Search Results (33)

Cold environments challenge the structural and functional integrity of membrane proteins, requiring specialized adaptations to maintain activity under low thermal energy. Here, we investigate the molecular basis of cold tolerance in the peptide transporter PepT1 from the Antarctic icefish (Chionodraco hamatus, ChPepT1) using molecular dynamics simulations, binding free energy calculations (MM/GBSA), and dynamic network analysis. We compare ChPepT1 to its human ortholog (hPepT1), a non-cold-adapted variant, to reveal key features enabling psychrophilic function. Our simulations show that ChPepT1 displays enhanced global flexibility, particularly in domains adjacent to the substrate-binding site and the C-terminal domain (CTD). While hPepT1 loses substrate binding affinity as temperature increases, ChPepT1 maintains stable peptide interactions across a broad thermal range. This thermodynamic buffering results from temperature-sensitive rearrangement of hydrogen bond networks and more dynamic lipid interactions. Importantly, we identify a temperature-responsive segment (TRS, residues 660–670) within the proximal CTD that undergoes an α-helix to coil transition, modulating long-range coupling with transmembrane helices. Dynamic cross-correlation analyses further suggest that ChPepT1, unlike hPepT1, reorganizes its interdomain communication in response to temperature shifts. Our findings suggest that cold tolerance in ChPepT1 arises from a combination of structural flexibility, resilient substrate binding, and temperature-sensitive interdomain dynamics. These results provide new mechanistic insight into thermal adaptation in membrane transporters and offer a framework for engineering proteins with enhanced functionality in extreme environments. Full article

Lyn is a multifunctional Src-family kinase (SFK) that regulates immune signaling and has been implicated in diverse types of cancer. Unlike other SFKs, its full-length structure and regulatory dynamics remain poorly characterized. In this study, we present the first long-timescale molecular dynamics analysis of full-length Lyn, including the SH3, SH2, and SH1 domains, across wildtype, ligand-bound, and cancer-associated mutant states. Using principal component analysis, dynamic cross-correlation matrices, and network-based methods, we show that ATP binding stabilizes the kinase core and promotes interdomain coordination, while the ATP-competitive inhibitor dasatinib and specific mutations (e.g., E290K, I364N) induce conformational decoupling and weaken long-range communication. We identify integration modules and develop an interface-weighted scoring scheme to rank dynamically central residues. This analysis reveals 44 allosteric hubs spanning SH3, SH2, SH1, and interdomain regions. Finally, a random forest classifier trained on 16 MD-derived features highlights key interdomain descriptors, distinguishing functional states with an AUC of 0.98. Our results offer a dynamic and network-level framework for understanding Lyn regulation and identify potential regulatory hotspots for structure-based drug design. More broadly, our approach demonstrates the value of integrating full-length MD simulations with network and machine learning techniques to probe allosteric control in multidomain kinases. Full article

Multi-hop inter-domain wireless networks play a vital role in future heterogeneous communication systems by improving data transmission efficiency and security assurance. Despite the advances in secure routing techniques in areas such as node authentication and encryption, they still suffer from the shortcomings of frequent key updates, high computational overhead, and poor adaptability to large-scale dynamic topologies. To address these limitations, we propose a new routing method—the Secure Cross-Layer Route—designed for multi-hop inter-domain wireless networks to achieve unified optimization of security, delay, and throughput. First, we construct a multi-objective optimization model that integrates authentication delay, link load, and resource states, enabling balanced trade-offs between security and transmission performance in dynamic conditions. Second, we introduce a cross-layer information fusion mechanism that allows nodes to adapt routing costs in real time under heterogeneous network conditions, thereby improving path reliability and load balancing. Furthermore, a risk-aware dynamic key update strategy is developed to handle behavioral uncertainty among nodes, reducing authentication overhead and enhancing attack resilience. Experimental evaluations conducted on four datasets with varying network scales demonstrate the superior performance of the proposed method. Experimental results demonstrated that the proposed method achieves at least 28% improvement in effective throughput, reduces average authentication delay by approximately 30%, and increases the secure link ratio by at least 10%, outperforming mainstream routing algorithms under multi-constraint conditions. Full article

Living organisms must adapt and communicate effectively in their environment to survive. Cells communicate through various mechanisms, including releasing growth factors, chemokines, small bioactive molecules, and cell–cell contact. In recent years, a new and sophisticated cell communication mechanism based on extracellular vesicles (EVs) has been described in all three domains of life: archaea, bacteria, and eukaryotes. EVs are small, bilayer proteolipid vesicles released by cells into the extracellular space. This review aims to analyze and compare the current literature on bacterial, archaeal, and eukaryotic EVs and their possible clinical applications. This framework will address three key points: (a) The role of EVs in bacteria, eukaryotes, and archaea. (b) What is the impact of EVs in archaea on disease? (c) How archaea use EVs to communicate with other domains (bacteria/eukaryotes). Full article

Recently, there has been an explosive growth in wireless devices capable of connecting to the Internet and utilizing various services anytime, anywhere, often while on the move. In the realm of the Internet, such devices are called mobile nodes. When these devices are in motion or traverse different domains while communicating, effective mobility management becomes essential to ensure the continuity of their services. Software-defined networking (SDN), a new paradigm in networking, offers numerous possibilities for addressing the challenges of mobility management. By decoupling the control and data planes, SDN enables greater flexibility and adaptability, making them a powerful framework for solving mobility-related issues. However, communication can still be momentarily disrupted due to frequent changes in IP addresses, a drop in radio signals, or configuration issues associated with gateways. Therefore, this paper introduces Routage Inter-domains in SDN (RI-SDN), a novel anchor-based routing method designed for inter-domain mobility in SDN architectures. The method identifies a suitable anchor domain, a critical intermediary domain that contributes to reducing delays during data transfer because it is the closest domain (i.e., node) to the destination. Once the anchor domain is identified, the best routing path is determined as the route with the smallest metric, incorporating elements such as bandwidth, flow operations, and the number of domain hops. Simulation results demonstrate significant improvements in data transfer delay and handover latency compared to existing methods. By leveraging SDN’s potential, RI-SDN presents a robust and innovative solution for real-world scenarios requiring reliable mobility management. Full article

The security requirements for SDN (Software-Defined Network) cross-domain communication are diverse and dynamically changing; thus, a security service negotiation function is required for the SDN interdomain. However, the SDN interdomain distributed communication environment leads to a lack of trustworthiness and security. Therefore, this paper proposes a blockchain-based SDN interdomain security service negotiation mechanism, BSSN-SDNs, to provide automatic, secure, and trustworthy SDN interdomain security service negotiation. BSSN-SDNs proposes a three-layer reference architecture that enables joint on-chain and off-chain work by extending the security service negotiation module and blockchain client on the controller and deploying security service negotiation smart contracts on the blockchain. It especially adopts non-interactive key exchange and the message authentication code to ensure the confidentiality of the secure service negotiated on-chain. Finally, the timeliness as well as security and trustworthiness of BSSN-SDNs are analyzed, and the FISCO BCOS-based experiment results show that the delay of BSSN-SDNs is acceptable and is positively correlated with the number of policies and the number of SDN domains involved in negotiation. Full article

Global Navigation Satellite Systems (GNSS) offer comprehensive position, navigation, and timing (PNT) estimates worldwide. Given the growing demand for reliable location awareness in both indoor and outdoor contexts, the advent of fifth-generation mobile communication technology (5G) has enabled expansive coverage and precise positioning services. However, the power received by the signal of interest (SOI) at terminals is notably low. This can lead to significant jamming, whether intentional or unintentional, which can adversely affect positioning receivers. The diagnosis of jamming types, such as classification, assists receivers in spectrum sensing and choosing effective mitigation strategies. Traditional jamming diagnosis methodologies predominantly depend on the expertise of classification experts, often demonstrating a lack of adaptability for diverse tasks. Recently, researchers have begun utilizing convolutional neural networks to re-conceptualize a jamming diagnosis as an image classification issue, thereby augmenting recognition performance. However, in real-world scenarios, the assumptions of independent and homogeneous distributions are frequently violated. This discrepancy between the source and target distributions frequently leads to subpar model performance on the test set or an inability to procure usable evaluation samples during training. In this paper, we introduce LJCD-Net, a deep adversarial migration-based cross-domain jamming generalization diagnostic network. LJCD-Net capitalizes on a fully labeled source domain and multiple unlabeled auxiliary domains to generate shared feature representations with generalization capabilities. Initially, our paper proposes an uncertainty-guided auxiliary domain labeling weighting strategy, which estimates the multi-domain sample uncertainty to re-weight the classification loss and specify the gradient optimization direction. Subsequently, from a probabilistic distribution standpoint, the spatial constraint imposed on the cross-domain global jamming time-frequency feature distribution facilitates the optimization of collaborative objectives. These objectives include minimizing both the source domain classification loss and auxiliary domain classification loss, as well as optimizing the inter-domain marginal probability and conditional probability distribution. Experimental results demonstrate that LJCD-Net enhances the recognition accuracy and confidence compared to five other diagnostic methods. Full article

The introduction of NaCl in freshwater caused by winter runoffs is a problem whose consequences are still little understood. We sought to analyze the effect of NaCl addition on microbial communities of the hypolimnion and bottom sediments of a Canadian lake. Using microcosms comprising a salinity gradient varying between 0.01 and 3.22 ppt (10–3220 mg/L⁻¹) NaCl, we investigated the effect of salinity on prokaryotic absolute abundance and diversity, following a three- and six-week exposure, and detected the presence of a salinity threshold for microbial communities’ differentiation. We observed a significant decline of bacterial diversity after six weeks in hypolimnetic samples. In the sediments, no clear effect of NaCl was observed on abundance or diversity, despite the presence of variations throughout the salinity gradient. The implication of nutrient fluctuations as well as the co-occurrence of species and inter-domain interactions is likely and would strongly contribute to the development of salt-exposed prokaryotic communities. In hypolimnetic water and sediments, the archaeal and eukaryotic communities differed significantly from 0.93 ppt (930 mg/L⁻¹), while only conclusive at 1.9 ppt (1900 mg/L⁻¹) NaCl in bacteria, meaning that the regulations in place are possibly suitable for the protection of the microbial communities in the hypolimnion and sediment lake layers. Full article

The concepts of green infrastructures, nature-based solutions and ecosystem services are today considered an integral part of the broader theme of the urban bioregion, with an intrinsic character of complexity. It is certainly difficult to structure bioregional processes in a balanced and sustainable way, able to keep local energy production and consumption cycles closed. It is a complex issue of knowledge bases, and problems are increased by the participatory dimension of environmental planning. In fact, when rational planning models have failed in the face of prominent individual needs and environmental complexity, a path has emerged towards the inclusion of multiple citizens’ and stakeholders’ knowledge. The cognitive structure of the plans has thus changed from systems of exclusively expert, formal knowledge to systems of diffused, multi-agent knowledge. This has involved richness but also significant problems in understanding and managing knowledge bases. In this complexity, there are some common peculiarities when it comes to socio-environmental systems. A common feature of the reference domains of ecosystem services, nature-based solutions and green infrastructures is the water resource. A management model of hydrological data, which are structurally relevant and cross-sectoral in environmental planning actions, could represent a flagship initiative. The used approach could be conveyed to more complex and extensive areas of the environmental domain in a perspective of sustainable planning. The present paper is part of a research work oriented toward handling complex environmental subjects, such as green infrastructures, nature-based solutions or ecosystem services, with a knowledge modelling approach. This approach is based on semantic extensions, elaborated form the concept of semantic web, to allow shared interpretations of knowledge coming from different languages and scientific domains. It is also based on using applied ontologies, elaborated from the concept of ontology-based classification, to support a structured organization of knowledge contents. The main research objective is therefore to investigate about a knowledge management system with semantic extensions, populated with hydrological knowledge contents, as well as to propose a preliminary functional architecture. A simple ontology of data is extracted, aiming at clarifying and improving inter-domain communication, so as to enhance a common semantic understanding in a complex environmental system. Full article

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates the biological and toxicological effects of structurally diverse chemicals, including halogenated aromatic hydrocarbons. In this work, we investigate the effects of the binding of the AhR prototypical ligand, TCDD, on the stability of the AhR:ARNT complex, as well as the mechanisms by which ligand-induced perturbations propagate to the DNA recognition site responsible for gene transcription. To this aim, a reliable structural model of the overall quaternary structure of the AhR:ARNT:DRE complex is proposed, based on homology modelling. The model shows very good agreement with a previous one and is supported by experimental evidence. Moreover, molecular dynamics simulations are performed to compare the dynamic behaviour of the AhR:ARNT heterodimer in the presence or absence of the TCDD. Analysis of the simulations, performed by an unsupervised machine learning method, shows that TCDD binding to the AhR PASB domain influences the stability of several inter-domain interactions, in particular at the PASA-PASB interface. The inter-domain communication network suggests a mechanism by which TCDD binding allosterically stabilizes the interactions at the DNA recognition site. These findings may have implications for the comprehension of the different toxic outcomes of AhR ligands and drug design. Full article

As a promising paradigm, the Industrial Internet of Things (IIoT) provides a wide range of intelligent services through the interconnection and interaction of heterogeneous networks. The quality of these services depends on how the bandwidth is shared among different flows. Hence, it is critical to design a flexible flow control strategy in multi-region management scenarios. In this paper, we establish a flow optimization model based on the IIoT networks managed by multiple Software-Defined Networking (SDN) controllers. Specifically, it jointly optimizes the real-time delivery, route selection, and constrained resource allocation to maximize the total utilities of domains. Since the topology and resources within each domain are kept secret, the problem model belongs to a multi-block problem with coupling constraints, which is difficult to be solved directly. To this end, we first decompose the problem into several intra-domain subproblems, which can be solved in parallel. By considering the inter-domain communication problem, we then introduce the slack variables to implement the interaction among domains. Finally, we design a distributed Proximal Symmetric Alternating Direction Method of Multipliers (Prox-SADMM) algorithm to solve the above joint optimization problem. Through numerical simulations, we investigate the impact of data timeliness, multi-path routing, and resource constraints on the rate utility. The performance analysis confirms that the Prox-SADMM algorithm can be well applied to large-scale networks and provides guidance to set appropriate parameter values according to the realistic requirements of IIoT networks. Full article

With the development of 5G and the Internet of things (IoT), the multi-domain access of massive devices brings serious data security and privacy issues. At the same time, most access systems lack the ability to identify network attacks and cannot adopt dynamic and timely defenses against various security threats. To this end, we propose a blockchain-based access control and behavior regulation system for IoT. Relying on the attribute-based access control model, this system deploys smart contracts on the blockchain to achieve distributed and fine-grained access control and ensures that the identity and authority of access users can be trusted. At the same time, an inter-domain communication mechanism is designed based on the locator/identifier separation protocol and ensures the traffic of access users are authorized. A feedback module that combines traffic detection and credit evaluation is proposed, ensuring real-time detection and fast, proactive responses against malicious behavior. Ultimately, all modules are linked together through workflows to form an integrated security model. Experiments and analysis show that the system can effectively provide comprehensive security protection in IoT scenarios. Full article

Plants and their associated soil microorganisms interact with each other and form complex relationships. The effects of slash-and-burn agriculture and logging on aboveground plants and belowground microorganisms have been extensively studied, but research on plant–microbial interkingdom ecological networks is lacking. In this study, using old growth forest as a control, we used metagenomic data (ITS and 16S rRNA gene amplified sequences) and plant data to obtain interdomain species association patterns for three different soil disturbance types (slash-and-burn, clear cutting and selective cutting) in a tropical rainforest based on interdomain ecological network (IDEN) analysis. Results showed that the soil bacterial–fungal and plant–microbe ecological networks had different topological properties among the three forest disturbance types compared to old growth forest. More nodes, links, higher modularity and negative proportion were found in the selective cutting stand, indicating higher stability with increasing antagonistic relationships and niche differentiation. However, the area of slash-and-burn forest yield opposite results. Network module analysis indicated that different keystone species were found in the four forest types, suggesting alternative stable states among them. Different plant species had more preferential associations with specific fungal taxa than bacterial taxa at the genus level and plant–microbe associations lagged behind bacterial–fungal associations. Overall, compared with old growth forests, the bacterial–fungal and plant–microbe ecological networks in the slash-and-burn and clear cutting stands were simpler, while the network in the selective cutting stand was more complex. Understanding the relationships between aboveground plants and belowground microorganisms under differing disturbance patterns in natural ecosystems will help in better understanding the surrounding ecosystem functions of ecological networks. Full article

Environmental problems associated with marine pollution and climate warming create favorable conditions for the penetration and survival of pathogenic bacteria in marine ecosystems. These microorganisms have interspecific competitive interactions with marine bacteria. Co-culture, as an important research strategy that mimics the natural environment of bacteria, can activate silent genes or clusters through interspecies interactions. The authors used modern biotechnology of co-cultivation to dynamically study intercellular interactions between different taxa of bacteria—pathogenic enterobacteria Yersinia pseudotuberculosis and Listeria monocytogenes and saprotrophic marine bacteria Bacillus sp. and Pseudomonas japonica isolated in summer from the coastal waters of the recreational areas of the Sea of Japan. The results of the experiments showed that during the formation of polycultural biofilms, horizontal transfer of genes encoding some pathogenicity factors from Y. pseudotuberculosis and L. monocytogenes to marine saprotrophic bacteria with different secretion systems is possible. It was previously thought that this was largely prevented by the type VI secretion system (T6SS) found in marine saprotrophic bacteria. The authors showed for the first time the ability of marine bacteria Bacillus sp. and P. japonica to biofilm formation with pathogenic enterobacteria Y. pseudotuberculosis and L. monocytogenes, saprophytic bacteria with type III secretion system (T3SS). For the first time, a marine saprotrophic strain of Bacillus sp. Revealed manifestations of hyaluronidase, proteolytic and hemolytic activity after cultivation in a polycultural biofilm with listeria. Saprotrophic marine bacteria that have acquired virulence factors from pathogenic enterobacteria, including antibiotic resistance genes, could potentially play a role in altering the biological properties of other members of the marine microbial community. In addition, given the possible interdomain nature of intercellular gene translocation, acquired virulence factors can be transferred to marine unicellular and multicellular eukaryotes. The results obtained contribute to the paradigm of the epidemiological significance and potential danger of anthropogenic pollution of marine ecosystems, which creates serious problems for public health and the development of marine culture as an important area of economic activity in coastal regions. Full article

The Major Facilitator Superfamily (MFS) drug:H⁺ antiporter CaMdr1, from Candida albicans, is responsible for the efflux of structurally diverse antifungals. MFS members share a common fold of 12–14 transmembrane helices (TMHs) forming two N- and C-domains. Each domain is arranged in a pseudo-symmetric fold of two tandems of 3-TMHs that alternatively expose the drug-binding site towards the inside or the outside of the yeast to promote drug binding and release. MFS proteins show great diversity in primary structure and few conserved signature motifs, each thought to have a common function in the superfamily, although not yet clearly established. Here, we provide new information on these motifs by having screened a library of 64 drug transport-deficient mutants and their corresponding suppressors spontaneously addressing the deficiency. We found that five strains recovered the drug-resistance capacity by expressing CaMdr1 with a secondary mutation. The pairs of debilitating/rescuing residues are distributed either in the same TMH (T127A_TMH1- > G140D_TMH1) or 3-TMHs repeat (F216A_TMH4- > G260A_TMH5), at the hinge of 3-TMHs repeats tandems (R184A_TMH3- > D235H_TMH4, L480A_TMH10- > A435T_TMH9), and finally between the N- and C-domains (G230A_TMH4- > P528H_TMH12). Remarkably, most of these mutants belong to the different signature motifs, highlighting a mechanistic role and interplay thought to be conserved among MFS proteins. Results also point to the specific role of TMH11 in the interplay between the N- and C-domains in the inward- to outward-open conformational transition. Full article