RanDepict: Random chemical structure depiction generator.

The development of deep learning-based optical chemical structure recognition (OCSR) systems has led to a need for datasets of chemical structure depictions. The diversity of the features in the training data is an important factor for the generation of deep learning systems that generalise well and are not overfit to a specific type of input. In the case of chemical structure depictions, these features are defined by the depiction parameters such as bond length, line thickness, label font style and many others.

The LOTUS initiative for open knowledge management in natural products research.

Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified.

Aquifer system and depth specific chemical patterns in fractured-rock groundwater from the Critical Zone revealed by untargeted LC-MS-based metabolomics.

In the Earth's Critical Zone, water plays an essential role as a collector and transporter of metabolites and their transformation products. It is generally believed that the chemical profiles of groundwater are strongly impacted by land use. However, predictors for the effects of above-ground natural and anthropogenic activities on below-ground chemistry are rare.

The Next Frontier of Environmental Unknowns: Substances of Unknown or Variable Composition, Complex Reaction Products, or Biological Materials (UVCBs).

Substances of unknown or variable composition, complex reaction products, or biological materials (UVCBs) are over 70 000 "complex" chemical mixtures produced and used at significant levels worldwide. Due to their unknown or variable composition, applying chemical assessments originally developed for individual compounds to UVCBs is challenging, which impedes sound management of these substances. Across the analytical sciences, toxicology, cheminformatics, and regulatory practice, new approaches addressing specific aspects of UVCB assessment are being developed, albeit in a fragmented manner.

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids.

Exhaustive generation of molecular structures has numerous chemical and biochemical applications such as drug design, molecular database construction, exploration of alternative biochemistries, and many more. Mathematically speaking, these are graph generators with chemical constraints. In the field, the most efficient generator currently (MOLGEN) is a commercial product, limiting its use.

Rapid wet-chemical oxidative activation of graphite felt electrodes for vanadium redox flow batteries.

To boost the performance of vanadium redox flow batteries, modification of the classically used felt electrodes is required to enable higher cycling performance and longer life cycles. Alternative approaches to the standard thermal oxidation procedure such as wet chemical oxidation are promising to reduce the thermal budget and thus the cost of the activation procedure. In this work we report a rapid 1 hour activation procedure in an acidified KMnO solution.

Mackinawite formation from elemental iron and sulfur.

Sulfur-assisted corrosion is a process known to material scientists for many decades now. Though the corrosion of iron in the presence of sulfur has been studied extensively, it has never been used to intentionally synthesize mackinawite. In contrast to the conventional preparation of mackinawite by precipitation, the synthesis from the elements can be carried out without additional ions.

From model organism to application: Bacteria-induced growth and development of the green seaweed Ulva and the potential of microbe leveraging in algal aquaculture.

The marine green macroalga Ulva (Chlorophyta, Ulvales), also known as sea lettuce, coexists with a diverse microbiome. Many Ulva species proliferate in nature and form green algal blooms ("green tides"), which can occur when nutrient-rich wastewater from agricultural or densely populated areas is flushed into the sea. Bacteria are necessary for the adhesion of Ulva to its substrate, its growth, and the development of its blade morphology.

Sphingolipids control dermal fibroblast heterogeneity.

Human cells produce thousands of lipids that change during cell differentiation and can vary across individual cells of the same type. However, we are only starting to characterize the function of these cell-to-cell differences in lipid composition. Here, we measured the lipidomes and transcriptomes of individual human dermal fibroblasts by coupling high-resolution mass spectrometry imaging with single-cell transcriptomics.

Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones.

Aquatic ecosystems are frequently overlooked as fungal habitats, although there is increasing evidence that their diversity and ecological importance are greater than previously considered. Aquatic fungi are critical and abundant components of nutrient cycling and food web dynamics, e.g.

Draft genome assembly and sequencing dataset of the marine diatom cf. RCC75.

Diatoms (Bacillariophyceae) are a major constituent of the phytoplankton and have a universally recognized ecological importance. Between 1,000 and 1,300 diatom genera have been described in the literature, but only 10 nuclear genomes have been published and made available to the public up to date. is a cosmopolitan marine diatom, principally occurring in coastal regions, and is one of the most abundant members of the genus.

The APAF1_C/WD40 repeat domain-encoding gene from the sea lettuce Ulva mutabilis sheds light on the evolution of NB-ARC domain-containing proteins in green plants.

We advance Ulva's genetic tractability and highlight its value as a model organism by characterizing its APAF1_C/WD40 domain-encoding gene, which belongs to a family that bears homology to R genes. The multicellular chlorophyte alga Ulva mutabilis (Ulvophyceae, Ulvales) is native to coastal ecosystems worldwide and attracts both high socio-economic and scientific interest. To further understand the genetic mechanisms that guide its biology, we present a protocol, based on adapter ligation-mediated PCR, for retrieving flanking sequences in U.

Room-Temperature Synthesis of [BMIm][SnOCl] with (SnOCl) Strands in a Saline [BMIm][SnCl] Matrix.

The novel tin(II) oxychloride [BMIm][SnOCl] (BMIm = 1-butyl-3-methylimidazolium) is obtained by the room-temperature reaction (25 °C) of black SnO and SnCl in [BMIm]Cl/SnCl as an ionic liquid. The title compound can be described as composed of noncharged, infinite (SnOCl) strands that are embedded in a saline matrix of [BMIm] and [SnCl]. The (SnOCl) strands consist of a backbone of edge-sharing OSn tetrahedra, which represent one-dimensional (1D) strands cut out of the layer-type structure of SnO.

Case Report: Local Treatment of a Leishmania tropica Infection in a Syrian Child with a Novel Filmogenic Preparation of Pharmaceutical Sodium Chlorite (LeiProtect®).

Cutaneous leishmaniasis (CL) frequently entails chronic skin lesions that heal only slowly. Until now, the available therapeutic options are very limited. Here, we present a case of a 5½-year-old Syrian refugee with two progressive lower-leg skin ulcers caused by Leishmania tropica.

One-step synthesis of indolizino[3,4,5-]isoindoles by manganese(I)-catalyzed C-H activation: structural studies and photophysical properties.

Herein, a regioselective synthesis of indolizino[3,4,5-]isoindoles, a valuable class of heterocycles with interesting luminescence properties, is described using manganese(I)-catalyzed C-H activation. The reported transformation proceeds in one-step and employs readily available 2-phenylpyridines as starting materials. Furthermore, the obtained single products exhibit blue-greenish fluorescence with high quantum yields.

Transcriptional dynamics of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP-RK transcription factor linked to reproduction.

Background: The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications.

Results: Gametogenesis of Ulva mutabilis, a model organism for green seaweeds, was studied.

Cysteinolic Acid Is a Widely Distributed Compatible Solute of Marine Microalgae.

Phytoplankton rely on bioactive zwitterionic and highly polar small metabolites with osmoregulatory properties to compensate changes in the salinity of the surrounding seawater. Dimethylsulfoniopropionate (DMSP) is a main representative of this class of metabolites. Salinity-dependent DMSP biosynthesis and turnover contribute significantly to the global sulfur cycle.

Development of a Highly Sensitive Luciferase-Based Reporter System To Study Two-Step Protein Secretion in Cyanobacteria.

Cyanobacteria, ubiquitous oxygenic photosynthetic bacteria, interact with the environment and their surrounding microbiome through the secretion of a variety of small molecules and proteins. The release of these compounds is mediated by sophisticated multiprotein complexes, also known as secretion systems. Genomic analyses indicate that protein and metabolite secretion systems are widely found in cyanobacteria; however, little is known regarding their function, regulation, and secreted effectors.

Bimetallic Mn, Fe, Co, and Ni Sites in a Four-Helix Bundle Protein: Metal Binding, Structure, and Peroxide Activation.

Bimetallic active sites in enzymes catalyze small-molecule conversions that are among the top 10 challenges in chemistry. As different metal cofactors are typically incorporated in varying protein scaffolds, it is demanding to disentangle the individual contributions of the metal and the protein matrix to the activity. Here, we compared the structure, properties, and hydrogen peroxide reactivity of four homobimetallic cofactors (Mn(II), Fe(II), Co(II), Ni(II)) that were reconstituted into a four-helix bundle protein.

Draft Genome Sequence of Vibrio jasicida 20LP, an Opportunistic Bacterium Isolated from Fish Larvae.

We present the genome sequence of Vibrio jasicida 20LP, a bacterial strain retrieved from larvae of gilthead seabream (Sparus aurata), a highly valuable, model fish species in land-based aquaculture. Annotation of the V. jasicida 20LP genome reveals multiple genomic features potentially underpinning opportunistic associations with diverse marine animals.

High-Resolution Fluorescence Spectra of Airborne Biogenic Secondary Organic Aerosols: Comparisons to Primary Biological Aerosol Particles and Implications for Single-Particle Measurements.

Aqueous extracts of biogenic secondary organic aerosols (BSOAs) have been found to exhibit fluorescence that may interfere with the laser/light-induced fluorescence (LIF) detection of primary biological aerosol particles (PBAPs). In this study, we quantified the interference of BSOAs to PBAPs by directly measuring airborne BSOA particles, rather than aqueous extracts. BSOAs were generated by the reaction of -limonene (LIM) or α-pinene (PIN) and ozone (O) with or without ammonia in a chamber under controlled conditions.

A Modular Approach to the Antifungal Sphingofungin Family: Concise Total Synthesis of Sphingofungin A and C.

Sphingofungins are fungal natural products known to inhibit the biosynthesis of sphingolipids which play pivotal roles in various cell functions. Here, we report a short and flexible synthetic approach towards the sphingofungin family. Key step of the synthesis was a decarboxylative cross-coupling reaction of chiral sulfinyl imines with a functionalized tartaric acid derivative, which yielded the core motif of sphingofungins carrying four consecutive stereocenters and a terminal double bond.

A Catalog of Natural Products Occurring in Watermelon-.

Sweet dessert watermelon () is one of the most important vegetable crops consumed throughout the world. The chemical composition of watermelon provides both high nutritional value and various health benefits. The present manuscript introduces a catalog of 1,679 small molecules occurring in the watermelon and their cheminformatics analysis for diverse features.

Discovering pesticides and their TPs in Luxembourg waters using open cheminformatics approaches.

The diversity of hundreds of thousands of potential organic pollutants and the lack of (publicly available) information about many of them is a huge challenge for environmental sciences, engineering, and regulation. Suspect screening based on high-resolution liquid chromatography-mass spectrometry (LC-HRMS) has enormous potential to help characterize the presence of these chemicals in our environment, enabling the detection of known and newly emerging pollutants, as well as their potential transformation products (TPs). Here, suspect list creation (focusing on pesticides relevant for Luxembourg, incorporating data sources in 4 languages) was coupled to an automated retrieval of related TPs from PubChem based on high confidence suspect hits, to screen for pesticides and their TPs in Luxembourgish river samples.