and ETRmax. These findings shed light on the relative sensitivity of different endpoints for the assessment of diuron toxicity.

Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor.

The F-box protein MORE AXILLARY GROWTH 2 (MAX2) is a central component in the signaling cascade of strigolactones (SLs) as well as of the smoke-derived karrikins (KARs) and the so far unknown endogenous KAI2 ligand (KL). The two groups of molecules are involved in overlapping and unique developmental processes, and signal-specific outcomes are attributed to perception by the paralogous α/ß-hydrolases DWARF14 (D14) for SL and KARRIKIN INSENSITIVE 2/HYPOSENSITIVE TO LIGHT (KAI2/HTL) for KAR/KL. In addition, depending on which receptor is activated, specific members of the SUPPRESSOR OF MAX2 1 (SMAX1)-LIKE (SMXL) family control KAR/KL and SL responses. As proteins that function in the same signal transduction pathway often occur in large protein complexes, we aimed at discovering new players of the MAX2, D14, and KAI2 protein network by tandem affinity purification in Arabidopsis cell cultures. When using MAX2 as a bait, various proteins were copurified, among which were general components of the Skp1-Cullin-F-box complex and members of the CONSTITUTIVE PHOTOMORPHOGENIC 9 signalosome. Here, we report the identification of a novel interactor of MAX2, a type 5 serine/threonine protein phosphatase, designated PHYTOCHROME-ASSOCIATED PROTEIN PHOSPHATASE 5 (PAPP5). Quantitative affinity purification pointed at PAPP5 as being more present in KAI2 rather than in D14 protein complexes. In agreement, mutant analysis suggests that PAPP5 modulates KAR/KL-dependent seed germination under suboptimal conditions and seedling development. In addition, a phosphopeptide enrichment experiment revealed that PAPP5 might dephosphorylate MAX2 in vivo independently of the synthetic SL analog, rac-GR24. Together, by analyzing the protein complexes to which MAX2, D14, and KAI2 belong, we revealed a new MAX2 interactor, PAPP5, that might act through dephosphorylation of MAX2 to control mainly KAR/KL-related phenotypes and, hence, provide another link with the light pathway.

Interlaboratory Validation of Toxicity Testing Using the Duckweed Lemna minor Root-Regrowth Test.

The common duckweed (Lemna minor), a freshwater monocot that floats on the surfaces of slow-moving streams and ponds, is commonly used in toxicity testing. The novel Lemna root- regrowth test is a toxicity test performed in replicate test vessels (24-well plates), each containing 3 mL test solution and a 2-3 frond colony. Prior to exposure, roots are excised from the plant, and newly developed roots are measured after 3 days of regrowth. Compared to the three internationally standardized methods, this bioassay is faster (72 h), simpler, more convenient (requiring only a 3-mL) and cheaper. The sensitivity of root regrowth to 3,5-dichlorophenol was statistically the same as using the conventional ISO test method. The results of interlaboratory comparison tests conducted by 10 international institutes showed 21.3% repeatability and 27.2% reproducibility for CuSO4 and 21.28% repeatability and 18.6% reproducibility for wastewater. These validity criteria are well within the generally accepted levels of <30% to 40%, confirming that this test method is acceptable as a standardized biological test and can be used as a regulatory tool. The Lemna root regrowth test complements the lengthier conventional protocols and is suitable for rapid screening of wastewater and priority substances spikes in natural waters.

Agrobacterium strains and strain improvement: Present and outlook.

Almost 40 years ago the first transgenic plant was generated through Agrobacterium tumefaciens-mediated transformation, which, until now, remains the method of choice for gene delivery into plants. Ever since, optimized Agrobacterium strains have been developed with additional (genetic) modifications that were mostly aimed at enhancing the transformation efficiency, although an optimized strain also exists that reduces unwanted plasmid recombination. As a result, a collection of very useful strains has been created to transform a wide variety of plant species, but has also led to a confusing Agrobacterium strain nomenclature. The latter is often misleading for choosing the best-suited strain for one's transformation purposes. To overcome this issue, we provide a complete overview of the strain classification. We also indicate different strain modifications and their purposes, as well as the obtained results with regard to the transformation process sensu largo. Furthermore, we propose additional improvements of the Agrobacterium-mediated transformation process and consider several worthwhile modifications, for instance, by circumventing a defense response in planta. In this regard, we will discuss pattern-triggered immunity, pathogen-associated molecular pattern detection, hormone homeostasis and signaling, and reactive oxygen species in relationship to Agrobacterium transformation. We will also explore alterations that increase agrobacterial transformation efficiency, reduce plasmid recombination, and improve biocontainment. Finally, we recommend the use of a modular system to best utilize the available knowledge for successful plant transformation.

Development of a novel and rapid phenotype-based screening method to assess rice seedling growth.

BACKGROUND: Rice (Oryza sativa) is one of the most important model crops in plant research. Despite its considerable advantages, (phenotypic) bioassays for rice are not as well developed as for Arabidopsis thaliana. Here, we present a phenotype-based screening method to study shoot-related parameters of rice seedlings via an automated computer analysis. RESULTS: The phenotype-based screening method was validated by testing several compounds in pharmacological experiments that interfered with hormone homeostasis, confirming that the assay was consistent with regard to the anticipated plant growth regulation and revealing the robustness of the set-up in terms of reproducibility. Moreover, abiotic stress tests using NaCl and DCMU, an electron transport blocker during the light dependent reactions of photosynthesis, confirmed the validity of the new method for a wide range of applications. Next, this method was used to screen the impact of semi-purified fractions of marine invertebrates on the initial stages of rice seedling growth. Certain fractions clearly stimulated growth, whereas others inhibited it, especially in the root, illustrating the possible applications of this novel, robust, and fast phenotype-based screening method for rice. CONCLUSIONS: The validated phenotype-based and cost-efficient screening method allows a quick and proper analysis of shoot growth and requires only small volumes of compounds and media. As a result, this method could potentially be used for a whole range of applications, ranging from discovery of novel biostimulants, plant growth regulators, and plant growth-promoting bacteria to analysis of CRISPR knockouts, molecular plant breeding, genome-wide association, and phytotoxicity studies. The assay system described here can contribute to a better understanding of plant development in general.

Assessment of five live-cell characteristics in periphytic diatoms as a measure of copper stress.

Metal pollution of fluvial systems remains a major problem and biomonitoring can be a useful tool for assessing the metal contamination. To assess their potential as new bioindicators of copper stress, we treated a field-collected live periphytic diatom community (dominated by Amphora, Navicula, and Nitzschia) with dissolved Cu under optimal growth conditions. We studied the effects of Cu on five live-cell attributes: motility, protoplasmic content, lipid body number and biovolume, and frustule morphology. In all three genera, motility and protoplasmic content decreased, whereas the LB number, biovolume and deformity increased when Cu and exposure time increased. The sensitivity to Cu was highest for % MF, % CPC and % BCLB in Navicula and the LB number and deformity in Nitzschia. Amphora appeared to be more tolerant to Cu in comparison with other genera. The five cell attributes were inter-related. A heatmap showed that a recommended indicator for rapid screening of Cu toxicity was % BCLB for Amphora and % MF for Navicula and Nitzschia. % MF might be the most common representative indicator that can be applied to all three genera to evaluate the lethal effects of Cu stress if only one of the five cell attributes must be selected.

Rapid toxicity assessment of six antifouling booster biocides using a microplate-based chlorophyll fluorescence in Undaria pinnatifida gametophytes.

Biocides of antifouling agents can cause problems in marine ecosystems by damaging to non-target algal species. Aquatic bioassays are important means of assessing the quality of water containing mixtures of contaminants and of providing a safety standard for water management in an ecological context. In this study, a rapid, sensitive and inexpensive test method was developed using free-living male and female gametophytes of the brown macroalga Undaria pinnatifida. A conventional fluorometer was employed to evaluate the acute (48 h) toxic effects of six antifouling biocides: 4,5-Dichloro-2-octyl-isothiazolone (DCOIT), diuron, irgarol, medetomidine, tolylfluanid, zinc pyrithione (ZnPT). The decreasing toxicity in male and female gametophytes as estimated by EC50 (effective concentration at which 50% inhibition occurs) values was: diuron (0.037 and 0.128 mg l-1, respectively) > irgarol (0.096 and 0.172 mg l-1, respectively) > tolylfluanid (0.238 and 1.028 mg l-1, respectively) > DCOIT (1.015 and 0.890 mg l-1, respectively) > medetomidine (12.032 and 12.763 mg l-1, respectively). For ZnPT, 50% fluorescence inhibition of U. pinnatifida gametophytes occurred at concentrations above 0.4 mg l-1. The Undaria method is rapid, simple, practical, and cost-effective for the detection of photosynthesis-inhibiting biocides, thus making a useful tool for testing the toxicity of antifouling agents in marine environments.

Application of a programmed semi-automated Ulva pertusa bioassay for testing single toxicants and stream water quality.

A toxicity test based on inhibition of reproduction in the green macroalga Ulva pertusa involves quantifying the change in thallus color as reproduction progresses. However, interpretation of this color change is reliant on the skill level of the examiner. This study aimed to validate a new toxicity test based on inhibition of reproduction in the green macroalga U. pertusa using a vital stain and programmed semi-automated analysis (using Image J) of the change in thallus color. The toxicity rank by inverse EC50 values was: irgarol (0.048 mg L-1) > Ag (0.132 mg L-1) > As (0.172 mg L-1) > simazine (0.378 mg L-1) > formaldehyde (0.442 mg L-1) > DCOIT (0.783 mg L-1) > ZnPT (3.556 mg L-1) > medetomidine (11.600 mg L-1) > phenol (29.316 mg L-1) > methanol (2,736 mg L-1) > ethanol (3,306 mg L-1). The sensitivity of the U. pertusa test to stream waters was similar to or lower than those of the commonly-used Lemna minor and Daphnia magna bioassays. The U. pertusa bioassay is sensitive to, and suitable for, testing various toxicants including metals, volatile organic compounds, herbicide, antifouling agents and phenol and can also be applied to testing freshwater quality after salinity adjustment.