MIWE: detecting the critical states of complex biological systems by the mutual information weighted entropy.

Complex biological systems often undergo sudden qualitative changes during their dynamic evolution. These critical transitions are typically characterized by a catastrophic progression of the system. Identifying the critical point is critical to uncovering the underlying mechanisms of complex biological systems. However, the system may exhibit minimal changes in its state until the critical point is reached, and in the face of high throughput and strong noise data, traditional biomarkers may not be effective in distinguishing the critical state. In this study, we propose a novel approach, mutual information weighted entropy (MIWE), which uses mutual information between genes to build networks and identifies critical states by quantifying molecular dynamic differences at each stage through weighted differential entropy. The method is applied to one numerical simulation dataset and four real datasets, including bulk and single-cell expression datasets. The critical states of the system can be recognized and the robustness of MIWE method is verified by numerical simulation under the influence of different noises. Moreover, we identify two key transcription factors (TFs), CREB1 and CREB3, that regulate downstream signaling genes to coordinate cell fate commitment. The dark genes in the single-cell expression datasets are mined to reveal the potential pathway regulation mechanism.

Preparation of ZIF-67/C3N4 composite material and adsorption of tetracycline hydrochloride.

In recent years, wastewater treatment to remove tetracycline hydrochloride (TCH) has received much attention in water treatment problems. ZIF-67/C3N4 composite adsorbent, a nanosheet structured material stacked with MOFs, was prepared by in situ growth method, which has high adsorption activity for tetracycline hydrochloride in wastewater. Comparing the effect of monomeric and composite adsorbents, Z6C2 had the best adsorption effect (206 mg·g-1), which was 77.6% higher than that of ZIF-67 (116 mg·g-1) and 10.8 times higher than that of C3N4 (19 mg·g-1). The structure of ZIF-67 stacked on C3N4 nanosheets has an excellent specific surface area and number of active sites, as well as π-π interactions, electrostatic interactions, and hydrogen bonding interactions between the adsorbent and TCH, which combine to enhance the adsorption performance. The adsorption process is accompanied by a combination of chemisorption, mass transport, and internal diffusion rate-limiting. It was shown that the adsorption process is favorable for monolayer adsorption as well as a heat absorption reaction that proceeds spontaneously. The adsorbent exhibits good stability and adsorption capacity, which may be suitable for efficient and low-cost water purification.

Toll-like receptor 4-mediated microglial inflammation exacerbates early white matter injury following experimental subarachnoid hemorrhage.

Neuroinflammation has been reported to be associated with white matter injury (WMI) after subarachnoid hemorrhage (SAH). As the main resident immune cells of the brain, microglia can be activated into proinflammatory and anti-inflammatory phenotypes. Toll-like receptor 4 (TLR4), expressed on the surface of the microglia, plays a key role in microglial inflammation. However, the relationship between TLR4, microglial polarization, and WMI following SAH remains unclear. In this study, a total of 121 male adult C57BL/6 wild-type (WT) mice, 20 WT mice at postnatal day 1 (P1), and 41 male adult TLR4 gene knockout (TLR4-/-) mice were used to investigate the potential role of TLR4-induced microglial polarization in early WMI after SAH by radiological, histological, microstructural, transcriptional, and cytological evidence. The results indicated that microglial inflammation was associated with myelin loss and axon damage, shown as a decrease in myelin basic protein (MBP), as well as increase in degraded myelin basic protein (dMBP) and amyloid precursor protein (APP). Gene knockout of TLR4 revised microglial polarization toward the anti-inflammatory phenotype and protected the white matter at an early phase after SAH (24 h), as shown through reduction of toxic metabolites, preservation of myelin, reductions in APP accumulation, reductions in white matter T2 hyperintensity, and increases in FA values. Cocultures of microglia and oligodendrocytes, the cells responsible for myelin production and maintenance, were established to further elucidate the relationship between microglial polarization and WMI. In vitro, TLR4 inhibition decreased the expression of microglial MyD88 and phosphorylated NF-κB, thereby inhibiting M1 polarization and mitigating inflammation. Decrease in TLR4 in the microglia increased preservation of neighboring oligodendrocytes. In conclusion, microglial inflammation has dual effects on early WMI after experimental SAH. Future explorations on more clinically relevant methods for modulating neuroinflammation are warranted to combat stroke with both WMI and gray matter destruction.

The Ovs surface defecting of an S-scheme g-C3N4/H2Ti3O7 nanoheterostructures with accelerated spatial charge transfer.

Semiconductor photocatalysis was a rising star in the sustainable transformation of solar energy for environmental problems governance. Herein, an S-scheme g-C3N4/H2Ti3O7 heterostructure was constructed and applied to tetracycline hydrochloride (TCH) destruction. The g-C3N4/H2Ti3O7 composite has a superior photocatalytic property to degrade TCH in contrast with bare g-C3N4 and H2Ti3O7. The 20% g-C3N4/H2Ti3O7 (CNHTO20) composite exhibited the optimum photocatalytic performance, and the degradation efficiency of 20 mg/L TCH reached 87.37% within 3 h (K = 0.572 min-1). The affluent active sites of the g-C3N4 nanosheet and effective interfacial charge separation of the S-scheme pathway facilitated the excellent performance. Moreover, the ample oxygen vacancies (Ovs) act as the electron mediator, not only reducing the band gap energy by producing the formation of defect levels, but also broadening the photo response range and promoting the interfacial charge transfer. The coordination complexes formed between TCH molecules and Ti (IV) ions in CNHTO20 composites induce strong visible light absorption through ligand-metal charge transfer (LMCT). The Ti4+/Ti3+ metal cycle in CNHTO20 was conducive to the separation of the photogenerated electron-hole pairs on the heterojunction interface as well. The ESR characterization and trapping experiments certified that the dominant substances were OH, O2- and h+. The AQY calculated by the COD removal rate was 0.16%. Conclusively, the S-scheme heterojunction between H2Ti3O7 and g-C3N4 enabled the CNHTO photocatalyst with high redox ability and boosted photocatalytic performance accordingly. This study may shed some enlightenment on the construction of heterojunctions and the realistic treatment of wastewater.

Deletion of Bak1 alleviates microglial necroptosis and neuroinflammation after experimental subarachnoid hemorrhage.

Microglial necroptosis exacerbates neurodegenerative diseases, central nervous system (CNS) injury, and demonstrates a proinflammatory process, but its contribution to subarachnoid hemorrhage (SAH) is poorly characterized. BCL-2 homologous antagonist-killer protein (Bak1), a critical regulatory molecule of endogenous apoptosis, can be involved in the pathologic process of necroptosis by regulating mitochondrial permeability. In this study, we revealed microglia undergo necroptosis after SAH in vivo and vitro. Western blot revealed that Bak1 was elevated at 24 h after SAH. Knocked down of Bak1 by adeno-associated virus attenuates microglial necroptosis, alleviates neuroinflammation, and improves neurologic function after SAH in mice. Furthermore, oxyhemoglobin (10 µM) induced necroptosis in BV2 microglia, increasing Bak1 expression and mediating proinflammatory phenotype transformation, exacerbating oxidative stress and neuroinflammation. Abrogating BV2 Bak1 could reduce necroptosis by down-regulating the expression of phosphorylated pseudokinase mixed lineage kinase domain-like protein (p-MLKL), then down-regulating proinflammatory phenotype gene expression. RNA-Seq showed that disrupting BV2 Bak1 down-regulates multiple immune and inflammatory pathways and ameliorates cell injury by elevating thrombospondin 1 (THBS1) expression. In summary, we identified a critical regulatory role for Bak1 in microglial necroptosis and neuroinflammation after SAH. Bak1 is expected to be a potential target for the treatment strategy of SAH.

Three Different Interaction Patterns between MCM-41 and Proteins.

As one of the most studied mesoporous silica nanoparticles (MSNs) in drug delivery systems, Mobil Composition of Matter No. 41 (MCM-41) possesses unique properties including perfect channel architecture, excellent load capacity, and good biocompatibility. However, the applications of MCM-41 nanoparticles in drug delivery have not yet been industrialized, due to the interaction between MCM-41 and biomolecules (especially proteins) that affect their in vivo behaviors after dosing. To investigate the interactions between MCM-41 and proteins, this study selected bovine serum albumin (BSA), lysozyme (Lyso), and bovine hemoglobin (BHb) as model proteins and characterized the ultraviolet-visible, fluorescence, circular dichroism spectra and the protein adsorption of MCM-41-protein complex. The UV-Vis spectra exhibited the different absorption increment degrees of three proteins. The fluorescence spectra showed that the fluorescence intensity of proteins changed by different trends. The CD spectra indicated that the secondary structure changes were ranked as BSA > Lyso > BHb, which is consistent with the protein's adsorption capability on MCM-41. It was shown that there were three different patterns of MCM-41-proteins interactions. The hydrophilic and low-charged BSA followed the strong interaction pattern, the hydrophilic but heavily charged Lyso followed the moderate interaction pattern, and the hydrophobic BHb followed the weak interaction pattern. Different interaction patterns would lead to different effects on the structural properties of proteins, the surface chemistry of MCM-41, and the absorption capability of proteins on MCM-41. We believe our study will provide a better insight into the application of MCM-41 nanoparticles in drug delivery systems.

The Effect of Sulfobetaine Coating in Inhibiting the Interaction between Lyotropic Liquid Crystalline Nanogels and Proteins.

The injective lyotropic liquid crystalline nanogels (LLCNs) were widely used in drug delivery systems. But when administered in vivo, LLCNs exposed to the biological environment interact with proteins. Recently, it has been shown that nanoparticles coated with zwitterions can inhibit their interaction with proteins. Thus, in this study, the interaction between proteins and LLCNs coated with the zwitterionic material sulfobetaine (GLLCNs@HDSB) was investigated using bovine serum albumin (BSA) as a model protein. Interestingly, it was found that GLLCNs@HDSB at higher concentrations (≥0.8 mg/mL) could block its interaction with BSA, but not at lower concentrations (<0.8 mg/mL), according to the results of ultraviolet, fluorescence, and circular dichroism spectra. In the ultraviolet spectra, the absorbance of GLLCNs@HDSB (0.8 mg/mL) was 1.9 times higher than that without the sulfobetaine coating (GLLCNs) after incubation with protein; the fluorescence quenching intensity of GLLCNs@HDSB was conversely larger than that of the GLLCNs; in circular dichroism spectra, the ellipticity value of GLLCNs@HDSB was significantly smaller than that of the GLLCNs, and the change in GLLCNs@HDSB was 10 times higher than that of the GLLCNs. Generally, nanoparticles coated with sulfobetaine can inhibit their interaction with proteins, but in this study, LLCNs showed a concentration-dependent inhibitory effect. It could be inferred that in contrast to the surface of nanoparticles covered with sulfobetaine in other cases, the sulfobetaine in this study interacted with the LLCNs and was partially inserted into the hydrophobic region of the LLCNs. In conclusion, this study suggests that coating-modified nanoparticles do not necessarily avoid interacting with proteins, and we should also study coating-modified nanoparticles interacting with proteins both in vitro and in vivo. In the future, finding a coating material to completely inhibit the interaction between LLCNs and proteins will generate a great impetus to promote the clinical transformation of LLCNs.

Research on Potential Network Markers and Signaling Pathways in Type 2 Diabetes Based on Conditional Cell-Specific Network.

Traditional methods concerning type 2 diabetes (T2D) are limited to grouped cells instead of each single cell, and thus the heterogeneity of single cells is erased. Therefore, it is still challenging to study T2D based on a single-cell and network perspective. In this study, we construct a conditional cell-specific network (CCSN) for each single cell for the GSE86469 dataset which is a single-cell transcriptional set from nondiabetic (ND) and T2D human islet samples, and obtain a conditional network degree matrix (CNDM). Since beta cells are the key cells leading to T2D, we search for hub genes in CCSN of beta cells and find that ATP6AP2 is essential for regulation and storage of insulin, and the renin-angiotensin system involving ATP6AP2 is related to most pathological processes leading to diabetic nephropathy. The communication between beta cells and other endocrine cells is performed and three gene pairs with obvious interaction are found. In addition, different expression genes (DEGs) are found based on CNDM and the gene expression matrix (GEM), respectively. Finally, 'dark' genes are identified, and enrichment analysis shows that NFATC2 is involved in the VEGF signaling pathway and indirectly affects the production of Prostacyclin (PGI2), which may be a potential biomarker for diabetic nephropathy.

Irisin Contributes to Neuroprotection by Promoting Mitochondrial Biogenesis After Experimental Subarachnoid Hemorrhage.

Subarachnoid hemorrhage (SAH) is a devastating form of stroke, which poses a series of intractable challenges to clinical practice. Imbalance of mitochondrial homeostasis has been thought to be the crucial pathomechanism in early brain injury (EBI) cascade after SAH. Irisin, a protein related to metabolism and mitochondrial homeostasis, has been reported to play pivotal roles in post-stroke neuroprotection. However, whether this myokine can exert neuroprotection effects after SAH remains unknown. In the present study, we explored the protective effects of irisin and the underlying mechanisms related to mitochondrial biogenesis in a SAH animal model. Endovascular perforation was used to induce SAH, and recombinant irisin was administered intracerebroventricularly. Neurobehavioral assessments, TdT-UTP nick end labeling (TUNEL) staining, dihydroethidium (DHE) staining, immunofluorescence, western blot, and transmission electron microscopy (TEM) were performed for post-SAH assessments. We demonstrated that irisin treatment improved neurobehavioral scores, reduced neuronal apoptosis, and alleviated oxidative stress in EBI after SAH. More importantly, the administration of exogenous irisin conserved the mitochondrial morphology and promoted mitochondrial biogenesis. The protective effects of irisin were partially reversed by the mitochondrial uncoupling protein-2 (UCP-2) inhibitor. Taken together, irisin may have neuroprotective effects against SAH via improving the mitochondrial biogenesis, at least in part, through UCP-2 related targets.

Network pharmacology-based study of the molecular mechanisms of Qixuekang in treating COVID-19 during the recovery period.

OBJECTIVE: In this research, the analytical method of network pharmacology was used to explore Qixuekang molecular mechanism in treating Coronavirus 2019 (COVID-19) during the recovery period. METHODS: Traditional Chinese Medicine Systems Pharmacology (TCMSP) database was used to collect the active components and corresponding targets of Qixuekang. Disease targets, related to COVID-19 during the recovery period, were collected from the GeneCards database. Protein-Protein interaction (PPI) network was built by using the String database, and analyzing and using Cytoscape 3.7.0 software to screen out hub genes. GO enrichment and KEGG pathway enrichment analysis were analyzed by R 3.6.1 software. RESULTS: 34 active components of Qixuekang were screened out, and 161 common targets of drug and disease were identified. GO enrichment suggested 141 biologic processes, mainly involving nuclear receptor activity, transcription factor activity, and direct ligand regulated sequence-specific DNA binding. KEGG pathway enrichment suggests 96 signaling pathways, mainly including TNF signaling pathway, IL-17 signal pathway, and C-type lectin receptor signal pathway. The hub genes, screened in the PPI network, were mainly inclusive of CXCL8, CXCL2, CXCL10, ADRA2A, and ADRA2C. CONCLUSION: Qixuekang has numerous components and targets in treating COVID-19 during the recovery period. It is mainly applied in anti-inflammatory action and regulating immune defense, which may guide clinical trials in the later stage.

TSPO ligand Ro5-4864 modulates microglia/macrophages polarization after subarachnoid hemorrhage in mice.

Brain injury after subarachnoid hemorrhage (SAH) is closely related to microglia/macrophages-induced neuroinflammation. Translocator protein (TSPO) is a hall marker of activated microglia/macrophages, and the TSPO ligands have been proved to be beneficial for controlling neuroinflammation. Ro5-4864, one of the TSPO ligands, has been reported to be able to regulate inflammation in neurological diseases. Here, we investigated the effects of Ro5-4864 on microglia/macrophages polarization in a SAH mice model, which was induced by endovascular perforation. Ro5-4864 was administered intraperitoneally dissolved in DMSO-saline. Post-SAH assessments included neurological tests, SAH grade, western blotting, ELISA assay and immunohistochemistry. The results showed that brain injury was accompanied by the accumulation of TNF-α and IL-1ß, as well as the increase of iNOS protein levels. Finally, we found that Ro5-4864 improved neurological function, increased the expression of anti-inflammatory factors, and influenced phenotypes of M2 microglia/macrophages after SAH. Together, these data reveal a protective role of TSPO ligand Ro5-4864 in inflammatory processes of SAH as well as a potential alternative for SAH treatment.

RNA-Seq Reveals Underlying Transcriptomic Mechanisms of Bone Marrow-Derived Mesenchymal Stem Cells in the Regulation of Microglia-Mediated Neuroinflammation After Subarachnoid Hemorrhage.

Subarachnoid hemorrhage (SAH) is a life-threatening cerebrovascular disease with high rates of morbidity and mortality. Microglia, the resident immune cells of the central nervous system, are involved in initiating inflammatory response post-SAH through releasing a variety of inflammatory mediators. Regulation of neuroinflammation triggered by activated microglia has become a promising therapeutic strategy for SAH. Recent studies reported that bone marrow-derived mesenchymal stem cells (BM-MSCs) have therapeutic effects, resulting from the regulation of microglia activation and production of inflammatory cytokines post-SAH. However, the underlying molecular mechanisms of BM-MSCs in targeting microglia-mediated neuroinflammation after SAH are still unclear. In this study, we used murine microglia cell line BV2 treated with oxyhemoglobin (OxyHb) to mimic the SAH conditions in vitro. The results showed that BM-MSCs coculture modulated OxyHb-induced BV2 activation as well as polarization. We further implemented RNA-seq approaches to investigate differences in transcriptomes between OxyHb-stimulated BV2 cocultured with and without BM-MSCs. The RNA-seq results suggested that the levels of inflammatory genes were strongly altered when OxyHb-stimulated BV2 cells were cocultured with BM-MSCs. Moreover, we identified epigenetic regulators involved in the regulation of microglia-mediated inflammation by BM-MSCs. This study clarifies detailed transcriptomic mechanisms underlying the interaction between BM-MSCs and activated microglia and may lead to a new therapeutic strategy using stem cell therapy for SAH.

Biglycan regulates neuroinflammation by promoting M1 microglial activation in early brain injury after experimental subarachnoid hemorrhage.

Neuroinflammation can be caused by various factors in early brain injury after subarachnoid hemorrhage (SAH). One of the most important features of this process is M1 microglial activation. In turn, the TLR4/NF-κB pathway plays an essential role in activating M1 phenotypic microglia. Biglycan, a small leucine-rich proteoglycan, functions as an endogenous ligand of TLR4 and TLR2 in macrophages. However, the underlying mechanisms associated with microglial activation in stroke pathogenesis are poorly understood. Here, we aimed to identify the role of biglycan in neuroinflammation following SAH. In our study, SAH was induced by endovascular perforation in young male C57BL/6J mice. Lentiviral vector was administered intracerebroventricularly to knock down Biglycan. Post-SAH assessments included neurobehavioral tests, immunofluorescence, western blot, qRT-PCR, Co-IP, flow cytometry, and ELISA. The biglycan level was markedly elevated following SAH in vivo. Of particularly note, knockdown of biglycan significantly improved neurological outcomes. TLR4 was bound with soluble biglycan in vitro. In addition, biglycan down-regulation suppressed the expression of phosphorylated-NF-κB p65 (p-NF-κB) and inducible nitric oxide synthase (iNOS), as well as the cytokine (TNF-α, IL-1ß, and IL-6) production in vivo and in vitro. Moreover, we detected a decreased expression of CD16/32 and CD86, M1 markers when biglycan was inhibited in vitro. Our work suggests that biglycan can induce neuroinflammation by promoting M1 microglial activation at least in part through TLR4/NF-κB signaling pathway after experimental SAH. Targeting biglycan may be a promising strategy for the clinical management of SAH.

[Expression of Translocator Protein in Early Brain Injury After Subarachnoid Hemorrhage in Mice].

OBJECTIVE: To evaluate the expression of translocator protein (TSPO) in brain tissue within 72 h after subarachnoid hemorrhage (SAH) in mice. METHODS: Forty-four C57BL/6J mice were randomly divided into two groups, 17 in the Sham group and 27 in the SAH group. SAH mice model was performed by endovascular perforation as previously described with slight modifications. Sham group mice were performed by the same method but without piercing the blood vessels. Before and 6 h, 24 h, 48 h, 72 h after modeling, the two groups were scored with modified Garcia score for neurological function. At 6 h, 24 h, 48 h, 72 h after modeling, the mice were sacrificed. Sham group mice were sacrificed at 24 h after modeling. The expression of TSPO in brain tissue was evaluated by Western blot, positron emission tomography-computed tomography (PET-CT) and immunofluorescence staining. Fluorescent double staining was used to assess the relationship of TSPO and microglia. RESULTS: The neurological function scores of the SAH group mice decreased with time and then increased. The expression of TSPO in the brain tissue increased first and then decreased with time, and there was a negative correlation between them (r=-0.615 6, P < 0.01). PET-CT showed that the tracer intake of mouse brain tissue after SAH was higher than that of Sham group, and the difference was statistically significant (P < 0.05). Immunofluorescence staining showed that TSPO increased in the parietal cortex and basal cortex of the SAH group. And fluorescent double staining suggested that TSPO colocalized with Iba-1 which was a specific marker of microglia. CONCLUSIONS: In the early brain injury after SAH, the expression of TSPO in brain is widely increased, and the expression level increases first and then decreases. TSPO could participate in the activation of microglia and regulate the occurrence and development of brain injury after SAH.