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.

Interactive Effects of Blue Light and Water Turbulence on the Growth of the Green Macroalga (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 .

Green Synthesis of Cation Exchange Membranes: A Review.

Cation exchange membranes (CEMs) play a significant role in the transition to a more sustainable/green society. They are important components for applications such as water electrolysis, artificial photosynthesis, electrodialysis and fuel cells. Their synthesis, however, is far from being sustainable, affecting safety, health and the environment.

Giant Duckweed () 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 () as a bioindicator of metal pollution.

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

We aimed to identify functional differences between different sections of the thallus of and develop tissue-endpoint combinations to assess the toxicity of six metals (i.e., Ag, As, Cd, Cr, Cu, and Ni).

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.

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.

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.

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

The phenylpropanoid cinnamic acid (CA) is a plant metabolite that can occur under a - or -form. In contrast to the proven bioactivity of the -form (-CA), the activity of -CA (-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.

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

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. 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.

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

is a natural source of fine chemicals for multiple biotechnological applications. We determined the optimal environmental conditions for 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.

A PEI/TMC membrane modified with an ionic liquid with enhanced permeability and antibacterial properties for the removal of heavy metal ions.

Heavy metal ions in drinking water severely threaten public health in various places worldwide. Nanofiltration (NF) membrane technology is an attractive option for heavy metal ions removal; however, improving NF membrane filtration performance is required to make their industrial application viable. In this study, a positively charged THPC/PEI-TMC NF membrane was designed via simple one-step incorporation of Tetrakis (hydroxymethyl) phosphonium chloride (THPC) biocide on the surface of PEI-TMC membranes, significantly optimizing surface morphology, roughness, hydrophilicity, and zeta potential of PEI-TMC membranes.

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

The common duckweed (), a freshwater monocot that floats on the surfaces of slow-moving streams and ponds, is commonly used in toxicity testing. The novel 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.

Assessment of Various Toxicity Endpoints in Duckweed () 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 at the physiological (growth and photosynthetic efficiency), biochemical (pigment biosynthesis and reactive oxygen species (ROS) levels), and molecular ( transcript) levels.

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/β-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.

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.

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

Background: Rice () 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 . Here, we present a phenotype-based screening method to study shoot-related parameters of rice seedlings via an automated computer analysis.

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.

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.

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.

Reappraisal of the toxicity test method using the green alga Ulva pertusa Kjellman (Chlorophyta).

This study was aimed to develop an objective way of quantifying the reproductive status of the green macroalga, Ulva pertusa using a vital stain and programmed automated analysis (by Image J program). The EC values (with 95% CI), the concentrations of toxicants inducing a reduction of 50% in sporulation after 96 h exposure, from the newly developed method were similar to those obtained by the conventional method: 0.651 (0.

Towards a multi-bioassay-based index for toxicity assessment of fluvial waters.

Despite their proven reliability for revealing 'acceptable' degrees of toxicity in waste- and reclaimed waters, bioassays are rarely used to assess the toxicity of hazardous contaminants present in natural waters. In this study, we used organisms from different trophic levels to assess the toxicity of water samples collected from four different South Korean rivers. The main objective was to develop a multi-descriptor index of toxicity for undiluted river water.

Testing the toxicity of metals, phenol, effluents, and receiving waters by root elongation in Lactuca sativa L.

Phytotoxicity tests using higher plants are among the most simple, sensitive, and cost-effective of the methods available for ecotoxicity testing. In the present study, a hydroponic-based phytotoxicity test using seeds of Lactuca sativa was used to evaluate the water quality of receiving waters and effluents near two industrial sites (Soyo and Daejon) in Korea with respect to the toxicity of 10 metals (As, Cd, Cr, Cu, Fe, Pb, Mn, Hg, Ni, Zn) and phenol, and of the receiving waters and effluents themselves. First, the L.