Shift Experiments Research Articles

Self-supervised Learning for Accelerometer-based Human Activity Recognition: A Survey

Self-supervised learning (SSL) has emerged as a promising alternative to purely supervised learning, since it can learn from labeled and unlabeled data using a pre-train-then-fine-tune strategy, achieving state-of-the-art performances across many research areas. The field of accelerometer-based human activity recognition (HAR) can benefit from SSL since unlabeled data can be collected cost-efficiently due to the ubiquitous nature of sensors embedded in smart devices, which is in contrast to labeled data, that require a costly annotation process. Motivated by the success of SSL and the lack of surveys on SSL for HAR, this survey comprehensively examines 52 SSL methods applied to HAR, and categorizes them into four SSL paradigms based on pre-training objectives. We discuss SSL strategies, evaluation protocols, and utilized datasets. We highlight limitations in current methodologies, including little large-scale pre-training, the absence of foundation models, as well as the scarcity of systematic domain shift experiments and domain knowledge utilization. Notably, the diversity in evaluation protocols across papers poses a considerable challenge when comparing methods. Future directions outlined in this survey include the development of an SSL framework for HAR to enable standardized benchmarking and large-scale pre-training, along with integrating domain knowledge to enhance model performance.

Large radial shift experiments in RHIC and their implications for EIC design

The Hadron Storage Ring (HSR) in the future Electron-Ion Collider (EIC) (EIC collaboration, 2020; Montag et al., 2022; Liu et al., 2022) must operate over a broad range of design circumferences. In 2018 preliminary beam studies on the circumference adjustment capabilities of the Relativistic Heavy Ion Collider (RHIC) (Accelerator Division, 2006) were performed by applying a small momentum offset to the circulating bunches without adjusting any bending magnets (Robert-Demolaize et al., 2019). The off-momentum linear optics were corrected back to on-momentum conditions. Applying a similarly small deviation to the dipole fields of a select set of bending magnets provides a large radial shift over much of the RHIC (or HSR) circumference while leaving the design trajectory unchanged in the insertion regions.This paper presents the design of the different lattice configurations foreseen as the most viable options for the required HSR circumference changes, and highlights the modifications necessary for regular operations and to allow for testing these new settings in RHIC. Experimental results from 2021 and 2022 are reviewed and compared to model predictions obtained from both MAD-X and Bmad (MAD, 2002; Bmad, 2006). The implications of these results for HSR design are discussed.

PePalA/B/C are required for virulence and patulin biosynthesis by regulating the PePacC-processing proteolytic activity in Penicillium expansum

Abstract Background The Pal/Rim signaling pathway is crucial for fungal responses to ambient pH conditions. It comprises the transcription factor PacC/Rim101 and six upstream Pal proteins. While the role of PacC has been extensively studied, there is limited information on the functions of the upstream Pal proteins. Results In the genome of Penicillium expansum, genes encoding the endosomal membrane complex (PalA/B/C) were identified. Among these, only the expression of PePalB, not PePalA or PePalC, is pH-dependent. Subcellular localization and functional analyses showed that PePalA/B/C are localized to the cytosol and peripheral punctate structures. Deletion of PePalA/B/C resulted in reduced growth and conidiation of P. expansum across various pH conditions. The virulence of the ΔPePalA/B/C mutant was significantly reduced in pear and apple fruits. Additionally, the mutants exhibited a loss of patulin production under both acidic and alkaline conditions and the down-regulation of genes in the patulin biosynthetic cluster. pH shift experiments further demonstrated that PePalA/B/C are essential for both the PePacC expression and the pH-dependent proteolytic activation of PePacC. Conclusions These findings highlight the significant roles of PePalA/B/C in regulating growth, conidiation, virulence, and patulin production in P. expansum, thereby enhancing our understanding of the regulatory mechanisms underlying the Pal/Rim signaling pathway.

Highly efficient hydrogenation of CO2 to heavy hydrocarbons via NaFeGa catalysts

Transforming CO2 into heavy hydrocarbons via thermal catalytic hydrogenation has garnered interest for its potential to address resource shortages and reduce atmospheric CO2. In this research, NaFeGa catalysts enriched with Ga additives were synthesized by the coprecipitation method. Various characterization techniques, including Mössbauer spectroscopy, were employed alongside reverse water-gas shift and Fischer-Tropsch synthesis experiments to elucidate the Fe-Ga interaction. This interaction effectively modulated the ratio of active sites Fe5C2 and enhanced CO species adsorption. The Ga additive's anti-hydrogenation effect limited intermediate hydrogenation, leading to increased carbon-hydrogen product yields. The catalyst underwent direct hydrogenation of CO2 under high throughput conditions (space velocity of 50,000 h−1), resulting in efficient CO2 conversion as well as remarkable heavy hydrocarbon selectivity. The catalyst demonstrated a remarkable heavy hydrocarbon space-time yield (STY) of 1460.2 g·kgcat−1·h−1, surpassing the threshold for commercial viability and offering a promising solution for large-scale production of liquid fuels from CO2.

Cross-Domain Adaptation Techniques for Robust Plant Disease Detection: A DANN-CORAL Hybrid Approach

Plant disease detection with deep learning models has shown promising results, but these models often struggle with generalizing across diverse agricultural environments due to domain shifts in imaging conditions. This paper presents a novel hybrid approach focusing on cross-domain adaptation techniques to address the challenge of domain shift. Our proposed method combines the Domain-Adversarial Neural Network (DANN) with Correlation Alignment (CORAL) to mitigate domain shifts between datasets. The DANN framework enforces domain-invariant feature learning through adversarial training. Using the PlantVillage Dataset, with controlled environment images, and the New Plant Village Dataset, with varied conditions, the model is first trained on PlantVillage and then adapted to New Plant Village using the CORAL loss to support the second-order statistics. In case of domain shift experiments with various datasets, DANN-CORAL achieved accuracies 91.39%, precision 93.36%, recall 88.9% and F1-scores 91.05% indicating the robustness and generalizability of our model is better than the other baseline models. This approach enhances model robustness and adaptability, providing insights into combining adversarial and statistical alignment for cross-domain adaptation in agricultural imaging.

Abstract 114: Inhibition Of Lecithin Cholesterol Acyl Transferase By A Novel Anti-apolipoprotein A1 Antibody Fragment

Apolipoprotein A1 (APOA1), the most abundant protein in high-density lipoproteins (HDL), is the primary activator of lecithin cholesterol acyl transferase (LCAT). LCAT’s cholesteryl esterification activity is key for maturing nascent HDL discs into the spherical forms commonly found in plasma. However, the molecular mechanism for APOA1 activation of LCAT is poorly understood. Using phage display selection against nanodiscs (lipid complexes stabilized by an APOA1 variant commonly used in transmembrane protein structural biology), we have identified, isolated, and expressed a novel Fab fragment (Fab16). Size exclusion chromatography elution shift experiments showed that Fab16 readily bound reconstituted HDL (rHDL) particles containing human purified plasma APOA1 with nearly quantitative binding at a 1:1 molar ratio of Fab16 to APOA1. Negative stain electron microscopy (NSEM), confirmed that 1-2 Fab16 bound to each rHDL particle in a specific pattern around the disc periphery. Additionally, Fab16 effectively bound both large and small spherical HDL particles isolated from human plasma. Chemical cross-linking / mass spectrometry experiments indicated that Fab16 binds an APOA1 epitope between residues 94 and 118 (i.e., within amphipathic helix 4). As our previous work has shown that APOA1 helix 4 is important for LCAT activation, we hypothesized that Fab16 would inhibit LCAT activity. Using a novel gas chromatography cholesterol esterification assay, we found that Fab16 applied at a 1.5:1 molar ratio to APOA1 inhibited LCAT cholesterol esterification activity by 56±7%. The symmetrical nature of both discoidal and spherical HDL particles has hampered the application of cryogenic electron microscopy (cryo EM) for understanding HDL structure. Fab16 may provide a valuable ‘landmark’ to assist in deriving a high-resolution structure of the complex. Work to optimize conditions for collecting high quality cryo EM datasets of discoidal and spherical HDL in the presence and absence of LCAT is ongoing. Deriving a high-resolution understanding of HDL structure and its interaction with remodeling factors such LCAT has been a long-standing problem but is crucial for deriving new strategies to manipulate HDL function for therapeutic benefit.

Prediction of cytochrome P450-mediated bioactivation using machine learning models and in vitro validation.

Cytochrome P450 (P450)-mediated bioactivation, which can lead to the hepatotoxicity through the formation of reactive metabolites (RMs), has been regarded as the major problem of drug failures. Herein, we purposed to establish machine learning models to predict the bioactivation of P450. On the basis of the literature-derived bioactivation dataset, models for Benzene ring, Nitrogen heterocycle and Sulfur heterocycle were developed with machine learning methods, i.e., Random Forest, Random Subspace, SVM and Naïve Bayes. The models were assessed by metrics like "Precision", "Recall", "F-Measure", "AUC" (Area Under the Curve), etc. Random Forest algorithms illustrated the best predictability, with nice AUC values of 0.949, 0.973 and 0.958 for the test sets of Benzene ring, Nitrogen heterocycle and Sulfur heterocycle models, respectively. 2D descriptors like topological indices, 2D autocorrelations and Burden eigenvalues, etc. contributed most to the models. Furthermore, the models were applied to predict the occurrence of bioactivation of an external verification set. Drugs like selpercatinib, glafenine, encorafenib, etc. were predicted to undergo bioactivation into toxic RMs. In vitro, IC50 shift experiment was performed to assess the potential of bioactivation to validate the prediction. Encorafenib and tirbanibulin were observed of bioactivation potential with shifts of 3-6 folds or so. Overall, this study provided a reliable and robust strategy to predict the P450-mediated bioactivation, which will be helpful to the assessment of adverse drug reactions (ADRs) in clinic and the design of new candidates with lower toxicities.

Differential acclimation kinetics of the two forms of type IV chromatic acclimaters occurring in marine Synechococcus cyanobacteria.

Synechococcus, the second most abundant marine phytoplanktonic organism, displays the widest variety of pigment content of all marine oxyphototrophs, explaining its ability to colonize all spectral niches occurring in the upper lit layer of oceans. Seven Synechococcus pigment types (PTs) have been described so far based on the phycobiliprotein composition and chromophorylation of their light-harvesting complexes, called phycobilisomes. The most elaborate and abundant PT (3d) in the open ocean consists of cells capable of type IV chromatic acclimation (CA4), i.e., to reversibly modify the ratio of the blue light-absorbing phycourobilin (PUB) to the green light-absorbing phycoerythrobilin (PEB) in phycobilisome rods to match the ambient light color. Two genetically distinct types of chromatic acclimaters, so-called PTs 3dA and 3dB, occur at similar global abundance in the ocean, but the precise physiological differences between these two types and the reasons for their complementary niche partitioning in the field remain obscure. Here, photoacclimation experiments in different mixes of blue and green light of representatives of these two PTs demonstrated that they differ by the ratio of blue-to-green light required to trigger the CA4 process. Furthermore, shift experiments between 100% blue and 100% green light, and vice-versa, revealed significant discrepancies between the acclimation pace of the two types of chromatic acclimaters. This study provides novel insights into the finely tuned adaptation mechanisms used by Synechococcus cells to colonize the whole underwater light field.

5-Aminolevulinic acid improves cold resistance through regulation of SlMYB4/SlMYB88-SlGSTU43 module to scavenge reactive oxygen species in tomato.

Cold stress severely affects the growth and quality of tomato. 5-Aminolevulinic acid (ALA) can effectively improve tomato's cold stress tolerance. In this study, a tomato glutathione S-transferase gene, SlGSTU43, was identified. Results showed that ALA strongly induced the expression of SlGSTU43 under cold stress. SlGSTU43-overexpressing lines showed increased resistance to cold stress through an enhanced ability to scavenge reactive oxygen species. On the contrary, slgstu43 mutant lines were sensitive to cold stress, and ALA did not improve their cold stress tolerance. Thus, SlGSTU43 is a key gene in the process of ALA improving tomato cold tolerance. Through yeast library screening, SlMYB4 and SlMYB88 were preliminarily identified as transcription factors that bind to the SlGSTU43 promoter. Electrophoretic mobility shift, yeast one-hybrid, dual luciferase, and chromatin immunoprecipitation assays experiments verified that SlMYB4 and SlMYB88 can bind to the SlGSTU43 promoter. Further experiments showed that SlMYB4 and SlMYB88 are involved in the process of ALA-improving tomato's cold stress tolerance and they positively regulate the expression of SlGSTU43. The findings provide new insights into the mechanism by which ALA improves cold stress tolerance. SlGSTU43, as a valuable gene, could be added to the cold-responsive gene repository. Subsequently, it could be used in genetic engineering to enhance the cold tolerance of tomato.

Identification of α-tubulin alpha-1B chain as a target of asiatic acid using chemical proteomics in HepG2 hepatoma cells.

Asiatic acid (AA) is a naturally occurring pentacyclic triterpene isolated from Centella asiatica and has various biological effects, most notably anticancer effects. While numerous investigations have demonstrated the possible mechanism underlying AA's anticancer action, the precise protein target of AA remains unclear. In this study, the protein target of AA in HepG2 hepatoma cells was identified using the AfBPP-based chemoproteomic approach. Initially, a diazirine and alkyne group modified AA photoaffinity probe was synthesized. Then, using mass spectrometry analysis, 13 putative target proteins were identified with high confidence. Combined with the competition bands in in situ fluorescence scanning, the α-tubulin alpha-1B chain (TUBA1B) was identified as the target protein of AA. Subsequently, the direct interaction between AA and TUBA1B was verified by surface plasmon resonance, pull-down and cellular thermal shift experiments, drug affinity responsive target stability assay, and molecular docking. This research will offer fresh perspectives on how AA prevents liver cancer at the molecular level.

Polyphasic characterization of a novel hot-spring cyanobacterium Thermocoleostomius sinensis gen et sp. nov. and genomic insights into its carbon concentration mechanism.

Thermophilic cyanobacteria play a crucial role as primary producers in hot spring ecosystems, yet their microbiological, taxonomic, and ecological characteristics are not extensively studied. This study aimed to characterize a novel strain of thermophilic cyanobacteria, PKUAC-SCTA174 (A174), using a combination of traditional polyphasic methods and modern genomic-based approaches. The study included 16S rRNA-based phylogeny, ITS secondary structure prediction, morphological and habitat analyses, as well as high-quality genome sequencing with corresponding phylogenomic analyses. The results of the 16S rRNA, 16S-23S ITS secondary structure, morphology, and habitat analyses supported the classification of the strain as a member of a novel genus within the family Oculatellaceae, closely related to Albertania and Trichotorquatus. Genomic analysis revealed the presence of a sophisticated carbon-concentrating mechanism (CCM) in the strain, involving two CO2 uptake systems NDH-I3, and NDH-I4, three types of bicarbonate transporters (BCT1, bicA, sbtA,) and two distinct putative carboxysomal carbonic anhydrases (ccaA1 and ccaA2). The expression of CCM genes was investigated with a CO2 shift experiment, indicating varying transcript abundance among different carbon uptake systems. Based on the comprehensive characterization, the strain was delineated as Thermocoleostomius sinensis, based on the botanical code. The study of the complete genome of strain A174 contributes valuable insights into the genetic characteristics of the genus Thermocoleostomius and related organisms and provides a systematic understanding of thermophilic cyanobacteria. The findings presented here offer valuable data that can be utilized for future research in taxogenomics, ecogenomics, and geogenomics.

Synthesis and characterization of the N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) alternate substrate analog N,N-dimethyl-l,l-SDAP

Growing antibiotic resistance by pathogenic bacteria has led to a global crisis. The bacterial enzyme N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) provides a very attractive target for the discovery of a new class of antibiotics, as it resides exclusively in many pathogenic bacterial strains and is a key enzyme in the lysine biosynthetic pathway. This pathway is responsible for the production of lysine as well as meso-diaminopimelate (m-DAP), both of which are required for peptidoglycan cell-wall synthesis, and lysine for peptide synthesis. The enzyme DapE catalyzes the hydrolysis of N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) to succinate and l,l-diaminopimelic acid (l,l-DAP), and due to its absence in humans, inhibition of DapE avoids mechanism-based side effects. We have executed the asymmetric synthesis of N,N-dimethyl-SDAP, an l,l-SDAP substrate analog and an analog of the synthetic substrate of our previously described DapE assay. Previous modeling studies advocated that N,N-dimethyl-SDAP might function as an inhibitor, however the compound behaves as a substrate, and we have demonstrated the use of N,N-dimethyl-SDAP as the substrate in a modified ninhydrin-based DapE assay. Thermal shift experiments of DapE in the presence of N,N-dimethyl-SDAP are consistent with a melt temperature (Tm) shifted by succinate, the product of enzymatic hydrolysis.

Sequence- and structure-specific RNA oligonucleotide binding attenuates heterogeneous nuclear ribonucleoprotein A1 dysfunction.

The RNA binding protein heterogeneous nuclear ribonucleoprotein A1 (A1) regulates RNA metabolism, which is crucial to maintaining cellular homeostasis. A1 dysfunction mechanistically contributes to reduced cell viability and loss, but molecular mechanisms of how A1 dysfunction affects cell viability and loss, and methodologies to attenuate its dysfunction, are lacking. Utilizing in silico molecular modeling and an in vitro optogenetic system, this study examined the consequences of RNA oligonucleotide (RNAO) treatment on attenuating A1 dysfunction and its downstream cellular effects. In silico and thermal shift experiments revealed that binding of RNAOs to the RNA Recognition Motif 1 of A1 is stabilized by sequence- and structure-specific RNAO-A1 interactions. Using optogenetics to model A1 cellular dysfunction, we show that sequence- and structure-specific RNAOs significantly attenuated abnormal cytoplasmic A1 self-association kinetics and A1 cytoplasmic clustering. Downstream of A1 dysfunction, we demonstrate that A1 clustering affects the formation of stress granules, activates cell stress, and inhibits protein translation. With RNAO treatment, we show that stress granule formation is attenuated, cell stress is inhibited, and protein translation is restored. This study provides evidence that sequence- and structure-specific RNAO treatment attenuates A1 dysfunction and its downstream effects, thus allowing for the development of A1-specific therapies that attenuate A1 dysfunction and restore cellular homeostasis.

Present and future of pure shift NMR in metabolomics.

NMR is one of the most powerful techniques for the analysis of biological samples in the field of metabolomics. However, the high complexity of fluids, tissues, or other biological materials taken from living organisms is still a challenge for state-of-the-art pulse sequences, thereby limiting the detection, the identification, and the quantification of metabolites. In this context, the resolution enhancement provided by broadband homonuclear decoupling methods, which allows for simplifying 1 H multiplet patterns into singlets, has placed this so-called pure shift technique as a promising approach to perform metabolic profiling with unparalleled level of detail. In recent years, the many advances achieved in the design of pure shift experiments has paved the way to the analysis of a wide range of biological samples with ultra-high resolution. This review leads the reader from the early days of the main pure shift methods that have been successfully developed over the last decades to address complex samples, to the most recent and promising applications of pure shift NMR to the field of NMR-based metabolomics.

Functional Redundancy Secures Resilience of Chain Elongation Communities upon pH Shifts in Closed Bioreactor Ecosystems.

For anaerobic mixed cultures performing microbial chain elongation, it is unclear how pH alterations affect the abundance of key players, microbial interactions, and community functioning in terms of medium-chain carboxylate yields. We explored pH effects on mixed cultures enriched in continuous anaerobic bioreactors representing closed model ecosystems. Gradual pH increase from 5.5 to 6.5 induced dramatic shifts in community composition, whereas product range and yields returned to previous states after transient fluctuations. To understand community responses to pH perturbations over long-term reactor operation, we applied Aitchison PCA clustering, linear mixed-effects models, and random forest classification on 16S rRNA gene amplicon sequencing and process data. Different pH preferences of two key chain elongation species─one Clostridium IV species related to Ruminococcaceae bacterium CPB6 and one Clostridium sensu stricto species related to Clostridium luticellarii─were determined. Network analysis revealed positive correlations of Clostridium IV with lactic acid bacteria, which switched from Olsenella to Lactobacillus along the pH increase, illustrating the plasticity of the food web in chain elongation communities. Despite long-term cultivation in closed systems over the pH shift experiment, the communities retained functional redundancy in fermentation pathways, reflected by the emergence of rare species and concomitant recovery of chain elongation functions.

Rewiring of hormones and light response pathways underlies the inhibition of stomatal development in an amphibious plant Rorippa aquatica underwater

Land plants have evolved the ability to cope with submergence. Amphibious plants are adapted to both aerial and aquatic environments through phenotypic plasticity in leaf form and function, known as heterophylly. In general, underwater leaves of amphibious plants are devoid of stomata, yet their molecular regulatory mechanisms remain elusive. Using the emerging model of the Brassicaceae amphibious species Rorippa aquatica, we lay the foundation for the molecular physiological basis of the submergence-triggered inhibition of stomatal development. A series of temperature shift experiments showed that submergence-induced inhibition of stomatal development is largely uncoupled from morphological heterophylly and likely regulated by independent pathways. Submergence-responsive transcriptome analysis revealed rapid reprogramming of gene expression, exemplified by the suppression of RaSPEECHLESS and RaMUTE within 1h and the involvement of light and hormones in the developmental switch from terrestrial to submerged leaves. Further physiological studies place ethylene as a central regulator of the submergence-triggered inhibition of stomatal development. Surprisingly, red and blue light have opposing functions in this process: blue light promotes, whereas red light inhibits stomatal development, through influencing the ethylene pathway. Finally, jasmonic acid counteracts the inhibition of stomatal development, which can be attenuated by the red light. The actions and interactions of light and hormone pathways in regulating stomatal development in R.aquatica are different from those in the terrestrial species, Arabidopsis thaliana. Thus, our work suggests that extensive rewiring events of red light to ethylene signaling might underlie the evolutionary adaption to water environment in Brassicaceae.

Concentration shift experiment with an electrode of active material for precise electrochemical analysis.

To precisely evaluate the electrochemical properties of a battery of active material, we proposed a "concentration shift experiment" using single-particle electrochemical measurement (SPEM) and a diluted electrode sheet (DES). SPEM can be used for information, such as the charge-discharge and resistance properties of only the active material (extremely dilute condition: ≈0). DES consists of concentrations varying from 1% to 100% of the active material (LiCoO2) and inactive material (α-Al2O3), electrically conductive additive and binder polymer onto an Al current collector. The resistance components derived from the LiCoO2 single particles were measured and calculated. Their apparent activation energy (Ea) was 27 kJ mol-1, which is relatively low compared with the applied-type sheet electrode (30-60 kJ mol-1). Simple electric/ionic conductive route was analyzed using SPEM cell, and the fundamental LiCoO2 originated Ea could be calculated. Resistance components attributed to LiCoO2 were also measured and extracted by alternating current impedance measurements using DES. The resistance non-linearly decreased with LiCoO2 concentration, and the percolation and inhomogeneity of LiCoO2 particles were suspected. The planful isolation of an active material particle should be critical for the overall information on an electrode particle.

Ultrahigh-Resolution Homo- and Heterodecoupled 1H and TOCSY NMR Experiments.

The original homonuclear decoupled (pure shift) experiments provide ultrahigh-resolution 1H spectra of compounds containing NMR-active heteronuclei of low natural isotopic abundance (e.g., 13C or 15N). In contrast, molecules containing highly abundant heteronuclei (like 31P or 19F) give doublets or a multiple of doublets in their homonuclear decoupled spectra, depending on the number of heteronuclear coupling partners and the magnitude of the respective coupling constants. In these cases, the complex and frequently overlapping signals may hamper the unambiguous assignment of resonances. Here, we present new heteronuclear decoupled (HD) PSYCHE 1H and TOCSY experiments, which result in simplified spectra with significantly increased resolution, allowing the reliable assessment of individual resonances. The utility of the experiments has been demonstrated on a challenging stereoisomeric mixture of a platinum-phosphine complex, where ultrahigh resolution of the obtained HD PSYCHE spectra made the structure elucidation of the chiral products feasible. HD PSYCHE methods can be potentially applied to other important 31P- or 19F-containing compounds in medicinal chemistry and metabolomics.

RIPK3 inhibitor-AZD5423 alleviates acute kidney injury by inhibiting necroptosis and inflammation

Acute kidney injury (AKI) is a clinical syndrome that is defined as a sudden decline in renal function and characterized by inflammation and programmed cell death of renal tubular epithelial cells. Necroptosis is a form of regulated cell death that requires activation of receptor interacting protein kinase 3 (RIPK3) and its phosphorylation of the substrate MLKL. RIPK3 plays an important role in acute kidney injury, and hence developing its inhibitors is considered as one of the promising strategies aimed at prevention and treatment of AKI. Recently, we discovered AZD5423 as a novel potent RIPK3 inhibitor using a computer-aided hybrid virtual screening strategy according to three-dimensional structure of RIPK3. Our findings revealed that AZD5423 strongly inhibits activation of RIPK3, and MLKL phosphorylation upon cisplatin-, hypoxia/reoxygenation (H/R)- and TNF-α stimuli as compared with GSK872, which is a previously identified RIPK3 inhibitor. Importantly, AZD5423 exerts effective protection against cisplatin- and ischemia/reperfusion (I/R)-induced AKI mouse model. The results of cellular thermal shift assay and experiments in RIPK3 knockout cells indicated that AZD5423 could directly target RIPK3 to inhibit RIPK3 kinase activity. Mechanistically, the docking of AZD5423 and RIPK3 suggested that the kinase domain of RIPK3 for Lys50, Arg313, Lys29, Arg37 might form hydrogen bonds with AZD5423. Site-directed mutagenesis further revealed that AZD5423 reduces injury response via interacting with the key RIPK3 amino acid residues of Lys50 and Arg313. In conclusion, our study has demonstrated that AZD5423 may serve as a potent inhibitor of RIPK3 kinase and a promising clinical candidate for AKI treatment.

Case-only design identifies interactions of genetic risk variants at SIGLEC5 and PLG with the lncRNA CTD-2353F22.1 implying the importance of periodontal wound healing for disease aetiology.

The basis of phenotypic variation of periodontitis is genetic variability. Disease relevant effects of individual risk alleles are considered to result from genetic interactions. We investigated gene × gene (G×G) interactions of suggestive periodontitis susceptibility alleles. We used the case-only design and investigated single-nucleotide polymorphism (SNPs) that showed associations in our recent genome-wide association study (GWAS) and GWAS meta-analysis with p < 5 × 10-6 . CRISPR-dCas9 gene activation followed by RNA-sequencing and gene-set enrichment analyses elucidated differentially expressed genes and gene networks. With the databases of SNPInspector and Transfac professional, luciferase reporter gene assays and antibody electrophoretic mobility shift experiments, we analysed allele-specific effects on transcription factor binding. SNPs at the genes sialic acid binding Ig-like lectin 5 (SIGLEC5) and plasminogen (PLG) showed G×G interactions with rs1122900 at the long non-coding RNA (lncRNA) CTD-2353F22. Associated chromatin cis-activated CTD-2353F22.1 6.5-fold (p=.003), indicating CTD-2353F22.1 as target gene of this interaction. CTD-2353F22.1 regulated GADD45A (padj < 4.9 × 10-11 , log2 fold change (FC)=-0.55), THBS1, SERPINE1 and Tissue Factor F3 (padj < 5 × 10-7 , log2 FC ≥ -0.35) and the gene set "angiogenesis" (area under the curve=0.71, padj =8.2 × 10-5 ). rs1122900 effect C-allele decreased reporter gene activity (5.5-fold, p=.0003) and PRDM14 binding (76%). CTD-2353F22.1 mediates interaction of SIGLEC5 and PLG, together with genes that function in periodontal wound healing.