Transmembrane Transport Research Articles

Nonequilibrium Dynamic Phase Diagram for Transmembrane Transport of Active Particles.

In recent years, there has been considerable push toward the biomedical applications with active particles, which have great potential to revolutionize disease diagnostics and therapy. The direct penetration of active particles through the cell membrane leads to more efficient intracellular delivery than previously considered endocytosis processes but may cause membrane disruption. Understanding fundamental behaviors of cell membranes in response to such extreme impacts by active particles is crucial to develop active particle-based biomedical technologies and manage health and safety issues in this emerging field. Unfortunately, the physical principles underlying the nonequilibrium behaviors from endocytosis to direct penetration remain elusive, and experiments are challenging. Here, we present a computed dynamic phase diagram for transmembrane transport of active particles and identify four characteristic dynamic phases in endocytosis and direct penetration according to the particle activity and membrane tension. The boundaries dividing these phases are analytically obtained with theoretical models, elucidating the nonequilibrium physics and criteria for the transition between different phases. Furthermore, we numerically and experimentally show three distinct dynamic regimes related to the interplay between necking and wrapping during the endocytosis process of active particles, which strikingly contrast the regimes for passive particles. Overall, these findings could be useful for sharpening the understanding of basic principles underlying biological issues related to the safe and efficient biomedical applications of such emerging matters.

Kinetic Diagram Analysis: A Python Library for Calculating Steady-State Observables of Biochemical Systems Analytically.

Kinetic diagrams are commonly used to represent biochemical systems in order to study phenomena such as free energy transduction and ion selectivity. While numerical methods are commonly used to analyze such kinetic networks, the diagram method by King, Altman and Hill makes it possible to construct exact algebraic expressions for steady-state observables in terms of the rate constants of the kinetic diagram. However, manually obtaining these expressions becomes infeasible for models of even modest complexity as the number of the required intermediate diagrams grows with the factorial of the number of states in the diagram. We developed Kinetic Diagram Analysis (KDA), a Python library that programmatically generates the relevant diagrams and expressions from a user-defined kinetic diagram. KDA outputs symbolic expressions for state probabilities and cycle fluxes at steady-state that can be symbolically manipulated and evaluated to quantify macroscopic system observables. We demonstrate the KDA approach for examples drawn from the biophysics of active secondary transmembrane transporters. For a generic 6-state antiporter model, we show how the introduction of a single leakage transition reduces transport efficiency by quantifying substrate turnover. We apply KDA to a real-world example, the 8-state free exchange model of the small multidrug resistance transporter EmrE of Hussey et al. (J. Gen. Physiol., 2020, 152, e201912437), where a change in transporter phenotype is achieved by biasing two different subsets of kinetic rates: alternating access and substrate unbinding rates. KDA is made available as open source software under the GNU General Public License version 3.

Comparative Analysis of Angora Rabbit Colostrum and Mature Milk Using Quantitative Proteomics.

Colostrum intake is a crucial determinant of survival in newborn rabbits. Neonates rely entirely on passive immunity transfer from their mothers while suckling colostrum. The goal of this study was to explore the protein differences of rabbit milk during different lactation periods. Our findings showed that the daily milk yield exhibited an increasing trend from the 2nd to the 21st day of lactation. A data-independent acquisition proteomics approach identified a total of 2011 proteins. Significantly, different abundances were found for 525 proteins in the colostrum and the mature milk samples. Eleven differentially abundant proteins (DAPs) were examined using parallel reaction monitoring, which verified the reliability of the proteomic data. Gene Ontology analysis revealed that these DAPs were primarily associated with glycosyltransferase activity, macromolecule transmembrane transporter activity, and regulation of acute inflammatory response. The dominant metabolic pathways of the DAPs involve the complement and coagulation cascades. A protein-protein interaction analysis identified apolipoprotein B, apolipoprotein A1, triose phosphate isomerase 1, and albumin as the hub proteins responsible for distinguishing differences between biological properties in rabbit colostrum and mature milk. These findings enhance our comprehension of the rabbit milk proteome, particularly in expanding our knowledge regarding the requirements of neonatal rabbits.

Bioinformatic characterization and functional evaluation of Ph-Def: A novel marine antimicrobial peptide from Panulirus homarus

The present study describes the discovery of Ph-Def, the first marine antimicrobial peptide (AMP) isolated from Panulirus homarus, the Indian spiny lobster. Ph-Def is a 65-amino acid β-defensin (including signal peptide) with potential antimicrobial properties. Phylogenetic analysis revealed its close relationship to β-defensins in other Panulirus lobsters and suggested an evolutionary connection with vertebrate β-defensins. In silico analysis identified hot spot areas and a hydrophobic face, supporting its potential as a marine AMP with antimicrobial activity. A predicted bactericidal stretch spanning from Cys53–Tyr64 was notably identified, covering the mature peptide. Ph-Def demonstrated similarity to β-defensins in other lobster species and fish β-defensins, suggesting a shared functional role against microorganisms. Predicted biological processes associated with Ph-Def include metabolic regulation, cellular biosynthesis, transport, cation transmembrane transport, and immune system processes. These findings underscore the potential of Ph-Def as a marine AMP and expand our understanding of immune responses and defense mechanisms in P. homarus.

PpyLTP36 and PpyLTP39 are involved in the transmembrane transport of cuticular wax and are associated with the occurrence of pear fruit russeting

Non-specific lipid-transfer proteins (nsLTPs) are a group of small, cysteine-rich proteins that are involved in the transport of cuticular wax and other lipid compounds. Accumulating evidence suggests that dynamic changes in cuticular waxes are strongly associated with fruit russeting, an undesirable visual quality that negatively affects consumer appeal in pears. Currently, the regulatory role of nsLTPs in cuticular wax deposition and pear fruit skin russeting remains unclear. Here, we characterized the variations of cuticular waxes in non-treated (russeted) and preharvest bagging treated (non-russeted) pear fruits throughout fruit development and confirmed that the contents of cuticular waxes were significantly negatively correlated with the occurrence of pear fruit russeting. Based on RNA-Sequencing (RNA-Seq) and quantitative real-time PCR (qRT-PCR) analyses, two nsLTP genes (PpyLTP36 and PpyLTP39) were identified, which exhibited high expression levels in non-russeted pear fruit skins and were significantly repressed during fruit skin russeting. Subcellular localization analysis demonstrated that PpyLTP36 and PpyLTP39 were localized to the plasma membrane (PM). Further, transient Virus-Induced Gene Silencing (VIGS) analyses of PpyLTP36 and PpyLTP39 in pear fruits significantly reduced cuticular wax deposition. In conclusion, PpyLTP36 and PpyLTP39 are involved in the transmembrane transport of cuticular wax and are associated with pear fruit skin russeting.

Role of Enzymes Capable of Transporting Phosphatidylserine in Brain Development and Brain Diseases.

Phosphatidylserine (PS) is a common type of phospholipid, typically located in the inner leaflet of the cell membrane, especially abundant in the nervous system. It is an important component of the neuronal membrane and is considered to play a regulatory role in various brain functions, including memory and emotional stability, because its exposure to the outer leaflet of the neuronal membrane can result in abnormalities in various neurobiological processes such as synaptic transmission and neuronal apoptosis. Recently, research on two types of membrane proteins that synergistically mediate the transmembrane transport of phospholipid molecules in eukaryotic cells has become more in-depth and detailed. This review mainly explores the regulation of the expression of phosphatidylserine transporters and their impact on brain development and diseases.

Caveolin and NOS in the Development of Muscular Dystrophy.

Caveolin is a structural protein within caveolae that may be involved in transmembrane molecular transport and/or various intercellular interactions within cells. Specific mutations of caveolin-3 in muscle fibers are well known to cause limb-girdle muscular dystrophy. Altered expression of caveolin-3 has also been detected in Duchenne muscular dystrophy, which may be a part of the pathological process leading to muscle weakness. Interestingly, it has been shown that the renovation of nitric oxide synthase (NOS) in sarcolemma with muscular dystrophy could improve muscle health, suggesting that NOS may be involved in the pathology of muscular dystrophy. Here, we summarize the notable function of caveolin and/or NOS in skeletal muscle fibers and discuss their involvement in the pathology as well as possible tactics for the innovative treatment of muscular dystrophies.

Quercetin Supplementation Improves Intestinal Digestive and Absorptive Functions and Microbiota in Rats Fed Protein-Oxidized Soybean Meal: Transcriptomics and Microbiomics Insights.

To clarify the nutritional mechanisms of quercetin mitigation in the digestive and absorptive functions in rats fed protein-oxidized soybean meal, 48 three-week-old male SD rats were randomly allocated into a 2 × 2 factorial design with two soybean meal types (fresh soybean meal or protein-oxidized soybean meal) and two quercetin levels (0 or 400 mg/kg) for a 28-day feeding trial. The protein-oxidized soybean meal treatment decreased (p < 0.05) the relative weights of the pancreas, stomach, and cecum, duodenal villus height, pancreatic and jejunal lipase activities, apparent ileal digestibility of amino acids, and apparent total tract digestibility of dry matter, crude protein, and ether extract. The supplementation of quercetin in the protein-oxidized soybean meal diet reversed (p < 0.05) the decreases in the duodenal length, ileal villus height, lipase activity, apparent ileal digestibility of amino acids, and apparent total tract digestibility of dry matter, crude protein, and ether extract. Transcriptomics revealed that the "alanine transport" and "lipid digestion and absorption" pathways were downregulated by the protein-oxidized soybean meal compared with fresh soybean meal, while the "basic amino acid transmembrane transporter activity" and "lipid digestion and absorption" pathways were upregulated by the quercetin supplementation. Microbiomics revealed that the protein-oxidized soybean meal increased the protein-degrading and inflammation-triggering bacteria in the cecum, while the relative abundances of beneficial bacteria were elevated by the quercetin supplementation.

The effect of rs2910686 on ERAP2 expression in IBD and epithelial inflammatory response

BackgroundERAP2 is an aminopeptidase involved in antigen processing and presentation, and harbor genetic variants linked to several inflammatory diseases such as Inflammatory Bowel Disease (IBD). The lack of an ERAP2 gene homologue in mice has hampered functional studies, and most human studies have focused on cells of hematopoietic origin. Using an IBD biobank as vantage point, this study explores how genetic variation in ERAP2 affects gene expression in human-derived epithelial organoids upon proinflammatory stimulation.MethodsAn IBD patient cohort was genotyped with regards to two single nucleotide polymorphisms (SNP) (rs2910686/rs2248374) associated with ERAP2 expression levels, and we examined the correlation between colon gene expression and genotype, specifically aiming to establish a relationship with ERAP2 expression proficiency. Human-derived colon organoids (colonoids) with known ERAP2 genotype were established and used to explore differences in whole genome gene expression between ERAP2-deficient (n = 4) and -proficient (n = 4) donors upon pro-inflammatory encounter.ResultsWhen taking rs2910686 genotype into account, ERAP2 gene expression is upregulated in the inflamed colon of IBD patients. Colonoids upregulate ERAP2 upon IFNɣ stimulation, and ERAP2 expression proficiency is dependent on rs2910686 genotype. Colonoid genotyping confirms that mechanisms independent of the frequently studied SNP rs2248374 can cause ERAP2-deficiency. A total of 586 genes involved in various molecular mechanisms are differentially expressed between ERAP2 proficient- and deficient colonoids upon proinflammatory stimulation, including genes encoding proteins with the following molecular function: catalytic activity (AOC1, CPE, ANPEP and MEP1A), regulator activity (TNFSF9, MDK, GDF15, ILR6A, LGALS3 and FLNA), transmembrane transporter activity (SLC40A1 and SLC5A1), and extracellular matrix structural constituents (FGL2, HMCN2, and MUC17).ConclusionsERAP2 is upregulated in the inflamed IBD colon mucosa, and expression proficiency is highly correlated with genotype of rs2910686. While the SNP rs2248374 is commonly used to determine ERAP2 expressional proficiency, our data confirms that mechanisms independent of this SNP can lead to ERAP2 deficiency. Our data demonstrates that epithelial ERAP2 presence affects the inflammatory response in colonoids, suggesting a pleiotropic role of ERAP2 beyond MHC class I antigen processing.

(Invited) Tuning Chirality of Graphene Quantum Dots to Empower Medical Imaging and Theranostic Applications

Chiral nanostructures from metals and semiconductor, including graphene-based materials, are increasingly recognized for their potential in polarization-sensitive optoelectronics. Particularly, graphene quantum dots (GQDs) modified with L/D amino acids exhibit unique chiral properties due to edge-specific interactions, offering new possibilities in biomedicine. Our study delves into the interaction of these chiral nanomaterials with biological systems, revealing significant implications for their application in biology and medicine. We discovered that attaching L/D amino acid moieties to GQDs induces nanoscale chirality by helical buckling, influenced by the chiral interactions at the graphene edges. The chirality of GQDs affects their interaction at the nanoscale with cells and tissues. Molecular dynamics simulations show that D-GQDs are more likely to accumulate within cellular membranes compared to L-GQDs. Additionally, experiments on chiral GQD permeation through lipid membranes of extracellular vesicles demonstrated that optimizing chirality via ligand tuning and GQD size can significantly enhance their permeation efficiency into lipid bilayers, exceeding 80%. Leveraging this enhanced transmembrane transport, chiral GQDs have been applied in imaging and efficient drug loading for therapeutic extracellular vesicles. Furthermore, we explored how GQD chirality affects transport in tumor-like cellular spheroids. The results indicate that L-GQDs exhibit a 1.7 times higher apparent diffusion coefficient than D-GQDs, enhancing their transport into these spheroids. In summary, our research underscores the importance of controlling and engineering GQD chirality. This approach not only enhances the transport of drug carriers through biological barriers but also opens new avenues for advanced imaging and theranostic applications.

Insect tracheal systems as inspiration for carbon dioxide capture systems

Membrane technology advancements within the past twenty years have provided a new perspective on environmentalism as engineers design membranes to separate greenhouse gases from the environment. Several scientific journals have published articles of experimental evidence quantifying carbon dioxide (CO2), a common greenhouse gas, separation using membrane technology and ranking them against one another. On the other hand, natural systems such as the respiratory system of mammals also accomplish transmembrane transport of CO2. However, to our knowledge, a comparison of these natural organic systems with engineered membranes has not yet been accomplished. The tracheal respiratory systems of insects transport CO2at the highest rates in the animal kingdom. Therefore, this work compares engineered membranes to the tracheal systems of insects by quantitatively comparing greenhouse gas conductance rates. We demonstrate that on a per unit volume basis, locusts can transport CO2approximately ∼100 times more effectively than the best current engineered systems. Given the same temperature conditions, insect tracheal systems transport CO2three orders of magnitude faster on average. Miniaturization of CO2capture systems based on insect tracheal system design has great potential for reducing cost and improving the capacities of industrial CO2capture.

Hemostatic Gelatin-Alginate Hydrogels Modified with Humic Acids and Impregnated with Aminocaproic Acid

The work is devoted to the development of safe and biocompatible multicomponent gelatin-alginate hydrogels modified with humic acids (HA) and impregnated with the antifibrinolytic agent aminocaproic acid (АА).These hydrogels are designed to be effective hemostatic materials with anti-inflammatory properties and the ability to deliver in less than 30 seconds to deep and hidden areas of hemorrhages. Studies of the crystal structure by X-ray diffraction analysis and non-covalent interactions of molecules by Fourier transform infrared spectroscopy of the developed hemostatic gelatin-alginate hydrogels modified with bactericidal and anti-inflammatory humic acids made it possible to identify the optimal concentrations of HA from 2.5 wt.%. up to 5 wt.%. At such concentrations of HA, gelatin-alginate hydrogels have a semicrystalline structure. Due to non-covalent bonds between polymer chains, they are thermo-responsive with a gel-sol transition temperature of about 37 °C. Impregnation of these hydrogels with aminocaproic acid led to an almost threefold increase in their swelling, which facilitated the dissolution of AA in the hydrogels and its subsequent delivery to the wound. Experiments simulating the transmembrane transport of aminocaproic acid from the developed gelatin-alginate hydrogels confirmed their ability to rapidly deliver up to 494± 3 mg of AA from 5 ml of hydrogel to the wound.

Kinetic Diagram Analysis: A Python Library for Calculating Steady-State Observables of Biochemical Systems Analytically.

Kinetic diagrams are commonly used to represent biochemical systems in order to study phenomena such as free energy transduction and ion selectivity. While numerical methods are commonly used to analyze such kinetic networks, the diagram method by King, Altman and Hill makes it possible to construct exact algebraic expressions for steady-state observables in terms of the rate constants of the kinetic diagram. However, manually obtaining these expressions becomes infeasible for models of even modest complexity as the number of the required intermediate diagrams grows with the factorial of the number of states in the diagram. We developed Kinetic Diagram Analysis (KDA), a Python library that programmatically generates the relevant diagrams and expressions from a user-defined kinetic diagram. KDA outputs symbolic expressions for state probabilities and cycle fluxes at steady-state that can be symbolically manipulated and evaluated to quantify macroscopic system observables. We demonstrate the KDA approach for examples drawn from the biophysics of active secondary transmembrane transporters. For a generic 6-state antiporter model, we show how the introduction of a single leakage transition reduces transport efficiency by quantifying substrate turnover. We apply KDA to a real-world example, the 8-state free exchange model of the small multidrug resistance transporter EmrE of Hussey et al (J General Physiology 152 (2020), e201912437), where a change in transporter phenotype is achieved by biasing two different subsets of kinetic rates: alternating access and substrate unbinding rates. KDA is made available as open source software under the GNU General Public License version 3.

Transmembrane and transcriptome analysis reveals the mechanism of dietary supplements in reducing cadmium absorption and toxicity

Dietary strategies have proven to be effective in preventing cadmium (Cd) poisoning, but the regulation of the bioavailability (BAV) and transport of Cd in the body, as well as their molecular mechanisms remain unclear. In this study, the Caco-2 cell models were applied to investigate the effects of 15 dietary supplements on Cd bioavailability (Cd-BAV) in Cd-contaminated water through a transmembrane transport assay and the mechanisms of three selected supplements in inhibiting Cd toxicity and uptake. The results demonstrated that the Cd-BAV in water varied from 7.89 % to 18.4 % using simulated gastrointestinal digestion and cell model. The addition of MT, Zn, and OPCs significantly reduced Cd-BAV by 82.5 %, 73 % and 60.5 % and also strengthened transmembrane electrical resistance (TEER), indicating the protective effects of these compounds against Cd-induced barrier dysfunction. Moreover, the results of transcriptomics revealed that these components can modulate the expression of specific pathway genes associated with the toxicity and absorption of dietary Cd, such as the apoptosis pathway (Jun, Ddit3), antioxidant-related pathways (Cat, Hmox1), and mineral absorption pathway (Mt, Slc39a4). This study highlights the importance of potential dietary interventions in public health and suggests that developing more effective measures to promote safer food consumption would be beneficial.

Inhibitory activity and antioomycete mechanism of citral against Phytophthora capsici

The natural terpenoid citral has antifungal activity against multiple fungi, but its bioactivity against oomycetes is unclear. Therefore, this study investigated the antioomycete activity and mechanism of citral against Phytophthora capsici, a highly destructive invasive oomycete. Results showed that citral not only had a great inhibition on the mycelial growth of P. capsici (EC50 = 94.15 mg/L), but also had a significant inhibition on multiple spores, such as sporangia formation, zoospore discharge and zoospore germination. Citral at 4000 mg/L exhibited favorable protective (73.33%) and curative efficacy (55.11%) against pepper Phytophthora blight. Citral significantly damaged the hyphal morphology, disrupted the cell membrane integrity, increased the permeability of cell membrane, and increased the glycerol content in P. capsici. A total of 250 upregulated and 288 downregulated proteins were identified in iTRAQ-based quantitative proteomic analysis. Downregulated proteins were mostly enriched in pathways of ABC transporters, cyanoamino acid metabolism and starch and sucrose metabolism, suggesting an inhibition of citral on transmembrane transporter (e.g., ABC transporters) and pathogenicity (e.g., β-glucosidases) proteins. Upregulated proteins were enriched in biosynthesis of unsaturated fatty acids, pyruvate metabolism and glycolysis/gluconeogenesis, suggesting an activation of citral on energy generation proteins, including acyl-CoA oxidase, D-lactate dehydrogenase, pyruvate kinase, acetyl-CoA synthetase and phosphoenolpyruvate carboxykinase. Biochemical and iTRAQ analysis suggested that cell membrane may be the target of citral in P. capsici.

Biomimetic MOFs/GO membranes with enhanced charge density for osmotic power generation

Osmotic power generation is a renewable energy technology that harnesses energy from the natural mixing of freshwater and saltwater, offering a promising solution for sustainable energy. However, it is still a challenge to achieve high energy output without compromising scalability and stability. Herein, inspired by the nano-constrained dynamics of neuronal cell transmembrane transport, an anodic oxidation electrodeposition method is employed to fabricate metal organic frameworks (MOFs) within 2D graphene oxide (GO) layers. The in-situ integration of high-density charges within nanometer pore with 0.34 nm entrance of MOFs facilitates rapid and selective cation transport, which significantly increases the diffusion voltage (363.8 mV, 106 fold concentration gradient). Our device demonstrates a maximum output power of 6.82 μW under a 10 fold concentration gradient at a load resistance of 5000 Ω, possessing an energy conversion efficiency of 48.8% at an effective area of 12.56 mm2, which substantially surpasses the performance reported before. More importantly, the device performs exceptionally well, showing robust and stable performance. This is proven by its ability to power various electronic devices. These findings underscore the potential of biomimetic ion channel membranes in sustainable energy applications, offering a promising avenue for the broader field of energy harvesting technologies.

Intracellular Trafficking Defects in Congenital Intestinal and Hepatic Diseases.

Enterocytes and liver cells fulfill important metabolic and barrier functions and are responsible for crucial vectorial secretive and absorptive processes. To date, genetic diseases affecting metabolic enzymes or transmembrane transporters in the intestine and the liver are better comprehended than mutations affecting intracellular trafficking. In this review, we explore the emerging knowledge on intracellular trafficking defects and their clinical manifestations in both the intestine and the liver. We provide a detailed overview including more investigated diseases such as the canonical, variant and associated forms of microvillus inclusion disease, as well as recently described pathologies, highlighting the complexity and disease relevance of several trafficking pathways. We give examples of how intracellular trafficking hubs, such as the apical recycling endosome system, the trans-Golgi network, lysosomes, or the Golgi-to-endoplasmic reticulum transport are involved in the pathomechanism and lead to disease. Ultimately, understanding these processes could spark novel therapeutic approaches, which would greatly improve the quality of life of the affected patients.

Characterizing and identifying of miRNAs involved in berberine modulating glucose metabolism of Megalobrama amblycephala.

The present study, as one part of a larger project that aimed to investigate the effects of dietary berberine (BBR) on fish growth and glucose regulation, mainly focused on whether miRNAs involve in BBR's modulation of glucose metabolism in fish. Blunt snout bream Megalobrama amblycephala (average weight of 20.36 ± 1.44g) were exposed to the control diet (NCD, 30% carbohydrate), the high-carbohydrate diet (HCD, 43% carbohydrate) and the berberine diet (HCB, HCD supplemented with 50mg/kg BBR). After 10weeks' feeding trial, intraperitoneal injection of glucose was conducted, and then, the plasma and liver were sampled at 0h, 1h, 2h, 6h, and 12h. The results showed the plasma glucose levels in all groups rose sharply and peaked at 1h after glucose injection. Unlike the NCD and HCB groups, the plasma glucose in the HCD group did not decrease after 1h, while remained high level until at 2h. The NCD group significantly increased liver glycogen content at times 0-2h compared to the other two groups and then liver glycogen decreased sharply until at times 6-12h. To investigate the role of BBR that may cause the changes in plasma glucose and liver glycogen, miRNA high-throughput sequencing was performed on three groups of liver tissues at 2h time point. Eventually, 20 and 12 differentially expressed miRNAs (DEMs) were obtained in HCD vs NCD and HCB vs HCD, respectively. Through function analyzing, we found that HCD may affect liver metabolism under glucose loading through the NF-κB pathway; and miRNAs regulated by BBR mainly play roles in adipocyte lipolysis, niacin and nicotinamide metabolism, and amino acid transmembrane transport. In the functional exploration of newly discovered novel:Chr12_18892, we found its target gene, adenylate cyclase 3 (adcy3), was widely involved in lipid decomposition, amino acid metabolism, and other pathways. Furthermore, a targeting relationship of novel:Chr12_18892 and adcy3 was confirmed by double luciferase assay. Thus, BBR may promote novel:Chr12_18892 to regulate the expression of adcy3 and participate in glucose metabolism.

Transcriptomic responses and evolutionary insights of deep-sea and shallow-water mussels under high hydrostatic pressure condition

Marine mussels inhabit a wide range of ocean depths, necessitating unique adaptations to cope with varying hydrostatic pressures. This study investigates the transcriptomic responses and evolutionary adaptations of the deep-sea mussel Gigantidas platifrons and the shallow-water mussel Mytilus galloprovincialis to high hydrostatic pressure (HHP) conditions. By exposing atmospheric pressure (AP) acclimated G. platifrons and M. galloprovincialis to HHP, we aim to simulate extreme environmental challenges and assess their adaptive mechanisms. Through comparative transcriptomic analysis, we identified both conserved and species-specific mechanisms of adaptation, with a notable change in gene expression associated with immune system, substance transport, protein ubiquitination, apoptosis, lipid metabolism and antioxidant processes in both species. G. platifrons demonstrated an augmented lipid metabolism, whereas M. galloprovincialis exhibited a dampened immune function. Additionally, the expressed pattern of deep-sea mussel G. platifrons were more consistent than shallow-water mussel M. galloprovincialis under hydrostatic pressures changed conditions which corresponding the long-term living stable deep-sea environment. Moreover, evolutionary analysis pinpointed positively selected genes in G. platifrons that are linked to transmembrane transporters, DNA repair and replication, apoptosis, ubiquitination which are important to cell structural integrity, substances transport, and cellular growth regulation. This indicates a specialized adaptation strategy in G. platifrons to cope with the persistent HHP conditions of the deep sea. These results offer significant insights into the molecular underpinnings of mussel adaptation to varied hydrostatic conditions and enhance our comprehension of the evolutionary forces driving their depth-specific adaptations.

Whole-genome resequencing identifies candidate genes associated with heat adaptation in chickens

The wide distribution and diverse varieties of chickens make them important models for studying genetic adaptation. The aim of this study was to identify genes that alter heat adaptation in commercial chicken breeds by comparing genetic differences between tropical and cold-resistant chickens. We analyzed whole-genome resequencing data of 186 chickens across various regions in Asia, including the following breeds: Bian chickens (B), Dagu chickens (DG), Beijing-You chickens (BY), and Gallus gallus jabouillei from China; Gallus gallus murghi from India; Vietnam native chickens (VN); Thailand native chickens (TN) and Gallus gallus spadiceus from Thailand; and Indonesia native chickens (IN), Gallus gallus gallus, and Gallus gallus bankiva from Indonesia. In total, 5,454,765 SNPs were identified for further analyses. Population genetic structure analysis revealed that each local chicken breed had undergone independent evolution. Additionally, when K = 5, B, BY, and DG chickens shared a common ancestor and exhibited high levels of inbreeding, suggesting that northern cold-resistant chickens are likely the result of artificial selection. In contrast, the runs of homozygosity (ROH) and the ROH-based genomic inbreeding coefficient (FROH) results for IN, TN, and VN chickens showed low levels of inbreeding. Low population differentiation index values indicated low differentiation levels, suggesting low genetic diversity in tropical chickens, implying increased vulnerability to environmental changes, decreased adaptability, and disease resistance. Whole-genome selection sweep analysis revealed 69 candidate genes, including LGR4, G6PC, and NBR1, between tropical and cold-resistant chickens. The genes were further subjected to GO and KEGG enrichment analyses, revealing that most of the genes were primarily enriched in biological synthesis processes, metabolic processes, central nervous system development, ion transmembrane transport, and the Wnt signaling pathway. Our study identified heat adaptation genes and their functions in chickens that primarily affect chickens in high-temperature environments through metabolic pathways. These heat-resistance genes provide a theoretical basis for improving the heat-adaptation capacity of commercial chicken breeds.