1.Geographical Inference Study of Dust Samples From Four Cities in China Based on ITS2 Sequencing
Wen-Jun ZHANG ; Yao-Sen FENG ; Jia-Jin PENG ; Kai FENG ; Ye DENG ; Ke-Lai KANG ; Le WANG
Progress in Biochemistry and Biophysics 2025;52(4):970-981
ObjectiveIn the realm of forensic science, dust is a valuable type of trace evidence with immense potential for intricate investigations. With the development of DNA sequencing technologies, there is a heightened interest among researchers in unraveling the complex tapestry of microbial communities found within dust samples. Furthermore, striking disparities in the microbial community composition have been noted among dust samples from diverse geographical regions, heralding new possibilities for geographical inference based on microbial DNA analysis. The pivotal role of microbial community data from dust in geographical inference is significant, underscoring its critical importance within the field of forensic science. This study aims to delve deeply into the nuances of fungal community composition across the urban landscapes of Beijing, Fuzhou, Kunming, and Urumqi in China. It evaluates the accuracy of biogeographic inference facilitated by the internal transcribed spacer 2 (ITS2) fungal sequencing while concurrently laying a robust foundation for the operational integration of environmental DNA into geographical inference mechanisms. MethodsITS2 region of the fungal genomes was amplified using universal primers known as 5.8S-Fun/ITS4-Fun, and the resulting DNA fragments were sequenced on the Illumina MiSeq FGx platform. Non-metric multidimensional scaling analysis (NMDS) was employed to visually represent the differences between samples, while analysis of similarities (ANOSIM) and permutational multivariate analysis of variance (PERMANOVA) were utilized to statistically evaluate the dissimilarities in community composition across samples. Furthermore, using Linear Discriminant Analysis Effect Size (LEfSe) analysis to identify and filter out species that exhibit significant differences between various cities. In addition, we leveraged SourceTracker to predict the geographic origins of the dust samples. ResultsAmong the four cities of Beijing, Fuzhou, Kunming and Urumqi, Beijing has the highest species richness. The results of species annotation showed that there were significant differences in the species composition and relative abundance of fungal communities in the four cities. NMDS analysis revealed distinct clustering patterns of samples based on their biogeographic origins in multidimensional space. Samples from the same city exhibited clear clustering, while samples from different cities showed separation along the first axis. The results from ANOSIM and PERMANOVA confirmed the significant differences in fungal community composition between the four cities, with the most pronounced distinctions observed between Fuzhou and Urumqi. Notably, the biogeographic origins of all known dust samples were successfully predicted. ConclusionSignificant differences are observed in the fungal species composition and relative abundance among the cities of Beijing, Fuzhou, Kunming, and Urumqi. Employing fungal ITS2 sequencing on dust samples from these urban areas enables accurate inference of biogeographical locations. The high feasibility of utilizing fungal community data in dust for biogeographical inferences holds particular promise in the field of forensic science.
2.Independent and Interactive Effects of Air Pollutants, Meteorological Factors, and Green Space on Tuberculosis Incidence in Shanghai.
Qi YE ; Jing CHEN ; Ya Ting JI ; Xiao Yu LU ; Jia le DENG ; Nan LI ; Wei WEI ; Ren Jie HOU ; Zhi Yuan LI ; Jian Bang XIANG ; Xu GAO ; Xin SHEN ; Chong Guang YANG
Biomedical and Environmental Sciences 2025;38(7):792-809
OBJECTIVE:
To assess the independent and combined effects of air pollutants, meteorological factors, and greenspace exposure on new tuberculosis (TB) cases.
METHODS:
TB case data from Shanghai (2013-2018) were obtained from the Shanghai Center for Disease Control and Prevention. Environmental data on air pollutants, meteorological variables, and greenspace exposure were obtained from the National Tibetan Plateau Data Center. We employed a distributed-lag nonlinear model to assess the effects of these environmental factors on TB cases.
RESULTS:
Increased TB risk was linked to PM 2.5, PM 10, and rainfall, whereas NO 2, SO 2, and air pressure were associated with a reduced risk. Specifically, the strongest cumulative effects occurred at various lags: PM 2.5 ( RR = 1.166, 95% CI: 1.026-1.325) at 0-19 weeks; PM 10 ( RR = 1.167, 95% CI: 1.028-1.324) at 0-18 weeks; NO 2 ( RR = 0.968, 95% CI: 0.938-0.999) at 0-1 weeks; SO 2 ( RR = 0.945, 95% CI: 0.894-0.999) at 0-2 weeks; air pressure ( RR = 0.604, 95% CI: 0.447-0.816) at 0-8 weeks; and rainfall ( RR = 1.404, 95% CI: 1.076-1.833) at 0-22 weeks. Green space exposure did not significantly impact TB cases. Additionally, low temperatures amplified the effect of PM 2.5 on TB.
CONCLUSION
Exposure to PM 2.5, PM 10, and rainfall increased the risk of TB, highlighting the need to address air pollutants for the prevention of TB in Shanghai.
China/epidemiology*
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Humans
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Air Pollutants/analysis*
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Tuberculosis/epidemiology*
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Incidence
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Meteorological Concepts
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Particulate Matter/adverse effects*
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Environmental Exposure
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Male
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Female
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Adult
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Air Pollution
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Middle Aged
3.Controversial points in the surgical treatment of gallbladder cancer with delayed diagnoses
Sen LE ; Yue ZUO ; Zhengdong DENG ; Jianming WANG
Journal of Surgery Concepts & Practice 2025;30(2):106-111
Gallbladder cancer with delayed diagnoses, as a malignant tumor diagnosed intraoperatively or postoperatively incidentally in benign gallbladder diseases, radical surgical treatment is its core treatment, and the necessity of re-operation, timing of surgery, choice of surgical procedure, definition of resection extent, and preoperative neoadjuvant therapy still remain controversial. Re-operation for gallbladder cancer with delayed diagnoses needs to balance tumor radicalization, postoperative risk, and survival benefit, and combining neoadjuvant therapy to facilitate radical treatment, and develop individualized protocols. The multidisciplinary team should integrate innovative technologies and multi-center prospective studies to promote the development of precise treatment strategies for gallbladder cancer with delayed diagnoses and optimize the survival of patients.
4.Bibliometric analysis of a leadership indicator system in the medical field
Sen YANG ; Hua JIN ; Jianwei SHI ; Chen CHEN ; Xuhua GE ; Hanzhi ZHANG ; Le MA ; Dehua YU
Chinese Journal of General Practitioners 2024;23(3):244-250
Objective:To investigate the current status of research on the construction of leadership indicator system in the medical field at home and abroad, and to analyze the characteristics of the indicator system therein.Methods:This was a bibliometric study. The group applied subject keywords to search relevant literature on the construction of leadership indicator system in the medical field at home and abroad on English websites PubMed, Web of Science, Google Scholar, CINAHL, Scopus and Chinese websites Baidu Academic, CNKI, CQVIP, Wanfang Data Knowledge Service Platform, with a time frame of 2016-2023. The basic characteristics of the literature, the theoretical framework of the research application and the research theme were extracted, and the content of the indicator system in the literature was reviewed and summarized.Results:A total of 21 literatures were included, including 7 Chinese literatures and 14 English literatures. Of these literatures, 10 focused on physician leadership, 5 on medical manager leadership, and 2 on general practitioner leadership. Among 16 research literatures, 9 informed the theoretical basis of leadership, and 4 literatures were applied research. Five main themes were identified: leadership studies of individual healthcare administrators, leadership development in healthcare, interest and attitudes of healthcare workers towards leadership learning, applications of leadership in healthcare, and the impact of leadership in healthcare on patients and healthcare organizations.Conclusions:At present, research on the construction of the leadership indicator system in the medical field presents is diverse, with differences in theoretical basis and content. The original and empirical research is still insufficient.
5.The Genetic Polymorphism and Structural Analysis of 47 Microhaplotypes in a Jiangsu Changshu Chinese Han Population
Kun-Peng PAN ; Yao-Sen FENG ; Wen-Shuai YU ; Zong-Wei LIU ; Yi-Ren YAO ; Jie ZHAO ; Ke-Lai KANG ; Chi ZHANG ; Le WANG ; Jian WU
Progress in Biochemistry and Biophysics 2024;51(2):423-434
ObjectiveTo investigate the genetic polymorphism and structure of 47 autosomal microhaplotypes in the Han population in Changshu City, Jiangsu Province, and to evaluate the forensic efficiencies and forensic parameters. MethodsThe DNA library of unrelated individual samples was prepared according to MHSeqTyper47 kit manual and sequenced on the MiSeq FGx platform. Microhaplotype genotyping and sequencing depth statistics were processed using MHTyper. The genetic information of samples was then evaluated. The fixation index and genetic distance between the Jiangsu Changshu population and the reference populations in the 1000 Genomes Project phase 3 (1KG) were calculated, and forensic parameters were evaluated. ResultsThe fixation index and genetic distance between the Han population in Changshu, Jiangsu, and the CHB (Han Chinese in Beijing, China) reference population in 1KG were the lowest. The effective allele number (Ae) of each locus is also the closest between the two populations. The combined matching probability (CMP) of the Changshu Han population is close to the 5 populations of the East Asian reference super-population in 1KG, which is 1.25×10-36, and the combined probability of exclusion reached 0.999 999 999 964 1. ConclusionThis study reported the genetic polymorphism and allele frequency of 47 microhaplotypes in a Han population in Changshu City, Jiangsu Province. This information provides a data basis for 47 microhaplotypes in forensic applications. In addition, the polymorphism differences between the 1KG reference population and the Han population in Changshu, Jiangsu were compared, and the genetic structure of 47 microhaplotypes in the Han population in Changshu, Jiangsu was revealed. In general, the reference data of the East Asian super-population in 1KG is more in line with the genetic characteristics of Han population in Changshu, Jiangsu.
6.Pharmacological inhibition of BAP1 recruits HERC2 to competitively dissociate BRCA1-BARD1, suppresses DNA repair and sensitizes CRC to radiotherapy.
Xin YUE ; Tingyu LIU ; Xuecen WANG ; Weijian WU ; Gesi WEN ; Yang YI ; Jiaxin WU ; Ziyang WANG ; Weixiang ZHAN ; Ruirui WU ; Yuan MENG ; Zhirui CAO ; Liyuan LE ; Wenyan QIU ; Xiaoyue ZHANG ; Zhenyu LI ; Yong CHEN ; Guohui WAN ; Xianzhang BU ; Zhenwei PENG ; Ran-Yi LIU
Acta Pharmaceutica Sinica B 2023;13(8):3382-3399
Radiotherapy is widely used in the management of advanced colorectal cancer (CRC). However, the clinical efficacy is limited by the safe irradiated dose. Sensitizing tumor cells to radiotherapy via interrupting DNA repair is a promising approach to conquering the limitation. The BRCA1-BARD1 complex has been demonstrated to play a critical role in homologous recombination (HR) DSB repair, and its functions may be affected by HERC2 or BAP1. Accumulated evidence illustrates that the ubiquitination-deubiquitination balance is involved in these processes; however, the precise mechanism for the cross-talk among these proteins in HR repair following radiation hasn't been defined. Through activity-based profiling, we identified PT33 as an active entity for HR repair suppression. Subsequently, we revealed that BAP1 serves as a novel molecular target of PT33 via a CRISPR-based deubiquitinase screen. Mechanistically, pharmacological covalent inhibition of BAP1 with PT33 recruits HERC2 to compete with BARD1 for BRCA1 interaction, interrupting HR repair. Consequently, PT33 treatment can substantially enhance the sensitivity of CRC cells to radiotherapy in vitro and in vivo. Overall, these findings provide a mechanistic basis for PT33-induced HR suppression and may guide an effective strategy to improve therapeutic gain.
7.Research progress of SARS-CoV-2 main protease inhibitors
Mian-ling YANG ; Yu-sen CHENG ; Le-tian SONG ; Bing YE ; Sheng-hua GAO ; Xin-yong LIU ; Peng ZHAN
Acta Pharmaceutica Sinica 2023;58(9):2581-2600
As a common protease with high similarity among coronavirus species, the main protease (Mpro) of SARS-CoV-2 is responsible for the catalytic hydrolysis of viral precursor proteins into functional proteins, which is essential for coronavirus replication and is one of the ideal targets for the development of broad-spectrum antiviral drugs. This paper reviews the main protease inhibitors of SARS-CoV-2, including their molecular structures, potencies and drug-like profiles, binding modes and structure-activity relationships, etc.
8.Screening methods of SARS-CoV-2 main protease inhibitors and current applications
Bing YE ; Sheng-hua GAO ; Le-tian SONG ; Yu-sen CHENG ; Mian-ling YANG ; Peng ZHAN ; Xin-yong LIU
Acta Pharmaceutica Sinica 2023;58(6):1528-1539
COVID-19 epidemic continues to spread around the world till these days, and it is urgent to develop more safe and effective new drugs. Due to the limited P3 biosafety laboratories for directly screening inhibitors of virulent viruses with high infectivity, it is necessary to develop rapid and efficient screening methods for viral proteases and other related targets. The main protease (Mpro), which plays a key role in the replication cycle of SARS-CoV-2, is highly conserved and has no homologous proteases in humans, making it an ideal target for drug development. From two different levels, namely, molecular level and cellular level, this paper summarizes the reported screening methods of SARS-CoV-2 Mpro inhibitors through a variety of representative examples, expecting to provide references for further development of SARS-CoV-2 Mpro inhibitors.
9.Gene Analysis for the Sebaceous Carcinoma of Scalp by Whole Exome Sequencing
Ben-rong ZHENG ; Yi-na WANG ; Bo-xiong JIANG ; Ya-le LIANG ; Sheng-jun CAI ; Na-na ZHANG
Journal of Sun Yat-sen University(Medical Sciences) 2023;44(4):712-717
ObjectiveTo reveal the differences of the related pathogenicity gene mutations between sebaceous adenocarcinoma (SC) of scalp and sebaceous adenoma (SA) of scalp on whole exome level. MethodsWhole exome sequencing was performed on a SC sample and a SA sample by Illumina Hiseq 2500 platform. Suspicious single nucleotide variation sites were selected for mutation conservation and functional analysis. SciClone was used to track subclone evolution and clonal map information was obtained for each tumor sample. The high-frequency significant gene mutations in the tumor sample were screened by MutSigCV software, and compared with the known driver genes. ResultsTwo driver genes TFDP1 and ACVR1B harboring mutations in scalp SC compared to SA were found. ConclusionsThe finding of mutation in driver genes TFDP1 and ACVR1B should be confirmed in a large cohort, which might reveal the mechanism of scalp SC development and find a therapeutic target for SC.
10.Clinical Significance of co-expression of RNA Binding Protein PTBP1 and p-AXL in Osteosarcoma
Xiang-xiang LI ; Wen-li XU ; Zheng-yu LU ; An-fang HE ; Zhen WANG ; Ni LIU ; Yu-ting LE ; Ting-sheng PENG
Journal of Sun Yat-sen University(Medical Sciences) 2023;44(3):446-455
ObjectiveTo explore the co-expression of PTBP1 and p-AXL in osteosarcoma and its clinicopathological significance for prognosis evaluation. MethodsThe expression of PTBP1 and AXL and their prognostic value in osteosarcoma were analyzed by GEO and Target data. Paraffin biopsy specimens and clinical information from 76 cases of osteosarcoma and 37 cases of non-malignant bone tissue (callus, osteofibrous dysplasia and osteoid ostema) were obtained from the First Affiliated Hospital of Sun Yat-sen University from March 2016 to October 2020. The expressions of PTBP1 and p-AXL proteins in osteosarcoma were detected by immunohistochemistry. ResultsGEO database showed that the expression levels of PTBP and AXL in osteosarcoma tumor group were higher than those in normal tissues, but did not reach statistical significance. Target database showed that the high expression of PTBP1 had shorter Overall survival(OS) and Progression-free survival(PFS) than low PTBP1 expression, but did not reach statistical significance (P=0.064; P=0.134). Immunohistochemical staining included 76 cases of osteosarcoma and 37 cases of non-malignant bone tissue. The expression rate of PTBP1 and p-AXL protein in osteosarcoma tissues was higher than that in non-malignant bone tissue. The expression of p-AXL is correlated with lung metastasis (P=0.025). Kaplan-Meier analysis showed that lung metastasis, recurrence, PTBP1 expression, co-expression of PTBP1/p-AXL influence the prognosis of patients in OS. Multivariate Cox regression analysis showed that lung metastasis (P<0.000 1) and positive expression of PTBP1 (P=0.041) were independent risk factors for osteosarcoma patients in OS. Co-expression of PTBP1 and p-AXL had shorter OS (P=0.017) and PFS (P=0.043) than non-coexpression osteosarcoma patients. ConclusionsPTBP1 and p-AXL were highly expressed in osteosarcoma tissues. The co-expression of PTBP1 and p-AXL was associated with poor prognosis of patients, and PTBP1 could be used as an independent prognostic indicator of patients with osteosarcoma.

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