Integrative Astral-DIA proteomics and transcriptomics reveal candidate salt-tolerance genes in the halophyte Hordeum marinum.

• Understanding the population dynamics of a high-density ungulate is challenging. • We built an age/sex-structured population model for a moose population. • Our model successfully reproduced changes in abundance and demographic drivers. • We offered a way to build and calibrate complex population models with scarce data. • We identified mechanisms at play in a protected area without hunting and wolves. High-density populations can threaten the ecological integrity of ecosystems through cascading effects. In such cases, management practices must be guided by sufficient knowledge of the biological mechanisms at play. Simulation models are powerful tools for acquiring such knowledge. The moose ( Alces alces americana ) is a species that recently became overabundant in some areas of eastern North America, sometimes requiring specific management measures. While numerous models exist for moose population dynamics, few are adapted to high density populations like the one in Forillon National Park (Quebec, Canada), a protected area in which the moose's apical predator (grey wolf Canis lupus ) is absent. We developed a sex- and age-structured population model respecting these conditions that we parameterized using pattern-oriented modelling to help explain the changes in moose density observed over nearly 4 decades. The most plausible sequence of vital rates identified exhibited negative density dependence in survival, reproduction and dispersal. Predation by alternative predators, black bears ( Ursus americanus ) and coyotes ( Canis latrans ), caused substantial mortality of calves each year. Unlike elsewhere in northeastern North America, winter tick only had a slight effect on calf survival. Variations in the population’s sex ratio were mainly explained by sex-biased dispersal. Our study provides new insights concerning the dynamics of high-density ungulate populations in the absence of their apical predator, and our modelling approach helped reveal new methodological challenges and opportunities. We also present a comprehensive process to build and parameterize a complex population model using scarce data.

Integrated proteomic and nitrosylomic profiling suggests a role for S-nitrosylation in choroidal dysregulation during myopia pathogenesis.

Glycoprotein hormones alpha 2 (GPA2) and beta 5 (GPB5) are considered to be ancestral members of the glycoprotein hormone (GPH) family. Despite their potential roles in regulating thyroxine production, the immune response, and ovarian function, their roles in the testis remains largely unknown. To further explore this regulation, catshark testicular explants containing late spermatid stages were treated in vitro with recombinant GPA2, GPB5 and single-chain GPB5#GPA2. The comparative proteomic analysis of the treated explants revealed that ScGPB5 and ScGPB5#ScGPA2 were the most effective, modulating abundance of 449 and 525 proteins, respectively. In contrast, ScGPA2 only modulated 212 proteins. Among the differentially abundant proteins (DAPs), 103 showed substantial abundance changes in response to at least one treatment, with mean Log2ratios of 2.5 and-2.5. Manual functional annotation linked these proteins to spermiogenesis and immunity. Key proteins and candidates involved in spermiogenesis were highlighted, including SPINK2, which is involved in acrosome protection, and LRRC69, which is related to human spermatogenic failure. These results reinforce the hypothesis of a GPA2/GPB5 paracrine regulation of catshark spermiogenesis. They also underscore the necessity of functional and comparative studies to elucidate the physiological functions of GPA2/GPB5 across a broad spectrum of taxa, from non-vertebrates to mammals. SIGNIFICANCE: To our knowledge, this study is the first to report the effects of stimulation with recombinant ScGPA2, ScGPB5, and single-chain ScGPB5#ScGPA2 on vertebrate testicular tissue in vitro. A large-scale, untargeted proteomic analysis revealed for the first time that all three-ScGPA2, ScGPB5, and single-chain ScGPB5#ScGPA2-can modulate the abundance of 103 of the 7619 identified proteins, including proteins related to spermiogenesis and immunity, as well as others that are less well characterized. This report reinforces the importance of functionally characterizing GPA2 and GPB5 by showing the first results toward the characterization of their spermatogenesis related function in a specie of evolutive interest, the small-spotted catshark. In the future, a complete characterization of GPA2 and GPB5 will further our understanding of the functional evolution of glycoprotein hormones-a keystone group of hormones for vertebrate physiology and critical targets for fertility modulation in both livestock and humans.

Analysis of gut microbiota and intestinal secondary bile acids metabolism in rats after short-term antibiotic treatment.

Ocean acidification reduces diatom and photosynthetic gene abundance on plastic in an coastal bay mesocosm experiment.

Sex and photoperiod shape hepatic redox homeostasis in diet-induced obesity in association with a melatonin-NRF2-circadian regulatory axis.

Allergic Rhinitis (AR) represents a significant global health challenge with extensive prevalence and profound impacts, necessitating the development of novel therapeutic approaches beyond conventional symptomatic treatment. Emerging research has elucidated the crucial role of nasal microbiota dysbiosis in both the pathogenesis and progression of AR. Although the dominant microbial phyla remain largely consistent, significant changes in microbial abundance, composition, and diversity are often observed. In addition, studies have shown a correlation between changes in nasal microbiota and immune markers such as immunoglobulin E levels, suggesting that microbiota changes can reflect the severity of AR. Therefore, targeted modulation of the aberrant nasal microbiota may offer a promising therapeutic approach for this disease. However, further research is crucial for elucidating the causal relationships between specific microbial characteristics, disease severity, and potential comorbidities. This article summarizes recent studies examining the pathogenic role of nasal microbiota dysbiosis, the differential microbial composition across nasal mucosal sites, and potential therapeutic targets in AR. The ultimate goal is to develop precision medicine-based therapeutic interventions that target the underlying pathophysiological mechanisms of AR through specific modulation of dysbiotic nasal microbiota, thereby potentially preventing disease progression and reducing the risk of associated comorbidities.

Long-term bioelectricity generation in microbial fuel cell exposed to perfluorooctanoic acid.

Retinoic acid (RA) is a key morphogen in human retinal development, activating transcriptional programs that drive retinal progenitor differentiation and photoreceptor development, ensuring proper spatial organisation within the neural retina, essential for vision. Despite its well-established role in retinal patterning, the concentration-dependent effects of RA on human retinal cell fate specification and the regional definition of the primate macula and peripheral retina remain poorly understood. Here, we show that temporal and dosage-dependant modulation of RA during human retinal organoid differentiation induces distinct changes in retinal cell abundance, maturation, and organisation. Single-cell transcriptomics and protein analysis reveal that RA dosage influences the relative abundance and maturation of photoreceptors and retinal interneurons. Spatial transcriptomics analyses demonstrates that low RA levels biases retinal organoids toward a macular-like regional identity, whereas high RA levels promotes peripheral-like development. Collectively, our findings emphasise the critical role of RA signalling in retinal maturation and regional specification. This study elucidates mechanisms involved in human retinal development and we anticipate that controlled RA modulation in retinal organoids provides a strategy to refine disease modelling of inherited retinal disorders and enhance the specific generation of photoreceptors suitable for transplantation and regenerative therapies.

Ranger patrols are a cornerstone of wildlife protection efforts around the world and occur across all ecological governance systems. Evidence that patrols reduce threats to wildlife and enable their recovery has not been systematically examined previously. Without evidence of patrol effectiveness in varying contexts, protected area managers risk wasting limited conservation resources and lack information required to improve the effectiveness of patrols. We conducted a meta-analysis evaluating the effectiveness of terrestrial patrols for conserving African, Asian, and Latin American wildlife directly threatened by exploitation. After filtering 57 studies, we calculated effect sizes from each of the remaining 15 studies that included a comparator and measurement of wildlife abundance and calculated standardised mean difference and % change in wildlife species abundance. Results suggest tentative support that areas implementing patrols (alongside other interventions) were associated with higher wildlife abundance levels compared to time periods or locations without patrols. We were unable to confirm causality between patrols and changes in wildlife population abundance because studies were inadequately designed to evaluate and report on effectiveness. Studies commonly lacked a comparator or counterfactual event, temporal or spatial replication, and consistent and/or long-term monitoring of population abundance, and had study designs that confounded conservation actions. Further, of the 15 included studies linking wildlife abundance to patrol efforts, five also reported a reduction in a poaching threat, but only three of these used a comparator in the threat reduction evaluation. Without monitoring threat trends alongside wildlife abundance, it is difficult to be confident that patrols resulted in increases in wildlife abundance. To help evaluate patrol interventions (i.e. not only whether they work but where and under what conditions they work), we identify opportunities to improve future patrol effectiveness research and provide recommendations on how to improve the evidence base.

The significance of less abundant genera within the gut microbiota, such as Parabacteroides, remains largely unexplored. Despite its low levels, Parabacteroides is highly conserved and potentially beneficial across populations. This trial aimed to evaluate whether a four-week intake of glucolacto-oligosaccharides (GLO), previously reported as an enhancer of Parabacteroides, improves defecation frequency as the primary outcome. It also assessed holistic gut health and underlying microbiota-based mechanisms. In this randomized, double-blind, placebo-controlled trial, 50 healthy Japanese participants with a defecation frequency of five or fewer times per week were enrolled. The mean (±SE) weekly defecation frequency in the GLO group was 3.2 ± 0.2 at baseline, increasing to 5.8 ± 0.6 at week 4, whereas that in the placebo group was 3.4 ± 0.3 at baseline, increasing to 4.4 ± 0.3 at week 4. The time-dependent weekly defecation frequency was significantly higher in the GLO group than in the placebo group (p = 0.029). Changes in the relative abundance of the genus Parabacteroides significantly increased in the GLO group compared with in the placebo group. Changes in fecal bile acid composition were also confirmed in the GLO group compared with the placebo group, which was thought to be due to the unique features of Parabacteroides. Furthermore, changes in alpha diversity indices were significantly higher in the GLO group than in the placebo group (Simpson, p = 0.041; Pielou, p = 0.022). Additional analysis demonstrated that the increase in alpha diversity in the GLO group was significantly correlated with the increase in the relative abundance of Parabacteroides (p = 0.006), which tended to be associated with decreases in serum gamma-glutamyltransferase (p = 0.089) and serum triglyceride (p = 0.075) levels. These data suggest that GLO intake improved defecation status, selectively increased Parabacteroides, and harmonized the gut environment.

Objective: This study investigates long-term trends (1991–2024) in the population dynamics of 13 major livestock species in Türkiye by examining changes in species abundance, breed composition and biodiversity structure, with emphasis on the impacts of intensive breeding practices on local genetic resources.Material and Methods: Annual livestock statistics from the Turkish Statistical Institute (TUIK) were used to analyse species and breed trends. Biodiversity was assessed using ecological indices including Shannon, Simpson, Pielou’s Evenness, Berger–Parker and Margalef. Multivariate analyses (PCA and hierarchical clustering) and visualizations (heat maps, radar charts and dendrograms) were conducted in Python 3.11. Data were normalized to ensure comparability among species.Results: Commercial cattle and broiler chicken populations increased markedly, whereas native sheep and goat breeds declined. Biodiversity indices showed reductions in species richness and evenness after 2000. Bray–Curtis analyses revealed significant differences in species composition across five-year periods (F = 8.06, p

Post-transcriptional processing of pre-mRNAs by alternative polyadenylation (APA) generates a diversity of transcript isoforms at the 3' untranslated region (3'UTR) that can affect their function and stability. The differential enrichment of transcript isoforms has been implicated in diseases ranging from cancer to neurodevelopmental disorders. However, the postembryonic developmental roles of the core ensemble of cleavage and polyadenylation (CPA) factors that mediate these post-transcriptional changes remain poorly characterized. Here, we report a stress-dependent role for the core CPA factor CFIM-1 in Caenorhabditis elegans germline integrity. Total loss-of-function of cfim-1 elicits a temperature-sensitive sterility phenotype in hermaphrodites but CFIM-1 protein levels do not change with temperature. Sterility is accompanied by sperm, oocyte, and germline morphology defects. Surveying the transcriptome of cfim-1(lf) worms revealed changes in transcript isoform abundance for dozens of genes with functions related to the development and maintenance of these structures. Collectively, our findings define a postembryonic role for a core CPA factor in tissue-specific development.

New biomarkers for the detection of fetal death derived from large-scale proteomic analysis of maternal plasma.

The gut microbiome can influence host health by facilitating digestion, immune function, and xenobiotic metabolism. Microbial metabolites can influence mitochondrial function by shifting bioenergetic pathways, potentially altering sensitivity to mitochondrial toxicants. However, mechanisms through which the gut microbiota can alter mitochondrial function and susceptibility to mitochondrial toxicity are not well characterized. We used the model organism Caenorhabditis elegans and the microbiome kit CeMbio, a characterized collection of native gut commensals, to explore the interactions between gut microbiota, mitochondrial function, and chemical susceptibility. C. elegans grown on selected bacterial strains had varying levels of steady-state whole-body ATP, with an ∼3 fold difference between the highest and lowest strains, as well as 2- and 3-fold changes in antioxidant and mitochondrial unfolded protein gene induction. Further, C. elegans grown on selected bacterial strains showed differential sensitivity to short-term exposure to chemicals that inhibit mitochondrial electron transport chain Complexes I, II, and V, and fatty acid oxidation. To test mechanistically how microbiome-mediated sensitivities could result in chemical susceptibility, we carried out follow-up experiments using the Complex I inhibitor rotenone. We found that C. elegans grown on BIGb0170 (Sphingobacterium multivorum) had much higher lethality after 24- and 48-hour exposures than when grown on MYb10 (Acinetobacter guillouiae), MYb11 (Pseudomonas lurida), and OP50 (Escherichia coli) strains. Metabolomic analysis revealed that C. elegans grown on BIGb0170 had lower amounts of triglycerides and acylcarnitines. ATP levels were partially rescued by supplementing BIGb0170 with pyruvate. This work suggests that BIGb0170 can impact mitochondrial function through changes in metabolite abundance, which can increase sensitivity to the Complex I inhibitor rotenone.

Proteomic studies have generated robust assessments of protein abundance changes in Alzheimer's disease (AD); however, identifying how the protein abundance changes affect specific biological processes remains a challenge. To address these hurdles, we used a multi-network computational analysis approach that integrated dendritic spine morphometry data with mass spectrometry-based proteomics from the same individuals. The samples exhibited a range of AD neuropathology and were categorized into three groups: controls, asymptomatic AD, and AD cases. Multiplex tandem mass tag mass spectrometry proteomic data (N = 8,212 proteins) was generated on Brodmann area 46 (BA46) dorsolateral prefrontal cortex (DLPFC) human samples (N = 41, 23 males and 18 females), from which dendritic spine morphometry analysis existed. To integrate the multi-scale data types, two computational network analysis methods were performed, including WeiGhted co-expression network analysis (WGCNA) and SpeakEasy2 (SE2). Both WGCNA and SE2 revealed that the mitochondria protein modules were decreased in AsymAD and AD cases compared to controls, whereas the DNA repair modules were increased in AsymAD and AD compared to controls. Synaptic protein modules that correlated to multiple spine morphology traits were identified in both WGCNA and SE2. Pearson correlation analyses identified over a dozen individual proteins linked to multiple dendritic spine density and morphology traits. Collectively, these findings demonstrate how integration of spine morphometry data with proteomics can contextualize proteins for functional validation and identify synaptic alterations in AD progression.Significance Statement Cognitive decline in Alzheimer's disease associates more strongly with synapse and dendritic spine loss than amyloid-beta or tau pathology. However, one in three individuals harbor Alzheimer's disease neuropathology at death but were cognitively indistinguishable from baseline in life. Preservation of spines and synapses is hypothesized to prevent cognitive decline in these individuals. Identifying the molecular drivers of synaptic changes in Alzheimer's disease could yield deeper understanding of disease progression. Here, we utilized two computational network approaches that integrated multi-scale data, including proteomics and dendritic spine morphometry from the same humans, to identify proteins relevant to synapses in Alzheimer's disease. Hundreds of proteins related to mitochondria, DNA repair, and synaptic signaling were associated with alterations in synapse structure and function in Alzheimer's disease.

Salt marshes in the northeastern United States support several specialized breeding bird species that are threatened by sea level rise (SLR) and coastal development, processes that drive habitat change and fragmentation. There have been rapid, widespread declines in some species, but mechanisms driving population change and whether declines continue remain unclear. We examined the influence of phenomena expected to modify salt marshes, including SLR, sediment delivery rates, and land use, on the population trajectories of saltmarsh breeding birds. We modeled population trajectories of 5 species with spatially extensive point count surveys conducted from Maine to Virginia from 2011 to 2022. We used Bayesian hierarchical abundance models and model selection to identify phenomena that had the strongest effect on population change. Clapper rails (Rallus crepitans) continued their long-term decline (-4.1%/year). Willets (Tringa semipalmata semipalmata) (2.6%/year) and saltmarsh sparrows (Ammospiza caudacuta) (4.1%/year) increased, and seaside (Ammospiza maritima) and Nelson's (Ammospiza nelsoni subvirgatus) sparrows exhibited no clear change in abundance. The estimated increase for saltmarsh sparrow was not consistent with trends over the previous 25years but aligned with prior demographic modeling, which predicted a short-term stabilization during the study years before an expected return to a long-term decline. Road density and other tidal restrictions near marshes were generally good predictors of abundance over the study period, as was marsh habitat composition. Local rates of SLR and sediment delivery were not as good predictors. During periods of relatively low rates of realized SLR, local-scale drivers of population trends had relatively stronger effects than global drivers on the persistence of several saltmarsh breeding birds. Conservation practitioners, however, should be attentive to global drivers, especially as rates of SLR accelerate in the future.

Seamount ecosystems are increasingly exposed to rapid oceanographic change, including warming waters, declining oxygen concentrations, and the upward migration of carbonate saturation horizons. Together, these processes are compressing the depth ranges of suitable habitat for many deep-sea organisms and altering the environmental conditions structuring benthic communities. While deep-sea environments have historically been considered relatively stable due to low environmental variability, empirical evidence documenting how populations respond to ongoing ocean change remains scarce. Here, we use high-resolution photogrammetric reconstructions of 12 monitoring sites (350-1111 m depth) across three Northeast Pacific seamounts to assess changes in the abundance and condition (i.e., health) of cold-water corals and sponges. Baseline reconstructions established in 2018 were compared with repeat surveys conducted 3-5 years later. Contrary to expectations for these slow-growing, long-lived species, significant declines in both abundance and condition were observed. Across the 12 sites, 163 of 844 individuals were lost between surveys, with abundance declining at five sites and condition declining at nine. The most severe losses occurred at a single site on Explorer Seamount, where 51% of individuals were lost, including approximately 80% of the dominant sponge species. Sponges experienced greater declines than corals across all metrics, and the most impacted sites were not consistently located within the lowest oxygen concentrations of the expanding oxygen minimum zone. Although abundance change did not differ significantly among oxygen zones, condition scores were lower at sites with the lowest oxygen levels. These findings suggest that early impacts of ocean change may already be occurring in deep-sea foundation species, highlighting the importance of repeat monitoring to detect rapid ecological change in environments traditionally assumed to be stable.

Protein structural dynamics drive changes in protein function, making the capture of such dynamics essential for interrogating biological systems. Here we review limited proteolysis coupled to mass spectrometry (LiP-MS), a structural and chemical proteomics method that uses changes in susceptibility to protease cleavage to profile proteome-wide protein structural changes within complex biological samples. In the decade since its development, LiP-MS has become a broadly used structural proteomics method, with peptide-level resolution. It has identified drug targets, delineated altered cellular pathways in response to complex perturbations, revealed structural information on otherwise challenging protein targets, and demonstrated the new concept of structural biomarkers of disease. Because LiP-MS simultaneously probes numerous types of molecular events, such as molecular binding, changes in enzyme activity, chemical modifications, allosteric conformational changes, aggregation, and unfolding, it supports a new proteomics workflow which we term 3D proteomics. This workflow enables the detection of specific functional sites within proteins that are altered upon perturbation, thereby guiding the generation of molecular hypotheses. Further, by globally profiling structural in addition to protein abundance changes, LiP-MS has proven able to greatly increase the information content of functional proteomics screens. In sum, LiP-MS has supported the development of a novel conceptual framework for generating, visualizing, and interpreting structural proteomics data with peptide level resolution, thereby comprehensively probing biological systems. Here we survey the applications of LiP-MS, discuss methodological variants developed by us and others, and describe the use of this new type of omics readout for structural, functional, chemical, and biomarker discovery proteomics.