Membrane-assisted tariquidar access and binding mechanisms of human ATP-binding cassette transporter P-glycoprotein.

The human multidrug transporter P-glycoprotein (P-gp) is physiologically essential and of key relevance to biomedicine. Recent structural studies have shed light on the mode of inhibition of the third-generation inhibitors for human P-gp, but the molecular mechanism by which these inhibitors enter the transmembrane sites remains poorly understood. In this study, we utilized all-atom molecular dynamics (MD) simulations to characterize human P-gp dynamics under a potent inhibitor, tariquidar, bound condition, as well as the atomic-level binding pathways in an explicit membrane/water environment. Extensive unbiased simulations show that human P-gp remains relatively stable in tariquidar-free and bound states, while exhibiting a high dynamic binding mode at either the drug-binding pocket or the regulatory site. Free energy estimations by partial nudged elastic band (PNEB) simulations and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method identify two energetically favorable binding pathways originating from the cytoplasmic gate with an extended tariquidar conformation. Interestingly, free tariquidar in the lipid membrane predominantly adopts extended conformations similar to those observed at the regulatory site. These results suggest that membrane lipids may preconfigure tariquidar into an active ligand conformation for efficient binding to the regulatory site. However, due to its conformational plasticity, tariquidar ultimately moves toward the drug-binding pocket in both pathways, explaining how it acts as a substrate at low concentrations. Our molecular findings propose a membrane-assisted mechanism for the access and binding of the third-generation inhibitors to the binding sites of human P-gp, and offer deeper insights into the molecule design of more potent inhibitors against P-gp-mediated drug resistance.

Chronic hypotony management using endoscopy-assisted vitrectomy after severe ocular trauma or vitrectomy.

AIM: To report outcomes of endoscopy-assisted vitrectomy (EAV) in patients with chronic hypotony following severe ocular trauma or vitrectomy. METHODS: This was a retrospective, noncomparative case series. Ciliary bodies were evaluated using ultrasound biomicroscopy pre-operatively and direct visualisation intraoperatively. All selected individuals (seven patients/seven eyes) underwent EAV. Removal of ciliary membrane and traction, gas/silicone oil tamponade (GT/SOT), and scleral buckling (SB) were performed in selected eyes. Outcome measurements mainly included intraocular pressure (IOP) and best-corrected visual acuity (BCVA). RESULTS: Seven eyes from 7 male aphakic patients with a mean age of 45 (range, 20-68)y were included in this study; the average follow-up time was 12 (9-15)mo. GT was performed in 2 eyes; membrane peeling (MP) and SOT in 2 eyes; and MP, SOT, and SB in 3 eyes. The mean pre- and post-operative IOP were 4.5 (range, 4.0±0.11 to 4.8±0.2) mm Hg and 9.9 (range, 5.6±0.17 to 12.1±0.2) mm Hg at 52wk (12mo), respectively. BCVA improved in six eyes; one eye still showed light perception, and no bulbi phthisis was observed. CONCLUSION: Endoscopy offers improved judgment and recognition and has an improved prognosis for chronic hypotony. Therefore, endoscopy can be an effective and promising operative technique for chronic traumatic hypotony management.

SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging.

High-throughput single-cell RNA-seq data have provided unprecedented opportunities for deciphering the regulatory interactions among genes. However, such interactions are complex and often nonlinear or nonmonotonic, which makes their inference using linear models challenging. We present SIGNET, a deep learning-based framework for capturing complex regulatory relationships between genes under the assumption that the expression levels of transcription factors participating in gene regulation are strong predictors of the expression of their target genes. Evaluations based on a variety of real and simulated scRNA-seq datasets showed that SIGNET is more sensitive to ChIP-seq validated regulatory interactions in different types of cells, particularly rare cells. Therefore, this process is more effective for various downstream analyses, such as cell clustering and gene regulatory network inference. We demonstrated that SIGNET is a useful tool for identifying important regulatory modules driving various biological processes.

Protective effects of lipoic acid-niacin dimers against blue light-induced oxidative damage to retinal pigment epithelium cells.

AIM: To evaluate the protective effects of lipoic acid-niacin (N2L) dimers against blue light (BL)-induced oxidative damage to human retinal pigment epithelium (hRPE) cells in vitro. METHODS: hRPE cells were divided into a control group (CG), a BL group, an N2L plus BL irradiation group, an α-lipoic acid (ALA) plus BL group, an ALA-only group, and an N2L-only group. hRPE cellular viability was detected by performing 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium (MTT) bromide assays, and apoptosis was evaluated by annexin-V-PE/7-AAD staining followed by flow cytometry. Ultrastructural changes in subcellular organelles were observed by transmission electron microscopy. Reactive oxygen species formation was assayed by flow cytometry. The expression levels of the apoptosis-related proteins BCL-2 associated X protein (BAX), B-cell leukmia/lymphoma 2 (BCL-2), and caspase-3 were quantified by Western blot analysis. RESULTS: BL exposure with a light density of 4±0.5 mW/cm2 exceeding 6h caused hRPE toxicity, whereas treatment with a high dose of N2L (100 mol/L) or ALA (150 mol/L) maintained cell viability at control levels. BL exposure caused vacuole-like degeneration, mitochondrial swelling, and reduced microvillus formation; however, a high dose of N2L or ALA maintained the ultrastructure of hRPE cells and their organelles. High doses of N2L and ALA also protected hRPE cells from BL-induced apoptosis, which was confirmed by Western blot analysis: BCL-2 expression significantly increased, while BAX and caspase-3 expression slightly decreased compared to the CG. CONCLUSION: High-dose N2L treatment (>100 mol/L) can reduce oxidative damage in degenerating hRPE cells exposed to BL with an efficacy similar to ALA.

Protection of tight junction between RPE cells with tissue factor targeting peptide.

AIM: To investigate the effect of tissue factor targeting peptide (TF-TP) on retinal pigment epithelium (RPE) cells tight junctions. METHODS: Cell counting kit-8 (CCK-8) was used to measure the proliferation of ARPE-19 cells. Expression of tight junction, ZO-1 in ARPE-19 cells was measured by Western blot and immunofluorescent staining. Western blot was also used to detect the expression of tissue factor (TF). CEC Transmigration Assay was used to measure the migration of ARPE-19 cells. The transport of fluorescent markers [fluorescein isothiocyanate dextrans of 4, 10, 20 (FD4, FD10, FD20)] and the transepithelial electrical resistance (TEER) were used to measure in ARPE-19 cell. RESULTS: CCK-8 assay showed that 5 µmol/L TF-TP can inhibit ARPE-19 cells abnormally proliferation stimulated by lipopolysaccharide (LPS; P<0.05). LPS increased the transport of fluorescent markers (FD4, FD10, FD20) and decreased TEER levels in ARPE-19 cells, respectively, which were prevented by 5 µmol/L TF-TP pretreatment (P<0.05). Furthermore, LPS significantly up-regulated the expression of TF and downregulated the expression of ZO-1 (P<0.05) in ARPE-19 cell which was inhibited by the TF-TP (P<0.05). In addition, TF-TP inhibited the abnormal migration induced by LPS in ARPE-19 cell (P<0.05). CONCLUSION: Our findings suggest that TF-TP suppressed proliferation and migration of ARPE-19 cells induced by LPS, and maintained the RPE tight junctions through inhibition of TF expression and increased expression of ZO-1.

Endoscopy-assisted vitrectomy in the anterior vitreous.

Endoscopy-assisted ocular surgery is a relatively old technique that is increasingly being recognized for its application in cases of vitreoretinal disease. This technique is especially useful when both the vitreous and retina are difficult to access because of media opacity, a small pupil, or a microcornea. In this context, the anterior vitreous is often difficult to dissect because of its complex pathological changes. This article reviews the common anatomical features and pathologies that are observed in the anterior vitreous, as well as the applications and indications of endoscopy-assisted vitrectomy in the anterior vitreous.

[Impacts of suspended solids on "tailing" phenomenon in disinfection of sewage with chlorine].

The impacts of suspended solids in secondary effluent on "tailing" phenomenon in disinfection of E. coli with chlorine were investigated using kinetic disinfection curves. Higher SS concentration led to earlier beginning of "tailing" region with lower inactivation level. Comparison between lg-lg regression analyses of disinfection curves demonstrated that the SS concentration correlated with overall inactivation rate, which decreased by 10 times while SS concentration increased from 6 to 85 mg/L. The results of segmental modeling of disinfection curves showed that the SS concentration (at a range of 10-55 mg/L) correlated with the starting time of "tailing" region as well as the log-kill at the starting point of tailing region (R2 > 0.99). The starting time was shortened from 330 min to 55 min, and the log-kill dropped from 5.8 down to 0.8 with SS concentration increasing. Better removal of SS will improve the lg-kill of E. coli at tailing region and the inactivation rate, resulting in lower cost of construction and running. In addition, higher chlorine dosage and lower pH value could slightly enhance the log-kill in the "tailing" region.