Cancer Cell. 2025 Jan 13:S1535-6108(24)00483-5. doi: 10.1016/j.ccell.2024.12.008. Online ahead of print.

ABSTRACT

Fewer than 50% of metastatic deficient mismatch repair (dMMR) colorectal cancer (CRC) patients respond to immune checkpoint inhibition (ICI). Identifying and expanding this patient population remains a pressing clinical need. Here, we report that an interferon-high immunophenotype locally enriched in cytotoxic lymphocytes and antigen-presenting macrophages is required for response. This immunophenotype is not exclusive to dMMR CRCs but comprises a subset of MMR proficient (pMMR) CRCs. Single-cell spatial analysis and in vitro cell co-cultures indicate that interferon-producing cytotoxic T cells induce overexpression of antigen presentation in adjacent macrophages and tumor cells, including MHC class II invariant chain CD74. dMMR CRCs expressing high levels of CD74 respond to ICI and a subset of CD74 high pMMR CRC patients show better progression free survival when treated with ICI. Therefore, CD74 abundance can identify the constitutive interferon-high immunophenotype determining clinical benefit in CRC, independently of tumor mutational burden or MMR status.

PMID:39824178 | DOI:10.1016/j.ccell.2024.12.008

J Hypertens. 2024 Nov 12. doi: 10.1097/HJH.0000000000003924. Online ahead of print.

ABSTRACT

OBJECTIVES: The effects of acute physical exercise in patients with resistant hypertension remain largely unexplored compared with hypertensive patients in general. We assessed the short-term effects of acute moderate-intensity (MICE) and high-intensity interval exercise (HIIE) on the clinic (BP) and 24-h ambulatory blood pressure (ABP) of patients with resistant hypertension.

METHODS: Using a crossover randomized controlled design, 10 participants (56 ± 7 years) with resistant hypertension performed three experimental sessions: MICE, HIIE, and control. MICE consisted of continuous treadmill exercise at an intensity of 3-4 metabolic equivalents of energy (METs) until completing 3 kcal/kg and was energy-matched to HIIE (which included six to eight intervals of 3 min duration at 6-7 METs interspersed with 1.5-min rests at 3 METs). In the control session, participants remained seated for 50 min. Flow-mediated vasodilation, autonomic nervous system balance (heart rate variability), exerkines [interleukin (IL)-6, IL-8, IL-15, vascular endothelial growth factor A, irisin, adiponectin, and angiopoietin] and 71 inflammatory-related proteins were also measured.

RESULTS: Compared with baseline, HIIE and MICE reduced clinic SBP immediately (P < 0.001 for both) and 90 min (P = 0.001 and P = 0.041, respectively) postexercise. HIIE and MICE also reduced clinic DBP immediately postexercise (P = 0.003 and P = 0.025). By contrast, no changes were found in the control session. On the other hand, no significant effects were noted for 24 h ABP measures or for the rest of variables.

CONCLUSION: Although in patients with resistant hypertension, acute aerobic exercise induces short-term reductions in clinic BP, this stimulus does not suffice to reduce 24 h ABP or to impact on potential biological mechanisms.

PMID:39823644 | DOI:10.1097/HJH.0000000000003924

STAR Protoc. 2025 Jan 16;6(1):103573. doi: 10.1016/j.xpro.2024.103573. Online ahead of print.

ABSTRACT

Drugs that target specific proteins often have off-target effects. We present a protocol using artificial neural networks to model cellular transcriptional responses to drugs, aiming to understand their mechanisms of action. We detail steps for predicting transcriptional activities, inferring drug-target interactions, and explaining the off-target mechanism of action. As a case study, we analyze the off-target effects of lestaurtinib on FOXM1 in the A375 cell line. For complete details on the use and execution of this protocol, please refer to Meimetis et al.1.

PMID:39823233 | DOI:10.1016/j.xpro.2024.103573

STAR Protoc. 2025 Jan 16;6(1):103577. doi: 10.1016/j.xpro.2024.103577. Online ahead of print.

ABSTRACT

The eukaryotic cell division cycle is a highly conserved process, featuring fluctuations in protein localization and abundance required for key cell cycle transitions. Here, we present a protocol for the spatiotemporal analysis of the proteome during the budding yeast cell division cycle using live-cell imaging. We describe steps for strain construction, cell cultivation, microscopy, and image analysis. Variations of this protocol can be applied for the spatiotemporal analysis of the proteome in different contexts, such as genetic and environmental perturbations. For complete details on the use and execution of this protocol, please refer to Litsios et al.1.

PMID:39823231 | DOI:10.1016/j.xpro.2024.103577

Nat Biotechnol. 2025 Jan 16. doi: 10.1038/s41587-024-02535-2. Online ahead of print.

ABSTRACT

The complex nature of the immunosuppressive tumor microenvironment (TME) requires multi-agent combinations for optimal immunotherapy. Here we describe multiplex universal combinatorial immunotherapy via gene silencing (MUCIG), which uses CRISPR-Cas13d to silence multiple endogenous immunosuppressive genes in the TME, promoting TME remodeling and enhancing antitumor immunity. MUCIG vectors targeting four genes delivered by adeno-associated virus (AAV) (Cd274/Pdl1, Lgals9/Galectin9, Lgals3/Galectin3 and Cd47; AAV-Cas13d-PGGC) demonstrate significant antitumor efficacy across multiple syngeneic tumor models, remodeling the TME by increasing CD8+ T-cell infiltration while reducing neutrophils. Whole transcriptome profiling validates the on-target knockdown of the four target genes and shows limited potential off-target or downstream gene alterations. AAV-Cas13d-PGGC outperforms corresponding shRNA treatments and individual gene knockdown. We further optimize MUCIG by employing high-fidelity Cas13d (hfCas13d), which similarly showed potent gene silencing and in vivo antitumor efficacy, without weight loss or liver toxicity. MUCIG represents a universal method to silence multiple immune genes in vivo in a programmable manner, offering broad efficacy across multiple tumor types.

PMID:39820813 | DOI:10.1038/s41587-024-02535-2

Brief Bioinform. 2024 Nov 22;26(1):bbaf015. doi: 10.1093/bib/bbaf015.

ABSTRACT

The volume of microbiome data is growing at an exponential rate, and the current methodologies for big data mining are encountering substantial obstacles. Effectively managing and extracting valuable insights from these vast microbiome datasets has emerged as a significant challenge in the field of contemporary microbiome research. This comprehensive review delves into the utilization of foundation models and transfer learning techniques within the context of microbiome-based classification and prediction tasks, advocating for a transition away from traditional task-specific or scenario-specific models towards more adaptable, continuous learning models. The article underscores the practicality and benefits of initially constructing a robust foundation model, which can then be fine-tuned using transfer learning to tackle specific context tasks. In real-world scenarios, the application of transfer learning empowers models to leverage disease-related data from one geographical area and enhance diagnostic precision in different regions. This transition from relying on "good models" to embracing "adaptive models" resonates with the philosophy of "teaching a man to fish" thereby paving the way for advancements in personalized medicine and accurate diagnosis. Empirical research suggests that the integration of foundation models with transfer learning methodologies substantially boosts the performance of models when dealing with large-scale and diverse microbiome datasets, effectively mitigating the challenges posed by data heterogeneity.

PMID:39820436 | DOI:10.1093/bib/bbaf015

Nat Commun. 2025 Jan 16;16(1):715. doi: 10.1038/s41467-025-56042-2.

ABSTRACT

Plants, with intricate molecular networks for environmental adaptation, offer groundbreaking potential for reprogramming with predictive genetic circuits. However, realizing this goal is challenging due to the long cultivation cycle of plants, as well as the lack of reproducible, quantitative methods and well-characterized genetic parts. Here, we establish a rapid (~10 days), quantitative, and predictive framework in plants. A group of orthogonal sensors, modular synthetic promoters, and NOT gates are constructed and quantitatively characterized. A predictive model is developed to predict the designed circuits' behavior accurately. Our versatile and robust framework, validated by constructing 21 two-input circuits with high prediction accuracy (R2 = 0.81), enables multi-state phenotype control in both Arabidopsis thaliana and Nicotiana benthamiana in response to chemical inducers. Our study achieves predictable design and application of synthetic circuits in plants, offering valuable tools for the rapid engineering of plant traits in biotechnology and agriculture.

PMID:39820378 | DOI:10.1038/s41467-025-56042-2

BMC Med Inform Decis Mak. 2025 Jan 16;25(1):29. doi: 10.1186/s12911-024-02821-8.

ABSTRACT

BACKGROUND: Molecular tumor boards (MTBs) play a pivotal role in personalized oncology, leveraging complex data sets to tailor therapy for cancer patients. The integration of digital support and visualization tools is essential in this rapidly evolving field facing fast-growing data and changing clinical processes. This study addresses the gap in understanding the evolution of software and visualization needs within MTBs and evaluates the current state of digital support. Alignment between user requirements and software development is crucial to avoid waste of resources and maintain trust.

METHODS: In two consecutive nationwide medical informatics projects in Germany, surveys and expert interviews were conducted as stage 1 (n = 14), stage 2 (n = 30), and stage 3 (n = 9). Surveys, via the SoSci Survey tool, covered participants' roles, working methods, and support needs. The second survey additionally addressed requirements for visualization solutions in molecular tumor boards. These aimed to understand diverse requirements for preparation, implementation, and documentation. Nine semi-structured expert interviews complemented quantitative findings through open discussion.

RESULTS: Using quantitative and qualitative analyses, we show that existing digital tools may improve therapy recommendations and streamline MTB case preparation, while continuous training and system improvements are needed.

CONCLUSIONS: Our study contributes to the field by highlighting the importance of developing user-centric, customizable software solutions that can adapt to the fast-paced environment of MTBs to advance personalized oncology. In doing so, it lays the foundation for further advances in personalized medicine in oncology and points to a shift towards more efficient, technology-driven clinical decision-making processes. This research not only enriches our understanding of the integration of digital tools into MTBs, but also signals a broader shift towards technological innovation in healthcare.

PMID:39819625 | DOI:10.1186/s12911-024-02821-8

Annu Rev Plant Biol. 2025 Jan 16. doi: 10.1146/annurev-arplant-083123-060254. Online ahead of print.

ABSTRACT

More than 500 million years ago, a streptophyte algal population established a foothold on land and started terraforming Earth through an unprecedented radiation. This event is called plant terrestrialization and yielded the Embryophyta. Recent advancements in the field of plant evolutionary developmental biology (evo-devo) have propelled our knowledge of the closest algal relatives of land plants, the zygnematophytes, highlighting that several aspects of plant cell biology are shared between embryophytes and their sister lineage. High-throughput exploration determined that routes of signaling cascades, biosynthetic pathways, and molecular physiology predate plant terrestrialization. But how do they assemble into biological programs, and what do these programs tell us about the principal functions of the streptophyte cell? Here, we make the case that streptophyte algae are unique organisms for understanding the systems biology of the streptophyte cell, informing on not only the origin of embryophytes but also their fundamental biology.

PMID:39819561 | DOI:10.1146/annurev-arplant-083123-060254

Elife. 2025 Jan 17;13:RP95273. doi: 10.7554/eLife.95273.

ABSTRACT

Induced pluripotent stem cell (iPSC) technology is revolutionizing cell biology. However, the variability between individual iPSC lines and the lack of efficient technology to comprehensively characterize iPSC-derived cell types hinder its adoption in routine preclinical screening settings. To facilitate the validation of iPSC-derived cell culture composition, we have implemented an imaging assay based on cell painting and convolutional neural networks to recognize cell types in dense and mixed cultures with high fidelity. We have benchmarked our approach using pure and mixed cultures of neuroblastoma and astrocytoma cell lines and attained a classification accuracy above 96%. Through iterative data erosion, we found that inputs containing the nuclear region of interest and its close environment, allow achieving equally high classification accuracy as inputs containing the whole cell for semi-confluent cultures and preserved prediction accuracy even in very dense cultures. We then applied this regionally restricted cell profiling approach to evaluate the differentiation status of iPSC-derived neural cultures, by determining the ratio of postmitotic neurons and neural progenitors. We found that the cell-based prediction significantly outperformed an approach in which the population-level time in culture was used as a classification criterion (96% vs 86%, respectively). In mixed iPSC-derived neuronal cultures, microglia could be unequivocally discriminated from neurons, regardless of their reactivity state, and a tiered strategy allowed for further distinguishing activated from non-activated cell states, albeit with lower accuracy. Thus, morphological single-cell profiling provides a means to quantify cell composition in complex mixed neural cultures and holds promise for use in the quality control of iPSC-derived cell culture models.

PMID:39819559 | DOI:10.7554/eLife.95273

Elife. 2025 Jan 17;13:RP95485. doi: 10.7554/eLife.95485.

ABSTRACT

Live-cell microscopy routinely provides massive amounts of time-lapse images of complex cellular systems under various physiological or therapeutic conditions. However, this wealth of data remains difficult to interpret in terms of causal effects. Here, we describe CausalXtract, a flexible computational pipeline that discovers causal and possibly time-lagged effects from morphodynamic features and cell-cell interactions in live-cell imaging data. CausalXtract methodology combines network-based and information-based frameworks, which is shown to discover causal effects overlooked by classical Granger and Schreiber causality approaches. We showcase the use of CausalXtract to uncover novel causal effects in a tumor-on-chip cellular ecosystem under therapeutically relevant conditions. In particular, we find that cancer-associated fibroblasts directly inhibit cancer cell apoptosis, independently from anticancer treatment. CausalXtract uncovers also multiple antagonistic effects at different time delays. Hence, CausalXtract provides a unique computational tool to interpret live-cell imaging data for a range of fundamental and translational research applications.

PMID:39819525 | DOI:10.7554/eLife.95485

ACS Chem Biol. 2025 Jan 17. doi: 10.1021/acschembio.4c00553. Online ahead of print.

ABSTRACT

Developing novel nonribosomal peptides (NRPs) requires a comprehensive understanding of the enzymes involved in their biosynthesis, particularly the substrate amino acid recognition mechanisms in the adenylation (A) domain. This study focused on the A domain responsible for adenylating l-2,4-diaminobutyric acid (l-Dab) within the synthetase of polymyxin, an NRP produced by Paenibacillus polymyxa NBRC3020. To date, investigations into recombinant proteins that selectively adenylate l-Dab─exploring substrate specificity and enzymatic activity parameters─have been limited to reports on A domains found in enzymes synthesizing l-Dab homopolymers (pldA from S. celluloflavus USE31 and pddA from S. hindustanus NBRC15115), which remain exceedingly rare. The polymyxin synthetase in NBRC3020 contains five A domains specific to l-Dab, distributed across five distinct modules (modules 1, 3, 4, 5, 8, and 9). In this study, we successfully obtained soluble A domain proteins from modules 1, 5, 8, and 9 by preparing module-specific recombinant proteins. These proteins were expressed in E. coli BAP-1, purified via Ni-affinity chromatography, and demonstrated high specificity for l-Dab. Through sequence homology analysis, three-dimensional structural modeling, docking simulations to estimate substrate-binding sites, and functional validation using alanine mutants, we identified Glu281 and Asp344 as critical residues for recognizing the side chain amino group of l-Dab, and Asp238 as essential for recognizing its main chain amino group in the A domain. Notably, these key residues were conserved not only across the A domains in modules 1, 5, 8, and 9 of P. polymyxa NBRC3020 but also in those of the P. polymyxa PKB1 strain, as confirmed by sequence homology analysis. Interestingly, in pldA and pddA, the key residues involved in recognizing the side-chain amino group of l-Dab, which are conserved among polymyxin synthetases of NBRC3020 and PKB1 strain, were not observed. This suggests a potentially different mechanism for l-Dab recognition.

PMID:39818748 | DOI:10.1021/acschembio.4c00553

J Adolesc Health. 2025 Jan 16:S1054-139X(24)00551-2. doi: 10.1016/j.jadohealth.2024.10.033. Online ahead of print.

ABSTRACT

PURPOSE: Despite growing concerns about trends in cocaine use, there is a shortage of longitudinal research that prospectively examines risk and protective factors associated with cocaine initiation and use in general youth populations. This study addresses this gap.

METHODS: Growing Up in Ireland is a nationally representative cohort. Individual, family, and socio-environmental exposures associated with incident past-year cocaine use at ages 17 (N = 5965) and 20 (n = 4549) were assessed with survey-weighted logistic regression using generalised estimating equations. Prevalent past-year cocaine use at 20 (N = 4679) was analysed using generalised estimating equations complemented by gradient-boosted decision trees and Shapley explanations.

RESULTS: 221 (3.7%) self-reported cocaine use at 17 and 1072 (22.9%) at 20. Alcohol use at 14 or younger was associated with eight times the odds of cocaine use at 17 (aOR 8.0, 95% CI 1.7-37.3) and 19 times at 20 (aOR 19.2, 95% CI 8.6-43.2). Peer cannabis use was associated with 7 times the odds of cocaine use at 17 (aOR 7.3, 95% CI 2.9-18.3) and double at 20 (aOR 2.4, 95% CI 1.8-3.2). Growing up in a neighbourhood where substance use was common doubled the odds of cocaine use at 17 (aOR 2.4, 95% CI 1.3-4.4). Shapley explanations revealed individual-specific positive or negative impacts of exposures.

DISCUSSION: Cocaine use among 20-year-olds in Ireland is higher than reported internationally, and increases sharply between the ages of 17 and 20, suggesting a need for interventions targeting this age group. However, associations with early adolescent factors suggest that early interventions may also be important.

PMID:39818654 | DOI:10.1016/j.jadohealth.2024.10.033

Int J Biol Macromol. 2025 Jan 14:139913. doi: 10.1016/j.ijbiomac.2025.139913. Online ahead of print.

ABSTRACT

The macromolecular components of the seed coat, particularly lignin, play a critical role in regulating seed viability. In the maize-soybean intercropping (MSI) system, shading stress was reported to enhance the viability of soybean seeds. However, the specific role of seed coat lignin in this process remains poorly understood. In this study, we demonstrated that soybean seed coats derived from the MSI system exhibit significantly higher lignin content and mechanical resistance compared to those from the sole cropping systems. Further investigations with artificial shading treatments revealed a substantial impact on the accumulation of phenylpropanoids in soybean seeds. Notably, shading applied during the reproductive stage resulted in decreased levels of anthocyanins, proanthocyanidins, and isoflavones, while simultaneously increasing lignin content. Moreover, both the mechanical resistance of the seed coats and the seeds' longevity under deteriorative conditions improved significantly compared to the normal light control. Gene expression and metabolomics analyses indicated that shading stress promotes the expression of key genes involved in lignin biosynthesis within the soybean seed coats, increasing the amount of several intermediate metabolites. Taken together, these findings reveal that shading stress in the MSI system promotes the biosynthesis and accumulation of lignin in soybean seed coats and thereby regulating seed longevity.

PMID:39818396 | DOI:10.1016/j.ijbiomac.2025.139913

Int J Biol Macromol. 2025 Jan 14:139900. doi: 10.1016/j.ijbiomac.2025.139900. Online ahead of print.

ABSTRACT

A new gene coding for an iron-containing enzyme was identified in the genome of Acinetobacter radioresistens. Bioinformatics analysis allowed the assignment of the protein to DyP peroxidases, due to the presence of conserved residues involved in heme binding and catalysis. Moreover, Ar-DyP is located in an operon coding also for other enzymes involved in iron uptake and regulation. The crystal structure of Ar-DyP determined at 1.85 Å resolution shows that the heme pocket Ar-DyP is "wet" forming a continuous hydrogen-bond network that enables the communication between heme and distal residues. Moreover, as shown by the crystal structure and covalent crosslinking experiments, Ar-DyP uses a long-range electron transfer pathway involving His-181 and Tyr-241, in the active site and on the surface of the enzyme, respectively. This pathway allows oxidation of substrates of different sizes, including Kraft lignin. Indeed, the biochemical characterization showed that Ar-Dyp oxidizes ABTS and Reactive Blue 19 (turnover numbers of 500 and 464 min-1, respectively), but also phenolic compounds such as guaiacol and pyrogallol (turnover numbers of 7.4 and 1.8 min-1 respectively). Overall, the data shows that Ar-DyP is a promising candidate for applications in lignin valorization, bioremediation and industrial processes involving the breakdown of phenolic compounds.

PMID:39818373 | DOI:10.1016/j.ijbiomac.2025.139900

Animal. 2024 Dec 19;19(2):101404. doi: 10.1016/j.animal.2024.101404. Online ahead of print.

ABSTRACT

Domestic pigs (Sus scrofa) raised under natural conditions can show their complete behavioural repertoire. However, rooting behaviour can have a great impact on the environment. In the context of the promotion of farm animal welfare and environmental concerns, this study investigated the potential of nose-clips as a less invasive alternative to nose-rings for the management of rooting behaviour of free-ranging pigs. We collected behavioural data and salivary cortisol levels on two groups: an experimental group (n = 17) with nose-clips and a control group (n = 17) without nose-clips. After the nose-clipping, we observed a temporary increase in anxiety-related behaviour and cortisol levels during the 1st week, followed by a return to pre-application levels in the following weeks. We found a temporary decrease in affiliative interactions involving the nose during the 1st week after the application of nose-clips, whereas no differences in affiliative interactions without nose contact and aggression levels were observed. Moreover, nose-clips effectively reduced destructive excavation behaviours, without leading to a simultaneous increase in other exploratory behaviours. In conclusion, our findings show that nose-clips could be a solution that mitigates destructive rooting while preserving social interactions and animal welfare. Further research is essential to consolidate these findings and assess the long-term implications of this approach.

PMID:39818027 | DOI:10.1016/j.animal.2024.101404

Elife. 2025 Jan 16;13:RP100545. doi: 10.7554/eLife.100545.

ABSTRACT

Viral adhesion to host cells is a critical step in infection for many viruses, including monkeypox virus (MPXV). In MPXV, the H3 protein mediates viral adhesion through its interaction with heparan sulfate (HS), yet the structural details of this interaction have remained elusive. Using AI-based structural prediction tools and molecular dynamics (MD) simulations, we identified a novel, positively charged α-helical domain in H3 that is essential for HS binding. This conserved domain, found across orthopoxviruses, was experimentally validated and shown to be critical for viral adhesion, making it an ideal target for antiviral drug development. Targeting this domain, we designed a protein inhibitor, which disrupted the H3-HS interaction, inhibited viral infection in vitro and viral replication in vivo, offering a promising antiviral candidate. Our findings reveal a novel therapeutic target of MPXV, demonstrating the potential of combination of AI-driven methods and MD simulations to accelerate antiviral drug discovery.

PMID:39817728 | DOI:10.7554/eLife.100545

Natl Sci Rev. 2024 Nov 26;12(1):nwae425. doi: 10.1093/nsr/nwae425. eCollection 2025 Jan.

ABSTRACT

Defining metabolic health is critical for the earlier reversing of metabolic dysfunction and disease, and fasting-based diagnosis may not adequately assess an individual's metabolic adaptivity under stress. We constructed a novel Health State Map (HSM) comprising a Health Phenotype Score (HPS) with fasting features alone and a Homeostatic Resilience Score (HRS) with five time-point features only (t = 30, 60, 90, 180, 240 min) following a standardized mixed macronutrient tolerance test (MMTT). Among 111 Chinese adults, when the same set of fasting and post-MMTT data as for the HSM was used, the mixed-score was highly correlated with the HPS. The HRS was significantly associated with metabolic syndrome prevalence, independently of the HPS (OR [95% CI]: 0.41 [0.18, 0.92]) and the mixed-score (0.34 [0.15, 0.69]). Moreover, the HRS could discriminate metabolic characteristics unseparated by the HPS and the mixed-score. Participants with higher HRSs had better metabolic traits than those with lower HRSs. Large interpersonal variations were also evidenced by evaluating postprandial homeostatic resiliencies for glucose, lipids and amino acids when participants had similar overall HRSs. Additionally, the HRS was positively associated with physical activity level and specific gut microbiome structure. Collectively, our HSM model might offer a novel approach to precisely define an individual's metabolic health and nutritional capacity.

PMID:39816947 | PMC:PMC11734281 | DOI:10.1093/nsr/nwae425

R Soc Open Sci. 2025 Jan 15;12(1):241252. doi: 10.1098/rsos.241252. eCollection 2025 Jan.

ABSTRACT

Adaptive divergence and increased genetic differentiation among populations can lead to reproductive isolation. In Lake Constance, Germany, a population of invasive three-spined stickleback (Gasterosteus aculeatus) is currently diverging into littoral and pelagic ecotypes, which both nest in the littoral zone. We hypothesized that assortative mating behaviour contributes to reproductive isolation between these ecotypes and performed a behavioural experiment in which females could choose between two nest-guarding males. Behaviour was recorded, and data on traits relevant to mate choice were collected. Both females of the same and different ecotypes were courted with equal vigour. However, there was a significant interaction effect of male and female ecotypes on the level of aggression in females. Littoral females were more aggressive towards pelagic males, and pelagic females were more aggressive towards littoral males. This indicates rejection of males of different ecotypes in spite of the fact that littoral males were larger, more intensely red-coloured and more aggressive than the pelagic males-all mating traits female sticklebacks generally select for. This study documents the emergence of behavioural barriers during early divergence in an invasive and rapidly diversifying stickleback population and discusses their putative role in facilitating reproductive isolation and adaptive radiation within this species.

PMID:39816745 | PMC:PMC11732402 | DOI:10.1098/rsos.241252

Front Antibiot. 2022 Sep 16;1:957942. doi: 10.3389/frabi.2022.957942. eCollection 2022.

ABSTRACT

We report here the identification of four gene functions of principal importance for the tolerance of meropenem stress in Escherichia coli: cell division, cell envelope synthesis and maintenance, ATP metabolism, and transcription regulation. The primary mechanism of β-lactam antibiotics such as meropenem is inhibition of penicillin binding proteins, thus interfering with peptidoglycan crosslinking, weakening the cell envelope, and promoting cell lysis. However, recent systems biology approaches have revealed numerous downstream effects that are triggered by cell envelope damage and involve diverse cell processes. Subpopulations of persister cells can also arise, which can survive elevated concentrations of meropenem despite the absence of a specific resistance factor. We used Transposon-Directed Insertion Sequencing with inducible gene expression to simultaneously assay the effects of upregulation, downregulation, and disruption of every gene in a model E. coli strain on survival of exposure to four concentrations of meropenem. Automated Gene Functional Classification and manual categorization highlighted the importance at all meropenem concentrations of genes involved in peptidoglycan remodeling during cell division, suggesting that cell division is the primary function affected by meropenem. Genes involved in cell envelope synthesis and maintenance, ATP metabolism, and transcriptional regulation were generally important at higher meropenem concentrations, suggesting that these three functions are therefore secondary or downstream targets. Our analysis revealed the importance of multiple two-component signal transduction mechanisms, suggesting an as-yet unexplored coordinated transcriptional response to meropenem stress. The inclusion of an inducible, transposon-encoded promoter allowed sensitive detection of genes involved in proton transport, ATP production and tRNA synthesis, for which modulation of expression affects survival in the presence of meropenem: a finding that would not be possible with other technologies. We were also able to suggest new targets for future antibiotic development or for synergistic effects between gene or protein inhibitors and existing antibiotics. Overall, in a single massively parallel assay we were able to recapitulate many of the findings from decades of research into β-lactam antibiotics, add to the list of genes known to be important for meropenem tolerance, and categorize the four principal gene functions involved.

PMID:39816415 | PMC:PMC11731830 | DOI:10.3389/frabi.2022.957942