Reactivation and long-term stabilization of the [NiFe] Hox hydrogenase of Synechocystis sp. PCC6803 by glutathione after oxygen exposure.

Hydrogenases are key enzymes forming or consuming hydrogen. The inactivation of these transition metal biocatalysts with oxygen limits their biotechnological applications. Oxygen-sensitive hydrogenases are distinguished from oxygen-insensitive (tolerant) ones by their initial hydrogen turnover rates influenced by oxygen.

Unveiling fungal strategies: Mycoremediation in multi-metal pesticide environment using proteomics.

Micropollutants, such as heavy metals and pesticides, inhibit microbial growth, threatening ecosystems. Yet, the mechanism behind mycoremediation of the pesticide lindane and multiple metals (Cd, Total Cr, Cu, Ni, Pb, Zn) remains poorly understood. In our study, we investigated cellular responses in Aspergillus fumigatus PD-18 using LC-MS/MS, identifying 2190 proteins, 1147 of which were consistently present under both stress conditions.

Contrasting fertilization and phenological stages shape microbial-mediated phosphorus cycling in a maize agroecosystem.

Phosphorus (P) is essential for plants but often limited in soils, with microbes playing a key role in its cycling. P deficiency in crops can be mitigated by applying by-products like sludge and struvite to enhance yield and sustainability. Here, we evaluated the contribution of four different types of fertilizers: i) conventional NPK; ii) sludge; iii) struvite; and iv) struvite+sludge in a semiarid maize plantation to the availability of P and the responses of the soil microbiome.

BioPrediction-RPI: Democratizing the prediction of interaction between non-coding RNA and protein with end-to-end machine learning.

Machine Learning (ML) algorithms have been important tools for the extraction of useful knowledge from biological sequences, particularly in healthcare, agriculture, and the environment. However, the categorical and unstructured nature of these sequences requiring usually additional feature engineering steps, before an ML algorithm can be efficiently applied. The addition of these steps to the ML algorithm creates a processing pipeline, known as end-to-end ML.

Chemical mixture effects on the simplified human intestinal microbiota: Assessing xenobiotics at environmentally realistic concentrations.

The microbial community present in our intestines is pivotal for converting indigestible substances into vital nutrients and signaling molecules such as short-chain fatty acids (SCFAs). These compounds have considerable influence over our immune system and the development of diverse human diseases. However, ingested environmental contaminants, known as xenobiotics, can upset the delicate balance of the microbial gut community and enzymatic processes, consequently affecting the host organism.

BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification.

The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification.

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species.

Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking.

Single and combined exposures to bisphenol A and benzophenone-3 during early mouse pregnancy have differential effects on fetal and placental development.

Endocrine disrupting chemicals (EDCs) possess the capability to interfere with the endocrine system by binding to hormone receptors, for example on immune cells. Specific effects have already been described for individual substances, but the impact of exposure to chemical mixtures during pregnancy on maternal immune regulation, placentation and fetal development is not known. In this study, we aimed to investigate the combined effects of two widespread EDCs, bisphenol A (BPA) and benzophenone-3 (BP-3), at allowed concentrations on crucial pregnancy processes such as implantation, placentation, uterine immune cell populations and fetal growth.

Microbiomes: A New Open Section in .

As the Editor-in-Chief of , it is my pleasure to introduce a new Section of this journal [...

The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.

Background: Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the generation of metagenomics data has increased exponentially, and so has the availability and reusability of data present in public repositories. However, identifying which datasets and associated metadata are available is not straightforward.

Evaluation of Antioxidant Activity and Biotransformation of Fruit: The Effect of In Vitro and Ex Vivo Gut Microbiota Metabolism.

biological effects are attributed to several bioactive metabolites. However, these actions could be altered in vivo by biotransformation reactions mainly via gut microbiota. This study assessed gut microbiota effect on the biotransformation of metabolites both in vitro and ex vivo.

Bacterial Dehydrogenases Facilitate Oxidative Inactivation and Bioremediation of Chloramphenicol.

Antimicrobial resistance represents a major threat to human health and knowledge of the underlying mechanisms is therefore vital. Here, we report the discovery and characterization of oxidoreductases that inactivate the broad-spectrum antibiotic chloramphenicol via dual oxidation of the C3-hydroxyl group. Accordingly, chloramphenicol oxidation either depends on standalone glucose-methanol-choline (GMC)-type flavoenzymes, or on additional aldehyde dehydrogenases that boost overall turnover.

DSM 2243 Alleviates Bile Acid Stress Response in and by Transformation of Bile Acids.

Bile acids are crucial for the uptake of dietary lipids and can shape the gut-microbiome composition. This latter function is associated with the toxicity of bile acids and can be modulated by bile acid modifying bacteria such as , but the molecular details of the interaction of bacteria depending on bile acid modifications are not well understood. In order to unravel the molecular response to bile acids and their metabolites, we cultivated eight strains from a human intestinal microbiome model alone and in co-culture with in the presence of cholic acid (CA) and deoxycholic acid (DCA).

Adaptation and Resistance: How Copes with the Bisphenol A Substitute Bisphenol F.

Bisphenols are used in the process of polymerization of polycarbonate plastics and epoxy resins. Bisphenols can easily migrate out of plastic products and enter the gastrointestinal system. By increasing colonic inflammation in mice, disrupting the intestinal bacterial community structure and altering the microbial membrane transport system in zebrafish, bisphenols seem to interfere with the gut microbiome.

Associated bacterial microbiome responds opportunistic once algal host Scenedesmus vacuolatus is attacked by endoparasite Amoeboaphelidium protococcarum.

The interactions of microalgae and their associated microbiomes have come to the fore of applied phycological research in recent years. However, the functional mechanisms of microalgal interactions remain largely unknown. Here, we examine functional protein patterns of the microalgae Scenedesmus vacuolatus and its associated bacterial community during algal infection by the endoparasite Amoeboaphelidium protococcarum.

BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria.

Recent technological advances have led to an exponential expansion of biological sequence data and extraction of meaningful information through Machine Learning (ML) algorithms. This knowledge has improved the understanding of mechanisms related to several fatal diseases, e.g.

Microbial community functioning during plant litter decomposition.

Microbial life in soil is fueled by dissolved organic matter (DOM) that leaches from the litter layer. It is well known that decomposer communities adapt to the available litter source, but it remains unclear if they functionally compete or synergistically address different litter types. Therefore, we decomposed beech, oak, pine and grass litter from two geologically distinct sites in a lab-scale decomposition experiment.

An Annotated Inventory of Tanzanian Medicinal Plants Traditionally Used for the Treatment of Respiratory Bacterial Infections.

This review comprehensively covers and analyzes scientific information on plants used in Tanzanian traditional medicine against respiratory diseases. It covers ethnobotanical and ethnopharmacological information extracted from SciFinder, Google Scholar, and Reaxys as well as the literature collected at the Institute of Traditional Medicine in Dar-es-Salaam. Crude extracts and fractions of 133 plant species have literature reports on antimicrobial bioassays.

Oxygen and nitrogen production by an ammonia-oxidizing archaeon.

Ammonia-oxidizing archaea (AOA) are one of the most abundant groups of microbes in the world’s oceans and are key players in the nitrogen cycle. Their energy metabolism—the oxidation of ammonia to nitrite—requires oxygen. Nevertheless, AOA are abundant in environments where oxygen is undetectable.