Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of mutations.

Mutations in splicing factor 3B subunit 1 () frequently occur in patients with chronic lymphocytic leukemia (CLL) and myelodysplastic syndromes (MDSs). These mutations have different effects on the disease prognosis with beneficial effect in MDS and worse prognosis in CLL patients. A full-length transcriptome approach can expand our knowledge on mutation effects on RNA splicing and its contribution to patient survival and treatment options.

Effects of environmental changes on soil respiration in arid, cold, temperate, and tropical zones.

Soil respiration (R) is projected to be substantially affected by climate change, impacting the storage, equilibrium, and movement of terrestrial carbon (C). However, uncertainties surrounding the responses of R to climate change and soil nitrogen (N) enrichment are linked to mechanisms specific to diverse climate zones. A comprehensive meta-analysis was conducted to address this, evaluating the global effects of warming, increased precipitation, and N enrichment on R across various climate zones and ecosystems.

Do nanoparticles and colloids replenish soil phosphorus in the rhizosphere of winter wheat?

The rhizosphere is generally depleted in nutrients, but as a hotspot of microbial activity it fosters crop P uptake. We hypothesized that P contents of water extractable nanoparticles (<0.1 μm) and small sized colloids (<0.

Draft genome sequence and annotation of the polyextremotolerant polyol lipid-producing fungus aureobasidium pullulans NRRL 62042.

Objectives: The ascomycotic yeast-like fungus Aureobasidium exhibits the natural ability to synthesize several secondary metabolites, like polymalic acid, pullulan, or polyol lipids, with potential biotechnological applications. Combined with its polyextremotolerance, these properties make Aureobasidium a promising production host candidate. Hence, plenty of genomes of Aureobasidia have been sequenced recently.

Amino acid-sulphur decomposition in agricultural soil profile along a long-term recultivation chronosequence.

The significance of sulphur (S) availability for crop yield and quality is highlighted under the global S deficiency scenario. However, little is known about the temporal trend in belowground organic S mineralisation when restoring land to productive agricultural systems, particularly for the deeper soil parts. Therefore, we investigated the decomposition of S-labelled methionine in surface (0-30 cm) and subsurface soil (30-60 cm and 60-90 cm) over a 48-year recultivation chronosequence (sampled after1, 8, 14, 24 and 48 years).

The Antioxidant and HDAC-Inhibitor α-Lipoic Acid Is Synergistic with Exemestane in Estrogen Receptor-Positive Breast Cancer Cells.

Anti-estrogenic therapy is established in the management of estrogen receptor (ER)-positive breast cancer. However, to overcome resistance and improve therapeutic outcome, novel strategies are needed such as targeting widely recognized aberrant epigenetics. The study aims to investigate the combination of the aromatase inhibitor exemestane and the histone deacetylase (HDAC) inhibitor and antioxidant α-lipoic acid in ER-positive breast cancer cells.

Quantification of nisin concentration from fluorescence-based antimicrobial activity assay using Bayesian calibration.

Bacteriocins are ribosomally synthesized peptides with the innate ability to kill or inhibit growth of other bacteria. In recent years, bacteriocins have received increased interest, as their antimicrobial activity enhances food safety and shelf life by combatting pathogens such as Listeria monocytogenes. They also have application potential as an active pharmaceutical compound to combat multidrug-resistant pathogens.

Mechanical forces orchestrate the metabolism of the developing oilseed rape embryo.

The initial free expansion of the embryo within a seed is at some point inhibited by its contact with the testa, resulting in its formation of folds and borders. Although less obvious, mechanical forces appear to trigger and accelerate seed maturation. However, the mechanistic basis for this effect remains unclear.

Establishing an itaconic acid production process with Ustilago species on the low-cost substrate starch.

Ustilago maydis and Ustilago cynodontis are natural producers of a broad range of valuable molecules including itaconate, malate, glycolipids, and triacylglycerols. Both Ustilago species are insensitive toward medium impurities, and have previously been engineered for efficient itaconate production and stabilized yeast-like growth. Due to these features, these strains were already successfully used for the production of itaconate from different alternative feedstocks such as molasses, thick juice, and crude glycerol.

Amphicarpic development in Cardamine chenopodiifolia.

Amphicarpy is an unusual trait where two fruit types develop on the same plant: one above and the other belowground. This trait is not found in conventional model species. Therefore, its development and molecular genetics remain under-studied.

Corrigendum: Genome reduction in DSM 365 for chassis development.

[This corrects the article DOI: 10.3389/fbioe.2024.

Balancing pH and yield: exploring itaconic acid production in Ustilago cynodontis from an economic perspective.

Background: Itaconic acid is a promising bio-based building block for the synthesis of polymers, plastics, fibers and other materials. In recent years, Ustilago cynodontis has emerged as an additional itaconate producing non-conventional yeast, mainly due to its high acid tolerance, which significantly reduces saline waste coproduction during fermentation and downstream processing. As a result, this could likely improve the economic viability of the itaconic acid production process with Ustilaginaceae.

Soil heavy metal pollution promotes extracellular enzyme production by mediating microbial community structure during vegetation restoration of metallic tailing reservoir.

Vegetation restoration in metallic tailing reservoirs is imperative to restore the post-mining degraded ecosystems. Extracellular enzymes determine microbial resource acquisition in soils, yet the mechanisms controlling the enzyme activity and stoichiometry during vegetation restoration in metallic tailing reservoirs remain elusive. Here, we investigated the variations and drivers of C-, N- and P-acquiring enzymes together with microbial community along a 50-year vegetation restoration chronosequence in the China's largest vanadium titano-magnetite tailing reservoir.

Novel calibration design improves knowledge transfer across products for the characterization of pharmaceutical bioprocesses.

Modern machine learning has the potential to fundamentally change the way bioprocesses are developed. In particular, horizontal knowledge transfer methods, which seek to exploit data from historical processes to facilitate process development for a new product, provide an opportunity to rethink current workflows. In this work, we first assess the potential of two knowledge transfer approaches, meta learning and one-hot encoding, in combination with Gaussian process (GP) models.

Molecular Mechanisms Underlying Single Nucleotide Polymorphism-Induced Reactivity Decrease in CYP2D6.

Cytochrome P450 2D6 (CYP2D6) is one of the most important enzymes involved in drug metabolism. Genetic polymorphism can influence drug metabolism by CYP2D6 such that a therapy is seriously affected by under- or overdosing of drugs. However, a general explanation at the atomistic level for poor activity is missing so far.

AutoBioTech─A Versatile Biofoundry for Automated Strain Engineering.

The inevitable transition from petrochemical production processes to renewable alternatives has sparked the emergence of biofoundries in recent years. Manual engineering of microbes will not be sufficient to meet the ever-increasing demand for novel producer strains. Here we describe the AutoBioTech platform, a fully automated laboratory system with 14 devices to perform operations for strain construction without human interaction.

Potato Berries as a Valuable Source of Compounds Potentially Applicable in Crop Protection and Pharmaceutical Sectors: A Review.

Potato () is a major agricultural crop cultivated worldwide. To meet market demand, breeding programs focus on enhancing important agricultural traits such as disease resistance and improvement of tuber palatability. However, while potato tubers get a lot of attention from research, potato berries are mostly overlooked due to their level of toxicity and lack of usefulness for the food production sector.

Reliable Genomic Integration Sites in Identified by Two-Dimensional Transcriptome Analysis.

Genomic integration is commonly used to engineer stable production hosts. However, so far, for many microbial workhorses, only a few integration sites have been characterized, thereby restraining advanced strain engineering that requires multiple insertions. Here, we report on the identification of novel genomic integration sites, so-called landing pads, for KT2440.

Benefits and limits of biological nitrification inhibitors for plant nitrogen uptake and the environment.

Plant growth and high yields are secured by intensive use of nitrogen (N) fertilizer, which, however, pollutes the environment, especially when N is in the form of nitrate. Ammonium is oxidized to nitrate by nitrifiers, but roots can release biological nitrification inhibitors (BNIs). Under what conditions does root-exudation of BNIs facilitate nitrogen N uptake and reduce pollution by N loss to the environment? We modeled the spatial-temporal dynamics of nitrifiers, ammonium, nitrate, and BNIs around a root and simulated root N uptake and net rhizosphere N loss over the plant's life cycle.

hopsy - a methods marketplace for convex polytope sampling in Python.

Summary: Effective collaboration between developers of Bayesian inference methods and users is key to advance our quantitative understanding of biosystems. We here present hopsy, a versatile open-source platform designed to provide convenient access to powerful Markov chain Monte Carlo sampling algorithms tailored to models defined on convex polytopes (CP). Based on the high-performance C++ sampling library HOPS, hopsy inherits its strengths and extends its functionalities with the accessibility of the Python programming language.

A meta-analysis of elevated O3 effects on herbaceous plants antioxidant oxidase activity.

Increases in near-surface ozone (O3) concentrations is a global environmental problem. High-concentration O3 induces stress in plants, which can lead to visible damage to plants, reduced photosynthesis, accelerated aging, inhibited growth, and can even plant death. However, its impact has not been comprehensively evaluated because of the response differences between individual plant species, environmental O3 concentration, and duration of O3 stress in plants.

Multi-year aboveground data of minirhizotron facilities in Selhausen.

Improved understanding of crops' response to soil water stress is important to advance soil-plant system models and to support crop breeding, crop and varietal selection, and management decisions to minimize negative impacts. Studies on eco-physiological crop characteristics from leaf to canopy for different soil water conditions and crops are often carried out at controlled conditions. In-field measurements under realistic field conditions and data of plant water potential, its links with CO and HO gas fluxes, and crop growth processes are rare.