Artificial intelligence: the human response to approach the complexity of big data in biology.

Since the late 2010s, artificial intelligence (AI), encompassing machine learning and propelled by deep learning, has transformed life science research. It has become a crucial tool for advancing the computational analysis of biological processes, the discovery of natural products, and the study of ecosystem dynamics. This review explores how the rapid increase in high-throughput omics data acquisition has driven the need for AI-based analysis in life sciences, with a particular focus on plant sciences, animal sciences, and microbiology.

Beyond Phase Equilibria: Selecting Suitable Solvent Systems for Reactive Extraction of Carboxylic Acids.

Reactive extraction is an attractive separation technology that can replace energy-intensive water evaporation steps in the industrial production of carboxylic acids. We systematically review the current literature on the extraction of low-value bioproducts and thereby identify the reduced availability of predictive models, limited selectivity, and challenging phase separation as possible bottlenecks in the industrial implementation of reactive extraction. Furthermore, we discuss requirements and strategies for closing the material cycles for batch and continuous processes.

Gaps and strategies for accurate simulation of waterlogging impacts on crop productivity.

With the changing climate, soil waterlogging is a growing threat to food security. Yet, contemporary approaches employed in crop models to simulate waterlogging are in their infancy. By analysing 21 crop models, we show that critical deficiencies persist in accurately simulating capillary rise, crop resistance to transient periods of waterlogging, crop recovery mechanisms, and the effects on soil nitrogen processes, phenology and yield components.

subMG automates data submission for metagenomics studies.

Background: Publicly available metagenomics datasets are crucial for ensuring the reproducibility of scientific findings and supporting contemporary large-scale studies. However, submitting a comprehensive metagenomics dataset is both cumbersome and time-consuming. It requires including sample information, sequencing reads, assemblies, binned contigs, metagenome-assembled genomes (MAGs), and appropriate metadata.

Engineering of Corynebacterium glutamicum for the synthesis of aromatic compounds.

A significant proportion of industrially important small molecules are aromatic, and the majority of these compounds are produced chemically, relying heavily on fossil resources. In bacteria and plants, the shikimate pathway and related biosynthetic routes serve as the primary sources of aromatic compounds. Microbial cell factories, which are poised to play a central role in the emerging bio-based economy, provide a sustainable alternative for producing commercially valuable aromatics from renewable resources.

Formation of spatial vegetation patterns in heterogeneous environments.

Functioning of many resource-limited ecosystems is facilitated through spatial patterns. Patterns can indicate ecosystems productivity and resilience, but the interpretation of a pattern requires good understanding of its structure and underlying biophysical processes. Regular patterns are understood to form autogenously through self-organization, for which exogenous heterogeneities are negligible.

Immobilization of Inorganic Phosphorus on Soils by Zinc Oxide Engineered Nanoparticles.

The overuse of inorganic phosphate fertilizers in soils has led to the transfer of inorganic phosphorus (Pi) to aquatic ecosystems, resulting in eutrophication. Adsorption-desorption studies in batch systems were used to evaluate the effect of adding 1% zinc oxide (ZnO) engineered nanoparticles (ENPs) on Pi retention in Ultisol, and Mollisol soils. The 1% ZnO-ENPs showed increased chemical properties such as pH, electrical conductivity, and organic matter content, and reduce nutrient bioavailability (P, N, and Zn), and physical properties such as surface area and pore size of the two soils.

The mycotoxin Beauvericin is an uncompetitive inhibitor of Cathepsin B.

Beauvericin (BEA), a cyclic depsipeptide, is a mycotoxin of the enniatin family and the secondary metabolite of various toxigenic fungi. Multiple biological functions of BEA have been well investigated, such as anti-cancer, anti-inflammatory, anti-microbial, and immune-activating functions. In a recent study, we showed that BEA can target Toll-like receptor 4 (TLR4) to induce dendritic cell (DC) activation.

Identification of non-charged 7.44 analogs interacting with the NHR2 domain of RUNX1-ETO with improved antiproliferative effect in RUNX-ETO positive cells.

The RUNX1/ETO fusion protein is a chimeric transcription factor in acute myeloid leukemia (AML) created by chromosomal translocation t(8;21)(q22;q22). t(8;21) abnormality is associated with 12% of de novo AML cases and up to 40% in the AML subtype M2. Previously, we identified the small-molecule inhibitor 7.

Yield Sensitivity of Mungbean ( L.) Genotypes to Different Agrivoltaic Environments in Tropical Nigeria.

Genotype by environment (G × E) interaction is a magnitude change in the performance of a genotype when grown in contrasting environments. The sensitivity of a genotype to different environmental conditions is an important determinant of its suitability for cultivation in a specific environment or across multiple environments. In many nations of the world, where the drive to achieve a net-zero CO emission by 2030 has spurred significant investments in clean energy sources such as photovoltaics with a resultant conversion of some agricultural lands to photovoltaic facilities, there is a need to find the right balance between addressing the food and energy crises.

Seed-to-plant-tracking: automated phenotyping of seeds and corresponding plants of Arabidopsis.

Plants adapt seed traits in response to different environmental triggers, supporting the survival of the next generation. To elucidate the mechanistic understanding of such adaptations it is important to characterize the distributions of seed traits by phenotyping seeds on an individual scale and to correlate these traits with corresponding plant properties. Here we introduce a seed-to-plant-tracking pipeline which enables automated handling and high precision phenotyping of Arabidopsis seeds as well as germination detection and early growth quantification of emerging plants.

TopCysteineDB: A Cysteinome-wide Database Integrating Structural and Chemoproteomics Data for Cysteine Ligandability Prediction.

Development of targeted covalent inhibitors and covalent ligand-first approaches have emerged as a powerful strategy in drug design, with cysteines being attractive targets due to their nucleophilicity and relative scarcity. While structural biology and chemoproteomics approaches have generated extensive data on cysteine ligandability, these complementary data types remain largely disconnected. Here, we present TopCysteineDB, a comprehensive resource integrating structural information from the PDB with chemoproteomics data from activity-based protein profiling experiments.

Characterisation and Harnessing of 5-Hydroxymethylfurfural Metabolism in Pseudomonas umsongensis GO16 for the Production of 2,5-Furandicarboxylic Acid.

In the search for biobased alternatives to traditional fossil plastics, 2,5-furandicarboxylic acid (FDCA) represents a potential substitute to terephthalic acid (TPA), a monomer of the ubiquitous polyester, polyethylene terephthalate (PET). Pseudomonas umsongensis GO16, which can metabolise TPA and ethylene glycol (EG), can also oxidise 5-hydroxymethylfurfural (HMF), a precursor to FDCA. The enzymes involved in the oxidation to FDCA, PsfA and PsfG, were identified and characterised.

Biosurfactant biosynthesis by Alcanivorax borkumensis and its role in oil biodegradation.

The marine bacterium Alcanivorax borkumensis degrades alkanes derived from phytoplankton, natural hydrocarbon seeps and oil spills. We study the biosynthesis and function of a glycine-glucolipid biosurfactant from A. borkumensis for alkane degradation and identify a gene cluster encoding a nonribosomal peptide synthetase, glycosyltransferase and phosphopantetheinyl transferase.

On the importance of rhizosphere conductance and soil-root contact in drying soils.

Background And Aims: Root water uptake (RWU) is influenced by rhizosphere conductance and soil-root contact, which vary with soil texture and root structure, including root hairs. Current simplified models often fail to capture the spatial complexity of these interactions in drying soils. This study aims to examine how rhizosphere conductance, soil-root contact, and root hairs affect RWU.

Introduction of a lipidomics scoring system for data quality assessment.

The scientific field of lipidomics has shown a constantly growing publication number in recent years, which is accompanied by an increasing need for quality standards. While the official shorthand nomenclature of lipids is a first and important step toward a reporting quality tool, an additional point score would reflect the quality of reported data at an even more detailed granularity. Thus, we propose a lipidomics scoring scheme that considers all the different layers of analytical information to be obtained by mass spectrometry, chromatography, and ion mobility spectrometry and awards scoring points for each of them.

Modeling Cut Rose Yield Over an 18-Month Period After Compost Amendment Using Repeated Sigmoidal Gompertz Curve Fitting.

Understanding the growth, development, and production patterns of perennial crops is crucial for optimizing agricultural practices and enhancing crop productivity. Growth models are valuable tools in this regard, offering insights into how crops respond to different experimental treatments. This study evaluates the suitability of repeated Gompertz growth curves for assessing the impact of compost amendment on the yield of cut roses over an 18-month period.

Human chitinases and chitinase-like proteins as emerging drug targets - a medicinal chemistry perspective.

Human chitinases and chitinase-like proteins (CLPs) provide the immune system with the ability to recognize or process chitin originating from chitinous pathogens. In addition to their role in host defense, most members of this protein family have evolved pleiotropic cellular effector functions broadly related to immune homeostasis, cell proliferation, and tissue remodeling. This wide-ranging ability to modulate crucial cellular processes proceeds the activation of cellular signal transduction cascades and appears to be fully independent of chitin recognition.

Inhibitory effect of plant flavonoid cyanidin on oral microbial biofilm.

Unlabelled: As primary colonizers of the tooth surface, oral streptococci play a crucial role in dental caries development. Numerous natural compounds, including flavonoids, are emerging as promising agents for inhibiting dental biofilm formation without compromising bacterial viability, underscoring their potential in non-bactericidal antibiofilm strategies. This study investigated the effects and mechanism of action of the unmodified plant flavonoid cyanidin on the growth and sucrose-dependent biofilm formation of oral streptococci, with a particular focus on the cariogenic pathogen .

Contribution of arbuscular mycorrhiza and exoenzymes to nitrogen acquisition of sorghum under drought.

Introduction: For low-fertile and degraded soils of sub-Saharan Africa, nitrogen (N) is often the most growth-limiting factor restricting crop yields. The often-suggested exploitation of advantageous rhizosphere traits such as enzyme secretion and/or the symbiosis with arbuscular mycorrhizal fungi (AMF) remains to be validated as a potential strategy to overcome N limitation, especially when N deficiency co-occurs with further abiotic stresses such as water scarcity.

Methods: Three sorghum genotypes were cultivated in soil mesocosms with a root-exclusion compartment, where only AMF could scavenge for nutrients under drought and optimal conditions.

PyPE_RESP: A Tool to Facilitate and Standardize Derivation of RESP Charges.

We introduce PyPE_RESP, a tool to facilitate and standardize partial atomic charge derivation using the Restrained Electrostatic Potential (RESP) approach. PyPE_RESP builds upon the open-source Python package RDKit for chemoinformatics and the AMBER suite for molecular simulations. PyPE_RESP provides an easy setup of multiconformer and multimolecule RESP fitting while allowing a comprehensive definition of charge constraint groups through multiple methods.

Legacy of severe soil degradation hinders the buildup of mineral-associated soil organic carbon.

Global efforts target a soil organic carbon (SOC) enhancement rate of 2.4 ‰ y in the upper 30 cm of agricultural soils to address declining soil productivity associated with declining SOC stocks. We explored a unique chronosequence of homogeneous soils formed after mining in Germany, which serve conventional agriculture and exhibit a large margin for SOC storage, but limited SOC accrual, to study SOC protection mechanisms and accrual constraints.

Effect of simulated acidification on soil properties and plant nutrient uptake of eggplant in greenhouse.

Soil acidification adversely affects plant growth and development by decreasing the accessibility of roots to essential nutrients. Thus, it decreases crop yield. However, there has been a lack of systematic research on how soil acidification influences nutrient absorption in eggplant cultivated in greenhouse.

A Study of Thin Films Based on Polylactide and Vanillic Acid-Crucial Properties Relevant to Packaging.

In recent years, there has been a growing emphasis on packaging made from biodegradable materials. These materials not only help to reduce environmental impact, but also extend the shelf life of food products, thereby contributing to a significant reduction in food waste. In order to develop novel biodegradable polymeric films for use as active packaging, polylactide materials filled with vanillic acid were prepared.

Unveiling microbial single-cell growth dynamics under rapid periodic oxygen oscillations.

Microbial metabolism and growth are tightly linked to oxygen (O). Microbes experience fluctuating O levels in natural environments; however, our understanding of how cells respond to fluctuating O over various time scales remains limited due to challenges in observing microbial growth at single-cell resolution under controlled O conditions and in linking individual cell growth with the specific O microenvironment. We performed time-resolved microbial growth analyses at single-cell resolution under a temporally controlled O supply.