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Circadian rhythms are a mechanism by which species adapt to environmental variability and fundamental to understanding species behavior. However, we lack data and a standardized framework to accurately assess and compare temporal activity for species during rapid ecological change. Through a global network representing 38 countries, we leveraged 8.9 million mammalian observations to create a library of 14,587 standardized diel activity estimates for 445 species. We found that less than half the species' estimates were in agreement with diel classifications from the reference literature and that species commonly used more than one diel classification. Species diel activity was highly plastic when exposed to anthropogenic change. Furthermore, body size and distributional extent were strongly associated with whether a species is diurnal or nocturnal. Our findings provide essential knowledge of species behavior in an era of rapid global change and suggest the need for a new, quantitative framework that defines diel activity logically and consistently while capturing species plasticity.

High-performance liquid chromatography (HPLC) together with mass spectrometry (MS) is routinely used to separate, identify and quantify chemicals. HPLC data also provides retention time (RT) which can be aligned with structural data. Recent developments in machine learning (ML) have improved our ability to predict RTs from known or postulated chemical structures, allowing RT data to be used more effectively in LC-MS-based compound identification. However, RT data is highly specific to each chromatographic method (CM) and hundreds of different CMs with interdependent parameters are used in separations. This has limited the application of ML-based RT predictions in compound identification. Here we introduce an easy-to-use RT prediction webserver (called RT-Pred) that predicts RTs for molecules across most chromatographic setups. RT-Pred not only supports its own in-house CM-specific RT predictors, it allows users to easily train a custom RT-Pred model using their own RT data on their own CM and to predict RTs with that custom model. RT-Pred also supports RT and compound searches against its own database of millions of predicted RTs spanning >40 different CMs. RT-Pred is also uniquely capable of accurately identifying compounds that will elute in the void volume or be retained on the column. Including this void/retained/eluted classifier significantly improves RT-Pred's performance. Tests indicate that RT-Pred had an average coefficient of determination (R²) of 0.95 over 20 different CMs. Comparisons of RT-Pred against other RT predictors showed that RT-Pred achieved lower mean absolute errors and higher R² scores than any other published RT predictor. RT-Pred is freely available at https://rtpred.ca., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025. Published by Elsevier B.V.)

The presence of parasites can elicit host responses even in the absence of infection. These risk-induced trait responses include altered host behaviours, morphology, and/or physiology, which can trade off with other fitness-related traits. Studies of predator-induced non-consumptive effects (NCEs) have demonstrated that exposure at one life stage can lead to NCEs in the next stage, but no studies to date have examined such an effect of parasite exposure. Numerous NCEs have been demonstrated in larval, pupal and adult stages of Drosophila nigrospiracula exposed to ectoparasitic mites ( Macrocheles subbadius ). Here we experimentally investigated whether parasite-induced NCEs carry over into subsequent developmental stages (i.e. interstadial effects). We tested the prediction that when flies are exposed to mites during the larval and pupal stages, the subsequent adult stage will exhibit decreased body mass, fecundity and longevity. However, we did not detect downstream effects of parasite exposure on adult body mass, fecundity or longevity. The probability of survival and lifetime fecundity were comparable for previously exposed and unexposed groups. We suggest that when parasite exposure is confined to one developmental stage, and the risk of infection is removed in the subsequent stage, the long-term effects of parasite exposure dissipate. The potential to recover from the interim costs of parasite exposure may provide an added benefit to host dispersal.

Limosilactobacillus reuteri is an immunomodulatory bacterium enriched in non-industrialized microbiomes, making it a therapeutic candidate for chronic diseases. However, effects of L. reuteri strains in mouse models of multiple sclerosis have been contradictory. Here, we show that treatment of spontaneous relapsing-remitting experimental autoimmune encephalomyelitis (EAE) mice with L. reuteri R2lc, a strain that activates the aryl hydrocarbon receptor (AhR) through the pks gene cluster, resulted in severe pathology. In contrast, a pks mutant and a pks-negative strain (PB-W1) failed to exacerbate EAE and exhibited reduced pathology compared to R2lc despite earlier disease onset in PB-W1 mice. Differences in pathology occurred in parallel with a pks-dependent downregulation of AhR-related genes, reduced occludin expression in the forebrain, and altered concentrations of immune cells. This work establishes a molecular foundation for strain-specific effects on autoimmunity, which has implications for our understanding of how microbes contribute to chronic conditions and the selection of microbial therapeutics., Competing Interests: Declaration of interests J.W. is an owner of a patent on Limosilactobacillus reuteri NCIMB 42835 (PB-W1), licensed to Novonesis A/S, of which income will be shared with the research institutes in Papua New Guinea and Canada that were involved in isolation and characterization of the strain. J.W. has further received honoraria and/or paid consultancy from PrecisionBiotics/Novonesis A/S. J.-P.v.P. Is the founder and owner of the consulting company Next-Gen Probiotics, LLC. J.-P.v.P. has received unrestricted funding from BioGaia AB, a probiotics company., (Copyright © 2025. Published by Elsevier Inc.)

Chronic wasting disease (CWD) is a prion disease that infects cervid species by direct and environmental transmission and is invariably fatal. CWD spread can be promoted by the attraction of animals to "hotspots" such as hay bales and grain bags stored in fields and at farm sites. The density and location of hotspots may impact contact rates. We used an individual-based movement model of mule deer ( Odocoileus hemionus ) to investigate the effects of density and configuration of hotspots (hereafter artificial attractants, AA) on contact rates at a constant density of 1 deer/km 2 during winter. The model tracks when two deer from the same or different groups come into contact under 6 AA densities (0-1 AA/km 2 ) and 6 AA configurations. We compared placing AA randomly versus clustered around farms, and removing them randomly versus biased by proximity to preferred habitat. Overall, the number of unique contacts per individual and the number of unique deer visiting an AA increased, and the number of AAs used by each deer decreased as AA density declined. Selectively removing field attractants near preferred habitat resulted in a larger increase in contacts per deer, with deer contacting more and different individuals, fewer deer using the remaining AA, and fewer visits per AA than random removal. There was a greater increase in contact rates when reducing AA density at farms by randomly removing all AA at a farm compared to randomly removing individual AA across farms. Deer responses to AA removal may not be as straightforward as originally believed. Deer contacts may increase, not decrease, with AA removal because deer are attracted to the remaining AA. Under moderate deer densities, AA removal may require a broad-scale, "all or nothing" approach to prevent deer from concentrating at remaining AA, but concomitantly lowering deer density needs further assessment., Competing Interests: The authors declare no conflicts of interest., (© 2025 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

The hydrophobic surface of plastics adsorbs hydrophobic persistent organic pollutants (POP) such as Perfluorooctanoic acid (PFOA). The potential for hydrophobic nanoparticles such as titanium dioxide (TiO 2 ) to associate with PFOA and alter accumulation rates has not been investigated. Nanoparticles form ecocorona by adsorption of multiple constituents in water, but few studies have examined if this results in differences in the rate of PFOA accumulation in freshwater animals. We demonstrate the PFOA associates with the hydrophobic surfaces of nano-sized TiO 2 particles and this increases the rate of uptake of PFOA into Daphnia magna. Accumulation of PFOA in daphnia was measurement over multiple concentrations, flux times and particle sizes using a radiotracer-based method ( 14 C-labelled PFOA). Our results show that TiO 2 NPs have a high sorption capacity for PFOA and PFOA sorption decreased aggregation of TiO 2 as evidenced by a decrease in average hydrodynamic diameter, decreased zeta potential and increased polydispersity index. Uptake of PFOA at 10 μg/L was found to be 45 % higher in the presence of 500 μg/L of 5 nm TiO 2 compared to control PFOA alone uptake. Potentiation of PFOA uptake using 25 nm TiO 2 NPs was 25 % higher than control PFOA alone. PFOA alone (0.5 mg/L) reduced metabolic oxygen consumption (MO 2 ) in daphnia by 52 %, but exposure to (100 mg/L) 5 nm TiO 2 NPs sorbed with (0.5 mg/L) PFOA decreased metabolic oxygen consumption (MO 2 ) by ~88 %. These findings show that TiO 2 nanoparticles act as vectors for hydrophobic organic pollutant accumulation and significantly potentiate PFOA accumulation and toxicity in aquatic organisms., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025. Published by Elsevier Inc.)

Key Message: An improved prime editing system precisely corrected a 14-bp deletion in the rc gene of white rice, restoring the production of brown pigments., Competing Interests: Declarations. Conflict of interest: The authors declare no conflict of interest in association with this work., (© 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Traumatic brain injuries (TBI) are diverse with heterogeneous injury pathologies, which creates challenges for the clinical treatment and prevention of secondary pathologies such as post-traumatic epilepsy and subsequent dementias. To develop pharmacological strategies that treat TBI and prevent complications, animal models must capture the spectrum of TBI severity to better understand pathophysiological events that occur during and after injury. To address such issues, we improved upon our recent larval zebrafish TBI paradigm emphasizing titrating to different injury levels. We observed coordination between an increase in injury level and clinically relevant injury phenotypes including post-traumatic seizures (PTS) and tau aggregation. This preclinical TBI model is simple to implement, allows dosing of injury levels to model diverse pathologies, and can be scaled to medium- or high-throughput screening., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2025. Published by The Company of Biologists Ltd.)

How animal cell types, tissues, and regional body plans arose is a fundamental question in EvoDevo. Many current efforts attempt to link genetic information to the morphology of cells, tissues and regionalization of animal body plans using single-cell sequencing of cell populations. However, a lack of in-depth understanding of the morphology of non-bilaterian animals remains a considerable block to understanding the transitions between bilaterian and non-bilaterian cells and tissues. Sponges (Porifera), one of the earliest diverging animal phyla, pose a particular challenge to this endeavour, because their body plans lack mouths, gut, conventional muscle and nervous systems. With a goal to help bridge this gap, we have studied the morphology, behaviour and transcriptomics of cells and tissue types of an easily accessible and well-studied species of freshwater sponge, Ephydatia muelleri. New features described here include: a polarized external epithelium, a new contractile sieve cell that forms the entry to incurrent canals, motile cilia on apopyle cells at the exit of choanocyte chambers, and non-motile cilia on cells in excurrent canals and oscula. Imaging cells in vivo shows distinct behavioural characteristics of motile cells in the mesohyl. Transcriptomic phenotypes of three cell types (cystencytes, choanocytes and archaeocytes) captured live indicate that cell-type transcriptomes are distinct. Importantly, individual archaeocytes show a range of transcriptomic phenotypes which is supported by the distinct expression of different genes by subsets of this cell type. In contrast, all five choanocyte cells sampled live revealed highly uniform transcriptomes with significantly fewer genes expressed than in other cell types. Our study shows that sponges have tissues whose morphology and cell diversity are both functionally complex, but which together enable the sponge, like other metazoans, to sense and respond to stimuli., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Exploring the relationship between phenotype, genotype, and environment is essential in quantitative genetics. Considering the complex genetic architecture of economically important traits, integrating genotype-by-environment interactions in a genome-wide association (GWAS) and genomic prediction (GP) framework is imperative. This integration is crucial for identifying robust markers with stability across diverse environments and improving the predictive accuracy of individuals' performance within specific target environments. We conducted a multi-environment GWAS and GP analysis for 30 productivity, defense, and climate-adaptability traits on 1540 white spruce trees from Alberta, Canada, genotyped for 467,224 SNPs and growing across three environments. We identified 563 significant associations (p-value < 1.07 ×10 -05 ) across the studied traits and environments, with 105 SNPs showing overlapping associations in two or three environments. Wood density, myrcene, total monoterpenes, α-pinene, and catechin exhibited the highest overlap (>50%) across environments. Gas exchange traits, including intercellular CO 2 concentration and intrinsic water use efficiency, showed the highest number of significant associations (>38%) but less stability (<1.2%) across environments. Predictive ability (PA) varied significantly (0.03-0.41) across environments for 20 traits, with stable carbon isotope ratio having the highest average PA (0.36) and gas exchange traits the lowest (0.07). Only two traits showed differences in prediction bias (PB) across environments, with 80% of site-trait PB falling within a narrow range (0.90 to 1.10). Integrating multi-environment GWAS and GP analyses proved useful in identifying site-specific markers, understanding environmental impacts on PA and PB, and ultimately providing indirect insights into the environmental factors that influenced this white spruce breeding program., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s), under exclusive licence to The Genetics Society.)

Background: Excessive hypercholesterolemia in pregnancy increases the risk of preeclampsia, though the mechanisms remain unclear. We recently showed that uterine artery function is impaired in hypercholesterolemia-preeclampsia via activation of the TLR4 (toll-like receptor 4)/PGHS1 (prostaglandin H synthase 1) pathway. Low-dose aspirin lowers preeclampsia risk in high-risk pregnancies by inhibiting PGHS1, but its effects in hypercholesterolemia-preeclampsia pregnancies are not known. Moreover, oxidized low-density lipoprotein levels rise in hypercholesterolemia-preeclampsia, potentially activating TLR4 and LOX-1 (lectin-like oxLDL receptor-1; scavenger receptor linked to vascular dysfunction in preeclampsia). However, whether this occurs in hypercholesterolemia-preeclampsia is not known., Methods: Sprague Dawley rats received a control or high-cholesterol diet (to induce hypercholesterolemia-preeclampsia) from gestational day 6 to 20, with placebo or low-dose aspirin (1.5 mg/daily) given from gestational day 10 to 20. On gestational day 20, pregnancy outcomes and uterine artery function were assessed., Results: Uterine artery blood flow velocity and placental weights were higher in hypercholesterolemia-preeclampsia placebo-treated dams versus controls, but these were reduced by low-dose aspirin. Endothelium-dependent vasodilation was impaired in the uterine arteries of the hypercholesterolemia-preeclampsia placebo group versus controls and was corrected by low-dose aspirin. Ex vivo inhibition of TLR4, PGHS1, or LOX-1 also normalized endothelium-dependent vasodilation in the hypercholesterolemia-preeclampsia placebo-treated dams. Exposure to oxidized low-density lipoprotein in the bath (modeling a secondary hit) further impaired endothelium-dependent vasodilation in the uterine arteries of the hypercholesterolemia-preeclampsia placebo group, partially via TLR4 and LOX-1, which was prevented by low-dose aspirin., Conclusions: Low-dose aspirin improved uterine artery endothelial function in hypercholesterolemia-preeclampsia pregnancies; likely by suppressing the TLR4/LOX-1/PGHS1 pathway.

The genus Rhinebothrium (Cestoda: Rhinebothriidea) comprises tapeworm species parasitizing elasmobranch hosts, particularly batoids. Despite numerous recent findings regarding the ecological importance of marine fish parasites throughout the world, the biodiversity of cestodes inhabiting fishes of the Persian Gulf and the Gulf of Oman remains understudied. Here, two new species of Rhinebothrium from stingrays from the Persian Gulf and Gulf of Oman are described: Rhinebothrium gossi sp. nov. and Rhinebothrium palmeri sp. nov. from Maculabatis arabica and Maculabatis randalli , respectively. However, each new cestode species is found with a lower frequency in the other host species, too. These new species were already subjected to a molecular analysis and the revealed genetic distinctiveness requires detailed morphological examinations at the species level. A combination of morphomeristic characteristics including body size, scolex features, proglottid morphology, and reproductive structures distinguish the new species from the other congeners. Although these new species are morphologically similar, however, they differ from each other in the number of testes (6-8 and 8-14), and bothridial loculi (50 and 42 in R. gossi sp. nov. and R. palmeri sp. nov., respectively). These findings contribute to our understanding of marine cestode diversity and underscore the importance of further research in this ecologically significant region.

Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small "many analyst" study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future., Competing Interests: Declarations. Ethics approval and consent to particpate: We obtained permission to conduct this research from the Whitman College Institutional Review Board (IRB). As part of this permission, the IRB approved the consent form ( https://osf.io/xyp68/ ) that all participants completed prior to joining the study. The authors declare that they have no competing interests. Competing interests: The authors declare that they have no competing interests., (© 2025. The Author(s).)

A nanomaterial life-cycle risk assessment (Nano LCRA) was conducted for second-generation functionalized cellulose nanomaterials (CNs) in five case studies, including applications in water filtration, food contact packaging (including as an additive and coating), and food additives, to identify and prioritize potential occupational, health, consumer, and environmental risks. Exposure scenarios were developed and ranked for each product life-cycle stage. A Safer-by-Design Toolbox (SbD Toolbox) representing a compendium of high-throughput physical, chemical, and toxicological new approach methodologies (NAMs) was used for a screening-level hazard assessment. Overall, risks identified for the CN-enabled products were low. Of the exposure scenarios, occupational inhalation exposures during product manufacturing and application ranked the highest. Despite differences in chemistry and morphology, the materials behaved similarly in oral, dermal, and inhalation models, supporting their grouping and read-across. The screening-level hazard assessment identified potential lung inflammation associated with CN exposure, and a review of the literature supported this funding, suggesting CNs behave as poorly soluble, low-toxicity dusts with the potential to irritate the lung. Key research gaps to reduce uncertainty include evaluating long-term, low-dose exposures typical of the workplace, as well as the potential release and toxicity of CN-containing composite particles.

While psychologists have extensively discussed the notion of a "theory crisis" arising from vague and incorrect hypotheses, there has been no debate about such a crisis in biology. However, biologists have long discussed communication failures between theoreticians and empiricists. We argue such failure is one aspect of a theory crisis because misapplied and misunderstood theories lead to poor hypotheses and research waste. We review its solutions and compare them with methodology-focused solutions proposed for replication crises. We conclude by discussing how promoting inclusion, diversity, equity, and accessibility (IDEA) in theoretical biology could contribute to ameliorating breakdowns in the theory-empirical cycle., Competing Interests: Declarations. Competing interests: The authors declare no competing interests except that SN, YY, and ML are the members of SORTEE., (© 2025. The Author(s).)

Fungi are well-known for their ability to both produce and catabolize complex carbohydrates to acquire carbon, often in the most extreme of environments. Glucuronoxylomannan (GXM)-based gel matrices are widely produced by fungi in nature and though they are of key interest in medicine and pharmaceuticals, their biodegradation is poorly understood. Though some organisms, including other fungi, are adapted to life in and on GXM-like matrices in nature, they are almost entirely unstudied, and it is unknown if they are involved in matrix degradation. Sporothrix epigloea is an ascomycete fungus that completes its life cycle entirely in the short-lived secreted polysaccharide matrix of a white jelly fungus, Tremella fuciformis. To gain insight into how S. epigloea adapted to life in this unusual microhabitat, we compared the predicted protein composition of S. epigloea to that of 21 other Sporothrix species. We found that the genome of S. epigloea is smaller than that of any other sampled Sporothrix, with widespread functional gene loss, including those coding for serine proteases and biotin synthesis. In addition, many predicted CAZymes degrading both plant and fungal cell wall components were lost while a lytic polysaccharide monooxygenase with no previously established activity or substrate specificity, appears to have been gained. Phenotype assays suggest narrow use of mannans and other oligosaccharides as carbon sources. Taken together, the results suggest a streamlined machinery, including potential carbon sourcing from GXM building blocks, facilitates the hyperspecialized ecology of S. epigloea in the GXM-like milieu., (© The Author(s) 2025. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Sponges (phylum Porifera) are an early diverging animal lineage without nervous and muscular systems, and yet they are able to produce coordinated whole-body contractions in response to disturbances. Little is known about the underlying signalling mechanisms in coordinating such responses. Previous studies demonstrated that sponges respond specifically to chemicals such as l-glutamate and γ-amino-butyric acid (GABA), which trigger and prevent contractions, respectively. Genes for purinergic P2X-like receptors are present in several sponge genomes, leading us to ask whether ATP works with glutamate to coordinate contractions in sponges as it does in other animal nervous systems. Using pharmacological approaches on the freshwater sponge Ephydatia muelleri, we show that ATP is involved in coordinating contractions. Bath application of ATP caused a rapid, sustained expansion of the excurrent canals in a dose-dependent manner. Complete contractions occurred when ATP was added in the presence of apyrase, an enzyme that hydrolyses ATP. Application of ADP, the first metabolic product of ATP hydrolysis, triggered complete contractions, whereas AMP, the subsequent metabolite, did not trigger a response. Blocking ATP from binding and activating P2X receptors with pyridoxalphosphate-6-azophenyl-2',4'-disulfonic acid (PPADS) prevented both glutamate- and ATP-triggered contractions, suggesting that ATP works downstream of glutamate. Bioinformatic analysis revealed two P2X receptor sequences, one of which groups with other vertebrate P2X receptors. Altogether, our results confirm that purinergic signalling by ATP is involved in coordinating contractions in the freshwater sponge., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2025. Published by The Company of Biologists.)

Various modeling efforts have been conducted to evaluate ecosystem services (ES) of agricultural conservation practices but typically these models are too complex for conservation stakeholders to use. This research developed a cloud-based WebGIS tool for communicating integrated ES modeling to conservation stakeholders. The integrated ES modeling was developed by linking farm economic, watershed hydrologic, and soil carbon modeling within a spatial optimization framework for identifying conservation practices to minimize economic costs subject to multiple ES targets including water quality and soil carbon improvement benefits. The WebGIS tool, named "Ecosystem Services Assessment Tool" (ESAT), has a suite of functions to visualize watershed characteristics, summarize the effectiveness of existing agricultural conservation practices, examine the cost, effectiveness, and cost-effectiveness of future agricultural conservation practices, and further, identify optimal sets of conservation practices for achieving cost-effectiveness. The study area for the integrated ES modeling and WebGIS tool development was the 4,820-km 2 Modeste watershed in Alberta, Canada. The ESAT application demonstrated its functionalities to support decision making, particularly in identifying cost-effective conservation practices for achieving sediment, phosphorus or nitrogen reduction, or soil carbon increase target. In the research, conservation stakeholders including municipal and provincial governments, conservation management agencies, and NGOs were actively engaged in data collection, modeling development, WebGIS tool development, and training for the use of the WebGIS tool. Conservation stakeholders assessed that the ESAT is a very useful tool for supporting decision making in agri-environmental programs. However, the WebGIS tool can be further simplified and streamlined to improve the user-friendliness of the ESAT., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Social insects, particularly honey bees, have exceptionally high genomic frequencies of genetic recombination. This phenomenon and underlying mechanisms are poorly understood. To characterise the patterns of crossovers and gene conversion in the honey bee genome, a recombination map of 187 honey bee brothers was generated by whole-genome resequencing. Recombination events were heterogeneously distributed without many true hotspots. The tract lengths between phase shifts were bimodally distributed, indicating distinct crossover and gene conversion events. While crossovers predominantly occurred in G/C-rich regions and seemed to cause G/C enrichment, the gene conversions were found predominantly in A/T-rich regions. The nucleotide composition of sequences involved in gene conversions that were associated with or distant from crossovers corresponded to the differences between crossovers and gene conversions. These combined results suggest two types of DNA double-strand break repair during honey bee meiosis: non-canonical homologous recombination, leading to gene conversion and A/T enrichment of the genome, and the canonical homologous recombination based on completed double Holliday Junctions, which can result in gene conversion or crossover and is associated with G/C bias. This G/C bias may be selected for to balance the A/T-rich base composition of eusocial hymenopteran genomes. The lack of evidence for a preference of the canonical homologous recombination for double-strand break repair suggests that the high genomic recombination rate of honey bees is mainly the consequence of a high rate of double-strand breaks, which could in turn result from the life history of honey bees and their A/T-rich genome., (© 2024 The Author(s). Insect Molecular Biology published by John Wiley & Sons Ltd on behalf of Royal Entomological Society.)

Urinary N 1 , N 12 -diacetylspermine (DAS) is a known biomarker for colorectal cancer (CRC). However, DAS levels in both healthy and CRC patients' urine samples are extremely low and often challenging to quantify. Complex and expensive methods do exist to detect DAS in urine, but simpler, less expensive methods to detect DAS are needed, especially in low resource settings. Here we describe a highly efficient, fast, precise, and inexpensive colorimetric assay to detect low levels of DAS in human urine samples. We used recombinant diacetylspermine oxidase (rDAS Ox), expressed and extracted from E. coli, to oxidize DAS, producing three products including hydrogen peroxide (H 2 O 2 ). The level of DAS present, which correlates with H 2 O 2 levels, was measured using horseradish peroxidase (HRP), which together with H 2 O 2 , oxidized Amplex™ Red to produce the pink-colored resorufin. The concentration of resorufin is directly proportional to H 2 O 2 (and DAS) levels. As urine contains metabolites which interfere with these oxidation reactions, we developed a simple two column-based protocol using ion exchange resins to remove these compounds and concentrate the DAS. With this novel cleaning and concentrating method, DAS was concentrated 15 times (confirmed by nuclear magnetic resonance (NMR) spectroscopy) and <1 μM DAS could be detected. Correlation graphs of urine samples spiked with known DAS concentrations versus assay-determined DAS concentrations had high coefficients of determination (R 2 ) for 0-10 μM DAS (0.94) and for 0-1 μM DAS (0.91), clearly demonstrating the excellent performance of the two-column protocol with the rDAS Ox reaction mixture. To the best of our knowledge, this is first reported colorimetric enzymatic assay that quantitates DAS in urine., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Genetic rescue, or the translocation of individuals among populations to augment gene flow, can help ameliorate inbreeding depression and loss of adaptive potential in small and isolated populations. Genetic rescue is currently under consideration for an endangered butterfly in Canada, the Half-moon Hairstreak (Satyrium semiluna). A small, unique population persists in Waterton Lakes National Park, Alberta, isolated from other populations by more than 400 km. However, whether genetic rescue would actually be helpful has not been evaluated. Here, we generate the first chromosome-level genome assembly and whole-genome resequence data for the species. We find that the Alberta population maintains extremely low genetic diversity and is genetically very divergent from the nearest populations in British Columbia and Montana. Runs of homozygosity suggest this is due to a long history of inbreeding, and coalescent analyses show that the population has been small and isolated, yet stable, for up to 40k years. When a population like this maintains its viability despite inbreeding and low genetic diversity, it has likely undergone purging of deleterious recessive alleles and could be threatened by the reintroduction of such alleles via genetic rescue. Ecological niche modelling indicates that the Alberta population also exhibits environmental associations that are atypical of the species. Together, these evolutionary and ecological divergences suggest that population crosses may result in outbreeding depression. We therefore infer that genetic rescue has a relatively unique potential to be harmful rather than helpful for this population at present. However, because of its reduced adaptive potential, the Alberta population may still benefit from future genetic rescue as climate and habitat conditions change. Proactive experimental population crosses should therefore be completed to assess reproductive compatibility and progeny fitness., (© 2025 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

Diapause is an adaptive developmental arrest commonly utilized by animals to cope with seasonal changes. Central to this process are hormonal events that bridge photoperiodic cues and physiological changes. In insect reproductive diapause, the absence of juvenile hormone (JH) serves as the primary endocrine event that governs key diapause traits, including ovarian developmental arrest and lipid accumulation. Conventionally, it is believed that the effects of JH are conveyed through the receptor Methoprene-tolerant (Met) and its transcriptional factor Krüppel homolog 1 (Kr-h1). However, our study with the bean bug Riptortus pedestris reveals that JH independently regulates lipid accumulation, bypassing Met and Kr-h1 pathways. R. pedestris enters reproduction under long-day (LD) conditions, while diapause occurs under short-day (SD) conditions. Treatment of SD females with the JH mimic methoprene stimulated reproductive activities, enhancing ovary development and reducing lipid accumulation. In contrast, silencing genes essential for JH biosynthesis in LD females led to pronounced diapause characteristics, including ovarian developmental arrest and substantial lipid accumulation. Interestingly, disruptions in the JH action genes, either Met or Kr-h1, solely affected ovary development, leaving lipid accumulation unchanged, indicating an independent pathway for regulating JH in lipid accumulation. This was further confirmed by RNA interference experiments in SD females, where knockdown of Met or Kr-h1 did not alter the effects of methoprene on lipid reduction. Collectively, these results suggest that JH controls ovary development through the established Met-Kr-h1 pathway, while it modulates lipid accumulation through an alternative, yet to be identified noncanonical pathway during reproductive diapause in R. pedestris., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The plant community has a strong track record of RNA sequencing technology deployment, which combined with the recent advent of spatial platforms (e.g. 10× genomics) has resulted in an explosion of single-cell and nuclei datasets that can be positioned in an in situ context within tissues (e.g. a cell atlas). In the genomics era, application of proteomics technologies in the plant sciences has always trailed behind that of RNA sequencing technologies, largely due in part to upfront cost, ease-of-use, and access to expertise. Conversely, the use of early analytical tools for characterizing small molecules (metabolites) from plant systems predates nucleic acid sequencing and proteomics analysis, as the search for plant-based natural products has played a significant role in improving human health throughout history. As the plant sciences field now aims to fully define cell states, cell-specific regulatory networks, metabolic asymmetry and phenotypes, the measurement of proteins and metabolites at the single-cell level will be paramount. As a result of these efforts, the plant community will unlock exciting opportunities to accelerate discovery and drive toward meaningful translational outcomes., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

The evolution of eukaryotes is a fundamental event in the history of life. The closest prokaryotic lineage to eukaryotes, the Asgardarchaeota, encode proteins previously found only in eukaryotes, providing insight into their archaeal ancestor. Eukaryotic cells are characterized by endomembrane organelles, and the Arf family GTPases regulate organelle dynamics by recruiting effector proteins to membranes upon activation. The Arf family is ubiquitous among eukaryotes, but its origins remain elusive. Here we report a group of prokaryotic GTPases, the ArfRs, which are widely present in Asgardarchaeota. Phylogenetic analyses reveal that eukaryotic Arf family proteins arose from the ArfR group. Expression of representative Asgardarchaeota ArfR proteins in yeast and X-ray crystallographic studies show that ArfR GTPases possess the mechanism of membrane binding and structural features unique to Arf family proteins. Our results indicate that Arf family GTPases originated in the archaeal ancestor of eukaryotes, consistent with aspects of the endomembrane system evolving early in eukaryogenesis., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s), under exclusive licence to Springer Nature Limited.)

Strigolactones (SLs) are plant hormones that play a crucial role in regulating various aspects of plant architecture, such as shoot and root branching. However, the knowledge of SL-responsive genes and transcription factors (TFs) that control the shaping of plant architecture remains elusive. Here, transcriptomic analysis was conducted using the SL-insensitive barley mutant hvd14.d (carried mutation in SL receptor DWARF14, HvD14) and its wild-type (WT) to unravel the differences in gene expression separately in root and shoot tissues. This approach enabled us to select more than six thousand SL-dependent genes that were exclusive to each studied organ or not tissue-specific. The data obtained, along with in silico analyses, found several TFs that exhibited changed expression between the analyzed genotypes and that recognized binding sites in promoters of other identified differentially expressed genes (DEGs). In total, 28 TFs that recognize motifs over-represented in DEG promoters were identified. Moreover, nearly half of the identified TFs were connected in a single network of known and predicted interactions, highlighting the complexity and multidimensionality of SL-related signalling in barley. Finally, the SL control on the expression of one of the identified TFs in HvD14- and dose-dependent manners was proved. Obtained results bring us closer to understanding the signalling pathways regulating SL-dependent plant development., Competing Interests: Declarations. Conflict of interest: The authors declare no competing interests., (© 2024. The Author(s).)

Environmental filtering and dispersal history limit plant distributions and affect biogeographical patterns, but how their relative importance varies across evolutionary timescales is unresolved. Phylogenetic beta diversity quantifies dissimilarity in evolutionary relatedness among assemblages and might help resolve the ecological and biogeographical mechanisms structuring biodiversity. Here, we examined the effects of environmental dissimilarity and geographical distance on phylogenetic and taxonomic turnover for ~270,000 seed plant species globally and across evolutionary timescales. We calculated past and present dispersal barriers using palaeogeographical reconstructions and calculated geographical linear and least-cost distances, accounting for dispersal over water, mountains or areas with unsuitable climates. Environmental dissimilarity and geographical distance jointly explained most of the deviance in taxonomic (up to 86.4%) and phylogenetic turnover (65.6%). While environmental dissimilarity consistently showed strongly positive effects, the effect of geographical distance on phylogenetic turnover was less pronounced further back in evolutionary time. Past physiogeographical barriers explained a relatively low amount of the variation across all timescales, with a slight peak at intermediate timescales (20-50 Myr BP). Our results suggest that while old lineages have generally dispersed widely, the imprint of environmental filtering on range expansion persists, providing insights into biogeographical and evolutionary processes underlying global biodiversity patterns., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Macronutrients such as nitrogen (N), phosphorus (P), potassium (K) and sulphur (S) are critical for plant growth and development. Field-grown canola (Brassica napus L.) is supplemented with fertilizers to maximize plant productivity, while deficiency in these nutrients can cause significant yield loss. A holistic understanding of the interplay between these nutrient deficiency responses in a single study and canola cultivar is thus far lacking, hindering efforts to increase the nutrient use efficiency of this important oil seed crop. To address this, we performed a comparative quantitative proteomic analysis of both shoot and root tissue harvested from soil-grown canola plants experiencing either nitrogen, phosphorus, potassium or sulphur deficiency. Our data provide critically needed insights into the shared and distinct molecular responses to macronutrient deficiencies in canola. Importantly, we find more conserved responses to the four different nutrient deficiencies in canola roots, with more distinct proteome changes in aboveground tissue. Our results establish a foundation for a more comprehensive understanding of the shared and distinct nutrient deficiency response mechanisms of canola plants and pave the way for future breeding efforts., (© 2024 The Author(s). Plant, Cell & Environment published by John Wiley & Sons Ltd.)

Purpose: Homoarginine (hArg) is an arginine metabolite that has been known for years, but its physiological role in the body remains poorly understood. For instance, it is well known that high hArg concentrations in the blood are protective against several disease states, yet the mechanisms behind these health benefits are unclear. This review compiles what is known about hArg, namely its synthetic pathways, its role in different diseases and conditions, and its proposed mechanisms of action in humans and experimental animals., Findings: Previous work has identified multiple pathways that control hArg synthesis and degradation in the body. Furthermore, endogenous hArg can modulate the cardiovascular system, with decreased hArg being associated with cardiovascular complications and increased mortality. Studies also suggest that hArg could serve as a diagnostic biomarker for a variety of immune, pancreatic, renal, and hepatic dysfunctions. Finally, in women, hArg concentrations rapidly increase throughout pregnancy and there are suggestions that alterations in hArg could indicate pregnancy complications like pre-eclampsia., Summary: Homoarginine is an under-appreciated amino acid with potential wide-ranging roles in systemic health, pregnancy, and pathophysiology. Although recent research has focused on its health or disease associations, there is a need for more investigations into understanding the mechanistic pathways by which hArg may operate. This could be aided using metabolomics, which provides a comprehensive approach to correlating multiple metabolites and metabolic pathways with physiological effects. Increasing our knowledge of hArg's roles in the body could pave the way for its routine use as both a diagnostic and therapeutic molecule., (© 2025 The Author(s). Acta Physiologica published by John Wiley & Sons Ltd on behalf of Scandinavian Physiological Society.)

Learned societies, as professional bodies for scientists, are an integral part of the scientific system. However, their membership fees have the potential to be prohibitive to the most vulnerable members of the scientific community. To shed light on how membership fees are structured, we conducted a survey of 182 international learned societies relevant to researchers in ecology and evolution. We found that 83% of these societies offered fee concessions to students, but only 26% to postdoctoral researchers. An average regular membership fee-US$67.8, student fee-US$27.4 (42.7% of the regular fee) and postdoctoral fee-US$42.7 (52.9%). Other types of individual concessions, such as for emeritus, family or unemployed, were rare (2-20%). Of the surveyed societies, 43% had discounts for members from developing countries (Global South). Such discounts were more common among societies located in high-income countries. Societies with a publicly visible commitment to equity, diversity and inclusion were more likely to offer different types of concessions. Currently, fees may prevent researchers from vulnerable and underprivileged groups from accessing multiple professional benefits offered by learned societies in ecology and evolution. This includes postdoctoral researchers, who should receive more support. We recommend tangible actions towards making learned societies more affordable and accessible.

Steroid hormones are powerful endocrine regulators, but little is known about how environmental conditions modulate steroidogenesis to reprogram developmental fates. Here, we use the Drosophila prothoracic gland (PG) to investigate how a nutrient restriction checkpoint (NRC) ensures or blocks developmental progression and sexual maturation via regulating steroidogenesis. Extensive transcriptome analysis of the PG reveals that pre-NRC starvation significantly downregulates mitochondria-associated genes. Pre-NRC starvation reduces prothoracicotropic neuropeptide hormone signaling, insulin signaling, and TORC1 activity in PG cells, which prevent mitochondrial fragmentation and import of Disembodied, a key steroidogenic enzyme. Ultimately, pre-NRC starvation causes severe mitophagy and proteasome dysfunction, blocking steroidogenesis and metamorphosis. By contrast, post-NRC starvation does not impair mitochondrial homeostasis in PG cells but reduces sit expression and induces moderate autophagy to promote steroidogenesis, leading to precocious metamorphosis. This study constitutes a paradigm for exploring how steroid hormone levels are controlled in response to environmental stress during developmental checkpoints., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Acidification is a key component of digestion throughout metazoans. The gut digestive fluid of many invertebrates is acidified by the vesicular-type H+-ATPase (VHA). In contrast, vertebrates generate acidic gut fluids using the gastric H+/K+-ATPase (HKA); an evolutionary innovation linked with the appearance of a true stomach that greatly improves digestion, absorption, and immune function. Hagfishes are the most basal extant vertebrates, and their mechanism of digestive acidification remains unclear. Herein we report that the stomachless Pacific hagfish (Eptatretus stoutii) acidify their gut using the VHA, while searches of E. stoutii gut transcriptomes and the genome of a closely related hagfish species (E. burgerii) indicate they lack HKA, consistent with its emergence following the 2R whole genome duplication. Immunostaining revealed prominent VHA presence in the apical membrane of enterocytes and sub-apical expression of both VHA and sAC. Interestingly, akin to vertebrates, VHA was also observed in immature pancreatic-like zymogen granules and was noticeably absent from the mature granules. Furthermore, isolated gut sacs from fed hagfish demonstrate increased VHA-dependent luminal H+ secretion that is stimulated by the cAMP pathway. Overall, these results suggest that the hagfish gut shares the trait of VHA-dependent acidification with invertebrates, while simultaneously performing some roles of the pancreas and intestine of gnathostomes., (© 2025. Published by The Company of Biologists.)

Background: Crohn's disease (CD) is a lifelong gastrointestinal inflammatory condition that often requires surgery, particularly for patients diagnosed in childhood. CD has been linked to a combination of microbial, genetic, and environmental factors, but pathogenesis remains unknown. We outline a framework for multicenter surgical biobanking across a large geographic area, required to enable meaningful research, and evaluate feasibility using the 2016 Consolidated Standards of Reporting Trials (CONSORT) extension to randomized pilot and feasibility trials. We also share proof-of-concept RNA sequencing and immunohistochemistry results demonstrating adequacy to generate high-quality translational results., Methods: CD patients (5-17.2 years) scheduled for intestinal resection were included. Intra-abdominal sepsis was excluded. Surgeons from 10 Canadian children's hospitals underwent virtual training on tissue collection. Bowel, mesenteric fat, and lymph nodes were collected intraoperatively, fixed in formalin and RNAlater, and shipped overnight to a single lab. Feasibility was determined by protocol adherence, study recruitment efficacy, and tissue viability., Results: Tissue has been collected from 18 patients at seven sites since the study launched in 2023. The biobank is on track to bank 30-50 % of the total estimated eligible yearly case volume. Adherence to shipping protocols was impacted by the day of the week of the operation and by shipping office closures. Proof-of-concept immunohistochemistry demonstrated high-quality multiplex images. RNA sequencing identified 560 genes discriminating between inflamed and non-inflamed bowel., Conclusions: Establishing a national biobank for surgically resected pediatric CD is feasible for translational investigations of CD pathogenesis. Preliminary experiments demonstrate functional protocols sufficient to collect research-quality tissue., Level of Evidence: Prognosis Study - Level IV., Competing Interests: Conflict of interest The authors have no conflicts or competing interests to declare., (Copyright © 2025 The Authors. Published by Elsevier Inc. All rights reserved.)

Coexistence with large carnivores represents one of the world's highest profile conservation challenges. Ecologists have identified ecological benefits derived from large carnivores (and large herbivores), yet livestock depredation, perceived competition for shared game, risks to pets and humans, and social conflicts often lead to demands for reduction of predator numbers from a range of stakeholder groups. Nearly 100 years ago, Vito Volterra predicted that increased mortality on both prey and predators results in increased abundance of prey and decreased abundance of predators. This principle appears to be robust and often consistent with the objectives of wildlife management. Although seldom recognized, and rarely tested in the field, the Volterra principle is a fundamental outcome of ecological theory with important implications for conservation., (© 2025 The Author(s). Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Industrialization adversely affects the gut microbiome and predisposes individuals to chronic non-communicable diseases. We tested a microbiome restoration strategy comprising a diet that recapitulated key characteristics of non-industrialized dietary patterns (restore diet) and a bacterium rarely found in industrialized microbiomes (Limosilactobacillus reuteri) in a randomized controlled feeding trial in healthy Canadian adults. The restore diet, despite reducing gut microbiome diversity, enhanced the persistence of L. reuteri strain from rural Papua New Guinea (PB-W1) and redressed several microbiome features altered by industrialization. The diet also beneficially altered microbiota-derived plasma metabolites implicated in the etiology of chronic non-communicable diseases. Considerable cardiometabolic benefits were observed independently of L. reuteri administration, several of which could be accurately predicted by baseline and diet-responsive microbiome features. The findings suggest that a dietary intervention targeted toward restoring the gut microbiome can improve host-microbiome interactions that likely underpin chronic pathologies, which can guide dietary recommendations and the development of therapeutic and nutritional strategies., Competing Interests: Declaration of interests NiMe is a trademark of A.M.A and J.W. J.W. is an owner of a patent on Limosilactobacillus reuteri PB-W1 (NCIMB 42835), licensed to Novonesis A/S, of which income will be shared with the research institutes in Papua New Guinea and Canada that were involved in isolation and characterization of the strain. J.W. has further received honoraria and/or paid consultancy from PrecisionBiotics/Novonesis A/S. A.G. is an employee of Danone Specialized Nutrition. C.M.P. has previously received honoraria and/or paid consultancy from Abbott Nutrition, Nutricia, Nestlé Health Science, Pfizer, AMRA Medical, and Novo Nordisk unrelated to this work., (Copyright © 2025 The Authors. Published by Elsevier Inc. All rights reserved.)

Reproductive diapause is an insect survival strategy in which reproduction temporarily halts in response to adverse environmental changes. This process is characterized by arrested ovarian development and lipid accumulation in females. A reduction in juvenile hormone (JH) biosynthesis is known to initiate reproductive diapause, but its regulatory mechanism remains unclear. Seven up (Svp), a transcription factor from the nuclear receptor family, plays a crucial role in various developmental processes in insects. In this study, using the cabbage beetle Colaphellus bowringi as a model, we observed higher expression of Svp in the heads of female adults under reproductive photoperiodic conditions (short-day [SD]) compared to diapause conditions (long-day [LD]). RNA interference-mediated knockdown of Svp in SD females induced typical diapause phenotypes, including ovarian arrest and lipid accumulation. The application of methoprene (ME), a JH receptor agonist, reversed these diapause phenotypes and restored reproduction, indicating that Svp's regulation of reproductive diapause is dependent on JH signaling. Additionally, Svp knockdown led to the downregulation of JH pathway genes and a reduction in JH titers. Further evidence suggested that Svp regulates the expression of JHAMT1, a critical gene in JH biosynthesis, which determines diapause entry in C. bowringi. These findings suggest that diapause-inducing photoperiods suppress Svp expression, blocking JH production and triggering diapause. This work reveals a critical transcription factor that regulates reproductive diapause initiation through modulating JH production, providing a potential target for controlling pests capable of entering reproductive diapause., (© 2025 Institute of Zoology, Chinese Academy of Sciences.)

Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence─the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies. Further refinement in identification levels have occurred, for example to accommodate use of ion mobility spectrometry in metabolomics workflows, and alternate approaches to communicate compound identification confidence also have been developed based on identification points schema. However, neither qualitative levels of identification confidence nor quantitative scoring systems address the degree of ambiguity in compound identifications in the context of the chemical space being considered. Neither are they easily automated nor transferable between analytical platforms. In this perspective, we propose that the metabolomics and related communities consider identification probability as an approach for automated and transferable assessment of compound identification and ambiguity in metabolomics and related studies. Identification probability is defined simply as 1/ N , where N is the number of compounds in a database that matches an experimentally measured molecule within user-defined measurement precision(s), for example mass measurement or retention time accuracy, etc. We demonstrate the utility of identification probability in an in silico analysis of multiproperty reference libraries constructed from a subset of the Human Metabolome Database and computational property predictions, provide guidance to the community in transparent implementation of the concept, and invite the community to further evaluate this concept in parallel with their current preferred methods for assessing metabolite identification confidence.

Many analytical methods have been developed for performing targeted metabolomics. By combining multiple analytical techniques, comprehensive coverage of the metabolome can be achieved. We combined multiple analytical techniques to comprehensively and quantitatively characterize the widely studied NIST human plasma reference material, SRM 1950. Our goal was to provide a large, well-validated list of confident metabolite concentration values (i.e., benchmarks) to assist the metabolomics community in its calibration and comparison efforts. We used four analytical platforms: high-resolution NMR spectroscopy, direct injection tandem MS (DI-MS/MS), liquid chromatography tandem MS (LC-MS/MS), and inductively coupled plasma MS (ICP-MS). Eight validated analytical assays were run, yielding accurate quantitative measurements for 728 unique metabolites or metabolite species. Through computer-aided literature mining, we identified another 330 unique metabolites previously quantified in SRM 1950. We compared NIST-certified values along with literature-derived concentrations/ranges to the metabolite concentrations measured by our four platforms and eight assays. From these assays/platforms, we generated a list of high-confidence concentration values of 1058 metabolites or metabolite species in SRM 1950 including data for 60 amino acids/related compounds, 48 bile acids, 72 amines/sugars/alcohols, 21 metals, 8 catecholamines, 11 vitamins, 92 organic acids, 40 fatty acids/steroids/nucleobases/indole derivatives, 5 polyfluorinated compounds, 7 carotenoids, 39 acylcarnitines, 76 oxylipins, 13 sterols, and 566 lipids/lipid species. This data set represents the most complete quantitative characterization of SRM 1950. An online database (SRM1950-DB) containing 1058 plasma metabolites/metabolite species in SRM 1950, their structures, HMDB IDs, mass, chemical class, concentrations, references, and reliability is freely available at https://srm1950-data.wishartlab.com.

Protein-O-mannosylation (POM) is a form of O-glycosylation that is ubiquitous and has been studied extensively throughout in fungi and animals. The key glycosyltransferase, protein O-mannosyltransferase (PMT), a member of family GT-39, is also found in over 3,800 bacterial genomes but has only been minimally examined from prokaryotes. In prokaryotes POM has only been investigated in terms of pathogenicity (in Mycobacterium tuberculosis) even though there are far more non-pathogenic bacteria that appear to carry out POM. To date, there is no consensus on what benefit POM imparts to the non-pathogenic bacteria that can perform it. Through the generation of a POM deficient mutant of Corynebacterium glutamicum - a widely utilized and known protein O-mannosylating actinobacteria - this work shows that even closely related actinobacterial GT-39 s (the enzymes responsible for the initiation of POM) can have different substrate specificities for targets of POM. Moreover, presented here is evidence that POM does not only occur in a SEC-dependent manner; POM also occurs with TAT and non-SEC secreted substrates in a specific and likely tightly regulated manner. Together these results highlight the need for further biochemical characterization of POM in these and other bacterial species to help elucidate the true nature of its biological functions., (© The Author(s) 2024. Published by Oxford University Press.)

The ectoparasitic mite Varroa destructor remains a great threat for the beekeeping industry, for example contributing to excessive winter colony loss in Canada. For decades, beekeepers have sequentially used the registered synthetic varroacides tau-fluvalinate, coumaphos, amitraz, and flumethrin, leading to the risk of resistance evolution in the mites. In addition to the widespread resistance to coumaphos and pyrethroids, a decline in amitraz efficacy has recently been reported in numerous beekeeping regions in Canada. The goals of this study were to assess the evolution of resistance to amitraz in Canadian mite populations and to evaluate the presence and incidence of mutations previously associated with resistance to amitraz and pyrethroids in V. destructor. Our bioassay results confirmed the presence of amitraz-resistant mites in the population of Alberta. These phenotypic results were complemented by targeted genotyping of the octopamine receptor gene Octβ 2 R which revealed the presence of the mutation Y215H in 90% of tested apiaries with local allele frequencies ranging from 5 to 95%. The phenotypic resistance showed a significant correlation with the presence of this mutation across apiaries. In parallel, the L925I and L925M mutations in the voltage-gated sodium channel were identified in 100% of the tested apiaries with frequencies ranging from 33 to 97%, suggesting that resistance to pyrethroids remains widespread. These results support the notion that the practice of relying on a single treatment for a prolonged period can increase rates of resistance to current varroacides. Our findings suggest the need for large-scale resistance monitoring via genotyping to provide timely information to beekeepers and regulators. This will enable them to make an effective management plan, including rotation of available treatments to suppress or at least delay the evolution of resistance in V. destructor populations., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogota's last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature involve both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 genes with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer with other bacteria and archaea that often grow at similar temperatures, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures., Competing Interests: Conflict of Interest: The authors declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

The Natural Products Magnetic Resonance Database (NP-MRD; https://np-mrd.org) is a comprehensive, freely accessible, web-based resource for the deposition, distribution, extraction, and retrieval of nuclear magnetic resonance (NMR) data on natural products (NPs). The NP-MRD was initially established to support compound de-replication and data dissemination for the NP community. However, that community has now grown to include many users from the metabolomics, microbiomics, foodomics, and nutrition science fields. Indeed, since its launch in 2022, the NP-MRD has expanded enormously in size, scope, and popularity. The current version of NP-MRD now contains nearly 7× more compounds (281 859 versus 40 908) and 7× more NMR spectra (5.5 million versus 817 278) than the first release. More specifically, an additional 4.6 million predicted spectra and another 11 000 spectra simulated from experimental chemical shifts were deposited into the database. Likewise, the number of NMR raw spectral data depositions has grown from 165 spectra per year to >10 000 per year. As a result of this expansion, the number of monthly webpage views has grown from 55 to 20 000 and the number of monthly visitors has increased from 7 to 2500. To address this growth and to better support the expanding needs of its diverse community of users, many additional improvements to the NP-MRD have been made. These include significant enhancements to the data submission process, notable updates to the database's spectral search utilities and useful additions to support better NMR spectral analysis/prediction. Significant efforts have also been undertaken to remediate and update many of NP-MRD's database entries. This manuscript describes these database improvements and expansion efforts, along with how they have been implemented and what future upgrades to the NP-MRD are planned., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

MarkerDB (https://markerdb.ca) has become a leading resource for comprehensive information on molecular biomarkers. Over the past 3 years, the database has evolved significantly, reflecting the dynamic landscape of biomarker research and increasing demands from its user community. This year's update, which is called MarkerDB 2.0, introduces key improvements to enhance the database's usability, consistency and the range of biomarkers covered. These improvements include (i) the addition of thousands of new biomarkers and associated health conditions, (ii) the inclusion of many new biomarker types and categories, (iii) upgraded searches and data filtering functionalities, (iv) new features for exploring and understanding biomarker panels and (v) significantly expanded and improved descriptions. These upgrades, along with numerous minor improvements in content, interface, layout and overall website performance, have greatly enhanced MarkerDB's usability and capacity to facilitate biomarker interpretation across various research domains. MarkerDB remains committed to providing a free, publicly accessible platform for consolidated information on a wide range of molecular (protein, genetic, chromosomal and chemical/small molecule) biomarkers, covering diagnostic, prognostic, risk, monitoring, safety and response-related biomarkers. We are confident that these upgrades and updates will improve MarkerDB's user friendliness, increase its utility and greatly expand its potential applications to many other areas of clinical medicine and biomedical research., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background/Objectives: Abnormal development of the second heart field significantly contributes to congenital heart defects, often caused by disruptions in tightly regulated molecular pathways. Smyd1 , a gene encoding a protein with SET and MYND domains, is essential for heart and skeletal muscle development. Mutations in SMYD1 result in severe cardiac malformations and misregulation of Hand2 expression in mammals. This study examines the role of Smyd1b in zebrafish cardiac morphogenesis to elucidate its function and the mechanisms underlying congenital heart defects. Methods: Smyd1b ( still heart ) mutant embryos were analyzed for cardiac defects, and changes in gene expression related to heart development using live imaging, in situ hybridization, quantitative PCR and immunofluorescent comparisons and analysis. Results: Smyd1b mutants displayed severe cardiac defects, including failure to loop, severe edema, and an expansion of cardiac jelly linked to increased has2 expression. Additionally, the expression of key cardiac transcription factors, such as gata4 , gata5 , and nkx2.5 , was notably reduced, indicating disrupted transcriptional regulation. The migration of cardiac progenitors was impaired and the absence of Islet-1-positive cells in the mutant hearts suggests a failed contribution of SHF progenitor cells. Conclusions: These findings underscore the essential role of Smyd1b in regulating cardiac morphogenesis and the development of the second heart field. This study highlights the potential of Smyd1b as a key factor in understanding the genetic and molecular mechanisms underlying congenital heart defects and cardiac development.

Prostate cancer (PCa) is one of the leading causes of cancer-related deaths among men. The heterogeneous nature of this disease presents challenges in its diagnosis, prognosis, and treatment. Numerous potential predictive, diagnostic, prognostic, and risk assessment biomarkers have been proposed through various population studies. However, to date, no metabolite biomarker has been approved or validated for the diagnosis, prognosis, or risk assessment of PCa. Recognizing that systematic reviews of case reports or heterogenous studies cannot reliably establish causality, this review analyzed 29 large prospective metabolomics studies that utilized harmonized criteria for patient selection, consistent methodologies for blood sample collection and storage, data analysis, and that are available in public repositories. By focusing on these large prospective studies, we identified 42 metabolites that were consistently replicated by different authors and across cohort studies. These metabolites have the potential to serve as PCa risk-assessment or predictive biomarkers. A discussion on their associations with dietary sources or dietary patterns is also provided. Further detailed exploration of the relationship with diet, supplement intake, nutrition patterns, contaminants, lifestyle factors, and pre-existing comorbidities that may predispose individuals to PCa is warranted for future research and validation., Competing Interests: Declaration of competing interest The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results., (Copyright © 2024. Published by Elsevier Inc.)

Many species exhibit social living which offers ecological advantages such as increased foraging opportunities, more efficient locomotion and reduced predation risk. Additionally, exposure to multiple individuals of the same species can decrease an individual's stress and metabolic demand, termed social buffering. If disruption to an animal's social structure occurs and prevents social buffering, an elevated metabolic rate and thus ventilation frequency and gill permeability are likely. A potential consequence of this physiological response could be the increased accumulation of toxicants. The objective of this study was to investigate whether inducing social stress in marine threespine stickleback (Gasterosteus aculeatus) through social isolation during a sublethal water-borne copper (Cu) exposure would affect Cu uptake and whether that would translate to differences in behaviour and biochemical functioning. We hypothesized that isolating threespine stickleback during a Cu exposure would increase Cu uptake and sublethal toxicity compared to a grouped exposure. Wild-caught fish were exposed to control, low Cu or high Cu conditions (0 - 150 µg/L of Cu, nominally), either in isolation or groups of six for 96 h. Isolated stickleback travelled three times less distance, took six times longer to consume food and exhibited moderately increased gill sodium-potassium ATPase activity than group exposed fish, with no effect of Cu. Isolated stickleback also demonstrated significantly higher Cu levels in their gill and liver tissue compared to the group exposed fish. However, this Cu distribution was also present within the control fish, which had not been exposed to Cu, suggesting that the social context affects endogenous Cu distribution under stressful conditions. Our results illustrate the differences in physiology and behaviour that can arise when social contexts are manipulated and stress the importance of considering sociality when conducting toxicity tests with social organisms., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Environmental RNA (eRNA) is an emerging technique with significant potential for the assessment of organismal function in field settings. It has the advantage of being non-invasive, facilitating insight into the physiological status of an organism without complications associated with processes such as capture, handling, and transportation from the field to the laboratory. It is hypothesised that eRNA approaches will be especially valuable for assessing sublethal stress of species living in environmental settings undergoing change and could therefore be integral for examining population health and for testing hypotheses regarding organismal physiology developed from laboratory studies. However, the successful application of eRNA approaches requires further data regarding the stability and persistence of eRNA in natural substrates; established and validated relationships between molecular biomarkers and the physiological processes they participate in; and an understanding of the contributions of different epithelia in direct contact with the environment (skin, gill, gut) to the eRNA transcriptome. The utility of microRNA as a component of the eRNA pool should be an area of specific future research focus. Ultimately, eRNA has the potential to provide fundamental physiological information regarding the responses of organisms in their natural settings and could increase the sensitivity and acuity of biomonitoring efforts., Competing Interests: Declaration of competing interest The author is Editor-in-Chief for Comparative Biochemistry and Physiology B and was not involved in the editorial review or the decision to publish this article., (Copyright © 2024 Elsevier Inc. All rights reserved.)