[This corrects the article DOI: 10.1016/j.apsb.2022.03.002.].

Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin regions, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at the single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences on TF binding. Notably, cFOOT-seq, combined with FootTrack analysis, enables de novo prediction of TF binding sites and tracking of TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.
Transcription Factors/genetics* ; Humans ; Chromatin/genetics* ; Animals ; Binding Sites ; Mice ; DNA Footprinting/methods*

Objective:To explore the effects of short-term particulate matter(PM)exposure and the melatonin receptor 1B(MTNR1B)gene on triglyceride-glucose(TyG)index utilizing data from Fang-shan Family-based Ischemic Stroke Study in China(FISSIC).Methods:Probands and their relatives from 9 rural areas in Fangshan District,Beijing,were included in the study.PM data were obtained from fixed monitoring stations of the National Air Pollution Monitoring System.TyG index was calculated by fasting triglyceride and glucose concentrations.The associations of short-term PM exposure and rs10830963 polymorphism of the MTNR1B gene with the TyG index were assessed using mixed linear models,in which covariates such as age,sex,and lifestyles were adjusted for.Gene-environment inter-action analysis was furtherly performed using the maximum likelihood methods to explore the potential effect modifier role of rs10830963 polymorphism in the association of PM with TyG index.Results:A total of 4 395 participants from 2 084 families were included in the study,and the mean age of the study participants was(58.98±8.68)years,with 53.90％females.The results of association analyses showed that for every 10 μg/m3 increase in PM2.5 concentration,TyG index increased by 0.017(95％CI:0.007-0.027),while for per 10 μg/m3 increment in PM1o,TyG index increased by 0.010(95％CI:0.003-0.017).And the associations all had lagged effects.In addition,there was a positive association between the rs10830963 polymorphism and the TyG index.For per increase in risk allele G,TyG index was elevated by 0.040(95％CI:0.004-0.076).The TyG index was 0.079(95％CI:0.005-0.152)higher in carriers of the GG genotype compared with carriers of the CC genotype.The inter-action of rs10830963 polymorphism with PM exposure had not been found to be statistically significant in the present study.Conclusion:Short-term exposure to PM2.5 and PM10 were associated with higher TyG index.The G allele of rs10830963 polymorphism in the MTNR1B gene was associated with the elevated TyG index.

Objective To monitor the antifungal resistance of clinical isolates of Candida spp.in the East China region.Methods MALDI-TOF MS or molecular methods were used to re-identify the strains collected from January 2018 to December 2022.Antifungal susceptibility testing was performed using the broth microdilution method.The susceptibility test results were interpreted according to the breakpoints of 2022 Clinical and Laboratory Standards Institute(CLSI)documents M27 M44s-Ed3 and M57s-Ed4.Results A total of 3 026 strains of Candida were collected,65.33％of which were isolated from sterile body sites,mainly from blood(38.86％)and pleural effusion/ascites(10.21％).The predominant species of Candida were Candida albicans(44.51％),followed by Candida parapsilosis complex(19.46％),Candida tropicalis(13.98％),Candida glabrata(10.34％),and other Candida species(0.79％).Candida albicans showed overall high susceptibility rates to the 10 antifungal drugs tested(the lowest rate being 93.62％).Only 2.97％of the strains showed dose-dependent susceptibility(SDD)to fluconazole.Candida parapsilosis complex had a SDD rate of 2.61％and a resistance rate of 9.42％to fluconazole,and susceptibility rates above 90％to other drugs.Candida glabrata had a SDD rate of 92.01％and a resistance rate of 7.99％to fluconazole,resistance rates of 32.27％and 48.24％to posaconazole and voriconazole non-wild-type strains(NWT),respectively,and susceptibility rates above 90％to other drugs.Candida tropicalis had resistance rates of 29.55％and 26.24％to fluconazole and voriconazole,respectively,resistance rates of 76.60％and 21.99％to posaconazole and echinocandins non-wild-type strains(NWT),and a resistance rate of 2.36％to echinocandins.Conclusions The prevalence and species distribution of Candida spp.in the East China region are consistent with previous domestic and international reports.Candida glabrata exhibits certain degree of resistance to fluconazole,while Candida tropicalis demonstrates higher resistance to triazole drugs.Additionally,echinocandins resistance has emerged in Candida albicans,Candida glabrata,Candida tropicalis,and Candida parapsilosis.

The management of antibiotic-resistant, bacterial biofilm infections in skin wounds poses an increasingly challenging clinical scenario. Pseudomonas aeruginosa infection is difficult to eradicate because of biofilm formation and antibiotic resistance. In this study, we identified a new benzothiazole derivative compound, SN12 (IC₅₀ = 43.3 nmol/L), demonstrating remarkable biofilm inhibition at nanomolar concentrations in vitro. In further activity assays and mechanistic studies, we formulated an unconventional strategy for combating P. aeruginosa-derived infections by targeting the two-component (Gac/Rsm) system. Furthermore, SN12 slowed the development of ciprofloxacin and tobramycin resistance. By using murine skin wound infection models, we observed that SN12 significantly augmented the antibacterial effects of three widely used antibiotics-tobramycin (100-fold), vancomycin (200-fold), and ciprofloxacin (1000-fold)-compared with single-dose antibiotic treatments for P. aeruginosa infection in vivo. The findings of this study suggest the potential of SN12 as a promising antibacterial synergist, highlighting the effectiveness of targeting the two-component system in treating challenging bacterial biofilm infections in humans.

Ganjiang (Zingiberis Rhizoma, ZR) and Jiangtan (Carbonized Zingiberis Rhizoma, CZR) have long been used in traditional Chinese medicine (TCM) with a rich history in the treatment of various ailments. While ZR and CZR obviously stem from the same botanical source, their attributes, chemical compositions, pharmacological behaviors, and clinical applications are different owing to variations in the extent of drying and processing they undergo. In this paper, data pertaining to ZR and CZR were retrieved from databases including China National Knowledge Infrastructure (CNKI), PubMed, Web of Science, and Google Scholar. These sources were scrutinized to elucidate the distinctions between ZR and CZR arising from carbonization processing in terms of their ethnopharmacology, quality control, chemical compositions, biological activities, pharmacological mechanisms, and clinical uses. In this study, a total of 56 chemical constituents were identified and isolated from ZR and CZR, which primarily encompassed volatile oils, gingerols, and diphenylheptane compounds. CZR's pharmacological effects include hemostatic, anti-oxidant, analgesic, antibacterial, anti-cancer, and other biological activities. ZR has pungent and warm properties. It is a Yang-supplementing herbal medicine for ailments exacerbated by cold or damp climatic influences. CZR is a product of ZR after undergoing high temperature, with diminished intensity of its pungent and warm attributes. This change leads to a more gradual treatment efficacy, renowned hemostatic effects and its ability to gently invigorate the spleen and effectively alleviate diarrhea. Currently, research on the pharmacological mechanism of CZR is mainly focused on the effects of CZR on coagulation and fibrinolysis. Although the healing effect of CZR has long been known, and some correlation has been found between the changing composition and the changing color of the decoctions, people still lack relatively clear processing mechanisms to reflect the characteristics and specific quality standards of the ingredients of CZR's hemostatic effect. This review provides a systematic summary on quality control, chemical composition, ethnopharmacology, and pharmacology of CZR, offering novel perspectives for advancing the exploration of additional carbonized herbal medicine and fostering their application in clinical settings

Hepatocellular carcinoma (HCC) is a common malignant tumor with poor prognosis and high mortality. In this study, we demonstrated a novel vaccine targeting HCC and tumor neovascular endothelial cells by fusing recombinant MHCC97H cells expressing porcine α-1,3-galactose epitopes (αGal) and endorphin extracellular domains (END) with dendritic cells (DCs) from healthy volunteers. END⁺/Gal⁺-MHCC97H/DC fusion cells induced cytotoxic T lymphocytes (CTLs) and secretion of interferon-gamma (IFN-γ). CTLs targeted cells expressing αGal and END and tumor angiogenesis. The fused cell vaccine can effectively inhibit tumor growth and prolong the survival time of human hepatoma mice, indicating the high clinical potential of this new cell based vaccine.

Objective:To analyze the relationship between arch index and foot kinematic parameters and their characteristics in stress fracture of lower extremity.Methods:A case-control study was performed for 108 recruits selected from a certain army unit in 2019. Before training, the recruits′ foot print images were collected by the capacitive plantar pressure measurement system to calculate their arch indices. The kinematic characteristics of the foot were analyzed by the dynamic gait posture analysis system. Spearman rank correlation analysis between arch index and foot kinematic parameters including landing elevation angle, toe-off angle, landing speed, landing varus angle, valgus amplitude and landing valgus speed were performed. Throughout the training, orthopedic physicians followed up the recruits, among whom 10 were excluded due to other types of lower extremity injuries. The arch index and foot kinematic characteristics were analyzed and compared between the remained recruits with stress fracture of lower extremity (fracture group, n=10) and those without lower extremity injury (control group, n=79). Results:(1) For the recruits, the arch index was 0.21(0.12,0.25), with landing elevation angle for (17.31±4.02)°, toe-off angle for (63.90±5.63)°, landing speed for (176.85±24.39)°/s, landing varus angle for (13.64±4.44)°, valgus amplitude for (12.16±3.42)°, and landing valgus speed for 382.50(311.05,474.80)°/s. (2) The landing varus angle ( r=0.25, P<0.01) and valgus amplitude ( r=0.14, P<0.05) were positively related to the arch index. (3) The arch index, toe-off angle and landing valgus speed were 0.20(0.07,0.24), (61.59±5.51)° and 336.00(251.02,428.67)°/s in fracture group, significantly lower than 0.23(0.17,0.26), (64.79±4.79)° and 381.20(313.63,470.92)°/s in control group ( P<0.05 or 0.01). There were no significant differences in the landing elevation angle, landing speed, landing varus angle and valgus amplitude between the two groups (all P>0.05). Conclusions:The change of the arch index can affect the landing varus angle and valgus amplitude of the foot. Recruits who suffer from stress fracture of lower extremity have the characteristics of higher arch, lower toe-off angle and lower landing valgus speed.

Objective:To investigate the possible functional roles and mechanisms of phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway, reactive oxygen species (ROS), and aldo-keto reductase family 1 member C3 (AKR1C3) in keloid formation.Methods:Nine keloid tissues from patients (six males, three females; aged: 24-40 years old) and six normal skin tissues from healthy controls (four males, two females; aged 24-45 years old) were collected. Tissue samples were embedded or used in fibroblasts isolation and culture. (1) The relative expression of protein kinase B serine phosphorylation site 473[p-AKT (S473)], protein kinase B threonine phosphorylation site 308[p-AKT (T308)], and AKR1C3 in keloid tissues and normal skin tissues was measured using immunohistochemistry. (2) The CCK-8 assay was employed to detect the inhibitory effect of PI3K-specific inhibitor LY294002 (0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50 mmol/L) on the proliferation of keloid fibroblasts and to screen the optimal experimental concentration of LY294002. (3) The ROS assay kit was used to detect the effects of different concentrations (0, 4, 6, 8, 10, 12 mmol/L) of the ROS inhibitor N-acetylcysteine (NAC) and 15 mmol/L LY294002 on ROS levels in keloid fibroblasts. (4) Fibroblasts derived from keloid tissues or normal skin tissues were divided into control group (without any treatment), respectively, dimethyl sulfoxide(DMSO) group (0.002% DMSO treatment), LY294002 group (15 mmol/L LY294002 treatment), and NAC group (6 mmol/L NAC treatment), respectively. Quantitative PCR (qPCR) and Western blotting assays were performed to detect the levels of AKT mRNA, AKR1C3 mRNA and the protein levels of p-AKT(S473), p-AKT(T308), and AKR1C3. Statistical analysis was performed with SPSS 22.0. Data was presented as Mean±SD. Independent sample t-test was used for comparison between two groups, one-way ANOVA was used for comparison between multiple groups, and SNK- q test was used for multiple comparisons between two groups. Results:(1) Immunohistochemistry showed that the expression levels of p-AKT(S473), p-AKT(T308), and AKR1C3 in keloid tissues were 16.75±3.30, 16.20±1.56, 26.69±2.50, which were significantly higher than those in normal skin tissues: 4.02±1.50, 1.82±0.50, 1.47±1.07 ( P<0.01). (2) The proliferation inhibition rate of keloid fibroblasts treated by different concentrations of LY294002 (15-50 mmol/L LY294002) for 24 h was significantly higher than in the control group (0 mmol/L) ( P<0.01). The optimal experimental concentration of LY294002 is 15 mmol/L. (3) After different concentrations of NAC were applied to keloid fibroblasts for 1 h, the differences in ROS level was groups were statistically significant ( P<0.01), and the lowest ROS level was found in the 6 mmol/L NAC group(0.72±0.03). The 15 mmol/L LY294002 group had significantly lower ROS levels than the control group (0 mmol/L) (0.80±0.01 vs. 0.86±0.01, P<0.01). (4) qPCR showed that the mRNA levels of AKT and AKR1C3 were 1.38±0.09 and 1.40±0.05 in keloid fibroblasts in control group, which were significantly higher than those in normal skin fibroblasts: 0.97±0.10, 0.98±0.03( P<0.01). The expression level of AKT mRNA in keloid fibroblasts treated with 15 mmol/L LY294002 was significantly lower than that in normal skin fibroblasts (0.73±0.05 vs. 0.89±0.06, P<0.01). The expression level of AKR1C3 mRNA in keloid fibroblasts treated with 6 mmol/L NAC was significantly lower than that in normal skin fibroblasts (0.43±0.05 vs. 0.86±0.03, P<0.01). Western blotting revealed the expression levels of p-AKT(S473), p-AKT(T308), and AKR1C3 in keloid fibroblasts were 1.19±0.21, 0.92±0.04, 0.73±0.08, significantly higher than those in normal skin fibroblasts (0.24±0.06, 0.33±0.05, 0.31±0.05, P<0.01). After treatment with 15 mmol/L LY294002 or 6 mmol/L NAC, the protein expression of p-AKT (S473) in keloid fibroblasts were 0.92±0.04 and 0.80±0.20; the protein levels of p-AKT (T308) were 0.42±0.04 and 0.81±0.05, which were all significantly higher than the expression levels in normal skin tissue (0.23±0.03, 0.22±0.05, 0.30±0.06, 0.32±0.05). However, The expression of AKR1C3 protein in keloid fibroblasts treated with 15 mmol/L LY294002 (0.23±0.05) was significantly lower than that in normal skin fibroblasts (0.30±0.07), the expression of AKR1C3 protein in keloid fibroblasts treated with 6 mmol/L NAC (0.33±0.07) was significantly higher than that in normal skin fibroblasts (0.28±0.06, P>0.05). Conclusions:Activation of PI3K/AKT signaling pathway and AKR1C3 promoted the proliferation of keloid fibroblasts and keloid formation. Meanwhile, the elevation of AKR1C3 accelerated the increase of ROS level in keloid fibroblasts.

Objective:To investigate the possible functional roles and mechanisms of phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway, reactive oxygen species (ROS), and aldo-keto reductase family 1 member C3 (AKR1C3) in keloid formation.Methods:Nine keloid tissues from patients (six males, three females; aged: 24-40 years old) and six normal skin tissues from healthy controls (four males, two females; aged 24-45 years old) were collected. Tissue samples were embedded or used in fibroblasts isolation and culture. (1) The relative expression of protein kinase B serine phosphorylation site 473[p-AKT (S473)], protein kinase B threonine phosphorylation site 308[p-AKT (T308)], and AKR1C3 in keloid tissues and normal skin tissues was measured using immunohistochemistry. (2) The CCK-8 assay was employed to detect the inhibitory effect of PI3K-specific inhibitor LY294002 (0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50 mmol/L) on the proliferation of keloid fibroblasts and to screen the optimal experimental concentration of LY294002. (3) The ROS assay kit was used to detect the effects of different concentrations (0, 4, 6, 8, 10, 12 mmol/L) of the ROS inhibitor N-acetylcysteine (NAC) and 15 mmol/L LY294002 on ROS levels in keloid fibroblasts. (4) Fibroblasts derived from keloid tissues or normal skin tissues were divided into control group (without any treatment), respectively, dimethyl sulfoxide(DMSO) group (0.002% DMSO treatment), LY294002 group (15 mmol/L LY294002 treatment), and NAC group (6 mmol/L NAC treatment), respectively. Quantitative PCR (qPCR) and Western blotting assays were performed to detect the levels of AKT mRNA, AKR1C3 mRNA and the protein levels of p-AKT(S473), p-AKT(T308), and AKR1C3. Statistical analysis was performed with SPSS 22.0. Data was presented as Mean±SD. Independent sample t-test was used for comparison between two groups, one-way ANOVA was used for comparison between multiple groups, and SNK- q test was used for multiple comparisons between two groups. Results:(1) Immunohistochemistry showed that the expression levels of p-AKT(S473), p-AKT(T308), and AKR1C3 in keloid tissues were 16.75±3.30, 16.20±1.56, 26.69±2.50, which were significantly higher than those in normal skin tissues: 4.02±1.50, 1.82±0.50, 1.47±1.07 ( P<0.01). (2) The proliferation inhibition rate of keloid fibroblasts treated by different concentrations of LY294002 (15-50 mmol/L LY294002) for 24 h was significantly higher than in the control group (0 mmol/L) ( P<0.01). The optimal experimental concentration of LY294002 is 15 mmol/L. (3) After different concentrations of NAC were applied to keloid fibroblasts for 1 h, the differences in ROS level was groups were statistically significant ( P<0.01), and the lowest ROS level was found in the 6 mmol/L NAC group(0.72±0.03). The 15 mmol/L LY294002 group had significantly lower ROS levels than the control group (0 mmol/L) (0.80±0.01 vs. 0.86±0.01, P<0.01). (4) qPCR showed that the mRNA levels of AKT and AKR1C3 were 1.38±0.09 and 1.40±0.05 in keloid fibroblasts in control group, which were significantly higher than those in normal skin fibroblasts: 0.97±0.10, 0.98±0.03( P<0.01). The expression level of AKT mRNA in keloid fibroblasts treated with 15 mmol/L LY294002 was significantly lower than that in normal skin fibroblasts (0.73±0.05 vs. 0.89±0.06, P<0.01). The expression level of AKR1C3 mRNA in keloid fibroblasts treated with 6 mmol/L NAC was significantly lower than that in normal skin fibroblasts (0.43±0.05 vs. 0.86±0.03, P<0.01). Western blotting revealed the expression levels of p-AKT(S473), p-AKT(T308), and AKR1C3 in keloid fibroblasts were 1.19±0.21, 0.92±0.04, 0.73±0.08, significantly higher than those in normal skin fibroblasts (0.24±0.06, 0.33±0.05, 0.31±0.05, P<0.01). After treatment with 15 mmol/L LY294002 or 6 mmol/L NAC, the protein expression of p-AKT (S473) in keloid fibroblasts were 0.92±0.04 and 0.80±0.20; the protein levels of p-AKT (T308) were 0.42±0.04 and 0.81±0.05, which were all significantly higher than the expression levels in normal skin tissue (0.23±0.03, 0.22±0.05, 0.30±0.06, 0.32±0.05). However, The expression of AKR1C3 protein in keloid fibroblasts treated with 15 mmol/L LY294002 (0.23±0.05) was significantly lower than that in normal skin fibroblasts (0.30±0.07), the expression of AKR1C3 protein in keloid fibroblasts treated with 6 mmol/L NAC (0.33±0.07) was significantly higher than that in normal skin fibroblasts (0.28±0.06, P>0.05). Conclusions:Activation of PI3K/AKT signaling pathway and AKR1C3 promoted the proliferation of keloid fibroblasts and keloid formation. Meanwhile, the elevation of AKR1C3 accelerated the increase of ROS level in keloid fibroblasts.