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*

Cognitive impairment is the main clinical manifestation of many nervous system diseases such as stroke,multiple sclerosis,and neurodegeneration,and neuroinflammation is one of the key mechanisms for the onset of cognitive disorders.Chemokines are a class of highly conserved small-molecule secretory proteins that bind to the corresponding chemokine receptors located on cell mem-brane,activating downstream signaling pathways and playing an important role in cell migration,proliferation,differentiation,and sur-vival.In the central nervous system,chemokines and their receptors are involved in immune response and can exert a certain regulatory effect on neuroinflammation.This article reviews the research advances in chemokines and their receptors in cognitive disorders,in or-der to provide new insights and targets for the early diagnosis and treatment of related diseases.

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.

Purpose: This study aimed to identify the altered pathways and genes associated with freezing damage in human sperm during cryopreservation by multiomics analysis. Materials and Methods: Fifteen fresh human semen samples were collected for transcriptomic analysis, and another 5 fresh human semen samples were obtained for metabolomic analysis. For each semen sample, 1 mL was cryopreserved, and another 1 mL was left untreated for paired design. The results were then combined with previously published proteomic results to identify key genes/pathways. Results: Cryopreservation significantly reduced sperm motility and mitochondrial structure. Transcriptomic analysis revealed altered mitochondrial function, including changes in tRNA-methyltransferase activity and adenosine tri-phosphate/adenosine di-phosphate transmembrane transporter activity. Metabolomic analysis showed that the citrate cycle in mitochondria was significantly altered. Combining transcriptomic, proteomic, and metabolomic analyses revealed 346 genes that were altered in at least two omics analyses. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that metabolic pathways were significantly altered and strongly associated with mitochondria. Five genes were altered in all three omics analyses: COL11A1, COL18A1, LPCAT3, NME1, and NNT. Conclusions Five genes were identified by multiomics analysis in human cryopreserved sperm. These genes might have specific functions in cryopreservation. Explorations of the functions of these genes will be helpful for sperm cryopreservation and sperm motility improvement or even for reproduction in the future.

Objective To investigate the infection sites,pathogen distribution and risk factors of nosocomial infection after craniocerebral surgery.Methods This is a case-control study.Eighty patients with a mean age of(63.2±8.2)years who developed hospital acquired infections after craniocerebral treatment at Suzhou Hospital of Integrated Traditional Chinese and Western Medicine from January 2018 to December 2021 were assigned to infection group.Eighty patients with a mean age of(61.7±7.8)years who underwent craniocerebral surgery during the same period but did not develop hospital acquired infections were allocated to control group.The medical records and laboratory examination data of the patients were reviewed.Infection sites and pathogen characteristics in patients with hospital acquired infections after craniocerebral surgery were analyzed.Univariate and multivariate analyses were used to explore the risk factors for hospital acquired infections after craniocerebral surgery.Results The respiratory system was mainly infected in the 80 patients with hospital acquired infection after craniocerebral surgery(58.75%),followed by urinary system(22.50%).The main pathogenic bacteria in patients with respiratory system,urinary system and nervous system infections were Gram-negative bacteria.Gram-negative and Gram-positive bacteria in patients with blood system infection accounted for 50%,respectively.There was no significant difference in the composition of pathogenic bacteria among patients with infections in different parts of the body(P>0.05).In 51 patients with Gram-negative bacterial infections,the main pathogenic bacteria were Escherichia coli(26.25%)and Acinetobacter baumannii(15.00%).In 29 patients with Gram-positive bacterial infections,the main pathogenic bacteria were Staphylococcus aureus(16.25%)and Enterococcus faecalis(11.25%).Logistic regression model showed that non class Ⅰ incision,external ventricular drainage,cerebrospinal fluid leakage,non-prophylactic use of antibiotics before surgery,and indwelling catheter were independent risk factors for infection related complications in patients undergoing craniocerebral surgery(all P<0.05).Conclusion The respiratory system and urinary system are mainly involved in patients with nosocomial infection after craniocerebral surgery.The main pathogenic bacteria are Gram-negative bacteria.Non class Ⅰ incisions,external ventricular drainage,leakage of cerebrospinal fluid,non-prophylactic use of antibiotics before surgery,and indwelling catheter may increase the risk of postoperative infection.

Objective To investigate the job burnout of marines and analyze the mediating role of psychological resilience between anxiety and job burnout of marines.Methods A total of 230 marines were chosen as research objects,and 147 servicemen stationed on island were enrolled as control.Military job burnout scale was used to evaluate their job burnout levels.Connor-Davidson resilience scale(CD-RISC)and state trait anxiety inventory(STAI)were used to evaluate their psychological resilience and anxiety,respectively.Results The degree of job burnout of marines was significantly lower than that of the control group(P<0.001).Job burnout was negatively correlated with psychological resilience(P<0.001)and positively correlated with anxiety(P<0.001).Psychological resilience was negatively correlated with anxiety(P<0.001).Psychological resilience played a mediating role in the influence of anxiety on the job burnout of marines(indirect effect was 0.011[95%CI 0.002 to 0.021]).Conclusion Marines have a low level of job burnout.Anxiety is an important factor of job burnout.Anxiety can not only directly cause job burnout,but also aggravate job burnout by affecting the level of psychological resilience.It is very important to relieve anxiety and improve psychological resilience for reducing job burnout of marines.

To revise GBZ 188 Technical Specification for Occupational Health Surveillance based on national laws, regulations, standards, specifications and legal documents of occupational disease, and combination with the actual situation in China. The main modifications are as follows: the occupational health surveillance for workers exposed to toluene (xylene may implement by reference), bromopropane, methyl iodide, ethylene oxide, chloroacetic acid, indium and its compounds, coal tar, coal tarasphalt, asphalt, β-naphthylamine, dust of metal and its compounds(tin, iron, antimony, barium and its compounds), hard metal dust, erionite dust, low temperature, laser, tick-borne encephalitis virus, Borrelia burgdorferi, and human immunodeficiency virus, for scraper or grind operators, and underground workers using squatting or kneeling position, crawling position, side-lying position, or shoulder position for a long period of time are included. The emergency health screening for workers exposed to arsenic, fluorine and its inorganic compounds, and acrylamide are included. The occupational medical examination (OME) for workers exposed to amino and nitro compounds of benzene, phosgene, monomethylamine, organic fluorine and dimethyl sulfate has been adjusted and made mandatory, with corresponding assessments required upon leaving the job. The special occupational health surveillance for workers exposed to mycobacterium tuberculosis and hepatitis virus is removed. The OME conclusion of reexamination is removed, and standardize recheck/additional inspection requirements. The optional items in OME performed before, during and after leaving post are removed, but the optional items in emergency medical examination are retained. Additional OME items are added. The Guideline for OME Summary Reports is added as informative appendix, and so on. The revised GBZ 188 Technical Specification for Occupational Health Surveillance is more scientific and practical.

Objective:To explore the team construction and treatment strategy of the Diabetic Foot-Multidisciplinary Team.Methods:The clinical data of 19 patients with severe ischemic diabetic foot treated by our Diabetic Foot-Multidisciplinary Team Center from Apr 2021 to Mar 2022 were collected, and the overall amputation rate, above-ankle major amputation rate, minor amputation rate and mortality, Diabetic Foot-Multidisciplinary Team consultation discipline participation rate and treatment participation degree were retrospectively analyzed.Results:Nineteen patients (15 males and 4 females) were enrolled, aged 26 to 94 (68.6±14.2). All were with severe ischemic diabetic foot ulcer:Rutherford grade 5 or up and dysfunction in 2 or more organs. Complications included arteriosclerosis obliterans of the lower extremities in 18 cases, heart diseases in 18, hypertension in 15, and renal insufficiencies in 10. The overall amputation rate was 36.8%, major amputation rate in 21.1%, minor amputation rate in 15.8%, and mortality rate was 15.8%. A total of 16 disciplines participated in Diabetic Foot-Multidisciplinary Team; the main participating disciplines were vascular surgery (19 times), endocrinology (12 times), and cardiology (11 times). The main treatment disciplines were vascular surgery (14 times), plastic surgery (3 times), and cardiology (2 times).Conclusion:For the diagnosis and treatment of diabetic foot, it is necessary to set up a multidisciplinary team as early as possible to control the causes of diabetic foot ulcer, prevent the recurrence of diabetic foot ulcer, reduce the mortality and amputation rate, and improve the quality of life of patients.

Objective:To investigate the expression of microRNA (miRNA, miR)-4699-3p in ovarian cancer cell lines, and observe its ability to regulate the expression of mitochondrial ribosomal protein S23 (MRPS23) and its effect on the migration and proliferation of ovarian cancer cells.Methods:Real-time fluorescence quantitative polymerase chain reaction (qRT-PCR) was used to detect the expression of miR-4699-3p in ovarian cancer cell lines (OVCAR-3, SKOV-3, HO-8910, OC3, A2780) and normal ovarian epithelial cells (IOSE80). The liposome transfection method was used to transfect miR-4699-3p mimic or negative control miR-NC to the cell line with the lowest miR-4699-3p expression, which was defined as the experimental group and the control group. qRT-PCR was used to verify transfection efficiency. Bioinformatics technology predicted the candidate target gene of miR-4699-3p, and the dual luciferase reporter gene experiment identified its ability to regulate the target gene. qRT-PCR and Western blot were used to detect the expression of target genes at the mRNA and protein levels. Cell counting method (CCK-8) and transwell migration experiment were used to detect the effect of miR-4699-3p on the proliferation and migration of ovarian cancer cells.Results:The expression of miR-4699-3p in ovarian cancer cell lines was significantly lower than that of normal ovarian epithelial cells ( P<0.05), and the lowest expression in OVCAR-3 cells ( P<0.01). After transfection of miR-4699-3p, the expression of miR-4699-3p in OVCAR-3 cells in the experimental group was significantly increased ( P<0.01), which proved that the transfection was successful. Bioinformatics technology predicted that the candidate target gene of miR-4699-3p may be MRPS23. The dual luciferase reporter gene experiment confirmed that miR-4699-3p can directly target the 3′-UTR of MRPS23 gene mRNA ( P<0.01). Compared with the OVCAR-3 cells in the control group, the mRNA and protein expression levels of the MRPS23 gene were significantly reduced, while the expressions of Twist, Slug, CDK6 and Cyclin D3 were significantly decreased ( P<0.01) in the experimental group after up-regulating miR-4699-3p expression ( P<0.01). After up-regulating miR-4699-3p expression, the proliferation ability of OVCAR-3 cells decreased ( P<0.05) and the migration ability of OVCAR-3 cells was reduced ( P<0.01). Conclusions:miR-4699-3p is under-expressed in ovarian cancer cell lines. Up-regulation of miR-4699-3p expression in OVCAR-3 cells can inhibit ovarian cancer cell proliferation and migration by interfering with MRPS23 gene expression.

Antibodies, Neutralizing ; Antibodies, Viral/isolation & purification* ; B-Lymphocytes/virology* ; COVID-19/virology* ; Humans ; Immunity/genetics* ; RNA, Viral/immunology* ; SARS-CoV-2/pathogenicity* ; Single-Cell Analysis