ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists.

ezSingleCell is an interactive and easy-to-use application for analysing various single-cell and spatial omics data types without requiring prior programing knowledge. It combines the best-performing publicly available methods for in-depth data analysis, integration, and interactive data visualization. ezSingleCell consists of five modules, each designed to be a comprehensive workflow for one data type or task. In addition, ezSingleCell allows crosstalk between different modules within a unified interface. Acceptable input data can be in a variety of formats while the output consists of publication ready figures and tables. In-depth manuals and video tutorials are available to guide users on the analysis workflows and parameter adjustments to suit their study aims. ezSingleCell's streamlined interface can analyse a standard scRNA-seq dataset of 3000 cells in less than five minutes. ezSingleCell is available in two forms: an installation-free web application ( https://immunesinglecell.org/ezsc/ ) or a software package with a shinyApp interface ( https://github.com/JinmiaoChenLab/ezSingleCell2 ) for offline analysis.

Unsupervised spatially embedded deep representation of spatial transcriptomics.

Optimal integration of transcriptomics data and associated spatial information is essential towards fully exploiting spatial transcriptomics to dissect tissue heterogeneity and map out inter-cellular communications. We present SEDR, which uses a deep autoencoder coupled with a masked self-supervised learning mechanism to construct a low-dimensional latent representation of gene expression, which is then simultaneously embedded with the corresponding spatial information through a variational graph autoencoder. SEDR achieved higher clustering performance on manually annotated 10 × Visium datasets and better scalability on high-resolution spatial transcriptomics datasets than existing methods. Additionally, we show SEDR's ability to impute and denoise gene expression (URL: https://github.com/JinmiaoChenLab/SEDR/ ).

Neutrophil Extracellular Traps Formation and Citrullinated Histones 3 Levels in Patients with Kawasaki Disease.

Background: Kawasaki disease (KD) is a vasculitis associated with vascular injury and autoimmune response. Inflammatory factors stimulate neutrophils to produce web-like structures called neutrophil extracellular traps (NETs). Citrullinated histone 3 (H3Cit) is one of the main protein components of neutrophil extracellular traps involved in the process of NETosis. The levels of NETs and H3Cit in the KD are not known. Objective: To determine the changes in the levels of NETs and H3Cit in KD. Methods: Children with KD were recruited and divided into the acute KD and the sub-acute KD group according to the disease phase and whether intravenous immunoglobulin (IVIG) was used or not. Peripheral venous blood was taken before and after the IVIG administration and sent for the examination of NETs by flow cytometry. The level of H3Cit was measured by enzyme-linked immunosorbent assay (ELISA). Results: The counts of NETs in the acute KD group significantly increased compared with the healthy controls (p<0.01). The level of H3Cit was significantly higher in the acute KD group than in the healthy control subjects. Of note, both the counts of NETs and the level of H3Cit decreased in the KD patients treated with IVIG compared with the acute KD group (p<0.01). Conclusion: Acute KD is characterized by an increased formation of NETs and high levels of H3Cit. IVIG significantly inhibited NETs formation and also reduced the level of plasma H3Cit in children with KD.

Resistance-proof antimicrobial drug discovery to combat global antimicrobial resistance threat.

Drug resistance is well-defined as a serious problem in our living world. To survive, microbes develop defense strategies against antimicrobial drugs. Drugs exhibit less or no effective results against microbes after the emergence of resistance because they are unable to cross the microbial membrane, in order to alter enzymatic systems, and/or upregulate efflux pumps, etc. Drug resistance issues can be addressed effectively if a "Resistance-Proof" or "Resistance-Resistant" antimicrobial agent is developed. This article discusses first the need for resistance-proof drugs, the imminent properties of resistance-proof drugs, current and future research progress in the discovery of resistance-proof antimicrobials, the inherent challenges, and opportunities. A molecule having imminent resistance-proof properties could target microbes efficiently, increase potency, and rule out the possibility of early resistance. This review triggers the scientific community to think about how an upsurge in drug resistance can be averted and emphasizes the discussion on the development of next-generation antimicrobials that will provide a novel effective solution to combat the global problem of drug resistance. Hence, resistance-proof drug development is not just a requirement but rather a compulsion in the drug discovery field so that resistance can be battled effectively. We discuss several properties of resistance-proof drugs which could initiate new ways of thinking about next-generation antimicrobials to resolve the drug resistance problem. This article sheds light on the issues of drug resistance and discusses solutions in terms of the resistance-proof properties of a molecule. In summary, the article is a foundation to break new ground in the development of resistance-proof therapeutics in the field of infection biology.

Prediction of Cancer Treatment Using Advancements in Machine Learning.

Many cancer patients die due to their treatment failing because of their disease's resistance to chemotherapy and other forms of radiation therapy. Resistance may develop at any stage of therapy, even at the beginning. Several factors influence current therapy, including the type of cancer and the existence of genetic abnormalities. The response to treatment is not always predicted by the existence of a genetic mutation and might vary for various cancer subtypes. It is clear that cancer patients must be assigned a particular treatment or combination of drugs based on prediction models. Preliminary studies utilizing artificial intelligence-based prediction models have shown promising results. Building therapeutically useful models is still difficult despite enormous increases in computer capacity due to the lack of adequate clinically important pharmacogenomics data. Machine learning is the most widely used branch of artificial intelligence. Here, we review the current state in the area of using machine learning to predict treatment response. In addition, examples of machine learning algorithms being employed in clinical practice are offered.

Comparison of O3, UV/O3, and UV/O3/PS processes for marine oily wastewater treatment: Degradation performance, toxicity evaluation, and flocs analysis.

Efficient on-site treatment technology is crucial for mitigating marine oily wastewater pollution. This work investigates the ozone (O3), ultraviolet (UV)/O3, UV/O3/persulfate (PS) processes for the treatment of marine oily wastewater, including degradation performance, acute toxicity evaluation, and oil flocs analysis in a benchtop circulating flow photoozonation reactor. Degradation performances have been studied by measuring the degradation rate of total oil concentrations, specific oil components (n-alkanes and polycyclic aromatic hydrocarbons (PAHs)), and total organic carbon (TOC). The results show that UV/O3/PS could significantly enhance the removal efficiency than the other two processes, with above 90% of removal efficiency in 30 min. Acute toxicity analysis further shows that the wastewater quality is significantly improved by four-fold of the EC50 of Vibrio fischeri, and the mortality of Artemia franciscana decreases from 100% to 0% after 48 h exposure. Further, the morphology and functional groups of flocs have been further characterized, showing that the floating flocs could be further degraded especially in UV/O3/PS process. Our study further raised discussions regarding the future on-site application of O3-based systems, based on the results generated from the treatment efficiency, toxicity, and flocs characterization. The regulation of the oxidation strength and optimization of the reaction systems could be a practical strategy for on-site marine oily wastewater treatment.

A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes.

The microbiome contributes to the development and maturation of the immune system. In response to commensal bacteria, intestinal CD4+ T lymphocytes differentiate into functional subtypes with regulatory or effector functions. The development of small intestine intraepithelial lymphocytes that coexpress CD4 and CD8αα homodimers (CD4IELs) depends on the microbiota. However, the identity of the microbial antigens recognized by CD4+ T cells that can differentiate into CD4IELs remains unknown. We identified ß-hexosaminidase, a conserved enzyme across commensals of the Bacteroidetes phylum, as a driver of CD4IEL differentiation. In a mouse model of colitis, ß-hexosaminidase-specific lymphocytes protected against intestinal inflammation. Thus, T cells of a single specificity can recognize a variety of abundant commensals and elicit a regulatory immune response at the intestinal mucosa.

Development of advanced oil/water separation technologies to enhance the effectiveness of mechanical oil recovery operations at sea: Potential and challenges.

Mechanical oil recovery (i.e., booming and skimming) is the most common tool for oil spill response. The recovered fluid generated from skimming processes may contain a considerable proportion of water (10 % ~ 70 %). As a result of regulatory prohibition on the discharge of contaminated waters at sea, vessels and/or storage barges must make frequent trips to shore for oil-water waste disposal. This practice can be time- consuming thus reduces the overall efficiency and capacity of oil recovery. One potential solution is on-site oil-water separation and disposal of water fraction at sea. However, currently available decanting processes may have limited oil/water separation capabilities, especially in the presence of oil-water emulsion, which is inevitable in mechanical oil recovery. The decanted water may not meet the discharge standards and cause severe ecotoxicological impacts. This paper therefore comprehensively reviews the principles and progress in oil/water separation, demulsification, and on-site treatment technologies, investigates their applicability on decanting at sea, and discusses the ecotoxicity of decanted water in the marine environment. The outputs provide the fundamental and practical knowledge on decanting and help enhance response effectiveness and consequently reducing the environmental impacts of oil spills.

DISCO: a database of Deeply Integrated human Single-Cell Omics data.

The ability to study cellular heterogeneity at single cell resolution is making single-cell sequencing increasingly popular. However, there is no publicly available resource that offers an integrated cell atlas with harmonized metadata that users can integrate new data with. Here, we present DISCO (https://www.immunesinglecell.org/), a database of Deeply Integrated Single-Cell Omics data. The current release of DISCO integrates more than 18 million cells from 4593 samples, covering 107 tissues/cell lines/organoids, 158 diseases, and 20 platforms. We standardized the associated metadata with a controlled vocabulary and ontology system. To allow large scale integration of single-cell data, we developed FastIntegration, a fast and high-capacity version of Seurat Integration. We also developed CELLiD, an atlas guided automatic cell type identification tool. Employing these two tools on the assembled data, we constructed one global atlas and 27 sub-atlases for different tissues, diseases, and cell types. DISCO provides three online tools, namely Online FastIntegration, Online CELLiD, and CellMapper, for users to integrate, annotate, and project uploaded single-cell RNA-seq data onto a selected atlas. Collectively, DISCO is a versatile platform for users to explore published single-cell data and efficiently perform integrated analysis with their own data.

Ischemic-Trained Monocytes Improve Arteriogenesis in a Mouse Model of Hindlimb Ischemia.

OBJECTIVE: Monocytes, which play an important role in arteriogenesis, can build immunologic memory by a functional reprogramming that modifies their response to a second challenge. This process, called trained immunity, is evoked by insults that shift monocyte metabolism, increasing HIF (hypoxia-inducible factor)-1α levels. Since ischemia enhances HIF-1α, we evaluate whether ischemia can lead to a functional reprogramming of monocytes, which would contribute to arteriogenesis after hindlimb ischemia. METHODS AND RESULTS: Mice exposed to ischemia by 24 hours (24h) of femoral artery occlusion (24h trained) or sham were subjected to hindlimb ischemia one week later; the 24h trained mice showed significant improvement in blood flow recovery and arteriogenesis after hindlimb ischemia. Adoptive transfer using bone marrow-derived monocytes (BM-Mono) from 24h trained or sham donor mice, demonstrated that recipients subjected to hindlimb ischemia who received 24h ischemic-trained monocytes had remarkable blood flow recovery and arteriogenesis. Further, ischemic-trained BM-Mono had increased HIF-1α and GLUT-1 (glucose transporter-1) gene expression during femoral artery occlusion. Circulating cytokines and GLUT-1 were also upregulated during femoral artery occlusion.Transcriptomic analysis and confirmatory qPCR performed in 24h trained and sham BM-Mono revealed that among the 15 top differentially expressed genes, 4 were involved in lipid metabolism in the ischemic-trained monocytes. Lipidomic analysis confirmed that ischemia training altered the cholesterol metabolism of these monocytes. Further, several histone-modifying epigenetic enzymes measured by qPCR were altered in mouse BM-Mono exposed to 24h hypoxia. CONCLUSIONS: Ischemia training in BM-Mono leads to a unique gene profile and improves blood flow and arteriogenesis after hindlimb ischemia.

Cx32 inhibits the autophagic effect of Nur77 in SH-SY5Y cells and rat brain with ischemic stroke.

The pathogenesis of cerebral ischemia-reperfusion (I/R) is complex. Cx32 expression has been reported to be up-regulated in ischemic lesions of aged human brain. Nevertheless, the function of Cx32 during cerebral I/R is poorly understood. Autophagy is of vital importance in the pathogenesis of cerebral I/R. In the current study, we found that oxygen-glucose deprivation/reoxygenation (OGD/R) or I/R insult significantly induced the up-regulation of Cx32 and activation of autophagy. Inhibition of Cx32 alleviated OGD/R or I/R injury, and further activated autophagy. In addition, Nur77 expression was found to be up-regulated after OGD/R or I/R. After inhibiting Cx32, the expression of Nur77 was further increased and Nur77 was translocated from nucleus to mitochondrial. Inhibition of Cx32 also activated mitophagy by promoting autophagosome formation and up-regulating the expression of mitochondrial autophagy marker molecules. Of note, in the siNur77-transfected cells, the number of dysfunctional mitochondrial was increased, and mitophagy was suppressed, which aggravated OGD/R-induced neuronal injury. In conclusion, Cx32 might act as a regulatory factor of Nur77 controlling neuronal autophagy in the brains. Understanding the mechanism of this regulatory pathway will provide new insight into the role Cx32 and Nur77 in cerebral ischemia, offering new opportunities for therapeutics.

A critical review on the environmental application of lipopeptide micelles.

The importance of lipopeptide micelles in environmental applications has been highlighted. These vessels exhibit various sizes, shapes, and surface properties under different environmental conditions. An in-depth understanding of the tunable assembling behavior of biosurfactant micelles is of great importance for their applications. However, a systematic review of such behaviors with assorted micro/nano micellar structures under given environmental conditions, particularly under low temperature and high salinity, remains untapped. Such impacts on their environmental applications have yet to be summarized. This review tried to fill the knowledge gaps by providing a comprehensive summary of the recent knowledge advancement in genetically regulated lipopeptides production, micelles associated decontamination mechanisms in low temperature and high salinity environments, and up-to-date environmental applications. This work is expected to deliver valuable insights to guide lipopeptide design and discovery. The mechanisms concluded in this study could inspire the forthcoming research efforts in the advanced environmental application of lipopeptide micelles.

Access-dispersion-recovery strategy for enhanced mitigation of heavy crude oil pollution using magnetic nanoparticles decorated bacteria.

Heavy crude oil (HCO) pollution has gained global attention, but traditional bioremediating practices demonstrate limited effectiveness. This study developed magnetic nanoparticles decorated bacteria (MNPB) using an oil-degrading and biosurfactant-producing Rhodococcus erythropolis species and identified a novel access-dispersion-recovery strategy for enhanced HCO pollution mitigation. The strategy entails (1) magnetic navigation of the MNPB towards HCO layer, (2) enhanced oil dispersion and formation of suspended oil-bacteria aggregates, and (3) magnetic recovery of these aggregates. The UV-spectrophotometer analysis showed that this strategy can enable up to 62% removal of HCO. The GC-MS analysis demonstrated that the MNPB enhanced the degradation of low-molecular-weight aromatics comparing with the pure bacteria, and the recovery process further removed oil-bacteria aggregates and entrained high-molecular-weight aromatics. The feasibility of using MNPB to mitigate HCO pollution could shed light on the emerging bioremediation applications.

Masitinib alleviated cerebral ischemia/reperfusion injury by inhibiting autophagy and apoptosis / 中国药科大学学报

@#To investigate the neuroprotective effect and possible mechanism of masitinib on cerebral ischemia-reperfusion injury in rats, healthy adult male Sprague-Dawley rats were divided into sham group (n = 12), model group (n = 12), masitinib low dosage group (n = 12), masitinib middle dosage group (n = 12), and masitinib high dosage group (n = 12). All rats was subjected to middle cerebral artery occlusion (MCAO) for two hours and reperfusion except sham group, and received treatment twice per day for 7 days once reperfusion started.Neurological score, infarct volume, and brain water content were detected; some autophagic markers, apoptotic and inflammatory cytokines were evaluated by Western blot and PCR after 7 d of reperfusion. Treatment with masitinib significantly ameliorated neurologic deficit, infarct volume and brain water after I/R injury. Masitinib also decreased the ratio of LC3II/I and the expression of Beclin-1 and increased the expression of p62 in the brain tissues of rats with I/R injury.Furthermore, it could inhibit apoptosis-related proteins and NF-κB expression. Masitinib could relieve the cerebral ischemia-reperfusion injury in rats through inhibiting autophagy and apoptosis.

Fish Waste Based Lipopeptide Production and the Potential Application as a Bio-Dispersant for Oil Spill Control.

There is a growing acceptance worldwide for the application of dispersants as a marine oil spill response strategy. The development of more effective dispersants with less toxicity and higher biodegradability would be a step forward in improving public acceptance and regulatory approvals for their use. By applying advances in environmental biotechnology, a bio-dispersant agent with a lipopeptide biosurfactant produced by Bacillus subtilis N3-1P as the key component was formulated in this study. The economic feasibility of producing biosurfactant (a high-added-value bioproduct) from fish waste-based peptone as a nutrient substrate was evaluated. Protein hydrolyzate was prepared from cod liver and head wastes obtained from fish processing facilities. Hydrolysis conditions (i.e., time, temperature, pH and enzyme to substrate level) for preparing protein hydrolyzates were optimized by response surface methodology using a factorial design. The critical micelle dilution (CMD) value for biosurfactant produced from the fish liver and head waste generated peptones was 54.72 and 47.59 CMD, respectively. Biosurfactant product generated by fish liver peptone had a low critical micelle concentration of 0.18 g L-1 and could reduce the surface tension of distilled water to 27.9 mN/m. Structure characterization proved that the generated biosurfactant product belongs to the lipopeptide class. An alternative to the key surfactant dioctyl sulfosuccinate sodium (DOSS) used in Corexit 9500 has been proposed based on a binary mixture of lipopeptides and DOSS that exhibited synergistic effects. Using the standard baffled flask test, a high dispersion efficiency of 76.8% for Alaska North Slope oil was achieved at a biodispersant composition of 80/20 (v/v) of lipopeptides/DOSS. The results show that fish waste can be utilized to produce a more effective, environmentally acceptable and cost-efficient biodispersant that can be applied to oil spills in the marine environment.

Discovery of coumarin-derived imino sulfonates as a novel class of potential cardioprotective agents.

The burst of reactive oxygen species (ROS) contributes to and exacerbates cardiac injury. Exogenous supplementation of antioxidants or upregulation of endogenous antioxidant defense genes should be the potential therapies for cardiovascular disease. Sixteen coumarin-derived imino sulfonates compounds were synthesized with the ability of attenuating oxidative stress directly by reducing intracellular ROS level via promoting Nrf2 pathway. The cell-based assays showed that most of the compounds had significant protective activity against H2O2-induced oxidative injury in H9c2 cells. Compound 5h with the highest activity and low cytotoxicity was demonstrated to remarkably remove the intracellular ROS accumulation by activating expressions of Nrf2 and its downstream antioxidant proteins (ie. HO-1 and NQO1), indicating a novel promising antioxidant and Nrf2 activator. Overall, these findings demonstrated that compound 5h could serve as a potential cardioprotective agent. Moreover, our study features developing new antioxidants and Nrf2 activators by introducing a sulfonyl group and nitrogen atom to the α,ß-unsaturated carbonyl entity in coumarin, rather than adding new functional groups or active fragments to coumarin itself.

A nanobody that recognizes a 14-residue peptide epitope in the E2 ubiquitin-conjugating enzyme UBC6e modulates its activity.

A substantial fraction of eukaryotic proteins is folded and modified in the endoplasmic reticulum (ER) prior to export and secretion. Proteins that enter the ER but fail to fold correctly must be degraded, mostly in a process termed ER-associated degradation (ERAD). Both protein folding in the ER and ERAD are essential for proper immune function. Several E2 and E3 enzymes localize to the ER and are essential for various aspects of ERAD, but their functions and regulation are incompletely understood. Here we identify and characterize single domain antibody fragments derived from the variable domain of alpaca heavy chain-only antibodies (VHHs or nanobodies) that bind to the ER-localized E2 UBC6e, an enzyme implicated in ERAD. One such VHH, VHH05 recognizes a 14 residue stretch and enhances the rate of E1-catalyzed ubiquitin E2 loading in vitroand interferes with phosphorylation of UBC6e in response to cell stress. Identification of the peptide epitope recognized by VHH05 places it outside the E2 catalytic core, close to the position of activation-induced phosphorylation on Ser184. Our data thus suggests a site involved in allosteric regulation of UBC6e's activity. This VHH should be useful not only to dissect the participation of UBC6e in ERAD and in response to cell stress, but also as a high affinity epitope tag-specific reagent of more general utility.

Fly ash based robust biocatalyst generation: a sustainable strategy towards enhanced green biosurfactant production and waste utilization.

Biosurfactants have been well recognized as an environmentally friendly alternative to chemical surfactants. However, their production remains challenging due to low productivity, short-term microbe stability and the potentially toxic by-products generated in the growth media. To overcome these challenges, the emerging biofilm-based biosynthesis was investigated in this study. A fresh insight into the biosynthesis process was provided through using waste fly ash as a carrier material. The biofilm produced by biosurfactant producer B. subtilis N3-1P attached onto the surface of fly ash acted as a robust and effective biocatalyst. Zeta potential analysis and scanning electron microscope (SEM) characterization were conducted to help unravel the biocatalyst formation. High-value biosurfactant products were then produced in an efficient and sustainable manner. Stimulation by a fly ash assisted biocatalyst on biosurfactant production was confirmed. The biosurfactant yield was boosted over ten times after 24 hours, at a fly ash dosage of 0.5%. The highest biosurfactant yield was achieved after five days, with a final productivity of 305 critical micelle dilution. The underlying mechanism of fly ash assisted biosurfactant production was tracked through it exerting an effect on the quorum sensing system. Fourier-transform infrared (FTIR) spectroscopy and matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis demonstrated that the final biosurfactant product belonged to the lipopeptides. This research output is expected to accelerate the development of more effective bioreactors, and make a continuous contribution to high-value product generation and waste reduction.

Immunometabolism features of metabolic deregulation and cancer.

Immunometabolism is a branch dealing at the interface of immune functionalities and metabolic regulations. Considered as a bidirectional trafficking, metabolic contents and their precursors bring a considerable change in immune cells signal transductions which as a result affect the metabolic organs and states as an implication. Lipid metabolic ingredients form a major chunk of daily diet and have a proven contribution in immune cells induction, which then undergo metabolic pathway shuffling inside their ownself. Lipid metabolic states activate relevant metabolic pathways inside immune cells that in turn prime appropriate responses to outside environment in various states including lipid metabolic disorders itself and cancers as an extension. Although data on Immunometabolism are still growing, but scientific community need to adjust and readjust according to recent data on given subject. This review attempts to provide current important data on Immunometabolism and consequently its metabolic ramifications. Incumbent data on various lipid metabolic deregulations like obesity, metabolic syndrome, obese asthma and atherosclerosis are analysed. Further, metabolic repercussions on cancers and its immune modalities are also analysed.

Targeted Delivery of Cyclotides via Conjugation to a Nanobody.

Many naturally occurring peptides have poor proteolytic stability, which limits their therapeutic applications. Cyclotides are plant-derived cyclic peptides that resist proteolysis due to their highly constrained structure, comprising a head-to-tail cyclic backbone and three disulfide bonds that form a cystine-knotted core. This structure makes them useful as scaffolds onto which peptide sequences (epitopes) can be grafted. In this study, VHH7, an alpaca-derived nanobody that targets murine class II MHC molecules, was used for the targeted delivery of cyclotides to antigen-presenting cells (APCs). The cyclotides MCoTI-I, and MCoTI-I with a HA-tag (YPYDVPDYA) grafted into loop 6 (MCoTI-HA), were tested for immunogenic properties. To produce the requisite VHH7-peptide conjugates, a site-specific sortase A-catalyzed reaction in combination with a copper-free strain-promoted cycloaddition reaction was used. MCoTI-I alone did not display any obvious antibody response, thus showing the capacity of cyclotides as immunologically silent scaffolds. By contrast, MCoTI-I conjugated to VHH7 elicited antibodies against cyclic or linear MCoTI-I, thus suggesting a simple and robust approach for targeting cyclotides to APCs, and potentially to other cell types. A similar antibody response was observed when MCoTI-HA was conjugated to VHH7, but there was no reactivity toward a linear HA-tag itself, suggesting differences in conformational constraint between cyclotide-presented and linear epitopes. Studies of commercially available HA antibodies applied to MCoTI-HA confirmed that the conformation of peptide immunogens affects their reactivity. Thus, the production of antibodies that recognize constrained epitopes may benefit from engraftment onto scaffolds such as cyclotides. More broadly, this study validates that a prototypic cyclotide, a member of a peptide family that has proven to be useful as drug design scaffolds in many other studies, can efficiently reach a specific target in vivo.