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*

BACKGROUND:The lower cervical vertebral pedicle is the main stress site of the posterior column of the spine,which is of great significance for the maintenance of the stability of the human center of gravity and the reduction of shock.At present,there are few reports on the characteristics of the internal bone trabeculae,and the characteristics of the joint site of the vertebral pedicle with the articular process and the vertebral body.It is urgent to understand the fine anatomical structure of the vertebral pedicle and the relationship and function of each part. OBJECTIVE:To observe the microanatomical morphology of the vertebral pedicle by Micro-CT scanning of cervical vertebra specimens,and to measure and analyze the microstructure and morphometric parameters of the bone trabecula in the cervical pedicle under normal conditions to evaluate the safety performance of the cervical spine. METHODS:Micro-CT scanning was performed on 31 sets of cervical vertebrae C3-C7.By checking and reconstructing the areas of interest in the bone trabecular within the vertebral pedicle,the morphological characteristics and distribution direction of the bone trabecular within the cervical pedicle were observed,and the bone microstructure parameters were detected,and the differences in the bone microstructure of the C3-C7 vertebral pedicle were analyzed and compared. RESULTS AND CONCLUSION:(1)The Micro-CT images showed that the honeycomb bone trabeculae of the pedicle of the lower cervical spine presented a complex network of microstructures.The trabeculae near the cortical bone were lamellar and relatively compact,extending forward toward the vertebral body and backward toward the articular process lamina.Abatoid bone trabeculae extended into the medullary cavity and transformed into a network structure,and then into rod-shaped bone trabeculae.The rod-shaped bone trabeculae were sparsely distributed in the medullary cavity.(2)Statistical results of morphological parameters of bone trabeculae showed that bone volume fraction values in C4 and C5 were higher than that in C7(P＜0.05).The bone surface/bone volume value in C7 was higher than that in C3,C4 and C6(P＜0.05).The bone surface density of bone trabeculae in C7 was higher than that in C3,C4,C5 and C6(P＜0.05).Trabecular thickness in C7 was higher than that in C3,C4 and C5(P＜0.05).Bone surface/bone volume and bone surface density of the left pedicle bone trabecular were greater than those on the right side(P＜0.05).(3)The microstructural changes of C3-C7 were summarized,in which the load capacity and stress of the C7 pedicle were poor,and the risk of injury was high in this area.

Tumor aerobic glycolysis is one of the main features of tumor metabolic reprogramming. This abnormal glycolytic metabolism provides bioenergy and biomaterials for tumor growth and proliferation. It is worth noting that aerobic glycolysis will not only provide biological materials and energy for tumor cells, but also help tumor cells to escape immune surveillance through regulation of immune microenvironment, thereby resisting tumor immunotherapy and promoting tumor progression. Based on the pathogenesis of renal cell carcinoma, this paper describes the characteristics of aerobic glycolysis, the effect of glycolytic metabolism on the immune microenvironment of renal cell carcinoma, the effect of glycolysis inhibitors on the immune microenvironment of renal cell carcinoma, and the prospect of glycolysis inhibitors combined with immune checkpoint inhibitors in the treatment of renal cell carcinoma.
Humans ; Carcinoma, Renal Cell/therapy* ; Immunotherapy ; Glycolysis ; Metabolic Reprogramming ; Kidney Neoplasms/therapy* ; Tumor Microenvironment

Objective:To compare the effects of unilateral thoracic paravertebal block with lidocaine on hemodynamic and the level of consciousness during double lumen endotracheal intubation.Methods:From June to october 2021,a total of 40 patients American Society of Anesthesiologists(ASA)physical status Ⅰ-Ⅱ,aged 19-65 years,scheduled for elective thoracic sugeries in Peking University Interna-tional Hospital block with under general anesthesia requiring orotracheal intubation were recruited and di-vided into two groups:The double-lumen endobronchial intubation(group C)and double-lumen endo-bronchial intubation after thoracic paravertebal block with lidocaine(group P).After an intravenous an-esthetic induction,the orotracheal double-lumen intubation was performed using a Macintosh direct laryn-goscopy,respectively.Invasive blood pressure(BP)and heart rate(HR)were recorded before and after anesthetic induction,immediately after intubation and 5 min after intubation with 1-minute interval and the intubation time was also noted.Rate-pressure product(RPP)were calculated.Results:After anes-thetic induction,BP and RPP in the two groups decreased significantly compared with their preinduction values.As comparison with their postinduction values,the orotracheal intubation in the two groups caused significant increases in BP,HR and RPP.Diastolic blood pressure(DBP)and mean arterial pressure(MAP)increased significantly and lasted for 1-minute in group C compared with the baseline values.Systolic blood pressure(SBP)was not significant change and DBP increased significantly immediately af-ter intubation in group P.HR of both groups after intubation were significantly higher than their baseline values and lasted for 4 min in group C,HR increased significantly immediately after intubation in group P.SBP,DBP,MAP,HR and RPP after intubation in group P were significantly lower than those of group C during the observation period.The value of BIS was similar between the two groups.Compared with group C,the incidence of SBP greater than 30％and RPP greater than 22 000 was significantly lower in group P in the observation period,and no patient in group P developed RPP greater than 22 000.At the end of the incidence of SBP less than 30％of the basal value and HR less than 30％of the baseline,no severe bradycardia occurred in both groups.Conclusion:During double-lumen endobronchial intubation,unilateral thoracic paravertebal block with lidocaine can provide less hemodynamic response and level of conscionsness.

In recent decades,the advent of coronaviruses has engendered multiple large-scale infectious outbreaks,leading to profound human casualties and posing a significant menace to global public health.At the crux of the coronavirus lifecycle,the assembly and release phases emerge as pivotal processes,necessitating meticulous investigation into the underlying mechanisms.This paper systematically expounds upon the intricate assembly and packaging mechanisms intrinsic to coronaviruses,scrutinizes the diverse release pathways employed by these viruses,and delves into the discourse surrounding targeted antiviral drugs.The comprehensive insights encapsulated in this exposition serve as valuable reference points for formulating effective strategies in the prevention and treatment of coronavirus infections.

Objective To investigate the effect of reactive oxygen species(ROS)/silent information regulator 1(SIRT1)on hyperoxia-induced mitochondrial injury in BEAS-2B cells.Methods The experiment was divided into three parts.In the first part,cells were divided into H0,H6,H12,H24,and H48 groups.In the second part,cells were divided into control group,H48 group,H48 hyperoxia+SIRT1 inhibitor group(H48+EX 527 group),and H48 hyperoxia+SIRT1 agonist group(H48+SRT1720 group).In the third part,cells were divided into control group,48-hour hyperoxia+N-acetylcysteine group(H48+NAC group),and H48 group.The ROS kit was used to measure the level of ROS.Western blot and immunofluorescent staining were used to measure the expression levels of SIRT1 and mitochondria-related proteins.Transmission electron microscopy was used to observe the morphology of mitochondria.Results Compared with the H0 group,the H6,H12,H24,and H48 groups had a significantly increased fluorescence intensity of ROS(P<0.05),the H48 group had significant reductions in the expression levels of SIRT1 protein and mitochondria-related proteins(P<0.05),and the H24 and H48 groups had a significant reduction in the fluorescence intensity of mitochondria-related proteins(P<0.05).Compared with the H48 group,the H48+SRT1720 group had significant increases in the expression levels of mitochondria-related proteins and the mitochondrial aspect ratio(P<0.05),and the H48+EX 527 group had a significant reduction in the mitochondrial area(P<0.05).Compared with the H48 group,the H48+NAC group had a significantly decreased fluorescence intensity of ROS(P<0.05)and significantly increased levels of SIRT1 protein,mitochondria-related proteins,mitochondrial area,and mitochondrial aspect ratio(P<0.05).Conclusions The ROS/SIRT1 axis is involved in hyperoxia-induced mitochondrial injury in BEAS-2B cells.

Aim To investigate the possible mecha-nism of UNC5B-AS1 in regulating the malignant biolog-ical behavior of osteosarcoma cells.Methods RT-qPCR was used to detect the expression of UNC5B-AS1 in osteosarcoma cells MG63,osteosarcoma cells U2OS and osteoblast cells hFOB1.19.After overexpression and knockdown of UNC5B-AS1 in osteosarcoma cells,the proliferation,migration and apoptosis of osteosarco-ma cells were detected by CCK-8 assay,Transwell as-say and flow cytometry,respectively.At the same time,RT-qPCR and Western blot were used to detect the effects of UNC5B-AS1 overexpression and knock-down on the mRNA and protein expression of key fac-tors in the NF-κB signaling pathway.Results Com-pared with normal osteoblast hFOB1.19,UNC5B-AS1 expression was differentially increased in osteosarcoma cells MG63 and U2OS.Overexpression of UNC5B-AS1 significantly promoted the proliferation of osteosarcoma cells and significantly increased the migration ability of osteosarcoma cells,while the apoptosis rate markedly decreased,and NF-κB signaling pathway-related mR-NA and protein expressions apparently increased.Knockdown of UNC5B-AS1 evidently inhibited the pro-liferation of osteosarcoma cells and significantly re-duced the migration ability of osteosarcoma cells,while the apoptosis rate markedly increased,the NF-κB sig-naling pathway related mRNA and protein expression significantly reduced.Conclusions lncRNA UNC5B-AS1 is highly expressed in osteosarcoma cells,which may affect the malignant biological behavior of osteo-sarcoma cells by activating the NF-κB signaling path-way.

Humans ; SARS-CoV-2 ; COVID-19 ; Antibodies ; Antibodies, Viral/therapeutic use* ; Antibodies, Neutralizing/therapeutic use*

Gastroesophageal reflux disease （GERD） is a frequently and commonly occurring disease in clinic. In recent decades， with the development in pathophysiology and drug researches， modern medicine has achieved remarkable progress and results in diagnosis and treatment. However， the treatments for non-erosive reflux disease， refractory gastroesophageal reflux disease， proton pump inhibitor resistance， overlap of disease symptoms， and extraesophageal symptoms are limited and ineffective. Traditional Chinese medicine （TCM） was widely used in clinical practice， which has been proved effective in relieving symptoms and improving the quality of life. Sponsored by China Association of Chinese Medicine （CACM） and undertaken by the Spleen and Stomach Disease Branch of CACM， "the 12^th Youth Salon of Clinical Predominance Disease Series （GERD）" invited 18 authoritative digestive experts of TCM and western medicine to discuss "the difficulties of clinical diagnosis and treatment of GERD and TCM advantages". The focus issues such as modern medical diagnosis and treatment achievements and contributions， improvement and maintenance of symptoms， response to overlapping disease symptoms， reduction and withdrawal of acid suppressors， and treatment of extra-esophageal symptoms were discussed in depth. TCM and western medicine exchanged and complemented each other's strengths， combing the difficulties of modern medical diagnosis and treatment， which clarified the positioning and advantages of TCM and provided guidance for clinical and scientific research.

OBJECTIVE: To investigate the effect of 300 mL carbohydrates intake two hours before sur-gery on the gastric volume (GV) in patients positioning in trendelenburg undergoing gynecological laparoscopic procedures by using gastric antrum sonography, and further assess the risk of reflux aspiration. METHODS: From June 2020 to February 2021, a total of 80 patients, aged 18-65 years, body mass index (BMI) 18-35 kg/m², falling into American Society of Anesthesiologists (ASA) physical status Ⅰ or Ⅱ, scheduled for gynecological laparoscopic procedures positioning in trendelenburg were recruited and divided into two groups: the observation group (n =40) and the control group (n=40). In the observation group, solid food was restricted after 24:00, the patients were required to take 300 mL carbohydrates two hours before surgery. In the control group, solid food and liquid intake were restricted after 24:00 the night before surgery. The cross-sectional area (CSA) of gastric antrum was measured in supine position and right lateral decubitus position before anesthesia. Primary outcome was gastric volume (GV) in each group. Secondary outcome included Perlas A semi-quantitative grading and gastric volume/weight (GV/W). All the patients received assessment of preoperative feeling of thirsty and hunger with visual analogue scale (VAS). RESULTS: Complete data were available in eighty patients. GV was (58.8±23.6) mL in the intervention group vs. (56.3±22.1) mL in the control group, GV/W was (0.97±0.39) mL/kg vs. (0.95±0.35) mL/kg, respectively; all the above showed no significant difference between the two groups (P > 0.05). Perlas A semi-quantitative grading showed 0 in 24 patients (60%), 1 in 15 patients (37.5%), 2 in 1 patient (2.5%) in the intervention group and 0 in 25 (62.5%), 1 in 13 (32.5%), 2 in 2 (5%) in the control group, the proportion of Perlas A semi-quantitative grading showed no significant difference between the two groups (P > 0.05). A total of 3 patients (1 in the intervention group and 2 in the control group) with Perlas A semi-quantitative grading 2 were treated with special intervention, no aspiration case was observed in this study. The observation group endured less thirst and hunger (P＜0.05). CONCLUSION Three hundred mL carbohydrates intake two hours before surgery along with ultrasound guided gastric content monitoring does not increase gastric volume and the risk of reflux aspiration in patients positioning in trendelenburg undergoing gynecological laparoscopic surgery, and is helpful in minimizing disturbance to the patient's physiological needs, therefore leading to better clinical outcome.
Female ; Humans ; Supine Position ; Prospective Studies ; Pyloric Antrum ; Laparoscopy/adverse effects* ; Carbohydrates