Re-engineering a transferase scaffold for indole C3 methylation in diketopiperazines.

The pyrroloindole (hexahydropyrrolo[2,3-b]indole, HPI) structural motif is present in a wide range of natural products with various biological activities, yet its chemical synthesis poses a challenge, particularly regarding methylation at the indole C3 position. In nature, S-adenosyl methionine (SAM)-dependent methyltransferases efficiently catalyze this reaction with high stereoselectivity. This study presents the investigation and rational re-design of a potential methyltransferase, termed SeMT, from the actinomycete Saccharopolyspora erythraea.

Enhanced short-term prediction of urban PM concentrations by improved hybrid deep learning.

Purpose: The aim of this study was to investigate the impact of improved deep learning model on the predictive performance of PM concentration.

Methods: We developed a new model combining one-dimensional convolutional neural network and bidirectional long short-term memory neural network to predict PM concentrations at hourly intervals. The air pollution observation data from 2020 to 2022 collected at several national air quality monitoring stations in Shenyang (Liaoning province, China) were employed to train our model.

Complete mitochondrial genomes of the Prototheca genus: comparative genomics and evolutionary insights.

Background: Prototheca (Chlorophyta: Trebouxiophyceae) is a genus of non-photosynthetic microalgae that causes increasingly frequent infections in both humans and animals, collectively referred to as protothecosis The genetic landscape of the Prototheca algae has remained largely uncharted until recent advances in sequencing and genomics. In this study, a combination of Illumina and Oxford Nanopore technologies was employed for sequencing of 18 mitochondrial genomes, representing all currently recognized Prototheca species.

Results: The genomes differed in terms of size and GC content, ranging from 38 kbp to 68 kbp and from 25 to 30%, respectively.

Computationally guided genome rewiring of Escherichia coli and its application for nanopolyethylene terephthalate (PET) biodegradation and upcycling.

Numerous strategies for the biodegradation and upcycling of polyethylene terephthalate (PET) are under investigation. Here, we present a proof-of-concept study for reprogramming the Escherichia coli BL21(DE3) strain to degrade PET nanoparticles (nPET) without introducing foreign DNA and compromising native cellular fitness. In brief, native proteins selected in silico from the genome were repurposed to acquire artificial PETase activity without compromising their function and were subsequently replaced via CRISPR/Cas9 editing.

Rice cycles between drought and well-watered-adapted phenotypes by changing lateral root formation.

Background And Aims: Natural rainfed conditions present drought episodes interspersed with periods of moderate to high soil moisture levels. This study investigates the genetic variation in root-to-shoot growth in response to a wet-drought-wet cycle and aims to identify rice (Oryza sativa) lines differing in drought recovery, focusing on detailed root trait investigations.

Methods: 100 different rice accessions were screened under fluctuating moisture across three field seasons for GWAS (genome wide association study) analysis.

Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize.

Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over 200,000 variants, genetic, epigenetic, or both (termed binding quantitative trait loci (bQTL)), linked to cis-element occupancy.

Probing the Mechanism of Selective Phosphate Adsorption from Wastewater Using Aqueous and Synchrotron X-ray Characterization.

Ion exchange shows promise for recovering phosphate from wastewater as value-added products but requires high phosphate selectivity to compete with conventional treatment. Hybrid anion exchange (HAIX) resins, which contain nonselective basic functional groups and selective iron oxide nanoparticles (FeOnp), can remove phosphate from wastewater. However, knowledge gaps remain regarding the mechanisms of phosphate selectivity and influence of competing ions, hindering efforts to model adsorption dynamics and design adsorption processes for varying wastewaters.

Engineering of 1,4-Butanediol and Adipic Acid Metabolism in Pseudomonas taiwanensis for Upcycling to Aromatic Compounds.

The overwhelming amount of plastic produced is an unprecedented challenge for humanity due to the lack of end-of-life solutions for heterogeneous plastic wastes. One possibility is feedstock recycling of mixed plastics and complex polymers with subsequent biological funnelling and upcycling. Major depolymerisation products of common plastics such as polyurethanes, polyesters and polyamides include aliphatic dicarboxylic acids or diols such as adipic acid (AA) and 1,4-butanediol (BDO), which can be metabolised by engineered Pseudomonas putida strains.

Radial oxygen loss of Typha latifolia outperforms microbial effects in heavy metal(loid) stabilization.

Wetland plants play a critical role in the remediation of tailings pond wetlands. Their unique radial oxygen loss (ROL) and rhizosphere microbial communities can modify soil properties (e.g.

Photosynthate distribution determines spatial patterns in the rhizosphere microbiota of the maize root system.

The spatial variation and underlying mechanisms of pattern formation in the rhizosphere microbiome are not well understood. We demonstrate that specific patterns in the distribution of recently fixed carbon within the plant root system influence the spatial organization of the rhizosphere microbiota. Non-invasive analysis of carbon allocation in the maize root system by C tracer-based positron emission tomography combined with magnetic resonance imaging reveals high spatial heterogeneity with highest C-signal accumulations at root tips and differences between root types.

Fuels Mediate the Influence of Climate Teleconnections on Wildfires in Dryland Ecosystems.

Climate teleconnections modulate regional wildfire occurrence. Understanding the underlying mechanisms is critical for sub-seasonal to annual wildfire predictions since the magnitude of certain teleconnection climate modes (TCMs) intensifies or they may undergo phase shifts. Here, we study how TCMs govern wildfire activity and compare the effects of weather and fuels in mediating the influence of TCMs on wildfires.

The bacterial ESCRT-III PspA rods thin lipid tubules and increase membrane curvature through helix α0 interactions.

The phage shock protein A (PspA), a bacterial member of the endosomal sorting complexes required for transport (ESCRT)-III superfamily, forms rod-shaped helical assemblies that internalize membrane tubules. The N-terminal helix α0 of PspA (and other ESCRT-III members) has been suggested to act as a membrane anchor; the detailed mechanism, however, of how it binds to membranes and eventually triggers membrane fusion and/or fission events remains unclear. By solving a total of 15 cryoelectron microscopy (cryo-EM) structures of PspA and a truncation lacking the N-terminal helix α0 in the presence of polar lipid membranes, we show in molecular detail how PspA interacts with and remodels membranes: Binding of the N-terminal helix α0 in the outer tubular membrane leaflet induces membrane curvature, supporting membrane tubulation by PspA.

Creating Rapid Oxygen Oscillations in Microbial Single-cell Growth Analysis using a Microfluidic Double-layer Device.

Microbial single-cell analysis using microfluidics coupled with time-lapse microscopy holds promise for investigating microbial growth behavior under confined environments with spatiotemporal resolution, offering insights that cannot be gained from conventional cultivation and analytical platforms. Oxygen plays a crucial role in determining microbial growth. However, temporal control in the range of seconds has not been implemented in microbial analysis using microfluidics.

Constitutive and Regulatory Responses of Arabidopsis thaliana to Harmonically Oscillating Light.

The rate of net CO uptake is proportional to dim light and saturates when the light exceeds the plant's assimilation capacity. This simple relationship between constant light and photosynthesis becomes intriguingly complex when the light oscillates. The rates of photosynthesis may differ between the descending and ascending phases of light oscillation.

Application of nanoparticles for salinity stress management and biofortification in wheat: a review of dual approaches and insights.

Salinity stress is one of the most challenging constraints affecting wheat production, limiting both yield and nutritional quality. Wheat is one of the most important staple cereals as well as a major source of carbohydrates for a considerable portion of the world population, yet wheat has suffered from significant productivity constraints due to salt stress. Such stress adversely affects germination, vegetative growth, reproductive organ development, enzymatic activity, photosynthesis photostability, and hormonal equilibrium, eventually causing oxidative stress and drastic loss of crop yield.

Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation.

The metagenome analysis of complex environments with thousands of datasets, such as those in the Sequence Read Archive, requires substantial computational resources for it to be completed within a reasonable time frame. Efficient use of infrastructure is essential, and analyses must be fully reproducible with publicly available workflows to ensure transparency. Here, we introduce the Metagenomics-Toolkit, a scalable, data-agnostic workflow that automates the analysis of short and long metagenomic reads from Illumina and Oxford Nanopore Technology devices, respectively.

Yeast as C1 cell factory: Transforming methanol and Formate into high-value compounds.

Microbial transformation of greenhouse gases, such as carbon dioxide and methane, into valuable biochemicals appears as a key strategy to sustainably decarbonize manufacturing industries. Numerous unresolved technological constraints still hamper the industrial adoption of these single‑carbon (C1) gas-based bioprocesses. Conversion of these gases into liquid C1 compounds like methanol and formate helps to reduce emissions and close the carbon loop.

PubPlant - a continuously updated online resource for sequenced and published plant genomes.

Advances in next-generation sequencing technologies over the last decade have substantially reduced the cost and effort required to sequence plant genomes. Whereas early efforts focused primarily on economically important crops and model species, attention has now turned to a broader range of plants, including those with larger and more complex genomes. In 2024, the genomes of 500 plant species were published, including 370 sequenced for the first time.

Functionalized in Triplicate: A Ring-By-Ring Approach to Tailored Prodiginine Derivatives for Site-Specific Conjugation Through Click Chemistry.

The tripyrrole prototype alkaloid prodigiosin and members of the prodigiosin family are structurally diverse bacterial secondary metabolites. The privileged scaffold accounts for versatile biological activities, for example, antimicrobial, antitumoral, and immunosuppressive. Its Lewis-basic lipophilic tripyrrole core and the aliphatic side chains allow for passive membrane diffusion, thereby trespassing the natural permeability barrier.

Non-Invasive Phenotyping of Sugar Beet and Maize Roots Using Field-Scale Spectral Electrical Impedance Tomography.

Root systems are essential for plant water and nutrient uptake, but are difficult to characterize in-situ due to their inaccessibility. Spectral electrical impedance tomography (sEIT) is a non-invasive geoelectrical method that has shown potential to quantify root traits at the laboratory scale. However, field applications remain scarce due to technical limitations and challenges in separating soil and root polarization signatures.

Molecular mechanisms underlying the early steps of floral initiation in seasonal flowering genotypes of cultivated strawberry.

Floral initiation is essential for sexual reproduction in angiosperms and plays a critical role in determining crop yields. In cultivated strawberry, however, the molecular mechanisms underlying floral initiation remain poorly understood, with most studies focusing on a single genotype under controlled conditions. To gain more insight into this process, we conducted a field-based study in two countries using two seasonal flowering cultivars.

Tomato genomics and its relatives are breaking the genomics barriers.

Recent advances in high-quality genome sequencing have revolutionized research in the tomato clade (Solanum section Lycopersicon), enabling the generation of long-read and even chromosome-scale assemblies for cultivated tomato and its wild relatives. These data have shed light on tomato domestication and population genetics, and have facilitated breeding using exotic germplasm. This review summarizes progress in tomato genomics, focusing on the diversity of section Lycopersicon and its function as a reservoir of stress tolerance genes, including drought tolerance from Solanum pennellii, and pathogen resistance from S.

Screening uncalibrated priority pollutants by improved AHP-CRITIC method at development land.

Unlisted uncalibrated pollutants in the industrial land of northeast China are continuously accumulating due to insufficient regulatory control, posing a serious threat to the ecological environment and human health. To address this challenge and begin to quantify the currently unlisted uncalibrated pollutants present in the industrial land in northeast China, 170 candidate pollutants were screened based on the literature research method. The Analytical Hierarchy Process (AHP) and the Criteria Importance Through Intercrieria Correlation (CRITIC) were utilized equally to screen for priority control of unlisted uncalibrated pollutants.

Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée.

Cultivar Désirée is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Désirée, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, resulting in a high-contiguity chromosome-level assembly. We implemented a comprehensive annotation pipeline incorporating gene models and functional annotations from the Solanum tuberosum Phureja DM reference genome alongside RNA-seq reads to provide high-quality gene and transcript annotations.