The association of BBR with DNA can suppress the interaction between TBP and the TATA box.

<p>(A) represents the suppressive effect of BBR on gene transcription in a cell-free system, where actinomycin D (AD) was used as the positive control drug because of its well-known transcription inhibitory activity. (B) represents the suppressive effect of BBR on the association between TBP and the TATA box. B (I) is an image taken via EMSA, and B (II) represents the effect of BBR on the binding of TBP to TATA box, (y = 11.468×, ln-(x)<i>+</i>.<i>60.55</i>, R² = 0.9344, n = 3. (C) represents the time-dependent suppressive effect of BBR (2.69 µmol) on the interaction between TBP and the TATA box in live cells observed using ChIP. C (I) is one of the images taken from a Western blot representing TBP, and C (II) displays the statistical results of brightness of TBP in Western blot images from three independent experiments. C (III) and C (IV) depict the quantitative analysis of the TATA box-containing DNA fragment in the CMV promoter and PPARγ promoter bound by TBP from four independent experiments, the data of which was represented as the ratio of the content of DNA fragments in BBR groups to the content in BBR-free groups at the same time-point (control group), input of each sample was used as inner reference. * P<0.05, ** p<0.01 vs the corresponding control indicated above. Data were presented as mean ± S.D, from three independent experiments (n = 3).</p

Cytotoxicity assay of berberine.

<p>(A) represents the cytotoxicity of BBR from the MTT assay: A(I) and A(II) represent the cytotoxicity of BBR to PC12 cells 12 hours and 24 hours after drug administration, respectively; (B) represents the LDH release of PC12 cells after BBR addition: B(I) and B(II) represent the amount of LDH released from PC12 cells 12 hours and 24 hours since BBR incubation. In the MTT assay, the group with 0 µmol of BBR was considered the control group; in LDH release assay, the spontaneous release of LDH from the BBR-free group (0 µmol) was considered the control group. The percentage of LDH release was calculated by the equation: LDH release (%) = (Experimental LDH release-Spontaneous LDH release)/Maximum LDH release. * p<0.05, ** p<0.01 vs control. Data were presented as mean ± S.D. from twelve independent experiments. (n = 12).</p

Distribution of berberine in a living cell.

<p>(A) (from I to V) depicts images of the subcellular location of BBR in PC12 cells one hour after BBR administration. The fluorescence of BBR is shown in blue in A (I); A (II) represents PC12 cells in visible light; A (III) and A (IV) represents the nucleus stained by PI and AO, respectively; figure A (V) is the merged image of A (I), A (II), A (III), and A (IV). (B) represents the process of BBR entering the nucleus. The fluorescence of BBR is shown in green in this figure, and the red arrow points to the nuclear region. All of the images in (B) were taken under the same conditions with a time interval of 1.2 min. (C) represents the fluorescence intensity of BBR in the nucleus. * p<0.05, ** p<0.01 vs control (0 minutes after BBR administration). (D) represents the time-resolution change of berberine in live cells and the nucleus, which was detected by HPLC. (E) represents the chemical structure of BBR. Data were presented as mean ± S.D. from three independent experiments (n = 3).</p

The suppressive effect of BBR on the transcription of artificial plasmids.

<p>A (I) and A (II) signify the type of artificial plasmid model used in this study. (B), (C), (D), (E), and (F) represent the effect of BBR on CMV-GFP, PPARγ-GFP, IgG-GFP, CMV-RFP, and TPH2-RFP plasmids, respectively. (G) illustrates the suppressive effect of BBR on the expression of these five plasmids 1 hour after drug administration. Data is the ratio of the target gene in the BBR group to the same target gene in the BBR-free group at the same time-point (control group) * p<0.05, ** p<0.01 vs the corresponding control indicated above. Data were presented as mean ± S.D, from three independent experiments (n = 3).</p

Spatial conformational change induced by berberine.

<p>(A) represents the dose-dependent alterations in circular dichroic spectrum of genome, chromatin, and plasmid, respectively. (B) represents the time-dependent alterations in circular dichroic spectrum of genome, chromatin, and plasmid, respectively. (C) represents the effect of BBR (500 µmol) on the intensity distribution (%) of chromatin (92.4 µmol), genome (423.2 µmol), and plasmid (808 µmol) in size (diameter) obtained from DLS measurements, respectively.</p

The suppressive effect of berberine on gene transcription in live cells.

<p>(A) portrays the time-dependent effect of BBR on gene transcription on a global level. (B) shows the time-dependent recovery of the global RNA level after the elimination of a 12 hour-BBR treatment. The linear equation of the control group in (B) is: <i>y</i> = 4.9836×<i>+21.516</i>, R² = 0.8162; the linear equation of the BBR group in (B)is: <i>y</i> = 6.6219×<i>+15.472</i>, R² = 0.8941. (C) displays the protective effect of BBR on the global RNA level. (D) depicts the protective effect of BBR on the mRNA level of the transfected artificial plasmid, pEGFP-N1. The dosage of BBR in all of the experiments was 2.69 µmol. Data in D was the ratio of target gene in the BBR group to the same target gene in the BBR-free group at the same time-point (control group). * p<0.05, ** p<0.01 vs the corresponding control indicated above. Data were presented as mean ± S.D. from four independent experiments (n = 4).</p

Artificial Peroxisome <i>h</i>NiPt@Co-NC with Tetra-enzyme Activities for Colorimetric Glutathione Sensing

Artificial peroxisome plays an important part in protocell system construction and disease therapy. However, it remains an enormous challenge to exploit a practicable artificial peroxisome with multiple and stable activities. Nanozymes with multienzyme mimetic activities stand out for artificial peroxisome preparation. Herein, a novel nanozymeCo-nanoparticle-embedded N-enriched carbon nanocubes (Co,N-CNC) decorated by hollow NiPt nanospheres (hNiPt@Co-NC) with featured tetra-enzyme mimetic activities of natural peroxisomewas prepared. Due to the synergistic effect of hollow NiPt nanospheres (hNiPtNS) and cubic porous Co,N-CNC support, hNiPt@Co-NC exhibited oxidase (OXD), peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD)-like activities with comparable catalytic efficiency, enabling it to be a competitive candidate for artificial peroxisome investigation. Based on the high OXD-mimetic activity of hNiPt@Co-NC, a facile colorimetric platform was proposed for reduced glutathione (GSH) detection with a wide linear range (0.1–5 μM, 5–100 μM) and a low detection limit (27 nM). Thus, the hNiPt@Co-NC with tetra-enzyme mimetic activities possessed bright prospects in diversified biotechnological applications, including artificial organelles, biosensing, and medical diagnostics

Image_1_Application of FGD-BCEL loss function in segmenting temporal lobes on localized CT images for radiotherapy.pdf

ObjectivesThe aim of this study was to find a new loss function to automatically segment temporal lobes on localized CT images for radiotherapy with more accuracy and a solution to dealing with the classification of class-imbalanced samples in temporal lobe segmentation.MethodsLocalized CT images for radiotherapy of 70 patients with nasopharyngeal carcinoma were selected. Radiation oncologists sketched mask maps. The dataset was randomly divided into the training set (n = 49), the validation set (n = 7), and the test set (n = 14). The training set was expanded by rotation, flipping, zooming, and shearing, and the models were evaluated using Dice similarity coefficient (DSC), Jaccard similarity coefficient (JSC), positive predictive value (PPV), sensitivity (SE), and Hausdorff distance (HD). This study presented an improved loss function, focal generalized Dice-binary cross-entropy loss (FGD-BCEL), and compared it with four other loss functions, Dice loss (DL), generalized Dice loss (GDL), Tversky loss (TL), and focal Tversky loss (FTL), using the U-Net model framework.ResultsWith the U-Net model based on FGD-BCEL, the DSC, JSC, PPV, SE, and HD were 0.87 ± 0.11, 0.78 ± 0.11, 0.90 ± 0.10, 0.87 ± 0.13, and 4.11 ± 0.75, respectively. Except for the SE, all the other evaluation metric values of the temporal lobes segmented by the FGD-BCEL-based U-Net model were improved compared to the DL, GDL, TL, and FTL loss function-based U-Net models. Moreover, the FGD-BCEL-based U-Net model was morphologically more similar to the mask maps. The over- and under-segmentation was lessened, and it effectively segmented the tiny structures in the upper and lower poles of the temporal lobe with a limited number of samples.ConclusionsFor the segmentation of the temporal lobe on localized CT images for radiotherapy, the U-Net model based on the FGD-BCEL can meet the basic clinical requirements and effectively reduce the over- and under-segmentation compared with the U-Net models based on the other four loss functions. However, there still exists some over- and under-segmentation in the results, and further improvement is needed.</p

DataSheet1_Design, synthesis and biological evaluation of 9-aryl-5H-pyrido[4,3-b]indole derivatives as potential tubulin polymerization inhibitors.pdf

A series of new 9-aryl-5H-pyrido[4,3-b]indole derivatives as tubulin polymerization inhibitors were designed, synthesized, and evaluated for antitumor activity. All newly prepared compounds were tested for their anti-proliferative activity in vitro against three different cancer cells (SGC-7901, HeLa, and MCF-7). Among the designed compounds, compound 7k displayed the strongest anti-proliferative activity against HeLa cells with IC50 values of 8.7 ± 1.3 μM. In addition, 7k could inhibit the polymerization of tubulin and disrupt the microtubule network of cells. Further mechanism studies revealed that 7k arrested cell cycle at the G2/M phase and induced apoptosis in a dose-dependent manner. Molecular docking analysis confirmed that 7k may bind to colchicine binding sites on microtubules. Our study aims to provide a new strategy for the development of antitumor drugs targeting tubulin.</p

Additional file 1 of A potent synthetic nanobody with broad-spectrum activity neutralizes SARS-CoV-2 virus and the Omicron variant BA.1 through a unique binding mode

Additional file 1: Table S1. Epitope binning of spike nanobodies. Table S2. Cryo-EM data collection, refinement and validation statistics. Table S3. Conservation of epitopic residues in RBD for C5G2 binding from natural occurring SARS-Cov-2 variants