Accurately identifying positive and negative regulation of apoptosis using fusion features and machine learning methods.

Apoptotic proteins play a crucial role in the apoptosis process, ensuring a balance between cell proliferation and death. Thus, further elucidating the regulatory mechanisms of apoptosis will enhance our understanding of their functions. However, the development of computational methods to accurately identify positive and negative regulation of apoptosis remains a significant challenge. This work proposes a machine learning model based on multi-feature fusion to effectively identify the roles of positive and negative regulation of apoptosis. Initially, we constructed a reliable benchmark dataset containing 200 positive regulation of apoptosis and 241 negative regulation of apoptosis proteins. Subsequently, we developed a classifier that combines the support vector machine (SVM) with pseudo composition of k-spaced amino acid pairs (PseCKSAAP), composition transition distribution (CTD), dipeptide deviation from expected mean (DDE), and PSSM-composition to identify these proteins. Analysis of variance (ANOVA) was employed to select optimized features that could yield the maximum prediction performance. Evaluating the proposed model on independent data revealed and achieved an accuracy of 0.781 with an AUROC of 0.837, demonstrating our model's potent capabilities.

Effect of tacrolimus on the expression of Park7 in glomerular podocytes injured by puromycin aminonucleoside. / ä»–å ‹èŽ«å¸å¯¹å˜Œå‘¤éœ‰ç´ æŸä¼¤çš„è‚¾å°çƒè¶³ç»†èƒžé‡ç»„äººå¸•é‡‘æ£®è›‹ç™½7表达的影响.

OBJECTIVES: To study the effect of puromycin aminonucleoside (PAN) on the apoptosis of mouse podocyte clone 5 (MPC-5) and the expression of recombinant human Parkinson's disease 7 (Park7) and to study the protective mechanism of tacrolimus (FK506) against MPC-5 injury. METHODS: MPC-5 cells were cultured in vitro and then divided into three groups: blank control (control), PAN, and FK506. The cells in the PAN group were added with PAN (with a concentration of 50 mg/L) to establish a model of MPC-5 injury, and those in the FK506 group were added with PAN (with a concentration of 50 mg/L) and FK506 (with a concentration of 5 mg/L). An inverted microscope was used to observe the morphology and structure of MPC-5 cells at 12, 24, and 48 hours after treatment. Flow cytometry was used to measure cell apoptosis rate. Quantitative real-time PCR was used to measure the mRNA expression of Park7. Western blot and immunofluorescent staining were used to measure the protein expression of Park7. RESULTS: The control group had a large number of foot processes of the cell body at all time points, with tight connections between cells and a normal morphology. Compared with the control group, the PAN group had a significantly smaller cell volume at all time points, with loose connections between cells and the presence of ruptured cells. Compared with the PAN group, the FK506 group had an increased cell volume at all time points, with tighter connections between cells and a better morphology. The PAN group had a significantly higher apoptosis rate than the control group at all time points. Compared with the PAN group, the FK506 group had a significant reduction in the apoptosis rate at all time points (P<0.01). The PAN group had a significantly higher mRNA expression level of Park7 than the control group at all time points. Compared with the PAN group, the FK506 group had a significant reduction in the mRNA expression level of Park7 at all time points (P<0.01). Western blot showed that the PAN group had a significantly higher protein expression level of Park7 than the control group at all time points. Compared with the PAN group, the FK506 group had a significant reduction in the protein expression level of Park7 at all time points (P<0.01). Immunofluorescent staining showed that in the PAN group, there was a significantly lower expression of Park7 protein in cell membrane and cytoplasm, with a dense cluster distribution and increased fluorescence intensity. Compared with the PAN group, the FK506 group had a significant improvement in the distribution of Park7 protein. CONCLUSIONS: PAN can act on MPC-5 cells and cause morphological and structural damage and apoptosis of MPC-5 cells, as well as upregulated mRNA and protein expression of Park7. FK506 can downregulate the mRNA and protein expression of Park7 in the model of MPC-5 injury, maintain cellular homeostasis, reduce proteinuria, and delay glomerulosclerosis.

Effects of tacrolimus on autophagy protein LC3 in puromycin-damaged mouse podocytes.

OBJECTIVE: To investigate the mechanism through which tacrolimus, often used to treat refractory nephropathy, protects against puromycin-induced podocyte injury. METHODS: An in vitro model of puromycin-induced podocyte injury was established by dividing podocytes into three groups: controls, puromycin only (PAN group), and puromycin plus tacrolimus (FK506 group). Podocyte morphology, number, apoptosis rate and microtubule associated protein 1 light chain 3 alpha (LC3) expression were compared. RESULTS: Puromycin caused podocyte cell body shrinkage and loose intercellular connections, but podocyte morphology in the FK506 group was similar to controls. The apoptosis rate was lower in the FK506 group versus PAN group. The low level of LC3 mRNA observed in untreated podocytes was decreased by puromycin treatment; however, levels of LC3 mRNA were higher in the FK506 group versus PAN group. Although LC3-I and LC3-II protein levels were decreased by puromycin, levels in the FK506 group were higher than the PAN group. Fewer podocyte autophagosomes were observed in the control and FK506 groups versus the PAN group. Cytoplasmic LC3-related fluorescence intensity was stronger in control and FK506 podocytes versus the PAN group. CONCLUSIONS: Tacrolimus inhibited puromycin-induced mouse podocyte damage by regulating LC3 expression and enhancing autophagy.

Insulin-like growth factor-1 improves diabetic cardiomyopathy through antioxidative and anti-inflammatory processes along with modulation of Akt/GSK-3ß signaling in rats.

Diabetic cardiomyopathy (DCM), a serious complication of diabetes mellitus, is associated with changes in myocardial structure and function. This study sought to explore the ability of insulin-like growth factor-1 (IGF-1) to modulate DCM and its related mechanisms. Twenty-four male Wistar rats were injected with streptozotocin (STZ, 60 mg/kg) to mimic diabetes mellitus. Myocardial fibrosis and apoptosis were evaluated by histopathologic analyses, and relevant proteins were analyzed by Western blotting. Inflammatory factors were assessed by ELISA. Markers of oxidative stress were tested by colorimetric analysis. Rats with DCM displayed decreased body weight, metabolic abnormalities, elevated apoptosis (as assessed by the bcl-2/bax ratio and TUNEL assays), increased fibrosis, increased markers of oxidative stress (MDA and SOD) and inflammatory factors (TNF-α and IL-1ß), and decreased phosphorylation of Akt and glycogen synthase kinase (GSK-3ß). IGF-1 treatment, however, attenuated the metabolic abnormalities and myocardial apoptosis, interstitial fibrosis, oxidative stress and inflammation seen in diabetic rats, while also increasing the phosphorylation levels of Akt and GSK-3ß. These findings suggest that IGF-1 ameliorates the pathophysiological progress of DCM along with an activation of the Akt/GSK-3ß signaling pathway. Our findings suggest that IGF-1 could be a potential therapeutic choice for controlling DCM.

[Study on the method for the determination of trace boron, molybdenum, silver, tin and lead in geochemical samples by direct current arc full spectrum direct reading atomic emission spectroscopy (DC-Arc-AES)].

The method for the determmation of trace boron, molybdenum, silver, tin and lead in geochemical samples by direct current are full spectrum direct reading atomic emission spectroscopy (DC-Arc-AES) was established. Direct current are full spectrum direct reading atomic emission spectrometer with a large area of solid-state detectors has functions of full spectrum direct reading and real-time background correction. The new electrodes and new buffer recipe were proposed in this paper, and have applied for national patent. Suitable analytical line pairs, back ground correcting points of elements and the internal standard method were selected, and Ge was used as internal standard. Multistage currents were selected in the research on current program, and each current set different holding time to ensure that each element has a good signal to noise ratio. Continuous rising current mode selected can effectively eliminate the splash of the sample. Argon as shielding gas can eliminate CN band generating and reduce spectral background, also plays a role in stabilizing the are, and argon flow 3.5 L x min(-1) was selected. Evaporation curve of each element was made, and it was concluded that the evaporation behavior of each element is consistent, and combined with the effects of different spectrographic times on the intensity and background, the spectrographic time of 35s was selected. In this paper, national standards substances were selected as a standard series, and the standard series includes different nature and different content of standard substances which meet the determination of trace boron, molybdenum, silver, tin and lead in geochemical samples. In the optimum experimental conditions, the detection limits for B, Mo, Ag, Sn and Pb are 1.1, 0.09, 0.01, 0.41, and 0.56 microg x g(-1) respectively, and the precisions (RSD, n=12) for B, Mo, Ag, Sn and Pb are 4.57%-7.63%, 5.14%-7.75%, 5.48%-12.30%, 3.97%-10.46%, and 4.26%-9.21% respectively. The analytical accuracy was validated by national standards and the results are in agreement with certified values. The method is simple, rapid, is an advanced analytical method for the determination of trace amounts of geochemical samples' boron, molybdenum, silver, tin and lead, and has a certain practicality.

[Determination of high content of tin in geochemical samples by solid emission spectrometry].

A method for the determination of high content of tin in geochemical samples by solid emission spectrometry was presented. The dedicated high content tin spectrum standard series was developed. K2S2O7, NaF, Al2O3 and carbon powder were used as buffers and Ge was used as internal standard, and the ratio of sample/matrix/buffer is 1 : 1 : 2. A weak sensitive line (Sn 242. 170 0 nm) was used as the analytical line. The technologies of vertical electrodes, AC arc overlap spectrograph, interception of the exposure, quantitative computer translation spectrum and background correction were used. The determination range is 100-22 350 microg x g(-1), the detection limit is 16.64 microg x g(-1), and the precision is (RSD, n = 12) 4.11%-6.46%. The accuracy of the method has been verified by determination of high content of tin in national geochemical standard samples and the results are in agreement with certified value. The method can be used for measurement directly without dilution of high content of tin in geochemical samples, and it greatly improved the detection upper limit for the determination of tin with solid emission spectroscopy and has certain practical value.

[Study on the differentially expressed genes of steroid-resistant and steroid-sensitive nephrotic syndrome].

OBJECTIVE: To identify the genes differentially expressed among the steroid-resistant nephrotic syndrome (SRNS), steroid-sensitive nephrotic syndrome (SSNS) and normal children, and understand the molecular mechanism of SRNS. METHODS: Affymetrix microarray technology was used to obtain such a profile. The differentially expressed genes among these groups were identified based on signal-to-noise ratios by GCOS software; real-time PCR analysis was performed to confirm the microarray results. RESULTS: There were 157 genes differentially expressed among these groups. The genes up-regulated both in SRNS and SSNS were involved primarily in ionic transportation, immuno-signal transduction and apoptosis. In particular, CLNS1A gene was down regulated in SRNS but up regulated in SSNS. CONCLUSION: Several differentially expressed genes, such as CLNS1A and HLA-DRB4 were found to be closely related to the pathogenesis of SRNS and SSNS. This DNA microarray analysis has provided some important clue to the molecular mechanism of SRNS.

[Effects of fosinopril on proliferation and secretion of extracellular matrix of rat glomerular mesangial cell].

OBJECTIVE: To observe the effects of fosinopril (FOS) on proliferation and secretion of extracellular matrix of rat glomerular mesangial cell induced by LPS. METHODS: In vitro culture method for glomerular mesangial cells (GMC) of rat was established and passages 3 - 10 of the cells were used in the experiment after identification. The experiment included the following 5 groups: control group (Ctrl), LPS group (LPS), high, medium and low dose FOS groups (FOS1, FOS2 and FOS3 groups, respectively). GMC proliferation was detected by methyl thiazolyl tetrazolium (MTT) incorporation method at 24 and 48 h; the changes of laminin (LN), fibronectin (FN) and ColIV protein secretion was detected by the enzyme-linked immunosorbent assay (ELISA). The changes of LNbeta(2) mRNA expression was detected by semi-quantitative real-time RT-PCR. RESULTS: (1) LPS could induce the mesangial cell proliferation, FOS inhibited this effect of proliferation induced by LPS. (2) Mesangial cells could secrete some extracellular matrix (ECM) protein in normal culture medium, mesangial cell secreted ECM protein was significantly higher in LPS group than that in Ctrl group (P < 0.01), but significantly lower in all FOS groups than that in LPS group (P < 0.01). (3) Mesangial cell could express LNbeta(2) mRNA in normal culture medium, LNbeta(2) mRNA expression was significantly higher in LPS group than that in Ctrl group at all time points, but was significantly lower in FOS group than that in LPS group. CONCLUSIONS: LPS could induce increased secretion of the ECM, including LN, FN, ColIV; FOS could inhibit the secretion of ECM in GMC in a dose-dependent manner at mRNA and protein levels.

[Therapeutic effect of Ginkgo biloba leaf extract on hypercholestrolemia in children with nephrotic syndrome].

OBJECTIVE: To explore the therapeutic effects of the extract of Ginkgo biloba leaf on hypercholestrolemia in children with primary nephritic syndrome (NS). METHODS: Thirty-five children with NS were randomized into 2 groups for treatment with prednisone plus Ginkgo biloba leaf extract (18 cases) or with prednisone plus dipyridamole (17 cases) for 8 weeks. After completion of the treatments, the therapeutic effects were evaluated and the changes in the blood biochemical markers assayed. RESULTS: The 8-week treatment with the extract significantly ameliorated the clinical symptoms and blood biochemistry as compared with prednisone plus dipyridamole group (P<0.01). The levels of urinic protein and blood lipid in Ginkgo leaf group were significantly lower than those in prednisome plus dipyridamole group (P<0.05). CONCLUSION: The extract from Ginkgo biloba leaf can lower blood lipid levels and urinic protein in children with NS and improve their clinical syptoms and the renal function, therefore has much clinical value as an adjuvant treatment of steroid therapy in such children.

[Protective effects of glycyrrhizin on adriamycin nephropathy in rats].

OBJECTIVE: To observe the effects of glycyrrhizin on laminin (LN) expression in kidney tissue and excretory quantity of urine protein of rats with adriamycin nephropathy, and to explore the protective effects of glycyrrhizin on glomerulosclerosis. METHODS: Eighteen SD rats were randomly divided into 3 groups: normal control group (n=6), untreated group (n=6) and glycyrrhizin-treated group (n=6). Adriamycin nephropathy was induced in rats in the last two groups by intravenous injection of adriamycin. The rats in the glycyrrhizin-treated group were fed glycyrrhizin for eight weeks, whereas the rats in the normal control group and untreated group were fed normal saline solution for eight weeks too. The levels of 24 h urine protein (Upr), serum creatinine (sCr), blood urea nitrogen (BUN) and serum cholesterol (Ch) of rats in each group were examined before treatment and after the treatment for four and eight weeks. The renal morphological changes were observed under a microscope. The expression level of LN in renal tissue was detected by streptavidin-biotin peroxidase complex (SABC) method. RESULTS: The levels of 24 h Upr after the treatment for four and eight weeks in the glycyrrhizin-treated group were both significantly decreased as compared with those in the untreated group. The pathological morphological changes of renal tissue in the glycyrrhizin-treated group were remarkably alleviated, and the expression level of LN in renal tissue was also decreased in the glycyrrhizin-treated group as compared with those in the untreated group. CONCLUSION: The glycyrrhizin exerts certain protective effects on adriamycin nephropathy in rats by reducing excretory quantity of urine protein, decreasing expression level of LN in renal tissue, improving renal function and lessening the severity degree of glomerulosclerosis so as to retard the development of glomerulosclerosis.