Search Results (279)

Pseudomonas aeruginosa is a notable opportunistic pathogen in the ESKAPE group due to its multidrug resistance (MDR) and its ability to cause severe healthcare-associated infections. Horizontal gene transfer (HGT) facilitates the dissemination of antibiotic resistance genes (ARGs) through mobile genetic elements (MGEs). A comprehensive genomic analysis of ARGs associated with these elements is essential to understand multidrug resistance in P. aeruginosa. Here, we analyzed 10,412 publicly available P. aeruginosa genome assemblies defined by the Genome Taxonomy Database (GTDB, release 226) species cluster, which provides standardized prokaryotic genome taxonomy. We identified plasmids, prophages, integrative and conjugative elements (ICEs), and integrative and mobilizable elements (IMEs) carrying ARGs. A group of highly prevalent ARG families was identified in P. aeruginosa, comprising mexD, fosA, catB7, blaPAO, and aph(3′)-IIb, each of which was detected in over 96% of the genome assemblies. In contrast, 313 ARG families were found in fewer than 20% of the genomes. Many ARGs were located on plasmids, with certain pairs co-occurring frequently, such as aph(3″)-Ib and aph(6)-Id, CmlA9 and aadA6, or aac(6′)-Ib3 and aph(3′)-XV, which were associated with specific plasmids. Some of these plasmids closely resembled plasmids from E. coli and K. pneumoniae. Moreover, other MGEs displayed distinct ARG cargo enrichment: mexD on IMEs, aph(3′)-IIb on prophages, and sul1, fosA, and catB7 on ICEs. Our study provides a high-resolution map of the P. aeruginosa MGE resistome and highlights the potential roles of MGEs in disseminating different resistance genes. Our results emphasize the significance of ICE- and plasmid-associated ARG dissemination, particularly sul1, which may be linked to class 1 integrons. They also suggest that interspecies plasmid exchange may contribute to the evolution of MDR in P. aeruginosa. Full article

Smart-city advanced metering infrastructure enables utility-scale remote analytics, but some forms of under-registration closely resemble lawful changes in demand and are hard to model as anomalies. We study a narrow, physically motivated event family at the single-meter level, namely multiplicative under-registration with unknown onset (a shunt-like attack), in which recorded active energy is approximately scaled by a factor $\alpha <1$ after a change-point while the daily-profile structure and spectral shape remain invariant. We formalize the problem and develop a physics-guided detector family based on weighted daily-profile regression (GLS) and its robust variant (RGLS), with quality-control filters, spectral-consistency checks, and an optional reactive-channel gate, designed to stay selective under confounders such as rooftop photovoltaics, electric-vehicle charging, and heat-pump onsets. On a device-disjoint Low Carbon London benchmark (487 households) the preferred GLS detector attains precision $0.915$, recall $0.978$, and $F_1=0.945$ at $\alpha =0.10$ while keeping the non-theft suspected rate near $1\%$; a cross-dataset check on Open Power System Data with real EV/PV/heat-pump overlays yields zero false alarms on all 72 cases, and Mendeley and WPuQ benchmarks add a second large family and a reactive-channel test. We compare against external baselines (classical change-point detection, Isolation Forest, autoencoder, LSTM, gradient boosting, and a supervised statistical pipeline) on the same protocol: generic anomaly detectors fail on this shape-preserving attack, and supervised models match the detector only in-distribution while, unlike it, failing to transfer to real lawful confounders. All metrics carry bootstrap confidence intervals, and a full reproducibility bundle accompanies the submission. Full article

Based on their domain organisation, four proteins from the protist Dictyostelium discoideum have been assigned to the IQGAP family of scaffold proteins. Although these proteins are shorter than animal IQGAPs, their involvement in the regulation of the actin cytoskeleton in cell motility, macroendocytosis, cytokinesis, and adhesion appears to be broadly conserved between these evolutionarily distant organisms. In this article, we show that the putative three-dimensional structure of Dictyostelium IQGAP-related proteins, as predicted by AlphaFold 3, closely corresponds to the C-terminal half of human IQGAP1, thus supporting their common origin. IqgD is the largest IQGAP-related protein in Dictyostelium, with an overall domain organisation similar to human IQGAPs. IqgD is localised in the cell cortex, interacts with F-actin and Rac1 GTPases, and primarily supports cell adhesion to the underlying surface and cell growth on bacterial lawns. DGAP1 and GAPA are truncated proteins that have retained a 700-residue-long C-terminal region of homology compared to their animal relatives. They play important, yet opposite, roles in regulating contractile cortical assemblies comprising F-actin, myosin II, and the actin-bundling proteins cortexillins, which are especially important for cytokinesis and epithelial morphogenesis. Finally, IqgC, although structurally resembling other IQGAPs, turns out to be more closely related to GAP1 proteins from fungi. This multifaceted protein carries RasGAP activity, interacts with several other small GTPases, and positively regulates macroendocytosis and cell–substratum adhesion. Full article

Although long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs) are typically passed down to descendants as part of the genome, the Bov-B LINE was likely horizontally transferred from a snake to the ancestor of ruminants. Plant RTE-clade LINEs and their associated SINEs possess a genomic insertion signature different from that of mammalian L1 LINEs. However, the reason for the increased frequency of horizontal transfer in RTE-clade LINEs such as Bov-B relative to that in L1-clade LINEs has not yet been clarified. In this study, we identified family members of the reptilian Bov-B LINE and associated Sauria SINE across various squamate species to determine the amplification timing of the LINE. The findings revealed that the LINE may be over 180 million years old. Moreover, profiling of target site duplications showed that a characteristic genomic insertion signature of the LINE and SINE closely resembled the signature of the plant RTE-clade LINEs. We conducted phylogenetic analyses of RTE-clade LINEs with characteristic genomic insertion signatures and estimated their divergence times. The findings suggest an ancient origin (over 411 MYA) of the retrotranspositional mechanism underlying this signature; however, a complex evolutionary trajectory of LINEs across species warrants further investigation. Full article

Chondroitin sulfate (CS) chains are major components of the extra- and pericellular matrix in the central nervous system (CNS), and their sulfation patterns influence CNS development and function. Highly sulfated CS preparations, including CS-D- and CS-E-enriched forms, have been shown to facilitate neurite outgrowth in cultured mouse hippocampal neurons. Notably, neurons cultured on CS-D- or CS-E-enriched substrates exhibited the following distinct morphological characteristics: CS-D promoted the extension of multiple short neurites, whereas CS-E induced the formation of a single elongated neurite with a polarization-like morphology. These features are consistent with early stages of neuronal polarization. However, the specific roles of these highly sulfated CS forms in polarization-like morphology remain unclear. In this study, we demonstrate that polarization-like morphological transitions in hippocampal neurons can be modulated on mixed CS-D/CS-E substrates by varying their ratios. Compared with CS-D-enriched substrates, CS-E-enriched substrates more effectively promoted polarization-like neuronal morphology, accompanied by enhanced activation of Src-family kinases. Furthermore, forced activation of Fyn kinase induced morphological changes resembling polarization-like features in a neuroblastoma cell line, even in the absence of CS-D/CS-E mixed substrates. In conclusion, highly sulfated CS subtypes may function as extracellular cues that regulate neuronal morphology via Src-family signaling, with likely involvement of Fyn. Full article

Background: The STAG1 gene has been related to a poorly known form of intellectual disability, known as Intellectual Developmental Disorder, Autosomal Dominant 47 (MRD47). Functionally, MRD47 is part of the Cohesinopathies, a small family of rare genetic disorders caused by defective cohesin complex, whose activity is essential for sister chromatid cohesion and therefore for chromatin organization. Chromatin state modulation is an entangled process finely modulated by a large number of actors that, if altered, give rise to the so-called Chromatinopathies. The clinical and biological overlap among these families of conditions on one hand poses significant challenges during diagnostic definition, and, on the other, may help delineate more accurate management guidelines. Methods: Starting from the report of a novel pathogenic variant in the STAG1 gene, we performed a retrospective clinical and molecular review of all previously reported patients affected by this rare disorder. Once clinical and photographic data of all published patients were collected, we used Face2Gene deep learning technology to analyze STAG1 facial phenotype, comparing it to both Chromatinopathy and Cohesinopathy profiles. Results: Our clinical and molecular re-evaluation of reported cases confirms MRD47 as a mainly neurodevelopmental disorder. Through artificial intelligence technology, we were able to first create the gestaltic profile of MRD47. Face2Gene analyses of this composite phenotype, although limited by the tool’s analysis modalities, demonstrates the strong overlap of STAG1 disorder with Chromatinopathies. Conclusions: The present literature review, together with gestaltic analyses of the STAG1-related phenotype, underscores the strong resemblance of MRD47 to epigenetic machinery disorders. The present case brings to light once more the biological and phenotypical entanglement of Cohesinopathies and Chromatinopathies, hinting at STAG1 as the joining chain. Full article

DNA damage requires repair via the endonuclease IV-mediated base excision repair (BER) pathway, which corrects apurinic/apyrimidinic (AP) sites. Chlamydophila pneumoniae AP endonuclease IV (CpEndoIV), the sole AP endonuclease in this pathogen, is crucial for genomic integrity. As humans lack a homologous protein, it represents a potential therapeutic target. In this study, we report the first crystal structure of CpEndoIV at 1.97 Å resolution. The structure reveals two Zn²⁺, one Mg²⁺, and a malonate molecule bound in the active site, marking the first observation of Mg²⁺ coordination in the EndoIV family. Compared to the three-Zn²⁺ model with a narrow, deep pocket for precise AP-site cleavage, the Zn²⁺/Mg²⁺-bound state has a wider, shallower pocket that might promote diverse catalytic activities. Combined with enzymatic assays, we suggest that the mixed Zn²⁺/Mg²⁺ model is better adapted for CpEndoIV to operate under host oxidative stress. Malonate binds to the metal ions, occupying the positions normally coordinated by water molecules. This binding mode may mimic the coordination of the substrate to the metal ions, and the protein conformation resembles that of the enzyme upon substrate binding at the active site. This study provides a structural basis for the functional characterization of CpEndoIV and offers a reference for the development of targeted inhibitors against diseases caused by Chlamydophila pneumoniae. Full article

Nitrogen metabolism is fundamental to all organisms, with ammonium transporters (Amt) playing a pivotal role in transmembrane ammonium transport. Brachiopods, as “living fossils”, offer unique insights into the evolutionary adaptation of marine invertebrates. This study systematically identified and characterized the Amt gene family in the brachiopod Lingula anatina. Five canonical Amt genes were identified, with nonrandom chromosomal distribution and evidence of lineage-specific duplication events. Phylogenetic analysis revealed that these Amt proteins cluster into three well-supported clades, showing closer affinity to Caenorhabditis elegans, reflecting conserved ancestral features predating protostome radiation. Structural predictions showed that LanAmtA and LanAmtB retain the canonical 11-transmembrane helix (TMH) topology with an extracellular N-terminus, while LanAmtC features a unique 12-TMH architecture with an intracellular N-terminus, resembling certain vertebrate Amt-related proteins. Critical functional residues involved in ammonium selectivity and transport were preserved across all paralogs. Expression profiling revealed non-redundant spatiotemporal patterns: LanAmtA1 and LanAmtB2 dominate early embryogenesis, with LanAmtB2 becoming the major isoform in late developmental stages; LanAmtC exhibits constitutive high expression across adult tissues. Collectively, our findings demonstrate that the L. anatina Amt family expanded via local duplications, evolving structural stability, regulatory diversity, and functional specificity. This study provides a comprehensive molecular framework for understanding the evolutionary adaptation of nitrogen-handling mechanisms in basal lophotrochozoans and sheds light on how intertidal organisms cope with dynamic environmental conditions. Full article

Background: The Calcineurin B-like (CBL) and CBL-interacting protein kinase (CIPK) system constitute critical signaling modules mediating plant responses to abiotic stress. Although these families have been studied across various species, their evolutionary dynamics across grasses and the functional plasticity of specific isoforms remain elusive. Methods: A genome-wide analysis of CBL and CIPK families was conducted across five major Poaceae species (Oryza sativa, Triticum aestivum, Zea mays, Sorghum bicolor, and Saccharum spontaneum). Phylogenetic and synteny analyses were analyzed to family expansion and evolution. Cis-regulatory elements analysis in gene promoter regions were examined to predict potential stress-responsive features. Expression profiles of OsCBL and OsCIPK gene families were examined by qRT-PCR under conditions involving PEG-induced osmotic stress, pathogen strain P6 inoculation, and exogenous application of the phytohormones abscisic acid (ABA) and methyl jasmonate (MeJA). Protein–protein interactions between selected CBL (OsCBL4) and CIPK pairs were assessed via Yeast Two-Hybrid (Y2H) and Luciferase Complementation Imaging assays (LCI). Results: Phylogenetic and synteny analyses indicated that segmental duplications have contributed substantially to the expansion of these gene families. Promoter analysis revealed that the majority of CBL and CIPK family members, exemplified by OsCBL4, traditionally characterized as a salt sensor, possesses a cis-element architecture (rich in ABREs and MBS) heavily biased towards dehydration responsiveness. Expression profiling showed that OsCBL4 is significantly hyper-induced by direct osmotic stress (PEG) but exhibits almost no response to exogenous ABA. A subset of kinases genes (e.g., OsCIPK2, 9, 18) displayed PEG-induced expression patterns resembling those of OsCBL4, whereas OsCIPK30 remained transcriptionally unresponsive under the same conditions. Protein interaction assays demonstrated that OsCBL4 physically interacts exclusively with PEG-responsive transcriptionally activated kinases such as OsCIPK9, but failed to interact with the non-responsive OsCIPK30. Conclusions: Our study provides a genomic characterization of CBL and CIPK families across five major Poaceae species. The combined expression and interaction data reveal that OsCBL4-assembles with specific CIPKs into signaling modules during osmotic stress responses in rice, pointing to roles that go beyond salt stress responses. The findings establish a foundation for further functional dissection of CBL-CIPK pathway diversification in abiotic stress adaptation. Full article

Desmodium styracifolium (Osb.) Merr., a member of the Leguminosae family, is an important medicinal plant widely used in traditional Chinese medicine. In September 2024, D. styracifolium plants exhibiting symptoms of little leaf and stunted growth were observed in a field of Zhanjiang, Guangdong province, China. Since the symptoms resembled those associated with phytoplasma infections, total DNA was extracted from the leaves of four symptomatic plants and one healthy plant for molecular identification. Universal primer pairs (P1/P7, R16mF2/mR1) for phytoplasma detection were used to amplify the 16S rDNA fragments (~1.8 kb and ~1.4 kb), while a specific primer pair secY-F/secY-R was employed to amplify a ~1.4 kb segment of the secY gene. Target fragments were successfully amplified from all symptomatic samples but not from the healthy control. These amplicons were cloned and sequenced. The obtained 16S rDNA sequence of D. styracifolium little leaf phytoplasma (DsLFP-GDZJ) showed the highest identity (99.67–100%) with strains of ‘Ca. Phytoplasma australasiaticum’ (subgroup 16SrII-A and 16SrII-D). Phylogenetic analysis also indicated that DsLFP-GDZJ formed a small evolutionary branch with strains of ‘Ca. Phytoplasma australasiaticum’ (subgroup 16SrII-A and 16SrII-D). Virtual RFLP (restriction fragment length polymorphism) analysis of the 16S rDNA sequence demonstrated DsLFP-GDZJ belongs to the 16SrII-A subgroup (GenBank accession number L33765). The secY gene sequence of DsLFP-GDZJ also showed the highest similarity and the closest relationship with those of the 16SrII-A subgroup phytoplasma strains. These results showed that DsLFP-GDZJ is a strain of ‘Ca. Phytoplasma australasiaticum’ (16SrII-A subgroup). To our knowledge, this is the first report of ‘Ca. Phytoplasma australasiaticum’—related phytoplasma associated with D. styracifolium little leaf disease in China, thereby establishing D. styracifolium (Osb.) Merr. as a new host plant of phytoplasma. Full article

Scoliidae are fossorial aculeate wasps (Hymenoptera: Apocrita) whose larvae develop as parasitoids of beetle grubs, mainly from the family Scarabaeidae. Despite their distinctive appearance and economic importance, the taxonomy and biology of Scoliidae are less well understood compared to other Hymenoptera. Recently, a new species of Scoliidae, Dielis tejensis Szafr., was described based on about a dozen male specimens from Texas (Nearctic realm). This article reports on mtDNA-verified discovery of the female D. tejensis. As in the case of other members of the tribe Campsomerini, D. tejensis exhibits strong sexual dimorphism in body structure and color pattern. Females of D. tejensis most closely resemble Dielis plumipes (Drury) and were previously confused with D. plumipes fossulana (Fabr.), with which D. tejensis is partially sympatric. D. tejensis has more than one generation per year, characterized by a male-biased sex ratio, perhaps resulting from the female immature stages entering a state of aestivation. The multi-generational developmental cycle of D. tejensis correlates with the existence of a partial seasonal polyphenism in this species. The data presented also shows a similarity in the distribution ranges of D. tejensis and one of its main nectaring plants, Hymenopappus artemisiifolius DC (Asteraceae), that may suggest similarity in the environmental requirements of both organisms or specialized trophic relationship between the still-unknown beetle host of the wasp larvae and H. artemisiifolius or another plant with a similar range. D. tejensis has been included in the accordingly modified key to the Nearctic species of Dielis Sauss. & Sichel, which is also presented here. Full article

Fusion-associated small transmembrane (FAST) proteins are viral nonstructural proteins known to be encoded by specific members of the Spinareoviridae, specifically within the Aquareovirus and Orthoreovirus genera. These proteins specialize in mediating cell–cell fusion, leading to syncytia. Unlike enveloped viruses, naked viruses do not rely on fusion proteins for cell entry; however, such proteins may facilitate viral spread between cells. Although not essential for virus replication, FAST proteins have been shown to enhance viral replication, particularly during the early stages of infection. More recently, proteins with characteristics resembling FAST proteins have been identified in a broader range of viruses, including several rotavirus species within the family Sedoreoviridae, and, unexpectedly, in some enveloped viruses within the Coronaviridae family. Here, we present protein sequence analyses suggesting that viruses of the recently established virus family Pistolviridae (order Ghabrivirales) also encode proteins with similarity to FAST proteins. Pistolviruses are small double-stranded RNA viruses that infect piscine species, and were initially referred to as “toti-like” viruses due to genomic similarities with members of the former Totiviridae, which infect single-celled organisms. The putative FAST proteins of the pistolviruses may be expressed either from small, distinct open reading frames or suggested to be produced as cleavage products derived from polyproteins. Full article

With the rapid advancement of artificial intelligence (AI) technology, training deep neural networks has become a core computational task that consumes significant energy in data centers. Researchers often employ various methods to estimate the energy usage of data center clusters or servers to enhance energy management and conservation efforts. However, accurately predicting the energy consumption and carbon footprint of a specific AI task throughout its entire lifecycle before execution remains challenging. In this paper, we explore the energy consumption characteristics of AI model training tasks and propose a simple yet effective method for predicting neural network training energy consumption. This approach leverages training task metadata and applies genetic programming-based symbolic regression to forecast energy consumption prior to executing training tasks, distinguishing it from time series forecasting of data center energy consumption. We have developed an AI training energy consumption environment using the A800 GPU and models from the ResNet{18, 34, 50, 101}, VGG16, MobileNet, ViT, and BERT families to collect data for experimentation and analysis. The experimental analysis of energy consumption reveals that the consumption curve exhibits waveform characteristics resembling square waves, with distinct peaks and valleys. The prediction experiments demonstrate that the proposed method performs well, achieving mean relative errors (MRE) of 2.67% for valley energy, 8.42% for valley duration, 5.16% for peak power, and 3.64% for peak duration. Our findings indicate that, within a specific data center, the energy consumption of AI training tasks follows a predictable pattern. Furthermore, our proposed method enables accurate prediction and calculation of power load before model training begins, without requiring extensive historical energy consumption data. This capability facilitates optimized energy-saving scheduling in data centers in advance, thereby advancing the vision of green AI. Full article

Numerous attempts to define art have been made from antiquity to the present, yet historical overviews often adopt a Eurocentric (and American-centric) perspective focused mainly on culturally dependent aesthetic approaches. As a universal social and cultural phenomenon, art resists center-periphery models. The cognitive turn reshaped art theory by reconsidering art as a cognitive dimension of humanity. Art has no limits on who can create or enjoy it. The ability to use and understand metaphor, for instance, demonstrates everyday human artistic cognition. The analysis relies on both field research (case studies) and academic literature; it argues for a revised theoretical frame for defining art and organizes it into a dynamic model of three main vectors: (1) art as communication (including art as agency); (2) art as creation; and (3) art as experience (involving both audience and artist). The model can incorporate the study of emotions into the third criterion while remaining open to both materialist and non-materialist approaches. Rather than offering a new definition, the study integrates the perspective of cognitive anthropology, cognitive semantics, and the anthropology of art in order to broaden understanding. Instead of searching for special aesthetic or economic values, these three dimensions of art appear more universal. A pragmatic analysis of how art “works” in individuals and groups provides a useful model for cognitive sciences. Instead of binary codes, it is a vectorial model, a 3D space for expressing family resemblance, since there is no common denominator (prototype) for all kinds of art. Full article

The M16 protease family comprises metalloendopeptidases, characterized by a unique molecular architecture. The active enzyme molecule is composed of two halves, which together form a structure resembling a clam shell. Although the active site residues are typically located in only one half, both parts are essential for proper enzyme function. The M16 family includes many proteins that are crucial for the physiology of the organism and, therefore, are the subject of intensive research. The flagship examples are insulin-degrading enzyme (IDE), mitochondrial processing peptidases (MPPs), and mitochondrial and chloroplast presequence peptidases (PrePs). The substrates of these enzymes include many biologically important peptides, such as insulin and amyloid β. Therefore, M16 peptidases are considered attractive therapeutic targets, and understanding their structure and mechanism of action is essential for the development of specific and selective modulatory compounds. Full article