PLOS Biology
● Public Library of Science (PLoS)
Preprints posted in the last 30 days, ranked by how well they match PLOS Biology's content profile, based on 408 papers previously published here. The average preprint has a 0.58% match score for this journal, so anything above that is already an above-average fit.
Gorelick, D. A.; Clark, A.
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Traditional peer review is often slowed by delays in identifying willing reviewers and waiting for completed review reports. In a 2024 pilot on the journal Biology Open, we showed that Fast & Fair peer review, which uses pre-contracted paid reviewers and a structured editorial timeline, could deliver rapid, high-quality peer. Here, we report the expanded implementation of Fast & Fair at Biology Open in 2025. From 1 April 2025 onward, all direct submissions to the journal were considered for Fast & Fair peer review unless appropriate pre-contracted reviewer expertise was unavailable. Reviewers were paid {pound}220 per manuscript only if they completed the review on time, and the review met editorial quality expectations. Among peer-reviewed manuscripts submitted in 2025, Fast & Fair reduced time to first decision with reviews from a mean of 37.7 working days under conventional peer review to 5.5 working days. Reviewer commitment also improved. Fast & Fair invitations were accepted more often than conventional invitations (67% versus 23%), had lower nonresponse (13% versus 39%), and had higher completion among accepted invitations (98% versus 87%). Faster review was not associated with reduced review quality. Handling editors scored each review for usefulness in editorial decision-making. Fast & Fair produced fewer low-scoring reports than conventional peer review. Editorial behavior was also unchanged, with similar first-decision profiles and final acceptance rates (59% versus 61%). While financial sustainability remains to be tested at scale, the Fast & Fair model addresses a major bottleneck in traditional peer review by replacing ad hoc reviewer recruitment with conditional compensation, predefined quality standards and a strict editorial timeline.
Dong, Z.; Wang, D.; Wang, B.; New, J. A.; Leung, Y. F.; Zhang, G.
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Mechanosensing and mechanotransduction are essential for all living cells. In mammals, Piezo1 and Piezo2 are two mechanically activated cation channels that serve as mechanosensors for a variety of physiological and pathological processes, ranging from touch sensing to sickle cell disease. These two channels are well evolutionarily conserved, and orthologous genes can be traced back to the origin of vertebrates, which underwent whole-genome duplications (WGDs). The number of paralogous genes originating from the vertebrate WGD varies across gene families. Thus, whether there are more PIEZO paralogous genes in vertebrates remains understudied. Here, we identified piezo3, a new paralog of the piezo gene family, and analyzed its evolutionary history using phylogenetic and synteny analyses. The piezo3 gene is present in most vertebrate lineages but absent in birds and most mammals, likely due to nonfunctionalization after WGDs. In addition, we demonstrated that this channel could mediate calcium flux in response to mechanical stimuli in HEK293T cells, suggesting that Piezo3 exhibits PIEZO1/2-like activation and conduction channel functions. Our CRISPR mutation analysis revealed that the zebrafish piezo3 gene is not developmentally essential, possibly because its expression overlaps with other PIEZO channels. Mutant zebrafish showed elevated sensitivity to mechanical force and increased locomotor activity under (photopic) light illumination. Our results suggest that this new mechanical-sensing Piezo channel is widespread in vertebrates and may be critical for vertebrate adaptation by modulating mechanical sensing and light responses during evolution. SIGNIFICANCEAll living cells must sense mechanical forces, whether endogenous or exogenous, and respond to them by transforming these forces into biological signals, which is essential to a wide range of cellular processes, including cell division, growth, and differentiation. PIEZO channels are well-characterized, critical, versatile mechanotransducers for touch and pain physiology and for human diseases. Currently, PIEZO1 and PIEZO2 are the only two known PIEZO channels in most vertebrates. In zebrafish, there are two Piezo2 channels (Piezo2a and Piezo2b) due to extra genome duplication in the ray-finned fishes. Here, we report Piezo3 channel, a long-missing paralog of Piezo1 and Piezo2, in most vertebrates. This channel is present in the majority of vertebrate lineages, except for most birds and mammals. The zebrafish piezo3 gene is expressed during early embryogenesis, and mutation of this gene leads to zebrafish larvae responding to tapping mechanical force and light with active movement. The widespread distribution of this Piezo3 channel across most vertebrate species, but its absence in birds and most mammals, suggests it may play important roles in vertebrate physiology and evolution.
Rock, D.; Stow, N.; Yu, C.; Nakagawa, Y.
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Elucidating the mechanisms that control the formation of the mammalian neocortex is crucial for understanding brain functions. Synaptic activity of thalamocortical axons (TCAs), mediated by glutamate, exerts a major extrinsic influence on the maturation of their target layer 4 neurons in postnatal primary sensory cortex. However, TCAs reach the sensory cortex during mid-embryonic stages in mice, when neurons of future superficial layers, including layer 4, are still being generated from radial glia (RGs) or intermediate progenitor cells (IPCs), well before the formation of direct synapses. We previously showed that TCAs are required for the production and specification of the proper number of layer 4 neurons in sensory areas, and that part of these area-specific roles is played by the thalamus-derived molecule VGF. However, the role of TCA-derived glutamate prior to synapse formation has remained unclear. In this study, we used mutant mice lacking vGluT2, a vesicular glutamate transporter expressed in the embryonic thalamus, and found that vesicular release of thalamus-derived glutamate is required for the proper production and specification of layer 4 neurons in the sensory cortex by the neonatal stage, through mechanism distinct from those involving VGF. Our findings reveal that multiple molecular cues produced by incoming TCAs play distinct roles in the production and specification of layer 4 neurons in the sensory cortex.
Peroni, E.; de Badts, C.-H.; Lepousez, G.; Hiridjee, A.; Renvoise, J.; Jacquemet, E.; Lledo, P.-M.; ALONSO, M.; Nissant, A.
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Adult neurogenesis in the olfactory bulb (OB) contributes to structural and functional plasticity, influencing olfactory perception, learning, and memory. Adult-born granule cells (abGCs) exhibit unique morphological, electrophysiological, and synaptic properties compared to their neonatally born counterparts, suggesting a specialized role in olfactory processing. In the OB, such processing relies both on sensory inputs from the olfactory epithelium as well as top-down cortical feedback, which encompass both glutamatergic and GABAergic projections from the olfactory cortex back to the OB. While abGCs are known to integrate both bottom-up sensory inputs and top-down cortical projections, the specific connectivity and functional influence of cortical GABAergic inputs on abGCs remain largely unexplored. In this study, we investigated whether activity of cortical GABAergic projections is modulated by olfactory learning, how they impact olfactory behavior and whether these connections selectively influence mature abGCs. Using in vivo fiber photometry following odor-reward associative conditioning, we found odor- and reward-dependent activity of cortical GABAergic projections during learning session. Furthermore, their functional role was revealed using optogenetic activation which impaired both the acquisition and the reversal of an odor-reward association. Ex vivo patch-clamp recordings demonstrated that olfactory learning potentiates cortical GABAergic inputs specifically onto abGCs, and morphological analysis confirmed that learning increases the number of cortical GABAergic synapses. These findings highlight a novel mechanism by which top-down inhibitory control from the olfactory cortex selectively targets abGC activity during olfactory learning. Our results provide new insights into the functional specialization of abGCs and their role in adaptive olfactory behaviors.
Dee, K.; Imrie, R.; MacLean, O.; Mojsiejczuk, L.; Smith, E.; Raveendran, S.; Lamb, K.; Chen, H.; Schultz, V.; Wang, Z.; Walsh, S. K.; Zhang, J.; Hutchinson, E. K.; Willett, B. J.; Thomson, E. C.; Hughes, J. C.; Robertson, D. L.; Illingworth, C. L.; Murcia, P.
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The emergence in 2025/26 of the influenza A/H3N2 K substrain (H3N2/K) was the cause of significant public health concern. This genetically divergent virus was assessed to have a strongly decreased reactivity to contemporary vaccine strains. Respectively prolonged and early influenza seasons in the Southern and Northern Hemispheres contributed to concerns about vaccine efficacy. Here we retrospectively assessed the genetic and antigenic properties of this virus, combining epidemiological surveillance data, computational antigenic analysis, and serological data using samples from a well-stratified UK cohort. In contrast to initial indications, we found that despite the genetic distinctiveness of H3N2/K the virus had undergone limited antigenic change, suggesting that its emergence was instead the result of selection for non-antigenic properties. We confirmed previous results showing that contemporary vaccines produced an enhanced neutralising response to H3N2/K but, in a stratified serological analysis, showed that responses to the J and K substrains were age-dependent, largely driven by patterns of vaccination. Our results have implications for antigenic surveillance and for public communication strategies in future influenza seasons.
de Wit, M. M.; Hoze, N.; De Jong, M. C. M.; Koopmans, M.; van Mastrigt, T.; Sikkema, R.; ten Bosch, Q.
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Serological testing is important for assessing past exposure and immunity, but interpretation can be complicated by antibody cross-reactivity between closely related viruses. We assess this challenge for Usutu virus (USUV) and West Nile virus (WNV), flaviviruses that recently emerged in Europe. We analysed samples from wild blackbirds collected in the Netherlands between 2016-2022. Samples (N=1742) were screened using an NS1-based protein micro-array, with positives confirmed by Focus Reduction Neutralization Tests (FRNT). We jointly estimated seroprevalence and antibody responses by fitting a Bayesian latent-variable model to FRNT values. Estimates of homologous and cross-reactive antibody responses were used to improve interpretation of observed titres for serosurveillance. Estimated seroprevalence varied across time and regions between 4.9% (95%CrI 3.5-6.7) to 18.5% (95%CrI 14.9-22.7) for USUV and between 2.4% (95%CrI 1.3-3.8) to 6.4% (95%CrI 3.9-9.6) for WNV. These were 1.5 (USUV) to 2.4 times (WNV) higher than estimates based on the current threshold-based algorithm. USUV induced a higher antibody response and was more likely to induce a cross-reactive response than WNV. Our classification algorithm informed by these estimates showed high sensitivity (WNV: 0.88, USUV: 0.97) and specificity (both: >0.99). Our results illustrate how quantitative frameworks can improve serological interpretation in settings with co-circulating pathogens.
Wang, X.; Wang, Q.; Xie, A.; Deng, L.; Huang, Z.; Zhao, Y.; Cao, Y.; Fu, R.; Huo, W.; Chen, Y.; Li, G.; Xu, A.; Yuan, S.
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Interferons (IFNs) are essential mediators of antiviral defense in vertebrates, having gradually replaced the RNA interference (RNAi) antiviral mechanism that predominates in invertebrates and plants. To date, IFNs have been identified exclusively in jawed vertebrates, leaving the origin of IFN-based antiviral mechanisms largely mysterious. In this study, by conducting a genome-wide screening of IFN homologs accross various species, we successfully identified seveal IFN homologs from agnatha and lancelet, but not other invertebrates. Notably, both agnatha and lancelet IFN homologs have ability to induce a set of interferon-stimulated genes (ISGs)-like genes, thus tracing the origin of IFN to basal chordate. Using VSV infected peripheral blood mononuclear cells (PBMCs) of Japanese lampreys, we found that lamprey IFNs have antiviral functionality by inducing the expression of hundreds of ISGs through interacting with a heterodimeric complex composed of CRFB7 and CRFB14. In addition to robustly mediating antiviral responses in monocytes, lamprey IFNs exert their effects on variable lymphocyte receptor B (VLRB)+ cells by remodeling the cytokine/chemokine networks to orchestrate antiviral innate and adaptive immunity. Furthermore, cross-species functional comparison of Dicer revealed that changes in residues essential for dsRNA processing occurred concurrently with the evolution of the IFN system. Collectively, these findings uncover the evolutionary origin of IFN and underscore its ancient roles in antiviral response and immune regulation, especially in the takeover of the RNAi antiviral mechanism during the early evolution of vertebrates. Significance StatementInterferons (IFNs) represent a hallmark of vertebrate antiviral immunity, yet their origin has remained elusive. Here, we reported bona fide IFN ligands and cognate receptors in both lamprey and lancelet, two key species placed at the transition from invertebrates to vertebrates. Using the VSV infection model, we further demonstrated the roles of lamprey IFN in antiviral defense and immune regulation. We also found that substitutions in residues essential for Dicer mediated dsRNA processing coincided with the emergence of the IFN system. Collectively, our findings provide key insights into the evolutionary origin of IFN-based immunity and its gradual replacement of RNAi as the dominant antiviral strategy in vertebrates.
Xu, Y.; Patterson, M. T.; Chang, M. D.; Ahlberg, I.; Liu, C.-Y.; Roll, C.; Hillman, H.; Kennedy, A.; Schrank, P. R.; Stuttgen, G. M.; Kubota, Y.; Ivanov, S.; Binstadt, B. A.; Williams, J. W.
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The adrenal glands are central regulators of systemic stress responses through tightly controlled glucocorticoid production. Yet, the contribution of local immune-vascular interactions to adrenal stress adaptation remains poorly understood. Here, we investigated the role of adrenal gland macrophages in coordinating stress-induced immune remodeling and vascular function. By integrating single-cell RNA sequencing datasets across four distinct stress models, including acute cold exposure, chronic social defeat, chronic inflammation, and systemic Candida albicans infection, we identified a conserved increase in monocyte recruitment to the adrenal gland, accompanied by dynamic macrophage transitions. Comparative transcriptomic and ligand-receptor analyses identified transforming growth factor-{beta} (TGF{beta}) as a dominant macrophage-derived signal targeting adrenal endothelial cells across all stress conditions. Pharmacological blockade of TGF{beta} receptor signaling reduced endothelial activation, vascular permeability, and monocyte infiltration into the adrenal gland following stress, without directly altering resident macrophage numbers. Using genetic fate-mapping and conditional knockout models, we demonstrate that macrophage-derived, but not endothelial-derived, TGF{beta} is required to promote enhanced endothelial adhesion molecule expression, vascular fenestration, permeability, and efficient monocyte recruitment. Loss of macrophage TGF{beta} production also led to exacerbated systemic stress hormone levels. Together, these findings uncover a previously unrecognized macrophage-endothelial axis in the adrenal gland, whereby macrophage-derived TGF{beta} regulates vascular properties to support immune cell recruitment and stress adaptation. This immune-vascular crosstalk provides new mechanistic insights into adrenal homeostasis and suggests potential therapeutic avenues for disorders associated with dysregulated chronic stress.
Zecchin, B.; Monne, I.; Dianati, M.; Bortolami, A.; Savegnago, E.; Shkodra, E.; Revilla Fernandezd, S.; Steensels, M.; Van Borm, S.; Ivanova, E.; Roncevic, I.; Savic, V.; Nagy, A.; Hjulsager, C. K.; Thorup, C.; Larsen, L. E.; Nurmoja, I.; Kauppinen, A.; Tammiranta, N.; Briand, F.-X.; Grasland, B.; Ahrens, A. K.; Pohlmann, A.; Gunther, A.; Harder, T.; Malik, P.; Garza Cuartero, L.; Cvetkova, S.; Kibilds, J.; Steingolde, Z.; Pumputis, E.; Pileviciene, S.; Snoeck, C. J.; Bourg, M.; Groza, O.; Bellido Martin, B.; Fouchier, R.; Thewessen, S.; Vuong, O.; Ballmann, M.; Engelsma, M.; Arnason Boe, C.;
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Since 2020, high pathogenicity avian influenza H5Nx viruses of clade 2.3.4.4b have become enzootic in Europe, causing recurrent epidemic waves characterized by extensive reassortment events. Here, we describe the emergence of a single high-fitness genotype (EA-2024-DI) that has driven two consecutive waves, evolving into distinct sub-lineages. While its circulation is ongoing, during the 2025-2026 wave it caused an unprecedented number of cases in wild birds. Using phylodynamic analyses of a large dataset of genomic sequences, we compared the spatial diffusion and host transmission pattern of the EA-2024-DI sub-lineages across the three most recent epidemic waves (2023-2024, 2024-2025 and 2025-2026). We show that the genotype has persisted over time and has spread primarily through wild Anseriformes, but with a marked change in the transmission patterns between the different waves and a shift in the epicenter from Eastern to Central Europe, the latter having emerged as an important hub for virus diffusion throughout Europe. Our results reveal a recent increase in the frequency of viruses from wild and domestic mammals carrying mutations enhancing virus replication in mammalian hosts, highlighting the importance of proactive monitoring of this group of hosts to better understand its role in the virus ecology and evolution.
Houghtaling, D.; Braun, E. L.; Kimball, R. T.
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Lysozyme has long been a model for understanding enzyme structure, function, and evolution. Early studies revealed a conflict between organismal phylogeny and the distribution of three functionally important amino acid residues in galliform birds. Lysozymes differing at all three amino acids appear functionally equivalent, but intermediates exhibit reduced stability and have not been observed in nature. However, the phylogeny suggests two independent occurrences of the three mutations, requiring two separate transitions through low fitness intermediates. We reexamined this apparent paradox using phylogenomic methods, accounting for incomplete lineage sorting and intralocus recombination. The lysozyme locus tree conflicts with an estimated species tree, but the conflict involves a short branch in coalescent units, consistent with incomplete lineage sorting. We also found evidence for recombination, with different parts of the lysozyme locus supporting alternative relationships. The three amino acids are encoded by exons located in different recombination-defined segments with different evolutionary histories. These results support a model where ancestral polymorphism, coupled with recombination between independently arising mutations, allowed rapid transitions between peaks in the fitness landscape without fixation of deleterious intermediates. Our findings resolve this long-standing question in lysozyme evolution and highlight the importance of considering complex genealogical processes such as incomplete lineage sorting and recombination when reconstructing ancestral proteins and interpreting apparent cases of molecular convergence.
Burns, M. W. N.; Chongsaritsinsuk, J.; Propheter, D. C.; YIN, J.; Zuo, V.; Huang, C.; Peng, L.; Ruhn, K. A.; Moremen, K. W.; Burstein, E.; Hooper, L.; Malaker, S. A.; Kohler, J. J.
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Mucus covers and protects colonic epithelial cells. Mucus is mainly composed of heavily O-glycosylated proteins called mucins, and disruption of normal mucin glycosylation occurs in ulcerative colitis (UC). Mucin-2 (MUC2) is the major colonic mucin, and MUC2 O-glycans are often extended with sulfated polyLacNAc, also known as keratan sulfate (KS). The GlcNAc residues in KS are added by B3GNT family members. B3GNT7 is highly expressed in the colon, and B3GNT7 expression is dramatically reduced in UC. However, the function of B3GNT7 in colonic physiology is unexplored. Here we show that B3gnt7 is a key player in colonic physiology through its function in controlling the structure of mucus glycans. We found that B3GNT7 prefers to extend a sulfated acceptor substrate and is required for production of polyLacNAc-modified mucus in a human goblet cell model. In vivo, B3GNT7 regulates Muc2, Muc13, and Muc17 O-glycosylation. Intestinal B3GNT7 deficiency increases susceptibility to colitis and enteric infection in mice, showing that B3GNT7-dependent glycosylation confers protective properties to colonic mucus. Taken together, these results demonstrate that B3GNT7 has a function distinct from other B3GNT family members and is critical for maintaining colonic homeostasis. SIGNIFICANCE STATEMENTUlcerative colitis is a chronic inflammatory bowel disease that affects 5 million people globally. The colonic mucus layer forms a protective barrier over colonic epithelial cells and is disrupted in ulcerative colitis. Mucus is composed of mucin proteins decorated by carbohydrates, called glycans. Glycans confer protective properties to the mucus barrier, and mucin glycans change in ulcerative colitis. B3GNT7 is an enzyme that elongates glycans and is downregulated in ulcerative colitis. In this study, we use in vitro and in vivo models to demonstrate that B3GNT7 regulates colonic mucus glycans and protects mice against colitis and infection. Our findings provide molecular insight into the contributions of B3GNT7-dependent glycans to colonic homeostasis.
Kelly, R. E.
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Null Hypothesis Significance Testing (NHST) remains the dominant paradigm for evaluation of empirical research findings in medicine and the social sciences despite concerns about frequent misinterpretations of those findings. Achievement of "statistical significance," the goal of NHST, often beckons unrealistic conclusions. Helpful would be the addition of a broader, Bayesian perspective of research in terms of progressive readjustment of hypothesis credibility from all sources of evidence. For this purpose, the Hypothesis Race Model (HRM) provides an intuitive Bayesian approach that builds upon NHST-concepts, helping to correct misunderstandings with minimal reeducation. The HRM is an extension of the Bayesian approach by Ioannidis in 2005 that helped to explain "why most published research findings are false." It is powerful enough to serve as the foundation for mathematical models to estimate and reduce the cost of empirical hypothesis testing.
Kanold, P. O.; Cardoso de Oliveira, M.
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Listening in complex environments requires the enhancement of relevant sounds and suppression of irrelevant ones. Corticothalamic neurons (CTNs) in auditory cortex layer (L) 6 provide modulatory feedback to thalamic nuclei and to upper cortical layers and are thought to be involved in gain control. However, their role in auditory processing remains unclear. We used in vivo two-photon imaging in mice to investigate the responses of L6 CTNs during active and passive listening. During a tone-in-noise detection task with varying levels of difficulty, L6 CTN responses exhibited higher gain in hit than miss trials, and this gain increased with task difficulty, indicating the active role of L6 CTNs. During passive listening, L6 CTNs exhibited diverse receptive fields and a heterogeneous tonotopic organization, with responses either suppressed or facilitated by background noise. Together, our results reveal diverse and dynamic context-dependent responses of L6 CTNs, consistent with a role in gain control.
Yu, J.; Li, H.-Z.; Wang, J.-J.; Liu, Y.-L.; Guo, Z.-Y.
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The mucosal chemoattractant C-X-C motif chemokine ligand 17 (CXCL17) was recently identified as a ligand for the orphan G protein-coupled receptor 25 (GPR25). Although CXCL17 orthologs have been identified in fishes, amphibians, and mammals, their presence in reptiles and birds remains unclear. In this study, we employed bioinformatic searches based on gene synteny and sequence features to identify CXCL17 orthologs in public databases. We identified functional CXCL17 orthologs in 46 reptilian species, including lizards, snakes, turtles, and alligators. In contrast, we found only non-functional gene relics in 22 bird species, suggesting the avian lineage lost functional CXCL17 during evolution. A recombinant reptilian CXCL17 from the loggerhead turtle (Caretta caretta), termed Cc-CXCL17, directly bound to and efficiently activated its corresponding receptor, Cc-GPR25, in a C-terminal fragment-dependent manner. Activation of Cc-GPR25 by Cc-CXCL17 also induced chemotactic movement of transfected human embryonic kidney (HEK) 293T cells. In cross-species activity assays, CXCL17s from human and tropical clawed frog could activate Cc-GPR25 albeit with lower potency, but fish orthologs lacked this activity; all tested CXCL17s had no detectable activity towards chicken GPR25, but Cc-CXCL17 had low activity towards mallard GPR25. Our findings demonstrate the presence of functional CXCL17 orthologs in extant reptiles and provide evidence for their evolutionary loss in birds, offering new insights into the phylogenetic distribution of the newly identified CXCL17-GPR25 signaling system.
Chawla, P.; Chen, Y.; Huynh, T. N.
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Bacteriophages, particularly temperate prophages that integrate directly into the host genome, are crucial drivers of bacterial evolution and act as fundamental architects of microbial communities. Listeria monocytogenes 10403S has two phage elements - prophage {Phi}10403S and monocin element. In this study, we found that c-di-AMP, a crucial second messenger in L. monocytogenes, regulates phage production. C-di-AMP accumulation down-regulates the gene expression of prophage and monocin gene loci and inhibits phage production, both spontaneous phage production as well as under phage induction through mitomycin-C treatment. We found that in genetically heterogenous cultures, super-infection of non-lysogenic strains with phage-containing strains can significantly amplify spontaneous prophage production. Using these cultures as an induction system, we found other inducers of spontaneous phage production. We found that ppGpp accumulation and nutrient starvation acts as an inducer of the spontaneous prophage production in L. monocytogenes. H2O2 can also play a role in inducing spontaneous phage production. Moreover, {Phi}10403S prophage production is suppressed in co-cultures of L. monocytogenes 10403S with L. monocytogenes F2365 and L. innocua CLIP11262. ImportanceMost Listeria and L. monocytogenes strains are lysogens, although the impact of phage genes on bacterial host metabolism or host fitness during bacterial competition is still unexplored. Bacteriophages have been shown to influence the evolution of their host and, in several cases, have a major effect on environmental fitness, pathogenicity and/or virulence of bacterial pathogens, either by regulating expression of critical genes or encoding beneficial genes. Prophages provide their hosts with a competitive edge through lysogenic conversion-- introducing novel toxins and defense systems--while simultaneously maintaining a molecular trigger, in the form of lysogenic-to-lytic switch, capable of initiating population-wide lysis in response to environmental stress. In the human pathogen Listeria monocytogenes, these prophages are near-ubiquitous and studies by other groups have described them as critical regulators of the bacteriums SOS pathways and its pathogenic lifestyle. This study identifies important novel regulators of phage induction in Listeria monocytogenes - c-di-AMP, ppGpp and H2O2, and how phage induction and production can shape the dynamics of bacterial competition of its host.
Raval, P. K.; Lim, S.; Gallie, J.; Agashe, D.
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Transfer RNA (tRNA) repertoires vary greatly across genomes, shaped by genetic drift and selection. A peculiar pattern across prokaryotes is the near-complete absence of tRNAs with unmodified adenine at the 34th (wobble) position (i.e., tRNAANN). Each of these tRNAs are just a single mutation away from several other tRNAs. Hence, their persistent absence suggests fundamental but hitherto unclear constraints. We engineered 36 Escherichia coli strains expressing tRNAs carrying each theoretically possible ANN anticodon to determine their functionality and fitness effects. Notably, there was no evidence of broad toxicity due to these tRNAs. All five tRNAANN tested underwent post-transcriptional maturation and all seven tested compensated for the deletion of their respective native tRNABNN (carrying G, C or U at the 34th position), demonstrating that tRNAANN are translationally active. Furthermore, tRNAANN from four-fold degenerate (4D) codon boxes were unmodified and were generally neutral or beneficial, whereas tRNAANN from two-fold degenerate (2D) boxes underwent A34-to-I34 modification and were more likely to impair fitness. We suggest superwobbling by tRNAANN -- decoding an entire four-codon set -- as one mechanism underlying these differential fitness effects. Maximal degeneracy in 4D boxes buffers or exploits tRNAANN superwobbling via synonymous decoding, whereas constrained degeneracy in 2D boxes renders it deleterious, likely through amino acid misincorporation. Thus, these differential fitness effects, sharpens the paradox of neutral or beneficial yet absent 4D tRNAANN, while beginning to empirically unravel underlying causes for the absence of 2D tRNAANN.
Loidolt, F.; Mazzoni, M.; Thamm, M.; Otieno, M.; Hasselmann, M.; Scheiner, R.
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Adaptation to local environments enables species to thrive in diverse and challenging habitats. Steep elevational gradients provide a compelling natural adaptation laboratory, because abiotic conditions change progressively over short geographical differences. Given that elevation can strongly reshape physiology and behavior of insects, neuromodulatory systems offer a promising lens through which to examine elevation-specific adaptation. We challenged the hypothesis that adaptation to elevation involves octopaminergic signaling in honey bees (Apis mellifera), an important pollinator species occupying different elevations along East African mountains. We collected foragers from two distinct elevations at Mount Kenya (1,150 m and 1,900 m above sea level) and analyzed elevation-dependent changes in octopaminergic signaling. Tissue-specific analysis revealed a striking upregulation of all three octopamine {beta} receptor genes in the thoracic flight muscles and elevated octopamine brain concentrations at high elevation. Expression differences in the brain and fat body were rather modest. We subjected CRISPR/Cas9-mediated octopamine {beta}2 receptor knockouts to cold stress to study the function of octopaminergic signaling in thermoregulation. Loss of AmOAR{beta}2 reduced both the slope and amplitude of heating phases, indicating altered thermogenic dynamics. Together, these results identify the octopaminergic system as a central neuromodulatory regulator of thermogenic performance across elevations in honey bees. More broadly, our study highlights how modulation of conserved aminergic signaling pathways can shape physiological resilience to environmental gradients, pointing to a general mechanism by which insects adapt to changing thermal landscapes. Highlights- Bees from high and low elevation differ in expression of octopamine {beta} receptor genes and octopamine brain concentrations - CRISPR/Cas9-mediated octopamine receptor knockout alters thermogenic behavior - Octopaminergic signaling emerges as a key neuromodulator in thermal adaptation to elevation in honey bees Significance statementAnimals living along mountain gradients must cope with rapidly changing temperatures, yet the mechanisms enabling this adaptation remain poorly understood. We show that honey bees from higher elevations have increased brain octopamine levels and enhanced expression of octopamine receptors in heat-producing flight muscles. Using gene editing, we demonstrate that disrupting one key receptor alters how bees generate heat under cold stress. These findings identify octopamine signaling as a central regulator of thermogenesis and reveal a mechanism by which insects adjust to colder environments. More broadly, our results highlight how conserved neuromodulatory systems can fine-tune physiological performance, offering insight into how insects may respond to changing climates and expanding environmental extremes.
Salazar, S.; Luong, K. T. Y.; Loaiza, A. D.; Cheng, D.; Drayman, N.; Koyuncu, O. O.
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Alpha herpesviruses (-HV) initially infect mucosal epithelial cells and subsequently establish lifelong latency in the peripheral nervous system (PNS). Herpes simplex virus-1 (HSV-1), a human pathogen persisting in the majority of the adult population, shares neuroinvasive properties with Pseudorabies virus (PRV), a swine -HV, commonly used as a model -HV. Utilizing primary peripheral neuronal cultures, we previously showed that IFN-{lambda} pre-treatment significantly reduced PRV yield. In this paper, we further characterized the early and late neuronal responses to IFN-{lambda} by RNA-seq, and the antiviral potential of this response against HSV-1. Notably, HSV-1 exhibited neuron-specific resistance to IFN-{lambda} mediated antiviral responses both in murine primary neurons and human neuronal cells. An ICP34.5-deficient HSV-1 ({Delta}34.5) mutant showed IFN-{lambda} sensitivity in neurons, while replicating normally in untreated neurons showing that ICP34.5 is responsible for the neuron specific IFN-{lambda} resistance of HSV-1. Our results further demonstrate that RSAD2 is strongly induced by IFN-{lambda} in neurons, localizing to ER-associated membranes, and effectively restricting -HV protein synthesis in the absence of ICP34.5. siRNA-mediated RSAD2 knockdown in IFN-{lambda}-primed primary neurons largely restored replication of {Delta}34.5 HSV-1, highlighting the role of this IFN-{lambda} induced host factor in neuronal infections. Together, neuronal IFN-{lambda}-induced RSAD2 and HSV-1 ICP34.5 define a neuron-specific antagonistic mechanism that collectively determines the replication efficiency of HSV-1 in the PNS.
Ding, L.; Mlejnek, J.; Zheng, H.; Lee, C.-H.; Chen, Y.-C.; Reinberg, D.; Desplan, C.
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In ants and other eusocial insects, reproductive division of labor is tightly regulated by juvenile hormone (JH), which suppresses reproduction in most individuals to maintain the worker caste. However, how social cues trigger systemic JH suppression to permit reproductive activation remains unclear. In the ant Harpegnathos saltator, workers respond to queen loss by engaging in sustained ritualistic dueling and transitioning into reproductive, long-lived pseudoqueens (gamergates). This provides a powerful model for investigating the molecular basis of socially induced plasticity. We examined the hemolymph proteome of transitioning ants and identified HCRG1, a lineage-restricted peptide upregulated during dueling, as a circulating factor that physically interacts with Hex70c, a broadly conserved JH-binding Hexamerin. HCRG1 promotes ovarian development by antagonizing JH signaling. Expression of ant HCRG1 in the heterologous solitary model Drosophila also extends lifespan. These findings identify an evolutionarily derived circulating factor that links social sensory perception to systemic JH suppression, enabling coordinated reproductive and longevity transitions in a social insect.
Vilain, M.; Mghabghab, R.; Aris-Brosou, S.
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The haemagglutinin (HA) and neuraminidase (NA) genes of seasonal influenza A evolve under continual immune-driven positive selection. To test whether the tempo of selection has changed over time, we mapped branch- and site-specific episodic diversifying selection (MEME) onto Bayesian relaxed-clock time trees for HA and NA in H1N1 and H3N2, across multiple countries and four sequence-subsampling schemes. We dated each selection episode and tested whether episodes accumulated through time after accounting for the growing number of sampled lineages. Positive-selection episodes increased over time in every gene-subtype combination, at about 2-6% per lineage-year, and rose faster for NA than HA. Episodes were concentrated at a small number of codon sites, especially recurrent sites in H3N2 HA that fell within canonical antigenic regions of the HA1 head. This increase was robust to subsampling scheme and time-bin width, and was driven disproportionately by recent lineages. A detrended spatial analysis found no association with latitude or temperature anomalies. Overall, positive selection on influenza surface antigens appears to be intensifying through time, most likely because of immune escape and expanded surveillance rather than climate warming.