Lanthanide coordination polymers@CuO nanoparticles: Enhanced self-cascade nanoenzyme activity and ratiometric fluorescence assay of glutathione.

Tandem enzyme can catalyze some cascade reactions with high efficiency, and some few tandem enzyme-like mimics have been discovered recently. Further improving the catalytic efficiency of tandem nanoenzymes with facile method may undoubtedly promote and broaden their applications in various fields. In this work, cupric oxide nanoparticles (CuO NPs) with dual-functional enzyme mimics were synthesized using the rapid deposition method in advance, which simultaneously combined with lanthanide infinite coordination polymers (Ln ICPs) during the self-assemble of Tb3+, guanine-5'-triphosphate (GTP) and auxiliary ligand terephthalic acid (TA). Excitingly, the obtained Tb-GTP/TA@CuO ICPs, not only displayed obviously enhanced tandem catalytic activity compared with pure CuO NPs, but also provided a versatile ratiometric platform for ultrahigh selective and sensitive detection of glutathione (GSH) under single-wavelength excitation. A good linear relationship between the ratio signal and the GSH concentration was spanning from 0.001 to 20 µM with an impressive detection limit of 0.50 nM. This study opens a new and universal avenue for preparing integrated multifunctional probes by coupling of nanoenzyme catalytic activity with superior luminescent Ln ICPs through facile method.

Testing of Anti-EMT, Anti-Inflammatory and Antibacterial Activities of 2',4'-Dimethoxychalcone.

Chalcone (1,3-diaryl-2-propen-1-one) is an α, ß-unsaturated ketone that serves as an active constituent or precursor of numerous natural substances, exhibiting a broad spectrum of pharmacological effects. In this study, the classical Claisen-Schmidt condensation method was used to synthesize the chalcone derivative 2',4'-dimethoxychalcone (DTC) and evaluate its pharmacological activity. By upregulating the expression of the epithelial cell marker E-cadherin and downregulating the expression of the mesenchymal cell marker vimentin, DTC was found to inhibit transforming growth factor-ß1 (TGF-ß1)-induced epithelial-mesenchymal transition (EMT) process in A549 cells, maintaining the cells' epithelial-like morphology and reducing the ability of the cells to migrate. Additionally, DTC demonstrated the ability to decrease the expression levels of nitric oxide (NO), tumor necrosis factor (TNF-α), interleukin-6 (IL-6), and interleukin-1ß (IL-1ß) in RAW264.7 cells, suggesting a possible anti-inflammatory effect. Furthermore, DTC was found to exhibit bacteriostatic activity against Staphylococcus aureus (S. aureus), Proteus vulgaris (P. vulgaris), methicillin-resistant Staphylococcus aureus (MRSA), and Candida albicans (C. albicans), indicating that this chemical may possess broad-spectrum antibacterial activity.

Saccharomyces cerevisiae cellular engineering for the production of FAME biodiesel.

The unsustainable and widespread utilization of fossil fuels continues to drive the rapid depletion of global supplies. Biodiesel has emerged as one of the most promising alternatives to conventional diesel, leading to growing research interest in its production. Microbes can facilitate the de novo synthesis of a type of biodiesel in the form of fatty acid methyl esters (FAMEs). In this study, Saccharomyces cerevisiae metabolic activity was engineered to facilitate enhanced FAME production. Initially, free fatty acid concentrations were increased by deleting two acetyl-CoA synthetase genes (FAA1, FAA4) and an acyl-CoA oxidase gene (POX1). Intracellular S-adenosylmethionine (SAM) levels were then enhanced via the deletion of an adenosine kinase gene (ADO1) and the overexpression of a SAM synthetase gene (SAM2). Lastly, the S. cerevisiae strain overproducing free fatty acids and SAM were manipulated to express a plasmid encoding the Drosophila melanogaster Juvenile Hormone Acid O-Methyltransferase (DmJHAMT). Using this combination of engineering approaches, a FAME concentration of 5.79 ± 0.56 mg/L was achieved using these cells in the context of shaking flask fermentation. To the best of our knowledge, this is the first detailed study of FAME production in S. cerevisiae. These results will provide a valuable basis for future efforts to engineer S. cerevisiae strains for highly efficient production of biodiesel.

Copper-doped Lanthanide Coordination Polymers as Luminescent Nanoenzyme for Ratiometric Sensing of H2O2 and Glutathione.

Design and fabrication of integrated multifunctional probes with intrinsic catalytic and detection abilities is of great importance to simplify the operation in biosensing application with high sensitivity. Herein, dual-emitting lanthanide coordination polymers (Ln-CPs) were facilely prepared by self-assembly of guanine diphosphate (GDP), terephthalic acid (TA), Tb3+ and Cu2+ designated as Tb/Cu-GDP/TA CPs. The doped Cu2+ endowed CPs with obviously enhanced peroxidase mimicking activity compared with free Cu2+. In the presence of H2O2, the probe catalyzed the oxidation of TA generating a new blue fluorescent product, while the fluorescence of Tb3+ decreased simultaneously. Therefore, a new sensitive ratiometric fluorescent sensor for H2O2 has been developed with a good linear range from 0.01 to 300 µM and limit of 1.62 nM. Moreover, the proposed platform could be extended to GSH ratiometric assay in the presence of H2O2, and interestingly, the detection performance could be easily adjusted by adding different concentration of H2O2. This work will facilitate the development of luminescent nanoenzymes based on Ln-CPs to construct the simple ratiomatric sensing platform.

Chemical Composition, Antibacterial and Antioxidant Activities of Essential Oil from Centipeda minima.

This study elucidated the chemical composition of essential oil from Centipeda minima (EOCM) and its antibacterial and antioxidant activities with two chemical monomers thymol and carvacrol. The main chemical composition of EOCM, analyzed by GC-MS, were trans-chrysanthenyl acetate, thymol, aromadendrene and ß-caryophyllene. In the screening of antibacterial activity against S. aureus, two monomers with antibacterial activity were obtained: thymol and carvacrol. The MIC of EOCM, thymol and carvacrol were 0.625 mg/mL, 0.156 mg/mL and 0.156 mg/mL, respectively. The experimental results were shown that three drugs could inhibit the growth of S. aureus and inhibit the formation of biofilm by changing the permeability of cell membrane and interfering with the metabolic activities in bacteria. The scavenging effects of the three drugs on DPPH radical and hydroxyl radical showed that the antioxidant effect of the three drugs was EOCM > carvacrol > thymol.

Optimization of the Extraction Process and Antioxidant Activity of Polysaccharide Extracted from Centipeda minima.

The purpose of this study is to optimize the extraction process and study antioxidant activity of Polysaccharide extracted from Centipeda minima. The Box-Behnken design-response surface methodology was adopted to optimize the extraction process of polysaccharides from Centipeda minima. We purified the crude polysaccharides from Centipeda minima, as well as determined the purity, monosaccharide composition, and molecular weight of the purified fraction. Fourier transform infrared spectrometer (FT-IR) and scanning electron microscopy (SEM) were used to analyze the structural features of the polysaccharides. Further, we investigated the antioxidant activities of different fractions of polysaccharides. Consequently, the results showed that the optimum extraction conditions for polysaccharides were: a liquid-solid ratio of 26 mL/g, extraction temperature of 85.5 °C, and extraction time of 2.4 h. Moreover, the yield of polysaccharides measured under these conditions was close to the predicted value. After purification, we obtained four components of Centipeda minima polysaccharides (CMP). The purity, monosaccharide composition, molecular weight, and structural characteristics of CMP were different, but with similar infrared absorption spectra. CMP exhibited a typical infrared absorption characteristic of a polysaccharide. Besides, CMP displayed good antioxidant activity, with potential to scavenge DPPH radical, hydroxyl radical, and superoxide radical. Therefore, this study provides a reference for future research on the structure and biological activity of CMP, and lays a theoretical foundation for food processing and medicinal development of CMP.

Acupuncture inhibits mammalian target of rapamycin, promotes autophagy and attenuates neurological deficits in a rat model of hemorrhagic stroke.

BACKGROUND: Intracerebral hemorrhage (ICH) accounts for approximately 15% of all stroke cases. Previous studies suggested that acupuncture may improve ICH-induced neurological deficits. Therefore, we investigated the effects of acupuncture on neurological deficits in an animal model of ICH. METHODS: Adult male Sprague-Dawley rats were injected with autologous blood (50 µL) into the right caudate nucleus. Additional rats underwent sham surgery as controls. ICH rats either received acupuncture (GV20 through GB7 on the side of the lesion) or sham acupuncture (1 cm to the right side of the traditional acupuncture point locations). Some ICH rats received acupuncture plus rapamycin injection into the right lateral ventricle. Neurological deficits in the various groups were assessed based on composite neurological score. The perihemorrhagic penumbra was analyzed by histopathology following hematoxylin-eosin staining. Levels of autophagy-related proteins light chain (LC)3 and p62 as well as of mammalian target of rapamycin (mTOR)-related proteins, and phosphorylated (p)-mTOR and p-S6K1 (ribosomal protein S6 kinase beta-1), were assessed by Western blotting. RESULTS: Acupuncture significantly improved composite neurological scores 7 days after ICH (17.7 ± 1.49 vs 14.8 ± 1.32, p < 0.01). Acupuncture augmented autophagosome and autolysosome accumulation based on transmission electron microscopy. Acupuncture significantly increased expression of LC3 (p < 0.01) but decreased expression of p62 (p < 0.01). Acupuncture also reduced levels of p-mTOR and p-S6K1 (both p < 0.01). CONCLUSION: Acupuncture improved neurological deficits in a rat model of ICH, possibly by inhibiting the mTOR pathway and activating autophagy.

Evaluation and intervention of postoperative delirium in pediatric otolaryngology: from best evidence to clinical practice / 中国实用护理杂志

Objective:To establish a scientific and standardized routine for perioperative nursing in pediatric otolaryngology, reduce the incidence of postoperative delirium, and improve the quality of postoperative recovery by implementing the best practice of evaluation and intervention of postoperative delirium in pediatric otolaryngology.Methods:By reviewing literature related to evaluation, prevention, intervention and management of postoperative delirium in pediatric otolaryngology from March 2018 to September 2019, fourteen best practice were concluded. By combining the best evidence and the clinical circumstances, the evidenced-based criteria were established and then applied in the Otolaryngology and Head and Neck Surgery Department, the Children ′s Hospital of Zhejiang University School of Medicine. Results:After three rounds of reviews, the results showed that the criteria 2, 3, 6, and 8 had 100.0% complacence. Comparison of before and after applying the evidence, there was no statistically significant difference for the occurrence of postoperative delirium or pain ( P>0.05); there was a statistically significant reduction of pain score at 60 minutes after returning to the ward ( χ2=9.93, P<0.05); there was a statistically significant reduction of preoperative anxiety score of children ′s family members from (33.36 ± 6.84) points to (29.54 ± 6.94) points ( F=6.33, P<0.05); there was a statistically significant increase of doctors ′ score of delirium knowledge based on evidence from (23.00 ± 3.94) points to (33.43 ± 8.25) points ( t=-3.02, P<0.05); and there was a statistically significant increase of nurses ′ score of delirium knowledge based on evidence from (33.11 ± 8.46) points to (57.79 ± 6.58) points ( t=-10.35, P<0.05) when the evidence was applied. Conclusion:The evidence-based practice didn ′t significantly relieve the postoperative delirium in pediatric otolaryngology, but it was helpful to relieve the postoperative pain level of children and the anxiety level of their families. The management of postoperative delirium in pediatric otolaryngology needs to be further explored.

[Effect of Bo's abdominal acupuncture as adjunctive therapy on rheumatoid arthritis and ESR, RF and CRP levels].

OBJECTIVE: To explore the therapeutic effect on rheumatoid arthritis treated with Bo's abdominal acupuncture for "guiding qi to the source" plus "opening four gates on the abdomen" and the relevant effect mechanism. METHODS: A total of 104 patients with rheumatoid arthritis were randomized into and an observation group (52 cases, 1 case dropped off) and a control group (52 cases, 3 cases dropped off). In the control group, methotrexate tablets were prescribed for oral administration, 5 mg each time, once a week. In the observation group, on the base of the treatment as the control group, Bo's abdominal acupuncture was combined. The acupoints included Zhongwan (CV 12), Xiawan (CV 10), Guanyuan (CV 4), Qihai (CV 6), Huaroumen (ST 24), Wailing (ST 26), etc. The treatment was given once every two days, 3 times weekly. Totally 12 weeks were required in the two groups. Before and after treatment, the score of TCM symptoms (including joint pain, the range of motion, joint swelling and morning stiffness), and the levels of erythrocyte sedimentation rate (ESR), rheumatoid factor (RF) and C-reactive protein (CRP) were observed and the clinical therapeutic effect was assessed in the two groups. RESULTS: After treatment, the total effective rate was 88.2% (45/51) in the observation group, higher than 73.5% (36/49) in the control group (P<0.05). The score of each TCM symptom and the total scores after treatment were all lower than those before treatment in the two groups (P<0.05), and these scores in the observation group were lower than the control group (P<0.05). After treatment, the levels of ESR, RF and CRP were all lower than those before treatment in the two groups (P<0.05), while the levels of those indexes in the observation group were lower than the control group (P<0.05). CONCLUSION: Bo's abdominal acupuncture for "guiding qi to the source" plus "opening four gates on the abdomen" as the adjunctive therapy effectively relieves the clinical symptoms in the patients with rheumatoid arthritis, which is related to the reduction of ESR, RF and CRP in mechanism.

Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae.

In Saccharomyces cerevisiae, Atg9 is an important autophagy-related (Atg) protein, and interacts with hundreds of other proteins. How many Atg9-interacting proteins are involved in macroautophagy/autophagy is unclear. Here, we conducted a multi-omic profiling of Atg9-dependent molecular landscapes during nitrogen starvation-induced autophagy, and identified 290 and 256 genes to be markedly regulated by ATG9 in transcriptional and translational levels, respectively. Unexpectedly, we found most of known Atg proteins and autophagy regulators that interact with Atg9 were not significantly changed in the mRNA or protein level during autophagy. Based on a hypothesis that proteins with similar molecular characteristics might have similar functions, we developed a new method named inference of functional interacting partners (iFIP) to integrate the transcriptomic, proteomic and interactomic data, and predicted 42 Atg9-interacting proteins to be potentially involved in autophagy, including 15 known Atg proteins or autophagy regulators. We validated 2 Atg9-interacting partners, Glo3 and Scs7, to be functional in both bulk and selective autophagy. The mRNA and protein expressions but not subcellular localizations of Glo3 and Scs7 were affected with or without ATG9 during autophagy, whereas the colocalizations of the 2 proteins and Atg9 were markedly enhanced at early stages of the autophagic process. Further analyses demonstrated that Glo3 but not Scs7 regulates the retrograde transport of Atg9 during autophagy. A working model was illustrated to highlight the importance of the Atg9 interactome. Taken together, our study not only provided a powerful method for analyzing the multi-omics data, but also revealed 2 new players that regulate autophagy.Abbreviations: ALP: alkaline phosphatase; Arf1: ADP-ribosylation factor 1; Atg: autophagy-related; Co-IP: co-immunoprecipitation; Cvt: cytoplasm-to-vacuole targeting; DEM: differentially expressed mRNA; DEP: differentially expressed protein; DIC: differential interference contrast; E-ratio: enrichment ratio; ER: endoplasmic reticulum; ES: enrichment score; FC: fold change; FPKM: fragments per kilobase of exon per million fragments mapped; GAP: GTPase-activating protein; GFP: green fluorescent protein; GO: gene ontology; GSEA: gene set enrichment analysis; GST: glutathione S-transferase; HA: hemagglutinin; iFIP: inference of functional interacting partners; KO: knockout; LR: logistic regression; OE: over-expression; PAS: phagophore assembly site; PPI: protein-protein interaction; RFP: red fluorescence protein; RNA-seq: RNA sequencing; RT-PCR: real-time polymerase chain reaction; SCC: Spearman's correlation coefficient; SD-N: synthetic minimal medium lacking nitrogen; THANATOS: The Autophagy, Necrosis, ApopTosis OrchestratorS; Vsn: variance stabilization normalization; WT: wild-type.

An integrative multi-omics approach uncovers the regulatory role of CDK7 and CDK4 in autophagy activation induced by silica nanoparticles.

Dysfunction of macroautophagy/autophagy has been postulated as a major cellular toxicological response to nanomaterials. It has been reported that excessive autophagy activation, induced by silica nanoparticles (SiNPs), contributes to autophagy dysfunction, whereas little is known how SiNPs trigger autophagy activation. Here, we treated normal rat kidney (NRK) cells using 3 different sizes of SiNPs (16, 29, and 51 nm) and observed that 16-nm SiNPs, with a final concentration of 60 µg/mL, dramatically induce autophagy activation without reducing cell viability. We further conducted a transcriptomic, proteomic, and phosphoproteomic profiling, and detected 23 autophagy-related (Atg) genes and 35 autophagy regulators regulated on at least one omic layer. To identify key regulators from the multi-omics data, we developed a new algorithm of computational prediction of master autophagy-regulating kinases (cMAK) to detect 21 candidates and revealed the CDK7-CDK4 cascade to be functional. The silence or inhibition of Cdk7 or Cdk4 significantly attenuated autophagic activation but not influenced autophagic flux blockage induced by 16-nm SiNPs. Further computational modeling indicated that the CDK7-CDK4 signaling axis potentially triggers autophagy activation by phosphorylating RB1 (RB transcriptional corepressor 1), activating two critical transcription factors, E2F1 (E2F transcription factor 1) and FOXO3 (forkhead box O3), and enhancing the transcriptional levels of at least 8 Atg genes and autophagy regulators in response to SiNPs. Our studies not only established a powerful method for predicting regulatory kinases from the multi-omics data but also revealed a potential mechanism of SiNP-triggered autophagy activation through modulating the CDK7-CDK4 cascade.Abbreviations: 3-MA: 3-methyladenine; Atg: autophagy-related; BECN1: beclin 1; CCK-8: cell counting kit-8; CDK4: cyclin dependent kinase 4; CDK7: cyclin dependent kinase 7; cMAK: computational prediction of master autophagy-regulating kinases; CQ: chloroquine; DMEM: Dulbecco's modified Eagle's medium; DMSO: dimethyl sulfoxide; E-ratio: enrichment ratio; E2F1: E2F transcription factor 1; EBSS: Earle's balanced salt solution; ER: endoplasmic reticulum; FOXO3: forkhead box O3; FPKM: fragments per kilobase of exon per million fragments mapped; GO: gene ontology; H2O2: hydrogen peroxide; iGPS: in vivo GPS; KEGG: Kyoto Encyclopedia of Genes and Genomes; LC-MS/MS: liquid chromatography-tandem mass spectrometry; LDH: lactate dehydrogenase; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; NRK: normal rat kidney; p-site: phosphorylation site; PBS: phosphate-buffered saline; PDI: polydispersity index; PTM: post-translational modification; QKS: quantitative kinase state; RB1: RB transcriptional corepressor 1; RBHs: reciprocal best hits; RNA-Seq: RNA sequencing; ROS: reactive oxygen species; rSiNPs: SiNPs fluorescently labeled with rhodamine B; SEM: scanning electronic microscopy; SiNPs: silica nanoparticles; siRNA: small interfering RNA; SQSTM1/p62: sequestosome 1; ssKSR: site-specific kinase-substrate relation; TEM: transmission electron microscopy; tfLC3: mRFP-GFP tandem fluorescent-tagged LC3.

EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes.

As an important post-translational modification (PTM), protein phosphorylation is involved in the regulation of almost all of biological processes in eukaryotes. Due to the rapid progress in mass spectrometry-based phosphoproteomics, a large number of phosphorylation sites (p-sites) have been characterized but remain to be curated. Here, we briefly summarized the current progresses in the development of data resources for the collection, curation, integration and annotation of p-sites in eukaryotic proteins. Also, we designed the eukaryotic phosphorylation site database (EPSD), which contained 1 616 804 experimentally identified p-sites in 209 326 phosphoproteins from 68 eukaryotic species. In EPSD, we not only collected 1 451 629 newly identified p-sites from high-throughput (HTP) phosphoproteomic studies, but also integrated known p-sites from 13 additional databases. Moreover, we carefully annotated the phosphoproteins and p-sites of eight model organisms by integrating the knowledge from 100 additional resources that covered 15 aspects, including phosphorylation regulator, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein-protein interaction, drug-target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, protein expression/proteomics and subcellular localization. We anticipate that the EPSD can serve as a useful resource for further analysis of eukaryotic phosphorylation. With a data volume of 14.1 GB, EPSD is free for all users at http://epsd.biocuckoo.cn/.

Effects of intense pulsed light and gamma irradiation on Bacillus cereus spores in mesquite pod flour.

This study was conducted to evaluate the inactivation of Bacillus cereus spore in mesquite flour with intense pulsed light (IPL) and gamma radiation. The physical, chemical, and toxicity of treated mesquite flour were also investigated. The results showed that up to 3.51 log10CFU/g B. cereus spore inactivation was achieved with 8 kGy of gamma radiation, and up to 1.69 log10CFU/g reductions could be achieved after 28s of catalytic IPL exposure. Although chemometric analysis showed 9-hydroxy-10,12-octadecadienoic acid was slightly increased after a 28s-catalytic IPL treatment, the concentration is within the acceptable range. No significant increase in acetic or propionic acids (typical off-flavor volatile compounds) was observed after either treatment. For cytotoxicity, the Caco-2 cell viability analysis revealed that these two technologies did not induce significant cytotoxicity to the treated mesquite flour. Overall, these two technologies exhibit strong potential for the decontamination of B. cereus in mesquite flour.

[Effect of acupuncture on NLRP3 inflammatory corpuscle in rats with intracerebral hemorrhage].

OBJECTIVE: To observe the effect of acupuncture at "Baihui" (GV 20) through "Qubin" (GB 7) on NLRP3 inflammatory corpuscle in rats with intracerebral hemorrhage (ICH), and to explore the action mechanism of acupuncture on promoting the recovery of neural function in rats with ICH. METHODS: Forty SPF six-week-old male SD rats were randomly divided into a sham operation group, a model group, a non-acupoint group and an acupuncture group, 10 rats in each group. The rats in the model group, non-acupoint group and acupuncture group were intervened with autologous blood injection to prepare ICH model, while the rats in the sham operation group were only intervened with operation but not injection with autologous blood. About 3 hours after the establishment of the model, the rats in the acupuncture group were intervened with acupuncture at "Baihui" (GV 20) through "Qubin" (GB 7), once every 12 hours, for 7 days; the rats in the non-acupoint group were intervened with acupuncture at the non-acupoint [parallel to the "Baihui" (GV 20), 1 cm next to the midline] on the affected side, and other treatment was the same as the acupuncture group. At the end of the intervention, the composite nerve function score of each group was evaluated; the histomorphology of the hemorrhage penumbra was observed by HE staining; the expression of NLRP3 inflammatory corpuscle in the brain was detected by immunohistochemistry; the relative protein expression levels of NLRP3, interleukin-1ß (IL-1ß) and interleukin-18 (IL-18) in brain were detected by the method of Western blot. RESULTS: Seven days into intervention, compared with the sham operation group, each item score and total score of composite nerve function in the model group were significantly reduced (P<0.01, P<0.05). There was edema and karyopyknosis in brain neuron as well as necrocytosis and inflammatory cell infiltration in the model group. Compared with the model group and the non-acupoint group, the total score of composite nerve function and the scores of symmetrical movement of limbs (LS) and proprioception of tentacles (VP) in the acupuncture group were increased (P<0.01, P<0.05), and the cell necrosis and inflammatory cell infiltration were relieved. Compared with the sham operation group, NLRP3 inflammatory corpuscle expression and the relative protein expression levels of NLRP3, IL-1ß and IL-18 in brain tissue in the model group were increased (P<0.01); compared with the model group and the non-acupoint group, NLRP3 inflammatory corpuscle expression and the relative protein expression levels of NLRP3, IL-1ß and IL-18 in brain tissue in the acupuncture group were reduced (P<0.01). CONCLUSION: Acupuncture at "Baihui" (GV 20) through "Qubin" (GB 7) could downregulate the expression of NLRP3, IL-1ß and IL-18 in the brain tissue of ICH rats, inhibit the inflammatory response, and promote the recovery of neural function.

DeepPhagy: a deep learning framework for quantitatively measuring autophagy activity in Saccharomyces cerevisiae.

Seeing is believing. The direct observation of GFP-Atg8 vacuolar delivery under confocal microscopy is one of the most useful end-point measurements for monitoring yeast macroautophagy/autophagy. However, manually labelling individual cells from large-scale sets of images is time-consuming and labor-intensive, which has greatly hampered its extensive use in functional screens. Herein, we conducted a time-course analysis of nitrogen starvation-induced autophagy in wild-type and knockout mutants of 35 AuTophaGy-related (ATG) genes in Saccharomyces cerevisiae and obtained 1,944 confocal images containing > 200,000 cells. We manually labelled 8,078 autophagic and 18,493 non-autophagic cells as a benchmark dataset and developed a new deep learning tool for autophagy (DeepPhagy), which exhibited superior accuracy in recognizing autophagic cells compared to other existing methods, with an area under the curve (AUC) value of 0.9710 from 10-fold cross-validations. We further used DeepPhagy to automatically analyze all the images and quantitatively classified the autophagic phenotypes of the 35 atg knockout mutants into 3 classes. The high consistency in our computational and biochemical results indicated the reliability of DeepPhagy for measuring autophagic activity. Moreover, we used DeepPhagy to analyze 3 additional types of autophagic phenotypes, including the targeting of Atg1-GFP to the vacuole, the vacuolar delivery of GFP-Atg19, and the disintegration of autophagic bodies indicated by GFP-Atg8, all with satisfying accuracies. Taken together, our study not only enables the GFP-Atg8 fluorescence assay to become a quantitative measurement for analyzing autophagic phenotypes in S. cerevisiae but also demonstrates that deep learning-based methods could potentially be applied to different types of autophagy.Abbreviations:Ac: accuracy; ALP: alkaline phosphatase; ALR: autophagic lysosomal reformation; ATG: AuTophaGy-related; AUC: area under the curve; CNN: convolutional neural network; Cvt: cytoplasm-to-vacuole targeting; DeepPhagy: deep learning for autophagy; fc_2: second fully connected; GFP: green fluorescent protein; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3 beta; HAT: histone acetyltransferase; HemI: Heat map Illustrator; JRE: Java Runtime Environment; KO: knockout; LRN: local response normalization; MCC: Mathew Correlation Coefficient; OS: operating system; PAS: phagophore assembly site; PC: principal component; PCA: principal component analysis; PPI: protein-protein interaction; Pr: precision; QPSO: Quantum-behaved Particle Swarm Optimization; ReLU: rectified linear unit; RF: random forest; ROC: receiver operating characteristic; ROI: region of interest; SD: systematic derivation; SGD: stochastic gradient descent; Sn: sensitivity; Sp: specificity; SRG: seeded region growing; t-SNE: t-distributed stochastic neighbor embedding; 2D: 2-dimensional; WT: wild-type.

[Penetrative needling improves neurological function by up-regulating expression of autophagy related protein LC3 in rats with hemorrhagic stroke].

OBJECTIVE: To observe the effect of penetrative needling from "Baihui" (GV20) to "Qubin" (GB7) on neurological function and expression of autophagy related protein microtubule-associated protein, light chain 3 (LC3) in rats with hemorrhagic stroke, so as to explore its mechanism underlying improvement of hemorrhagic stroke. METHODS: A total of 120 male SD rats were randomly divided into sham operation, model, non-acupoint, acupuncture and medication (Rapamycin) groups which were further divided into two time-point subgroups (3, 7 days after modeling, n=12/subgroup). The intracerebral hemorrhage model was established by injection of the rat's auto-blood (50 µL) into the putaman region. Penetrative needling from GV20 to GB7 or sham acupoints (about 1 cm beside GV20 and GB7) was conducted for 30 min, twice daily for 7 days. For rats of the medication group, Rapamycin solution (7 µmol/L) was injected into the right lateral ventricle. The neurological functions (locomotor and balance deficits) were evaluated according to suspended wire test (0-6 points) and horizontal board walking test (0-6 points). Immunohistochemistry and Western blot were used to detect the expression of total LC3 and expression of LC3-Ⅰ and LC3-Ⅱ proteins in the ischemic penumbra region of brain tissue, respectively. RESULTS: After modeling, the neurological function scores were significantly decreased on day 3 and 7, the levels of LC3-Ⅱ/Ⅰ and LC3 protein on day 3 and 7 were significantly increased in the model group relevant to the sham operation group (P<0.05). Following the interventions, the neurological function scores as well as LC3-Ⅱ/Ⅰ and LC3 protein expression were significantly increased in both acupuncture and medication groups compared with the model group (P<0.05). The effect of Rapamycin was obviously stronger than that of penetrative needling in up-regulating the expression of LC3-Ⅱ/Ⅰ and LC3 protein (P<0.05). CONCLUSION: Penetrative needling can improve neurologic function in hemorrhagic stroke rats, which is related with its effect in up-regulating the expression of autophagy-related protein LC3.

The evaluation of resistance to Co 2+ of lawn plant at seedling stage and its concentration property at adult stage.

In order to evaluate the resistance of lawn plant to Co2+ at germination stage and discuss its concentration property at adult stage, four kinds of lawn plant which have some growth advantages in Co2+ polluted environment were selected as experimental materials in this research. They are tall fescue, timothy grass, inflorescences, and annual ryegrass. The results show that the evaluation of resistance to Co2+ of tall fescue's seed is the highest; the evaluation of resistance to Co2+ of annual ryegrass seed is the lowest. The low consistence Co2+ could improve the seed germination. With Co2+ concentration increase, the accumulation coefficient of four plants increased at first and decreased later; the accumulation coefficient of underground portion is higher than the accumulation coefficient of aboveground; with Co2+ concentration increase, the transfer coefficient of four plants have a remarkable decline. In these plants, the accumulation coefficient of tall fescue and annual ryegrass is bigger than other two plants. As the concentration of Co2+ treatment increased to 100 mg/kg, the aboveground enrichment of Co2+ in F. elata reached 75 mg/kg, followed by L. multiflorum (68.9 mg/kg), P. pratense (48.8 mg/kg), and D. glomerata (27.2 mg/kg).The highest underground enrichment of Co2+ in F. elata reached 836.46 mg/kg, in contrast to the lowest underground enrichment in D. glomerata, 264.67 mg/kg. It shows that fescue and annual ryegrass have a better enrichment property to Co2+ and have a better prospect for the treatment of cobalt-contaminated soil. This research could provide some scientific basis and main technical approach for the soil contaminated by Co2+.