Adaptive Pathways Research Articles

Spatial Transcriptomic Signatures of Early Acute T Cell-mediated Rejection in Kidney Transplants.

Kidney transplantation significantly improves the quality of life for those with end-stage renal failure, yet allograft rejection resulting from immune cell interactions remains a persistent challenge. Although T cell-directed immunosuppressive drugs effectively contain graft rejection in most patients, a notable proportion still experiences acute T cell-mediated rejection (TCMR). Despite an emphasis on suppressing T cell-mediated immune responses, successful control over TCMR is not always achieved, suggesting the potential involvement of factors beyond T cells. Biopsy samples from suspicious (borderline) for acute TCMR (borderline TCMR) and non-TCMR patients were obtained 9 d postsurgery, and spatial transcriptomics profiling was conducted using the GeoMx Digital Spatial Profiler platform. Regions of interest in the glomerulus and interstitium were selected on the basis of immunohistochemistry staining anti-CD3 to identify areas with T-lymphocyte infiltration. Differential gene expression analysis was performed using unpaired t tests. Unbiased clustering of transcriptional profiles across all regions of interest showed distinct transcriptional profiles between glomeruli and interstitium in non-TCMR samples, whereas borderline TCMR samples displayed no distinct transcriptional profiles between these regions. Contrary to the prevailing T cell-centric view, we observed pathways and genes associated with innate immunity-related inflammatory conditions expressed in glomerular regions of borderline TCMR biopsies. Immunofluorescence staining for CD68 confirmed the presence of macrophages in the glomeruli of the post-TCMR sample in a validation cohort, indicating macrophage involvement in the glomerular response after TCMR. Activation of the innate immune response in borderline TCMR appears to impact not only the interstitium but also the glomerulus. Glomerulus-specific immune signatures suggest the role of the innate immune system in rejection. This nuanced understanding proposes the necessity for tailored therapeutic interventions targeting both innate and adaptive immune pathways to enhance transplant outcomes.

Impacts of early life adversity on the neurocircuitry of emotional memory in children.

Similar to adults with posttraumatic stress disorder, children with early life adversity show bias in memory for negative emotional stimuli. However, it is not well understood how childhood adversity impacts mechanisms underlying emotional memory. N = 56 children (8-14 years, 48% female) reported on adverse experiences including potentially traumatic events and underwent fMRI while attending to emotionally pleasant, neutral, or negative images. Post-scan, participants completed a cued recall test to assess memory for these images. Emotional difference-in-memory (DM) scores were computed by subtracting negative or positive from neutral recall performance. All children showed enhancing effects of emotion on recall, with no effect of trauma load. However, children with less trauma showed a larger emotional DM for both positive and negative stimuli when amygdala or anterior hippocampal activity was higher. In contrast, highly trauma-exposed children demonstrated a lower emotional DM with greater amygdala or hippocampal activity. This suggested that alternative neural mechanisms might support emotional enhancement of encoding in children with greater trauma load. Whole-brain analyses revealed that right fusiform activity during encoding positively correlated with both trauma load and successful later recall of positive images. Therefore, highly trauma-exposed children may use alternative, potentially adaptive neural pathways via the ventral visual stream to encode positive emotional events.

Autoimmune diseases and the risk and prognosis of latent autoimmune diabetes in adults.

The aim of this study was to clarify the impact of autoimmune disease (AD) comorbidity on the risk and prognosis of latent autoimmune diabetes in adults (LADA). We used data from a Swedish study comprising newly diagnosed cases of LADA (n=586, stratified into LADAlow and LADAhigh by autoantibody levels), type 2 diabetes (n=2003) and matched control participants (n=2355). Information on 33 ADs and diabetic retinopathy was obtained by linkage to regional and national registers. We estimated the ORs for LADA and type 2 diabetes in relation to ADs before diabetes diagnosis, and the HRs for diabetic retinopathy after diabetes diagnosis. We performed functional pathway analyses to explore biological mechanisms driving the associations. Individuals with ADs exhibit an increased susceptibility to LADA (OR 1.70; 95% CI 1.36, 2.13), particularly those with thyroid dysfunction (OR 1.88; 95% CI 1.38, 2.56), inflammatory bowel disease (OR 1.78; 95% CI 1.00, 3.16) or vitiligo (OR 3.91; 95% CI 1.93, 7.94), with stronger associations being observed for the LADAhigh phenotype. Only psoriasis was linked to type 2 diabetes (OR 1.47; 95% CI 1.08, 1.99). The biological pathways shared by LADA and ADs revolved around immune responses, including innate and adaptive immune pathways. The HRs for diabetic retinopathy in LADA patients with and without AD vs those with type 2 diabetes were 2.11 (95% CI 1.34, 3.32) and 1.68 (95% CI 1.15, 2.45), respectively. We confirm that several common ADs confer an excess risk of LADA, especially LADA with higher GADA levels, but having such a comorbidity does not appear to affect the risk of diabetic retinopathy.

Advancing Methodological Approaches in Affect-Adaptive Video Game Design: Empirical Validation of Emotion-Driven Gameplay Modification

Affect-adaptive video games are increasingly concerned with changing game material based on the emotional states of player to best elicit the optimal experience. However, conceptual uncertainties and unreliable methodologies make this process currently difficult and results inconclusive. Here we present a methodological approach to explicitly test mapping assumptions between in-game variables, player input, and subjective experience to build affect-adaptive video games. In Experiment 1, 161 participants played through a newly developed 2D action arcade game. Their data was used to identify associations between game input, presented material, and affective valence. Results made it possible to identify two potential pathways for emotion adaptation which were implemented and evaluated in Experiment 2 (N = 158) against a non-adaptive version of the same game. The player-based emotional adaptation showed a significant increase in self-reported valence compared to the control condition, providing evidence for the utility of the process.

A tale of two (Florida) cities: perceptions of flooding risk and adaptation in Tampa’s Hyde Park and Saint Augustine

AbstractSea level rise is not a problem for the future alone. It is already affecting many small to medium cities on the East Coast of the USA. These cities are adapting to their problems without sufficient help from the federal or state government. To escape the perils of short-term reactionary ad hoc measures to deal with such problems, there is a need to utilize longer-term visions and frameworks. One such approach, Adaptation Pathway Planning, requires the involvement of locally affected people. This study looks at the perceptions and preferred adaptation solutions of the residents of St. Augustine and the Hyde Park neighborhood in Tampa, FL, two cities that are already experiencing the worsening flooding effects caused by rising seas. The results show that those living in areas at higher risk, and which are already experiencing frequent tidal flooding, had a greater knowledge of this risk and a higher desire for increased action from multiple levels of government. Also, such people were more aware of what their municipalities were already doing to adapt. Finally, when faced with two different scenarios of the possible rise in sea levels by 2050, those presented with the higher scenarios were more likely to choose a wider range of adaptation countermeasures. All this indicates the need to carefully consider the awareness of residents regarding the effects of sea level rise and how long-term adaptation should be discussed with them.

Unlocking the dual role of LSD1 in tumor immunity: innate and adaptive pathways

Unlocking the dual role of LSD1 in tumor immunity: innate and adaptive pathways

Histone Deacetylases (HDACs) Roles in Inflammation-mediated Diseases; Current Knowledge.

The histone acetyl transferases (HATs) and histone deacetylases (HDACs), which are mostly recognized for their involvement in regulating chromatin remodeling via histone acetylation/deacetylation, have been shown to also change several non-histone proteins to regulate other cellular processes. Acetylation affects the activity or function of cytokine receptors, nuclear hormone receptors, intracellular signaling molecules, and transcription factors in connection to inflammation. Some small-molecule HDAC inhibitors are utilized as anticancer medications in clinical settings due to their capability to regulate cellular growth arrest, differentiation, and death. Here, we summarize our present knowledge of the innate and adaptive immunological pathways that classical HDAC enzymes control. The aim is to justify the targeted (or non-targeted) use of inhibitors against certain HDAC enzymes in inflammatory diseases such as arthritis, inflammatory bowel diseases (IBD), airways inflammation and neurological diseases.

Metabolic cross-feeding interactions modulate the dynamic community structure in microbial fuel cell under variable organic loading wastewaters.

The efficiency of microbial fuel cells (MFCs) in industrial wastewater treatment is profoundly influenced by the microbial community, which can be disrupted by variable industrial operations. Although microbial guilds linked to MFC performance under specific conditions have been identified, comprehensive knowledge of the convergent community structure and pathways of adaptation is lacking. Here, we developed a microbe-microbe interaction genome-scale metabolic model (mmGEM) based on metabolic cross-feeding to study the adaptation of microbial communities in MFCs treating sulfide-containing wastewater from a canned-pineapple factory. The metabolic model encompassed three major microbial guilds: sulfate-reducing bacteria (SRB), methanogens (MET), and sulfide-oxidizing bacteria (SOB). Our findings revealed a shift from an SOB-dominant to MET-dominant community as organic loading rates (OLRs) increased, along with a decline in MFC performance. The mmGEM accurately predicted microbial relative abundance at low OLRs (L-OLRs) and adaptation to high OLRs (H-OLRs). The simulations revealed constraints on SOB growth under H-OLRs due to reduced sulfate-sulfide (S) cycling and acetate cross-feeding with SRB. More cross-fed metabolites from SRB were diverted to MET, facilitating their competitive dominance. Assessing cross-feeding dynamics under varying OLRs enabled the execution of practical scenario-based simulations to explore the potential impact of elevated acidity levels on SOB growth and MFC performance. This work highlights the role of metabolic cross-feeding in shaping microbial community structure in response to high OLRs. The insights gained will inform the development of effective strategies for implementing MFC technology in real-world industrial environments.

Epigenetic trajectory predicts development of clinical rheumatoid arthritis in ACPA+ individuals: Targeting Immune Responses for Prevention of Rheumatoid Arthritis (TIP-RA).

The presence of autoantibodies to citrullinated protein antigens (ACPAs) in the absence of clinically-apparent inflammatory arthritis (IA) identifies individuals "at-risk" for developing future clinical rheumatoid arthritis (RA). However, it is unclear why some ACPA+ individuals convert to clinical RA while others do not. We explored the possibility in the Targeting Immune Responses for Prevention of Rheumatoid Arthritis (TIP-RA) study that epigenetic remodeling is part of the trajectory from an at-risk state to clinical disease and identifies novel biomarkers associated with conversion to clinical RA. ACPA-Controls, ACPA+ At-Risk, and Early RA individuals were followed for up to 5 years, including obtaining blood samples annually and at RA diagnosis. Peripheral blood mononuclear cells (PBMCs) were separated into CD19+ B cells, memory CD4+ T cells, and naïve CD4+ T cells using antibodies and magnetic beads. Genome-wide methylation within each cell lineage was assayed using the Illumina MethylationEPIC v1.0 beadchip. ACPA+ At-Risk participants who did or did not develop RA were designated "Pre-RA" or "Non-converters", respectively.Differentially methylated loci (DML) were selected using the Limma software package. Using the Caret package, we constructed machine learning models in test and validation cohorts and identified the most predictive loci of clinical RA conversion. Cross-sectional differential methylation analysis at baseline revealed DMLs that distinguish the Pre-RA methylome from ACPA+ Non-converters, the latter which closely resembled ACPA-Controls. Genes overlapping these DMLs correspond to aberrant NOTCH signaling and DNA repair pathways in B cells. Longitudinal analysis showed that ACPA-Control and ACPA+ Non-converter methylomes are relatively constant. In contrast, the Pre-RA methylome remodeled along a dynamic "RA methylome trajectory" characterized by epigenetic changes in active regulatory elements. Clinical conversion to RA, defined based on diagnosis, marked an epigenetic inflection point for cell cycle pathways in B cells and adaptive immunity pathways in naïve T cells. Machine learning revealed individual loci associated with RA conversion. This model significantly outperformed autoantibodies plus acute phase reactants as predictors of RA conversion. DNA methylation is a dynamic process in ACPA+ individuals at-risk for developing RA that eventually transition to clinical disease. In contrast, non-converters and controls have stable methylomes. The accumulation of epigenetic marks over time prior to conversion to clinical RA conforms to pathways that are associated with immunity and can be used to identify potential pathogenic pathways for therapeutic targeting and/or use as prognostic biomarkers.

Exploring the detrimental effects of microplastics on Asian seabass (Lates calcarifer) fingerlings survival and health

Microplastics (MPs) are widely used and disposed of indiscriminately, posing a potential threat to aquatic life. Herein, Asian seabass (Lates calcarifer) fingerlings were exposed to various concentrations (1, 10 and 100 ppt or g/kg) of dietary polyethylene MPs for 16 days. The results indicated a significant increase in mortality among the fish fed with dietary MPs compared to the control. Furthermore, histological analysis of the liver revealed moderate-to-severe morphological alterations, hepatocyte necrosis and vacuolisation as the concentration gradient of MPs increased. The severity of the alterations was highest at a concentration of 100 ppt, indicating a direct correlation between MP and liver damage. In addition, RNA sequencing and Gene Ontology term enrichment analysis revealed that a total of 4137 genes were significantly differentially expressed, with 1958 upregulated and 2179 downregulated genes. The significantly enriched terms included ‘oxidoreductase activity’, ‘endocytosis’, ‘mitochondrial’, ‘immune system process’ and ‘lipid catabolic process’. Moreover, the Kyoto Encyclopaedia of Genes and Genomes enrichment analysis demonstrated that dietary MPs triggered oxidative stress, immune response and adaptive mechanism pathways in fish. Thus, MPs can induce metabolic disorders in L. calcarifer, highlighting their potential threat to aquatic organisms.

Developing a Sustainable Digital Transformation Roadmap for SMEs: Integrating Digital Maturity and Strategic Alignment

Digital transformation (DT) is crucial for SMEs to streamline operational efficiency, foster innovation, and meet upcoming challenges. Integrating sustainability into this process not only enhances a company’s reputation but also attracts customers and investors who value environmental responsibility. Despite this opportunity, many SMEs operate without clear plans and strategies. The literature review identified a lack of roadmaps that integrate sustainability into the digital transformation process for SMEs. Thus, this paper aims to propose a sustainable digital transformation roadmap for SMEs that evaluates their digital maturity and facilitates gradual implementation in alignment with their strategic objectives. A systematic literature review using the Methodi Ordinatio defined six key dimensions of digital transformation. Consequently, the SDT-SMEs Roadmap was developed, drawing on ISO/IEC 33000 standards to offer well-defined processes for enhancing digital competencies. The roadmap features three organizational planning levels—strategic, tactical, and operational—and includes a maturity model that evaluates 75 processes across six dimensions: Digital Technologies, Customer Focus, Organizational Culture, Organizational Governance, People, and Sustainability. Validation through a case study confirmed the roadmap’s effectiveness in addressing real-world challenges and guiding SMEs through the digitization process. The SDT-SMEs Roadmap provides a comprehensive and integrated approach, ensuring continuous adaptation and improvement in sustainable digital transformation efforts. This roadmap addresses a significant gap in the literature and presents a practical, strategic, and adaptable pathway for SMEs embarking on their digital transformation journeys.

The roles and unexplored potential of policy experimentation in climate adaptation governance: A systematic literature review

AbstractPolicy experimentation has emerged globally as a novel governance approach to address complex socio‐environmental problems. In the climate adaptation literature, policy experiments that test technical and governance innovations on a small scale in real‐world conditions are increasingly utilized to explore new pathways for climate adaptation. However, there is a lack of empirical evidence on how policy experiments lead to transformative change in climate adaptation governance, particularly regarding their role as a change strategy. This systematic literature review aims to thoroughly investigate the topic by mapping the empirical characteristics of policy experiments, their role and their outcomes. An existing analytical framework was adapted to fulfill this objective by qualitatively and quantitatively analyzing 27 empirical papers. The findings reveal that policy experiments in climate adaptation often address multiple climate hazards, sectors and actors, yet they are spatially and temporally limited, being predominantly located in Europe. Moreover, the study highlights the transformative potential of policy experiments in climate adaptation governance, emphasizing their effectiveness in testing technical and governing innovations, as well as implementing adaptation policies. Policy experiments predominantly contribute to social learning rather than direct policy changes, requiring specific strategies to upscale the knowledge generated. We conclude the paper with a research agenda that stresses the need for more cumulative and comparative (post)assessments of climate adaptation experiments. This is important given the potential of policy experiments as governing approaches in the advancement of climate adaptation.

A GIS-MCDA approach to map environmental suitability of Posidonia oceanica meadows as blue nature-based solutions in the Mediterranean eco-region

The growing environmental risks induced by interacting climate and human-induced pressures threaten the survival and growth of marine coastal ecosystems (MCEs) and the ecosystem services they provide. Nature-based solutions (NBS), consisting of ecosystem-based approaches, have emerged as vital tools for climate adaptation and mitigation facing biodiversity loss and societal challenges. Identifying suitable environmental conditions for implementing Blue-NBS in marine coastal areas is a key priority to drive robust and cost-effective nature-based adaptation pathways. This study developed a suitability model for Blue-NBS, with a specific focus on Posidonia oceanica meadows in the Mediterranean Sea under a baseline scenario. GIS-based Multiple Criteria Decision Analysis (MCDA) was applied for data integration and prioritization of different environmental variables in geomorphological (e.g., depth), water quality (WQ) (e.g., salinity), and climatic (e.g., thermal stress) sub-groups. Suitability classes and scores for each variable were determined using statistical distributions, ensuring a data-driven approach to defining environmental suitability. Variables' weights were derived from the Analytic Hierarchy Process (AHP) based on expert judgment and then combined with scores to generate suitability maps for managing Blue-NBS on seagrasses. Depth was found to be the most dominant environmental variable, with shallow areas (e.g., Northern Adriatic, Gulf of Gabés) showing higher suitability. The southern part of the Mediterranean (e.g., Egypt) reported relatively low scores for both climate and WQ, while the Northern Adriatic had the lowest WQ scores. This study represents the first attempt to evaluate Blue-NBS suitability for seagrass meadows at the eco-regional scale with geomorphologic, WQ, and climatic variables, providing decision support for the selection and allocation of Blue-NBS in different environmental settings. The resulting environmental suitability maps represent a basis for the integration of socio-economic and governance-related indicators into a more complex, multi-tier approach to support NBS mainstreaming.

RpoS activates formation of Salmonella Typhi biofilms and drives persistence in the gall bladder.

The development of strategies for targeting the asymptomatic carriage of Salmonella Typhi in chronic typhoid patients has suffered owing to our basic lack of understanding of the molecular mechanisms that enable the formation of S. Typhi biofilms. Traditionally, studies have relied on cholesterol-attached biofilms formed by a closely related serovar, Typhimurium, to mimic multicellular Typhi communities formed on human gallstones. In long-term infections, S. Typhi adopts the biofilm lifestyle to persist in vivo and survive in the carrier state, ultimately leading to the spread of infections via the fecal-oral route of transmission. In the present work, we studied S. Typhi biofilms directly, applied targeted as well as genome-wide genetic approaches to uncover unique biofilm components that do not conform to the CsgD-dependent pathway established in S. Typhimurium. We undertook a genome-wide Tn5 mutation screen in H58, a clinically relevant multidrug resistance strain of S. Typhi, in gallstone-mimicking conditions. We generated New Generation Sequencing libraries based on the ClickSeq technology to identify the key regulators, IraP and RpoS, and the matrix components Sth fimbriae, Vi capsule and lipopolysaccharide. We discovered that the starvation sigma factor, RpoS, was required for the transcriptional activation of matrix-encoding genes in vitro, and for S. Typhi colonization in persistent infections in vivo, using a heterologous fish larval model. An rpoS null mutant failed to colonize the gall bladder in chronic zebrafish infections. Overall, our work uncovered a novel RpoS-driven, CsgD-independent paradigm for the formation of cholesterol-attached Typhi biofilms, and emphasized the role(s) of stress signaling pathways for adaptation in chronic infections. Our identification of the biofilm regulators in S. Typhi paves the way for the development of drugs against typhoid carriage, which will ultimately control the increased incidence of gall bladder cancer in typhoid carriers.

Learning About Sea Level Rise Uncertainty Improves Coastal Adaptation Decisions

AbstractAdaptive decision‐making allows decision‐makers to plan long‐term coastal infrastructure under uncertain sea level rise projections. To date, economic assessments of adaptive decision‐making that take into account future learning about sea level rise uncertainty are rare and the existing ones have relied on simple quantification of future learning not validated against sea level science. To address this gap, we develop an economic adaptive decision‐making framework that takes into account future learning about sea level rise uncertainty and apply it to a coastal case study in Lübeck, Germany, to answer the question of how adaptation to sea level rise can be improved through adaptive adaptation pathways as opposed to non‐adaptive pathways. To address this question, we use a Markov decision process to formulate the stochastic optimization problem. We quantify future learning about sea level rise uncertainty through sea level rise learning scenarios based on and validated against the latest scenarios of the Intergovernmental Panel on Climate Change. Our case study results show that the city of Lübeck is currently under‐protected against storm surges and that immediate adaptation actions are advisable in the face of future sea level rise. We find that adaptive adaptation pathways, in contrast to non‐adaptive pathways, generate sea level rise thresholds for adaptation actions that are similar across climate change scenarios and can reduce expected costs up to 1.8%.

Hypoxia-reoxygenation Extends the Lifespan of Caenorhabditis elegans via SKN-1- and DAF-16A-Dependent Stress Hormesis.

To study the role of hypoxia-reoxygenation and anoxia-starvation on the lifespan of C. elegans and elucidate the mechanism at molecular levels. Increasing evidence indicates that reactive oxygen species (ROS) act as signaling molecules that promote health. Hormesis occurs when a moderate stress level induces a beneficial adaptive response, protecting organisms against subsequent exposure to severe stress. Caenorhabditis elegans is a widely used model organism to study aging and displays a broad hormetic ability to couple with stress. To date, only few methods are available to induce stress hormesis in C. elegans. The objectives of this study were to explore the effects of hypoxia-reoxygenation and anoxia-starvation on the lifespan of C. elegans, exploring the involvement of ROS and oxidative stress-related pathways, and examining the hormetic property of H/R. The C. elegans were cultured in hypoxic conditions (1% O2) with OP50 bacteria for 24 h followed by reoxygenation (20% O2) (H/R) or in anoxic conditions (0% O2; 100% N2) without OP50 bacteria for 24 h followed by reoxygenation (20% O2) and food supplementation (A/S). Survivals were plotted and estimated for probability with Kaplan-Meier analysis. The H/R extended the lifespan of C. elegans, and H/R-pretreated worms showed improved resistance toward A/S compared to naïve worms. The C. elegans SKN-1 and DAF-16 are important oxidative stress response factors homologous to mammalian Nrf2 and FOXO3, respectively. Mutations in SKN-1 and DAF-16 blocked H/R-induced life extension. Next, H/R treatment in C. elegans activated both SKN-1 and DAF-16, as indicated by the upregulation of putative target genes of SKN-1 (gcs-1 and gss-1) and DAF-16 (sod-3). Moreover, pre-treatment with antioxidants (N-acetylcysteine, chlorogenic acid, and sulforaphane) reduced ROS levels and diminished the lifespan extension effect of H/R, indicating their dependency on ROS. These results provide evidence that H/R is beneficial for lifespan and stress resistance by activating the adaptive cellular response pathway (SKN-1 and DAF-16A) toward oxidative stress.

Type I IFN drives unconventional IL-1β secretion in lupus monocytes.

Opsonization of red blood cells that retain mitochondria (Mito+ RBCs), a feature of systemic lupus erythematosus (SLE), triggers type I interferon (IFN) production in macrophages. We report that monocytes (Mos) co-produce IFN and mature interleukin-1β (mIL-1β) upon Mito+ RBC opsonization. IFN expression depended on cyclic GMP-AMP synthase (cGAS) and RIG-I-like receptors' (RLRs) sensing of Mito+ RBC-derived mitochondrial DNA (mtDNA) and mtRNA, respectively. Interleukin-1β (IL-1β) production was initiated by the RLR antiviral signaling adaptor (MAVS) pathway recognition of Mito+ RBC-derived mtRNA. This led to the cytosolic release of Mo mtDNA, which activated the inflammasome. Importantly, mIL-1β secretion was independent of gasdermin D (GSDMD) and pyroptosis but relied on IFN-inducible myxovirus-resistant protein 1 (MxA), which facilitated the incorporation of mIL-1β into a trans-Golgi network (TGN)-mediated secretory pathway. RBC internalization identified a subset of blood Mo expressing IFN-stimulated genes (ISGs) that released mIL-1β and expanded in SLE patients with active disease.

Peroxisomal import stress activates integrated stress response and inhibits ribosome biogenesis.

Impaired organelle-specific protein import triggers a variety of cellular stress responses, including adaptive pathways to balance protein homeostasis. Most of the previous studies focus on the cellular stress response triggered by misfolded proteins or defective protein import in the endoplasmic reticulum or mitochondria. However, little is known about the cellular stress response to impaired protein import in the peroxisome, an understudied organelle that has recently emerged as a key signaling hub for cellular and metabolic homeostasis. To uncover evolutionarily conserved cellular responses upon defective peroxisomal import, we carried out a comparative transcriptomic analysis on fruit flies with tissue-specific peroxin knockdown and human HEK293 cells expressing dominant-negative PEX5C11A. Our RNA-seq results reveal that defective peroxisomal import upregulates integrated stress response (ISR) and downregulates ribosome biogenesis in both flies and human cells. Functional analyses confirm that impaired peroxisomal import induces eIF2α phosphorylation and ATF4 expression. Loss of ATF4 exaggerates cellular damage upon peroxisomal import defects, suggesting that ATF4 activation serves as a cellular cytoprotective mechanism upon peroxisomal import stress. Intriguingly, we show that peroxisomal import stress decreases the expression of rRNA processing genes and inhibits early pre-rRNA processing, which leads to the accumulation of 47S precursor rRNA and reduction of downstream rRNA intermediates. Taken together, we identify ISR activation and ribosome biogenesis inhibition as conserved adaptive stress responses to defective peroxisomal import and uncover a novel link between peroxisomal dysfunction and rRNA processing.

Physiological changes in the regulation of calcium and phosphorus utilization that occur after the onset of egg production in commercial laying hens.

At the onset of egg production, physiological changes governing calcium and phosphorus utilization must occur to meet demands for medullary bone formation and eggshell mineralization. The objective of this study was to identify these changes and determine if they are influenced by dietary supplementation with 1α-hydroxycholecalciferol (AlphaD3™, Iluma Alliance). Commercial laying hens fed either a control or AlphaD3-supplemented diet beginning at 18 weeks of age were sampled at 18 (n = 8) and 31 weeks (n = 8/diet) to evaluate mRNA expression associated with calcium and phosphorus utilization in kidney, shell gland, ileum, and liver, circulating vitamin D3 metabolites, and bone quality parameters in humerus, tibia, and keel bone. Though diet did not heavily influence gene expression at 31 weeks, several significant differences were observed between 18- and 31-week-old hens. Heightened sensitivity to hormones regulating calcium and phosphorus homeostasis was observed at 31 weeks, indicated by increased parathyroid hormone receptor 1, calcium-sensing receptor, calcitonin receptor, and fibroblast growth factor 23 receptors in several tissues. Increased renal expression of 25-hydroxylase and vitamin D binding protein ( DBP ) at 31 weeks suggests kidney participates in local vitamin D3 25-hydroxylation and DBP synthesis after egg production begins. Biologically active 1,25(OH)2D3 was higher at 31 weeks, with correspondingly lower inactive 24,25(OH)2D3. Increased expression of plasma membrane calcium ATPase 1 and calbindin in kidney, shell gland, and ileum suggests these are key facilitators of calcium uptake. Elevated renal inorganic phosphorus transporter 1 and 2 and sodium-dependent phosphate transporter IIa at 31 weeks suggests increased phosphorus excretion following hyperphosphatemia due to bone breakdown for eggshell formation. Diet did influence bone quality parameters. Bone mineral density in both humerus and tibia was higher in AlphaD3-supplemented hens at 31 weeks. Tibial bone mineral content increased between 18 and 31 weeks, with AlphaD3-supplemented hens increasing more than control hens. Moreover, control hens exhibited diminished tibial breaking strength at 31 weeks compared to hens at 18 weeks, while AlphaD3-supplemented hens did not. Together, these results indicate supplementation with AlphaD3 enhanced bone mineralization during the medullary bone formation period and elucidate the adaptive pathways regulating calcium and phosphorus utilization after the onset of lay.

Growth performance, antioxidant capacity, intestinal microbiota, and metabolomics analysis of Nile tilapia (Oreochromis niloticus) under carbonate alkalinity stress

To explore the effect of carbonate alkalinity stress on Nile tilapia (Oreochromis niloticus), fish were cultured at 3 alkalinity levels (0, 2 and 3 g/L NaHCO3) for six weeks. Survival, weight gain, and specific growth rate were measured. Liver samples were collected for measuring superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), total antioxidant capacity (T-AOC), and malondialdehyde (MDA) content. Intestinal microbiota was analyzed using 16S rRNA gene sequencing, and metabolomic profiling identified differentially abundant metabolites. The results showed that the survival rate decreased in the fish exposed to 3 g/L NaHCO3, while weight gain and specific growth rate were not affected by the increased carbonate alkalinity. In the group exposed to 3 g/L NaHCO₃, activities of superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), total antioxidant capacity (T-AOC), and malondialdehyde (MDA) content in liver increased, while in 2 g/L NaHCO₃, only SOD and T-AOC activities rose compared to the control. Long-term carbonate alkalinity stress increased the abundance of Luteolibacter in intestine but decreased the abundance of Cetobacterium, Bacteroides, and Lactiplantibacillus. Metabolomics results showed that differentially abundant metabolites were highly enriched in pathways such as purine metabolism, vitamin B6 metabolism, lysine degradation, glycerophospholipid metabolism, and biosynthesis of cofactors in fish cultured at 3 g/L NaHCO3. These results suggested that carbonate alkalinity stress affects intestinal health by increasing the proportion of pathogenic bacteria and reducing beneficial bacteria. The correlation between N6,N6,N6-trimethyllysine, Ne,Ne-dimethyllysine, and Luteolibacter may represent an effective physiological adaptation and tissue repair pathway for Nile tilapia under carbonate alkalinity stress.