PLoS Comput Biol. 2025 Apr 23;21(4):e1013011. doi: 10.1371/journal.pcbi.1013011. Online ahead of print.

ABSTRACT

Animal acoustic communication contains many structural features. Among these, temporal structure, or rhythmicity, is increasingly tested empirically and modelled quantitatively. Accelerando is a rhythmic structure which consists of temporal intervals increasing in rate over a sequence. Why this particular vocal behaviour is widespread in many different animal lineages, and how it evolved, is so far unknown. Here, we use evolutionary game theory and computer simulations to link two rhythmic aspects of animal communication, synchronization and overlap: We test whether rhythmic accelerando could evolve under a pressure for acoustic overlap in time. Our models show that higher acceleration values result in a higher payoff, driven by the higher relative overlap between sequences. The addition of a cost to the payoff matrix models a physiological disadvantage to high acceleration rates and introduces a divergence between an individual's incentive and the overall payoff of the population. Analysis of the invasion dynamics of acceleration strategies shows a stable, non-invadable range of strategies for moderate acceleration levels. Our computational simulations confirm these results: A simple selective pressure to maximise the expected overlap, while minimising the associated physiological cost, causes an initially isochronous population to evolve towards producing increasingly accelerating sequences until a population-wide equilibrium of rhythmic accelerando is reached. These results are robust to a broad range of parameter values. Overall, our analyses show that if overlap is beneficial, emergent evolutionary dynamics allow a population to gradually start producing accelerating sequences and reach a stable state of moderate acceleration. Finally, our modelling results closely match empirical data recorded from an avian species showing rhythmic accelerando, the African penguin. This shows the productive interplay between theoretical and empirical biology.

PMID:40267164 | DOI:10.1371/journal.pcbi.1013011

STAR Protoc. 2025 Apr 22;6(2):103786. doi: 10.1016/j.xpro.2025.103786. Online ahead of print.

ABSTRACT

Crabtree-positive yeasts rapidly consume glucose via glycolysis, making it difficult to experimentally estimate their actual glycolytic rate or flux. We present a stable isotope labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based protocol to quantitatively estimate glycolytic and related carbon metabolic fluxes using Saccharomyces cerevisiae. This approach defines time windows to capture glucose metabolic intermediate production before label saturation, enabling a comparison of glycolytic flux changes across different cells. This protocol provides a reliable, quantitative approach to study dynamic metabolic fluxes in these cells. For complete details on the use and execution of this protocol, please refer to Vengayil et al., 2024.1.

PMID:40266845 | DOI:10.1016/j.xpro.2025.103786

Insects. 2025 Mar 1;16(3):251. doi: 10.3390/insects16030251.

ABSTRACT

In insects, the number of life cycles varies inter- and intra-specifically, and it is widely accepted that the variation in the number of life cycles is an adaptive response to diverse environmental conditions. However, the molecular mechanism that underlies the variety and plasticity in the number of life cycles is largely unknown. In the silkworm, Bombyx mori, the Voltinism (V) locus has three alleles, V1(univoltine; dominant), V2 (bivoltine; standard), and V3 (polyvoltine; recessive), which are known to generate variation in the number of life cycles in a year under natural conditions, with obligatory diapause for the V1 allele, facultative diapause for V2, and non-diapause for V3. Here, we further confirm that the γ-aminobutyric acid (GABA)ergic neuron signal pathway modulates progeny diapause via controlling diapause hormone release. A population genetic analysis (Fst) revealed that the synaptic vesicle glycoprotein 2A and 2B (BmSV2A and BmSV2B) genes, tightly related to the transport of neurotransmitters, are located in the V locus. Importantly, using the CRISPR/Cas9 editing technique, we have discovered that the BmSV2A and BmSV2B genes increased or modified the expression of GABAergic neuron signal pathway genes, respectively. These results demonstrate that BmSV2A and BmSV2B, positioned within the V locus, could be involved in voltinism control via the GABAergic neuron signal pathway.

PMID:40266755 | DOI:10.3390/insects16030251

Vaccines (Basel). 2025 Feb 28;13(3):259. doi: 10.3390/vaccines13030259.

ABSTRACT

Background/Objectives: Limited research has compared tests assessing humoral and cellular immunity related to SARS-CoV-2 infection. This study evaluated immunoglobulin G for nucleocapsid (IgG(N)) and T-spot for nucleocapsid (T-spot(N)) assays against polymerase chain reaction (PCR) test results for identifying infected individuals. Methods: This study included participants who had completed five blood samplings since their second COVID-19 vaccination between 9 September 2021 and 6 November 2022. Chemiluminescent immunoassay (CLIA) tests measured the humoral immune response, IgG(S) and neutralizing activity tests the immune status, and IgG(N) tests the infection history. For cellar immunity, T-spot(S) indicated immune status, and T-spot(N) indicated infection history. Results: The primary outcome was the proportion of individuals who tested positive for PCR and the proportion who tested positive for IgG(N) and T-spot(N). Overall, this study included 2104 participants. In the PCR-negative group, 1838 individuals tested negative for IgG(N), whereas 64 tested positive at least once. The geometric mean of IgG(S) at T5 was 1541.7 AU/mL in the IgG(N)-negative group and 3965.8 AU/mL in the IgG(N)-positive group, which was 2.6 times higher. In the PCR-positive group, 25 individuals tested negative for IgG(N), while 177 tested positive at least once. The geometric mean of IgG(S) at T5 was 2700.6 AU/mL in the IgG(N)-negative group and 5400.8 AU/mL in the IgG(N)-positive group, showing higher values in the IgG(N)-positive group. Conclusions: A discrepancy was noted between PCR test results and the IgG(N) and T-spot(N) determinations. Combining multiple assays is required to accurately identify the past-infected population.

PMID:40266135 | DOI:10.3390/vaccines13030259

Vaccines (Basel). 2025 Feb 20;13(3):209. doi: 10.3390/vaccines13030209.

ABSTRACT

OBJECTIVES: Determination of reactogenicity and immunogenicity of a pentavalent candidate vaccine against S. flexneri 1b, 2a, 3a, 6, and Y (PLVF).

METHODS: The study involved 80 healthy adult volunteers aged 18-55 years. Groups were subcutaneously immunized twice at a 30-day interval with 62.5 μg/0.5 mL or 125 μg/0.5 mL of the vaccine.

RESULTS: During the entire 8-month period of post-vaccination observation, the vaccine was well tolerated, with no local or systemic reactions detected objectively. The results of laboratory studies demonstrated no effect on the main indicators of hemogram, biochemical blood test, or urinalysis. IgA, IgG, and IgM levels against LPS S. flexneri 1b, 2a, 3a, 6, and Y were examined before vaccination, a month after each vaccination, and 6 months after booster vaccination. One month after vaccination, IgA and IgG seroconversions were observed in 67.5-82.5% (depending on serotype) and 60-77.5% of volunteers, respectively. Booster immunization did not have a significant effect on vaccine immunogenicity. In two separate groups of 15 and 9 volunteers for mucosal sIgA, IgA, and IgG titer determination after immunization with a 125 μg vaccine dose, paired stool, and saliva samples were taken before and one month after vaccination. In 26.7-40% of volunteers, there was a 2-fold and higher increase in sIgA titer for the studied serotypes in the feces and in 66.7-88.9% in saliva. IgA and IgG 2-fold conversion rates were 26.7-53.3% and 33.3-46.7% in the feces, 33.3-77.9%, and 66.7-77.8% in saliva, respectively.

CONCLUSIONS: the tolerability of PLVF and the pronounced humoral immune response allow us to proceed to the phase 3 clinical trial stage.

PMID:40266069 | DOI:10.3390/vaccines13030209

Plants (Basel). 2025 Mar 17;14(6):935. doi: 10.3390/plants14060935.

ABSTRACT

Increasing global temperatures, in tandem with predicted increases in future frequencies of drought and flooding episodes, represent a threat to agricultural productivity [...].

PMID:40265884 | DOI:10.3390/plants14060935

Soft Matter. 2025 Apr 23. doi: 10.1039/d5sm00141b. Online ahead of print.

ABSTRACT

Granular materials are defined as collections of macroscopic dissipative particles. Although these systems are ubiquitous in our lives, the nature and the causes of their non-trivial collective dynamics still remain elusive and have attracted significant interest in non-equilibrium physics. Here, we focus on the vibrational dynamics of granular materials. While the vibrational dynamics of random packings have been examined concerning the jamming transition, previous research has overlooked the role of contact dissipations. We conducted numerical and analytical investigations into the vibrational dynamics of random packings influenced by the normal dissipative force, which is the simplest model for contact dissipations. Our findings reveal that the kinetic energy per mode diverges in the low-frequency range, following the scaling law with the frequency ωl, indicating that low-frequency modes experience strong excitation and that the equipartition of energy is violated. Additionally, the spatial structure factor of the velocity field displays the scaling law Sv(q) ∝ q-2 with the wavenumber q, which signifies that the velocity field has an infinitely long range. We demonstrate that these phenomena arise from the effects of weaker damping on softer modes, where the particle displacements parallel to the contacts are minimal in the low-frequency modes, rendering normal dissipation ineffective at damping these modes.

PMID:40265522 | DOI:10.1039/d5sm00141b

Comput Struct Biotechnol J. 2025 Apr 3;27:1511-1517. doi: 10.1016/j.csbj.2025.04.006. eCollection 2025.

ABSTRACT

Within the biopharmaceutical industry, the cell line development (CLD) process generates recombinant mammalian cell lines for the expression of therapeutic proteins. Analytical methods for the extensive characterisation of the protein product are well established; however, over recent years, next-generation sequencing (NGS) technologies have rapidly become an integral part of the CLD workflow. NGS can be used for different applications to characterise the genome, epigenome and transcriptome of cell lines. The resulting extensive datasets, especially when integrated with systems biology models, can give comprehensive insights that can be applied to optimize cell lines, media, and fermentation processes. NGS also provides comprehensive methods to monitor genetic variability during CLD. High coverage NGS experiments can indeed be used to ensure the integrity of plasmids, identify integration sites, and verify monoclonality of the cell lines. This review summarises the role of NGS in advancing biopharmaceutical production to ensure safety and efficacy of therapeutic proteins.

PMID:40265158 | PMC:PMC12013335 | DOI:10.1016/j.csbj.2025.04.006

Front Genet. 2025 Apr 8;16:1603498. doi: 10.3389/fgene.2025.1603498. eCollection 2025.

NO ABSTRACT

PMID:40264451 | PMC:PMC12011714 | DOI:10.3389/fgene.2025.1603498

Food Res Int. 2025 May;208:116288. doi: 10.1016/j.foodres.2025.116288. Epub 2025 Mar 16.

ABSTRACT

Induction of amyloid-like morphology in food proteins offers high potential to induce new techno-functional properties in food products (e.g. use as emulsifier, thickener or gelling agent in e.g. bakery and confectionery products). However, the health impact of amyloid-like fibril (ALF) consumption remains widely understudied and merits additional research. The aim of this study was to (partially) elucidate the general health impact of food-borne ALF consumption, using egg white ovalbumin as a case study. Based on in vitro cell culture models it was demonstrated that ovalbumin ALFs (i) do not induce direct cytotoxic effects on intestinal (Caco-2, IPEC-J2) and neuronal (SH-SY5Y) cell lines, but (ii) are able to induce a Toll-like-receptor-mediated innate immune response, similar to endogenous amyloids, in activated THP-1 cells. Furthermore, the consecutive in vitro digestion and absorption (enterocyte and M-cell) experiments demonstrated that ovalbumin ALFs (i) do not completely lose their ALF morphology upon in vitro gastrointestinal digestion, and that (ii) the ALF core sequences, located at the center of the ALF structure, are transported across Caco-2 based cell models, suggesting aggregate transport. In vivo, intestinal translocation of ingested ALFs would imply potential cross-seeding of endogenous, disease-related precursor proteins. The ability of ovalbumin ALFs to induce aggregation of a disease-related precursor protein, αSyn, was evaluated in a precursor overexpressing cell model. Here, it was illustrated that only homologous (αSyn) - but not heterologous (ovalbumin) - seeding resulted in intracellular aggregation bodies of (phosphorylated) αSyn. The lack of cross-seeding supports the assumption that ovalbumin ALF consumption is not a risk factor for the development of α-synucleinopathies like Parkinson's disease.

PMID:40263866 | DOI:10.1016/j.foodres.2025.116288

Food Res Int. 2025 May;208:116170. doi: 10.1016/j.foodres.2025.116170. Epub 2025 Mar 22.

NO ABSTRACT

PMID:40263834 | DOI:10.1016/j.foodres.2025.116170

Gene Ther. 2025 Apr 22. doi: 10.1038/s41434-025-00536-7. Online ahead of print.

ABSTRACT

Developing new strategies for local monitoring and delivery of immunosuppression is critical to making allografts safer and more accessible. Ex vivo genetic modification of grafts using machine perfusion presents a promising approach to improve graft function and modulate immune responses while minimizing risks of off-target effects and systemic immunogenicity in vivo. This proof-of-concept study demonstrates the feasibility of using normothermic machine perfusion (NMP) to mimic in vitro conditions for effective gene delivery. In this study, lentiviral vectors encoding the secreted biomarker Gaussia Luciferase (GLuc) and red fluorescent protein (RFP) were introduced ex vivo to rodent livers during a 72-h machine perfusion protocol. After an initial 24-h exposure to viral vectors, the organs were maintained in perfusion for an additional 48 h to monitor gene expression, aligning with in vitro benchmarks. Control livers were perfused in similar fashion, but without viral injections. Virally perfused livers exhibited nearly a 10-fold increase in luminescence compared to controls (p < 0.0001), indicating successful genetic modification of the organs. These findings validate the use of machine perfusion systems and viral vectors to genetically engineer whole organs ex vivo, laying the groundwork for a broad range of applications in transplantation through genetic manipulation of organ systems. Future studies will focus on refining this technology to enhance precision in gene expression and explore its implications for clinical translation.

PMID:40263629 | DOI:10.1038/s41434-025-00536-7

EMBO J. 2025 Apr 22. doi: 10.1038/s44318-024-00354-4. Online ahead of print.

NO ABSTRACT

PMID:40263601 | DOI:10.1038/s44318-024-00354-4

Mol Syst Biol. 2025 Apr 22. doi: 10.1038/s44320-025-00100-w. Online ahead of print.

ABSTRACT

Type 2 diabetes (T2D) presents a global health concern, with evidence highlighting the role of the human gut microbiome in metabolic diseases. This study employs metabolic modelling to elucidate changes in host-microbiome interactions in T2D. Glucose levels, diet, 16S sequences and metadata were collected for 1866 individuals. In addition, microbial community models, and ecological interactions were simulated for the gut microbiomes. Our findings revealed a significant decrease in metabolic fluxes provided by the host's diet to the microbiome in T2D patients, accompanied by increased within-community exchanges. Moreover, the diabetic microbiomes shift towards increased exploitative ecological interactions at the expense of collaborative interactions. The reduced microbiome-to-host butyrate flux, along with decreased fluxes of amino acids (including tryptophan), nucleotides, and B vitamins from the host's diet, further highlight the dysregulation in microbial-host interactions in diabetes. In addition, microbiomes of T2D patients exhibit enrichment in energy metabolism, indicative of increased metabolic activity and antagonism. This study sheds light on the increased microbiome autonomy and antagonism accompanying diabetes, and provides candidate metabolic targets for intervention studies and experimental validation.

PMID:40263590 | DOI:10.1038/s44320-025-00100-w

Nat Plants. 2025 Apr 22. doi: 10.1038/s41477-025-01984-0. Online ahead of print.

ABSTRACT

Auxins are a group of phytohormones that control plant growth and development. Their crucial role in plant physiology has inspired development of potent synthetic auxins that can be used as herbicides. Phenoxyacetic acid derivatives are a widely used group of auxin herbicides in agriculture and research. Despite their prevalence, the identity of the transporters required for distribution of these herbicides in plants is both poorly understood and the subject of controversial debate. Here we show that PIN-FORMED auxin transporters transport a range of phenoxyacetic acid herbicides across the membrane. We go on to characterize the molecular determinants of substrate specificity using a variety of different substrates as well as protein mutagenesis to probe the binding site. Finally, we present cryogenic electron microscopy structures of Arabidopsis thaliana PIN8 bound to either 2,4-dichlorophenoxyacetic acid or 4-chlorophenoxyacetic acid. These structures represent five key states from the transport cycle, allowing us to describe conformational changes associated with the transport cycle. Overall, our results reveal that phenoxyacetic acid herbicides use the same export machinery as endogenous auxins and exemplify how transporter binding sites undergo transformations that dictate substrate specificity. These results provide a foundation for future development of novel synthetic auxins and for precision breeding of herbicide-resistant crop plants.

PMID:40263580 | DOI:10.1038/s41477-025-01984-0

Sci Rep. 2025 Apr 22;15(1):13986. doi: 10.1038/s41598-025-96783-0.

ABSTRACT

Baeyer-Villiger monooxygenases (BVMOs) are versatile biocatalysts that catalyse the oxidation of ketones to esters with high regio- and enantioselectivity, operating under mild reaction conditions while reducing hazardous waste. Some BVMOs can convert cellulose-derived alkyl levulinates to 3-acetoxypropionates (3-APs), which are key intermediates in the production of 3-hydroxypropionic acid (3-HP), a versatile building block chemical. In this study, a BVMO from Acinetobacter radioresistens (Ar-BVMO) was tested as a biocatalyst for the conversion of three marketed alkyl levulinates: methyl, ethyl and butyl levulinate. The enzyme showed 4-fold higher catalytic efficiency (kcat/KM) and enhanced regioselectivity for the desired 3-AP product (4:1 ratio) when using butyl levulinate as a substrate. Escherichia coli whole-cells over-expressing Ar-BVMO were exploited to increase the product yield, achieving 85% conversion in 9 h. To further improve the sustainability of this biotransformation, butyl levulinate was obtained via microwave-assisted alcoholysis of pulp, a renewable cellulose feedstock, achieving 92.7% selectivity. Despite challenges posed by poor solubility of the resulting mixture in aqueous environment, Ar-BVMO in cell lysates was able to fully convert butyl levulinate within 24 h, efficiently producing 3-HP precursors without additional purification steps. These findings highlight the feasibility of this chemoenzymatic approach to convert cellulose-based raw materials to platform chemicals.

PMID:40263398 | DOI:10.1038/s41598-025-96783-0

Sci Rep. 2025 Apr 22;15(1):13844. doi: 10.1038/s41598-025-97105-0.

ABSTRACT

Accurate species identification is essential in biology, ecology, medicine, and agriculture, yet traditional methods relying on morphological characteristics often fail due to phenotypic plasticity and cryptic species. These limitations are particularly pronounced in small organisms with minimal distinguishing features. DNA barcoding has become a popular alternative; however, it requires invasive tissue sampling, making it unsuitable for delicate or rare organisms like insects and spiders. To address this challenge, we propose a non-invasive molecular method using proteomic analysis focused on species-specific protein sequences in spider silk, offering a viable solution for species identification without harming specimens. We developed a universal silk-dissolving method, followed by sequence similarity analysis to classify species into those identifiable at the species level and those distinguishable only to a group of closely related species. A bioinformatics pipeline was established to analyze peptide sequences, achieving 96% accuracy across 15 spider species, even in the presence of contaminants. This technique complements DNA barcoding and can be extended to other organisms producing biological materials. It holds promise in pest management, medical diagnostics, and improving public health by enabling accurate species identification without invasive procedures.

PMID:40263346 | DOI:10.1038/s41598-025-97105-0

Nature. 2025 Apr 22. doi: 10.1038/s41586-025-09021-y. Online ahead of print.

ABSTRACT

Engineering and characterizing proteins can be time-consuming and cumbersome, motivating the development of generalist CRISPR-Cas enzymes1-4 to enable diverse genome editing applications. However, such enzymes have caveats such as an increased risk of off-target editing3,5,6. To enable scalable reprogramming of Cas9 enzymes, here we combined high-throughput protein engineering with machine learning (ML) to derive bespoke editors more uniquely suited to specific targets. Via structure/function-informed saturation mutagenesis and bacterial selections, we obtained nearly 1,000 engineered SpCas9 enzymes and characterized their protospacer-adjacent motif7 (PAM) requirements to train a neural network that relates amino acid sequence to PAM specificity. By utilizing the resulting PAM ML algorithm (PAMmla) to predict the PAMs of 64 million SpCas9 enzymes, we identified efficacious and specific enzymes that outperform evolution-based and engineered SpCas9 enzymes as nucleases and base editors in human cells while reducing off-targets. An in silico directed evolution method enables user-directed Cas9 enzyme design, including for allele-selective targeting of the RHO P23H allele in human cells and mice. Together, PAMmla integrates ML and protein engineering to curate a catalog of SpCas9 enzymes with distinct PAM requirements, and motivates the use of efficient and safe bespoke Cas9 enzymes instead of generalist enzymes for various applications.

PMID:40262634 | DOI:10.1038/s41586-025-09021-y

Cell Syst. 2025 Apr 15:101266. doi: 10.1016/j.cels.2025.101266. Online ahead of print.

ABSTRACT

Biological analyses conducted at the single-cell scale have revealed profound impacts of heterogeneity and plasticity of chromatin states and gene expression on physiology and cancer. Here, we developed Parallel-seq, a technology for simultaneously measuring chromatin accessibility and gene expression in the same single cells. By combining combinatorial cell indexing and droplet overloading, Parallel-seq generates high-quality data in an ultra-high-throughput fashion and at a cost two orders of magnitude lower than alternative technologies (10× Multiome and ISSAAC-seq). We applied Parallel-seq to 40 lung tumor and tumor-adjacent clinical samples and obtained over 200,000 high-quality joint scATAC-and-scRNA profiles. Leveraging this large dataset, we characterized copy-number variations (CNVs) and extrachromosomal circular DNA (eccDNA) heterogeneity in tumor cells, predicted hundreds of thousands of cell-type-specific regulatory events, and identified enhancer mutations affecting tumor progression. Our analyses highlight Parallel-seq's power in investigating epigenetic and genetic factors driving cancer development at the cell-type-specific level and its utility for revealing vulnerable therapeutic targets.

PMID:40262617 | DOI:10.1016/j.cels.2025.101266

Cell Genom. 2025 Apr 17:100853. doi: 10.1016/j.xgen.2025.100853. Online ahead of print.

ABSTRACT

Mushroom-forming fungi (Agaricomycetes) are emerging as pivotal players in several fields of science and industry. Genomic data for Agaricomycetes are accumulating rapidly; however, this is not paralleled by improvements of gene annotations, which leave gene function notoriously poorly understood. We set out to improve our functional understanding of the model mushroom Coprinopsis cinerea by integrating a new, chromosome-level assembly, high-quality gene predictions, and functional information derived from broad gene-expression profiling data. The new annotation includes 5' and 3' untranslated regions (UTRs), polyadenylation sites (PASs), upstream open reading frames (uORFs), splicing isoforms, and microexons, as well as core gene sets corresponding to carbon starvation, light response, and hyphal differentiation. As a result, the genome of C. cinerea has now become the most comprehensively annotated genome among mushroom-forming fungi, which will contribute to multiple rapidly expanding fields, including research on their life history, light and stress responses, as well as multicellular development.

PMID:40262612 | DOI:10.1016/j.xgen.2025.100853