EvoAI enables extreme compression and reconstruction of the protein sequence space.

Designing proteins with improved functions requires a deep understanding of how sequence and function are related, a vast space that is hard to explore. The ability to efficiently compress this space by identifying functionally important features is extremely valuable. Here, we first establish a method called EvoScan to comprehensively segment and scan the high-fitness sequence space to obtain anchor points that capture its essential features, especially in high dimensions. Our approach is compatible with any biomolecular function that can be coupled to a transcriptional output. We then develop deep learning and large language models to accurately reconstruct the space from these anchors, allowing computational prediction of novel, highly fit sequences without prior homology-derived or structural information. We apply this hybrid experimental-computational method, which we call EvoAI, to a repressor protein and find that only 82 anchors are sufficient to compress the high-fitness sequence space with a compression ratio of 1048. The extreme compressibility of the space informs both applied biomolecular design and understanding of natural evolution.

Esketamine accelerates emergence from isoflurane general anaesthesia by activating the paraventricular thalamus glutamatergic neurones in mice.

BACKGROUND: Delayed emergence from general anaesthesia poses a significant perioperative safety hazard. Subanaesthetic doses of ketamine not only deepen anaesthesia but also accelerate recovery from isoflurane anaesthesia; however, the mechanisms underlying this phenomenon remain elusive. Esketamine exhibits a more potent receptor affinity and fewer adverse effects than ketamine and exhibits shorter recovery times after brief periods of anaesthesia. As the paraventricular thalamus (PVT) plays a pivotal role in regulating wakefulness, we studied its role in the emergence process during combined esketamine and isoflurane anaesthesia. METHODS: The righting reflex and cortical electroencephalography were used as measures of consciousness in mice during isoflurane anaesthesia with coadministration of esketamine. The expression of c-Fos was used to determine neuronal activity changes in PVT neurones after esketamine administration. The effect of esketamine combined with isoflurane anaesthesia on PVT glutamatergic (PVTGlu) neuronal activity was monitored by fibre photometry, and chemogenetic technology was used to manipulate PVTGlu neuronal activity. RESULTS: A low dose of esketamine (5 mg kg-1) accelerated emergence from isoflurane general anaesthesia (474 [30] s vs 544 [39] s, P=0.001). Esketamine (5 mg kg-1) increased PVT c-Fos expression (508 [198] vs 258 [87], P=0.009) and enhanced the population activity of PVTGlu neurones (0.03 [1.7]% vs 6.9 [3.4]%, P=0.002) during isoflurane anaesthesia (1.9 [5.7]% vs -5.1 [5.3]%, P=0.016) and emergence (6.1 [6.2]% vs -1.1 [5.0]%, P=0.022). Chemogenetic suppression of PVTGlu neurones abolished the arousal-promoting effects of esketamine (459 [33] s vs 596 [33] s, P<0.001). CONCLUSIONS: Our results suggest that esketamine promotes recovery from isoflurane anaesthesia by activating PVTGlu neurones. This mechanism could explain the rapid arousability exhibited upon treatment with a low dose of esketamine.

Probiotic Saccharomyces boulardii attenuates cardiopulmonary bypass-induced acute lung injury by inhibiting ferroptosis.

OBJECTIVE: Acute lung injury (ALI) is one of the most common and fatal complications of cardiopulmonary bypass (CPB). Probiotics treatment has been shown to reduce lung injury in different experimental models. However, the effect of probiotics on CPB-induced ALI is still poorly understood. This study aimed to investigate whether probiotic Saccharomyces boulardii CNCM I-745 treatment protects against lung injury in a rat model of CPB. METHODS: Rats were orally gavaged with Saccharomyces boulardii CNCM I-745 once a day for 5 days before being subjected to CPB. Rats were euthanized post-CPB, and samples of lung tissue were processed for later investigation. The levels of inflammatory cytokines were measured by ELISA. The expression levels of ferroptosis markers in lungs were assessed by western blot. The microbes in feces and proximal colon of rats were analyzed by using 16S rDNA amplicon sequencing method. The ratio and maturity of conventional dendritic cells (cDCs) were determined by flow-cytometry. RESULTS: Saccharomyces boulardii CNCM I-745 treatment improved lung function, attenuated pathologic lung changes and decelerated the exacerbation of inflammatory cytokine level after experimental CPB. Saccharomyces boulardii CNCM I-745 treatment also inhibited CPB-induced ferroptosis, as evidenced by the changes of main markers of ferroptosis, namely, the increase of Glutathione peroxidase 4 (GPX4) and the decrease of Acyl-CoA synthetase long chain family member 4 (ACSL4). In addition, after Saccharomyces boulardii CNCM I-745 treatment, the ratio and maturity of conventional dendritic cells (cDCs) in the guts of rats with CPB were significantly up-regulated. CONCLUSION: Our findings suggest that probiotic Saccharomyces boulardii CNCM I-745 reduces CPB-induced lung injury through suppression of the ferroptosis in lung and up-regulation of the ratio and maturity of cDCs in gut.

Understanding of remora's "hitchhiking" behaviour from a hydrodynamic point of view.

Symbiotic relationships have developed through natural evolution. For example, that of the remora fish attached to the body of a shark. From the remora's perspective, this could be associated to an increased hydrodynamic efficiency in swimming and this needs to be investigated. To understand the remora's swimming strategy in the attachment state, a systematic study has been conducted using the commercial Computational Fluid Dynamics (CFD) software, STAR-CCM + to analyse and compare the resistance characteristics of the remora in attached swimming conditions. Two fundamental questions are addressed: what is the effect of the developed boundary layer flow and the effect of the adverse pressure gradient on the remora's hydrodynamic characteristics? According to the results, the resistance of the remora can generally be halved when attached. Besides, the results have also demonstrated that the drag reduction rate increases with the developed boundary layer thickness and can be estimated using the boundary layer thickness ratio and velocity deficit. The paper demonstrates that the most frequent attachment locations are also the areas that provide the maximum drag reduction rate.

Transcriptome-Wide Gene Expression in a Murine Model of Ventilator-Induced Lung Injury.

BACKGROUND: Mechanical ventilation could lead to ventilator-induced lung injury (VILI), but its underlying pathogenesis remains largely unknown. In this study, we aimed to determine the genes which were highly correlated with VILI as well as their expressions and interactions by analyzing the differentially expressed genes (DEGs) between the VILI samples and controls. METHODS: GSE11434 was downloaded from the gene expression omnibus (GEO) database, and DEGs were identified with GEO2R. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using DAVID. Next, we used the STRING tool to construct protein-protein interaction (PPI) network of the DEGs. Then, the hub genes and related modules were identified with the Cytoscape plugins: cytoHubba and MCODE. qRT-PCR was further used to validate the results in the GSE11434 dataset. We also applied gene set enrichment analysis (GSEA) to discern the gene sets that had a significant difference between the VILI group and the control. Hub genes were also subjected to analyses by CyTargetLinker and NetworkAnalyst to predict associated miRNAs and transcription factors (TFs). Besides, we used CIBERSORT to detect the contributions of different types of immune cells in lung tissues of mice in the VILI group. By using DrugBank, small molecular compounds that could potentially interact with hub genes were identified. RESULTS: A total of 141 DEGs between the VILI group and the control were identified in GSE11434. Then, seven hub genes were identified and were validated by using qRT-PCR. Those seven hub genes were largely enriched in TLR and JAK-STAT signaling pathways. GSEA showed that VILI-associated genes were also enriched in NOD, antigen presentation, and chemokine pathways. We predicted the miRNAs and TFs associated with hub genes and constructed miRNA-TF-gene regulatory network. An analysis with CIBERSORT showed that the proportion of M0 macrophages and activated mast cells was higher in the VILI group than in the control. Small molecules, like nadroparin and siltuximab, could act as potential drugs for VILI. CONCLUSION: In sum, a number of hub genes associated with VILI were identified and could provide novel insights into the pathogenesis of VILI and potential targets for its treatment.