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*

Norovirus, as one of the main pathogens causing non-bacterial gastroenteritis, can cause serious public health problems and economic losses around the world. In recent years, the outbreaks caused by the virus in China are on the rise. Human Norovirus (HuNoV) can hardly be cultivated in-vitro. The nucleic acid detection method (such as RT-qPCR) has the highest sensitivity and specificity, but it was not established that the correlation between the detected viral genome and viral infectivity, which leads to inaccurate judgment of safety risks. Here, the in-vitro and in-vivo culture models, viral genome integrity and capsid protein integrity were cut into three aspects. The research progress and characteristics of infectious Norovirus identification technology in recent years were reviewed and discussed, and the future development trend of this technology was prospected. The aim is to further improve the accuracy of Norovirus quantitative detection and provide a theoretical basis for its application in the field of food safety testing.

The 11α-hydroxylation of 16α, 17-epoxyprogesterone (EP) catalyzed by Rhizopus nigricans is crucial for the steroid industry. However, lower conversion rate of the biohydroxylation restricts its potential industrial application. The 11α-steroid hydroxylase CYP509C12 from R. oryzae were reported to play a crucial role in the 11α-hydroxylation in recombinant fission yeast. In the present study, the CYP509C12 of R. oryzae (RoCYP) was introduced into R. nigricans using the liposome-mediated mycelial transformation. Heterologous expression of RoCYP resulted in increased fungal growth and improved intracellular reactive oxygen species content in R. nigricans. The H₂O₂ levels in RoCYP transformants were approximately 2-folder that of the R. nigricans wild type (RnWT) strain, with the superoxide dismutase activities increased approximately 45% and catalase activities decreased approximately 68%. Furthermore, the 11α-hydroxylation rates of EP in RoCYP transformants (C4, C6 and C9) were 39.7%, 38.3% and 38.7%, which were 12.1%, 8.2% and 9.4% higher than the rate of the RnWT strain, respectively. This paper investigated the effect of heterologous expression of RoCYP in R. nigricans, providing an effective genetic method to construct the engineered strains for steroid industry.

Objective To compare the minimum 5?year follow?up outcomes of surgical management by posterior only, anterior only and combined posterior and anterior approaches for lumbar tuberculosis in adults, evaluate the mid?term follow?up results of the surgery for the treatment of lumbar tuberculosis and explore its advantages and indications. Methods From Jun 2004 to Jan 2010, 311 adult patients with lumbar tuberculosis were treated surgically. The clinical data of 137 cases that met the enrolled criteria and had integrity following?up data was analyzed retrospectively. It included the patients who had the surgical indication of the posterior only surgery but underwent the anterior only or the combined posterior and anterior ap?proaches before 2008. There were 83 cases of male and 54 cases of female. The age ranged from 20 to 75 years, with a mean of 65.6 years. Among these patients, 63 cases were treated with single?stage posterior debridement, interbody fusion and instru?mentation (the posterior group); 42 cases were treated with posterior instrumentation, and anterior debridement and bone graft in a single or two?stage procedures (the combined group) and 32 cases were treated with anterior debridement and strut graft?ing with instrumentation (the anterior group). Trauma index (the operation time, blood loss, the length of hospital stay, compli?cations);imaging parameters (Segment kyphotic angle, corrective rate, loss angle, bone fusion time) and the quality?of?life indi?cators (Oswestry Disability Index、Frankle grade、visual analogue scale、Macnab score) were compared among three groups. Re?sults The mean operation time, mean blood loss and the complications rate were (207.9 ± 30.9) min, (409.5 ± 107.9) ml and 12.95%in the posterior group;(270.7±32.0) min, (649.0±120.0) ml and 30.95%in the anterior group;(349.7±38.9) min, (840.0± 168.7) ml and 25%in the combined group. The operation time, blood loss and the complications rate of the posterior group were less than the anterior group and the combined group, and the difference was significant;The combined group consumed the longest operation time, associated with the most intraoperative blood loss, the highest complication rate and the longest hospital stay among the three groups, and the difference was significant. The correction rate of kyphosis achieved of the anterior group ( 52%± 5.45%) was significantly inferior to the posterior group (74%±5.04%) and the combined group (69%±7.95%), while the loss of cor?rection in the anterior group (2.5°) was higher than both the posterior group (0.8°) and the combined group (1.1°), and the differ?ence was significant. The average follow?up was(6.5±1.96)years (range, 5-11). The mean bone fusion time of the posterior group, the anterior group and the combined group were (6.0±1.5) months, (6.2±1.3) months and (6.5±1.6) months respectively, and there was no statistic difference. After the surgery, the quality of life was improved obviously in all patients. At the time of the latest fol?low?up, the improvement rate of the ODI,VAS and the excellent and good rate according to the Macnab score were 80.6%±2.1%, 81.7%± 1.6%and 95.24%in the posterior group;79.8%± 1.5%, 79.7%± 2.0%and 92.95%in the anterior group;81.3%± 1.1%, 79.9%±0.8%and 90.63%in the combined group. There was no significant difference among the groups in the improvement rates of the ODI, VAS, Frankel grade and the excellent and good rate of the Macnab score. Conclusion The Mid?term follow?up of the different surgical procedures for the treatment of the lumbar tuberculosis in adults were basically satisfactory. Compared with the traditional surgery, the posterior?only surgery is a safe, minimally invasive and effective method in the management of monoseg?ment lumbar tuberculosis in adults.