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*

ObjectiveTo comprehensively evaluate the clinical value of Jintiange Capsules （JCs） in the treatment of osteoporosis （OP） and clarify the intrinsic advantages and clinical treatment characteristics of JCs， providing references for relevant departments of national health and medicine decision-making and the basis and clues for clinical and basic in-depth research. MethodBased on evidence-based medical evidence， this study integrated quantitative and qualitative methods and combined with questionnaires， official website data， human experience， pharmacoeconomic evaluation， and other research methods. From the effectiveness， safety， economy， innovation， suitability， accessibility， and traditional Chinese medicine （TCM） characteristics of the '6+1' dimension， the clinical evidence and value of JCs in the treatment of OP were comprehensively evaluated， forming the 'clinical evidence and value evaluation index'. The comprehensive evaluation of clinical value was based on the multi-criteria decision analysis framework. The expert meeting method was used to empower each dimension and value index. The clinical evidence and value evaluation software of Chinese patent medicine （CSC v2.0） was used to calculate the total value score， and the clinical advantages of JCs were comprehensively evaluated. ResultBased on randomized controlled clinical studies and systematic review， data analysis of spontaneous reporting system （SRS）， case reports， non-clinical safety studies， etc.， serious adverse drug reactions （ADRs） were reported after the launch of this product monitored by SRS， mainly involving abnormal liver function and adverse reactions of cardiovascular system. Therefore， the safety evidence adequacy of this product should be further improved， and the safety evaluation was Grade B. Meta-analysis showed that JCs were superior to the control group in improving the total clinical effective rate， improving bone mineral density， reducing visual analogue scale （VAS） score， and shortening fracture healing time. Combined with Grading of Recommendations Assessment， Development and Evaluation （GRADE） evidence evaluation， the comprehensive evaluation of effectiveness was Grade A. Pharmacoeconomic evaluation showed that JCs combined with calcium carbonate D₃ tablets were more cost-effective than calcium carbonate D₃ tablets alone in patients with OP. Compared with Gushukang capsules， JCs had more cost-effectiveness advantages， but the sample size included in the study was small， and the results needed to be verified by further studies. Combined with the results of the Comparative Assessment of Structure Prediction （CASP） evaluation list， the comprehensive economic evaluation was Grade B. JCs were the only bionic medicine of tiger bone in China with all intellectual property rights， with 3 national invention patents. Its process preparation and fingerprint detection had obvious technical advantages. It had innovative advantages in the supply base equipment， medicine resource management， production technology， and other aspects. Thus， its innovative comprehensive evaluation was Grade A. JCs were in capsule dosage form， which was relatively convenient for storage and transportation. The dosage form was suitable for indications， and the usage was easy for patients to grasp and accept. The statutory information and non-statutory information met the national standards. The comprehensive evaluation of suitability was Grade A. JCs did not contain toxic ingredients， had no restrictions on origin and prescription， and had abundant resources of original medicinal materials. The affordability of JCs in the treatment of OP was good in urban areas （14.97%） but not in rural areas （39.76%）. The price was higher than that of similar Chinese patent medicines， and the comprehensive evaluation of availability was Grade B. JCs had a reasonable proportion of natural animal bones， and their composition was basically the same as that of natural tiger bones. After marketing， more than 2 000 cases of real-world clinical research evidence was accumulated， and the comprehensive evaluation of TCM characteristics was Grade B. CSC v2.0 software was used for quantitative synthesis of the '6+1' dimension， and the comprehensive clinical value of JCs in the treatment of OP was Grade A. ConclusionJCs have good clinical value in the treatment of OP， and the TCM characteristics are prominent. It is suggested that JCs can be directly transformed into the related policy results of basic clinical drug management according to procedures.

Objective:To establish a computer-aided design and 3D printing system for precise implantation of micro implant anchorage, and accurately calibrate the position and direction of micro implant implantation.Methods:A retrospective selection was conducted on 15 patients (30 in total) who underwent micro implant implantation surgery from the Department of Stomatology, the Affiliated Hospital of Jiangnan University from November 2019 to November 2021, including 6 males and 9 females, aged (17.1±6.3)years old. The preoperative patient was photographed with cone beam computed tomography (CBCT) and the collected DICOM data format was output. A 3D scan was performed on the patient′s preoperative analysis model to obtain the STL file of the model scan. The CBCT data and model data were fitted and matched using 3Shape Implant Studio software, and the thickness of the guide plate, the amount of undercut compensation, and the size of the key component collar were designed. The 3D printer was used for printing after resizing. Using the assist method to implant micro implants, CBCT was taken postoperatively to compare the preoperative design with the postoperative results.Results:After fitting the postoperative CBCT with the designed CBCT of the micro implant, it was found that the micro implant was consistent with the preoperative design, maintained a safe distance and parallel to the adjacent tooth root, and did not damage the maxillary sinus and other areas. No detachment of the micro implant anchorage was observed 1 or 3 months after surgery. The application of assisted micro implant anchorage 3D guide plate was reliable, with accurate implantation position and direction, and can be implanted in most parts of the oral cavity.Conclusions:The use of computer-aided design and 3D printing system to create an assistive micro implant anchorage 3D guide plate can accurately locate the position and direction of the micro implant, which is worthy of clinical promotion and application.

Objective:To investigate the effect of radiofrequency radiation (RF) from 5G mobile phone communication frequency bands (3.5 GHz and 4.9 GHz) on the permeability of the blood-brain barrier (BBB) in mice.Methods:A total of 24 healthy adult male C57BL/6 mice (6-8 weeks old) were randomly divided into Sham, 3.5 GHz RF and 4.9 GHz RF groups, and 8 mice in each group. Mice in the RF groups were systemically exposed to 5G cell phone radiation for consecutive 35 d(1 h/d) with 50 W/m 2 power density. The BBB permeability of mice was detected by Evans Blue (EB) fluorescence experiment. The expression levels of the BBB tight junction-related proteins (ZO-1, occludin and claudin-11) and the gap junction-related protein Connexin 43 were determined by Western blot. Results:The number of spots, fluorescence intensity and comprehensive score of EB were significantly increased in 3.5 GHz RF group and 4.9 GHz RF group compared with the Sham group ( t=12.98, 17.82, P<0.001). Compared with the Sham group, the content of S100B in mouse serum was significantly increased in 3.5 GHz RF group and 4.9 GHz RF group ( t=19.34, 14.68, P<0.001). The BBB permeability was increased in the RF group. The expression level of occludin protein was significantly reduced in the 3.5 GHz RF group ( t=-3.13, P<0.05), and this decrease was much profound in the 4.9 GHz RF group ( t=-6.55, P<0.01). But the protein levels of ZO-1, Claudin-11 and Connexin 43 in the cerebral cortex of the RF groups had no significantly difference in comparison with the Sham group( P>0.05). Conclusions:The continuous exposure of mobile phone RF at 3.5 GHz or 4.9 GHz for 35 d (1 h/d) induces an increase of BBB permeability in the mouse cerebral cortex, perhaps by reducing the expression of occludin protein.

Objective:To prepare 68Ga-2-(4, 7-bis(carboxymethyl)-1, 4, 7-triazonan-1-yl)pentanedioic acid (NODAGA)-YHWYGYTPQNVI (GE11) and evaluate its feasibility of PET imaging for pancreatic cancer. Methods:GE11 peptide was conjugated with NODAGA and then labeled with 68Ga. The labeling yield, radiochemical purity, hydrophilicity, stability and specificity in vitro were determined. Human pancreatic cancer BxPC3 nude mice models ( n=9) were established. MicroPET imaging was then obtained after 30 and 90 min, and mice were sacrificed at 90 min to acquire the radioactivity distribution of main organs and tumors. Pair t test was used to analyze the data. Results:The labeling yield was (73.5±5.4)% and radiochemical purity was more than 98%. After incubation 120 min in mouse serum at 37 ℃, radiochemical purity was more than 92%. The uptake was specific in BxPC3 cell lines. MicroPET images showed that 68Ga-NODAGA-GE11 could accumulate quickly in tumor. Value of tumor uptake was significantly higher than that of normal pancreas at 90 min ((1.38±0.25) vs (0.49±0.07) %ID/g; t=12.67, P<0.05), and the radio-uptake of blood, muscle and bone was lower than that of tumor. Conclusions:68Ga-NODAGA-GE11 is easy to be prepared with high radiochemical purity and good stability, and can specifically target BxPC3 xenograft tumor. However, due to the high uptake in the kidneys and liver, the value of 68Ga-NODAGA-GE11 in PET imaging for pancreatic tumor needs further study.

Objective:To evaluate the clinical effect of Salviae Miltiorrhizae and Ligustrazine Hydrochloride injection on coronary heart disease in real world.Methods:Took the patients data with coronary heart disease of 24 tertiary-class A hospitals’ information system from October 2006 to December 2015 as the research targets. The patients injected by Salviae Miltiorrhizae and Ligustrazine Hydrochloride injection were selected as the observation group, and who were not injected were selected as the control group with ratio of 1:1, the same number on gender, similar age (+5 years difference) and similar condition upon hospitalization. Taking medication efficacy as the outcome evaluation index, the 30 confounding factors in this study were controlled by propensity scores, including hospital admission, co-morbidity, co-medication, occupation, cost category, and total hospitalization costs. Comparative analysis of the effect of Salviae Miltiorrhizae and Ligustrazine Hydrochloride injection on the clinical outcome of coronary heart disease by classical logistic regression and logistic regression weighted by propensity score.Results:30 confounding factors were identified and balanced, and 7 confounding factors were most affected factors that included clopidogrel bisulfate tablets, occupation, inosine tablets, levocarnidine injection, cerebroprotein hydrolysate injection, nitroglycerin and insulin. Both methods of logistic regression demonstrated that patients receiving parenterally administered Salviae Miltiorrhizae and Ligustrazine Hydrochloride injection had improved outcomes compared to those who did not receive the drug ( P<0.05). Conclusions:The study suggestes that the Salviae Miltiorrhizae and Ligustrazine Hydrochloride injection is a potential advantageous therapy in the treatment of coronary heart disease. However, a large amount of unknown confounding variable should be taken into account. Consider this research is a retrospective study, and the results need to be further verified by prospective studies.

Objective:To analyze the epidemiological and etiological characteristics of a dengue fever outbreak in Hunan province in 2018.Methods:Real-time PCR assay was performed for the laboratory diagnosis of 8 suspected dengue fever cases. Etiological surveillance was performed in 186 suspected dengue fever cases and fever cases who had close contacts with dengue fever patients. C6/36 cells was used for the virus isolation from acute phase serum. By sequencing the full length of E genes of 15 dengue virus strains, phylogenetic analysis was performed based on the sequences obtained, including reference sequences from the NCBI GenBank database, the serotypes and gene subtypes of the virus were analyzed to trace the possible source of transmission. An emergency monitoring of vector density and a retrospective survey of sero-epidemiology in healthy population were conducted in the epidemic area.Results:In the serum samples of 8 suspected patients, 6 were dengue virus RNA positive, and 4 were NS1 antigen positive. In 186 suspected patients, 96 were dengue virus nucleic acid, NS1 antigen or antibody positive in etiological test. A total of 64 dengue virus strains were isolated. The phylogenetic analysis showed that all the dengue virus strains belonged to type 2, which might be from Guangdong or Zhejiang provinces. The Bretub index was up to 65, indicating an extremely high risk of transmission. The positive rate of the dengue virus IgG antibody was 0.53%(2/377) in retrospective survey of 377 healthy people.Conclusion:The field epidemiologic and the molecular genetics analyses showed the outbreak of dengue fever in Hunan in 2018 was caused by imported cases and dengue virus 2.

Objective:To confirm the first imported Chikungunya fever (CHIK) epidemic in Hunan province.Methods:Serum samples of patients and colleagues were collected. The nucleic acids of Dengue virus (DENV), Yellow fever virus (YFV), Chikungunya virus (CHIKV) were detected by real- time fluorescent quantitative PCR. The positive PCR products were sequenced. Phylogenetic tree was constructed.Results:The serum samples of the patient and one of the five colleagues were positive for CHIKV. The Blast comparison of gene sequence showed 99% homology with CHIKV sequences. The infected CHIKV belonged to ECSA genotype in the phylogenetic tree.Conclusions:The first imported CHIK epidemic in Hunan province was confirmed through the epidemiological survey and etiologic detection.

Cryoelectron Microscopy ; Mycobacterium smegmatis ; genetics ; ultrastructure ; RNA, Ribosomal ; ultrastructure ; Ribosomal Proteins ; genetics ; isolation & purification ; Ribosomes ; genetics ; ultrastructure

Objective: To make etiological diagnosis and evaluate the protective effects of post-exposure prophylaxis(PEP) in an event of one dog injured seven persons. Methods: Direct immunofluorescence assay (DFA) and nested polymerase chain reaction (PCR) were employed to detect nucleoprotein and nucleoprotein(N) gene of rabies virus in the brain tissues of the dog, the positive samples were sequenced for the full length of N gene of rabies virus, then the homology of the N gene of rabies virus was analyzed after the phylogenetic tree was constructed. Rapid fluorescent focus inhibition test (RFFIT) was applied to detect the rabies virus neutralizing antibodies(RVNA) on day 0, 14 and 40 after PEP. Results: The cerebral, cerebellar and hippocampal tissues were positive by DFA and nested PCR. The phylogenetic tree indicated the rabies virus belonged to the rabies virus genotype I. The homology of the nucleotide and amino acid of the rabies virus N gene were over 86% with the vaccine strains. The titer of the RVNA increased significantly from the day 0 to day 14 after PEP, the lowest was 5.78 IU/ml and the highest was 26.15 IU/ml. On the day 40, the highest RVNA titer was 51.96 IU/ml. No rabies cases occurred in a one year follow-up visit. Conclusions Normative PEP can effectively prevent the occurrence of rabies cases.