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Ang Li

Publications and source records attributed to Ang Li.

At least 19 recordsLinked to original sources
PubMed2026

Modtector: ultra-fast modification signal mining on mapped sequencing reads.

SUMMARY: Existing tools for RNA epitranscriptomic modification and structural signal analysis are often fragmented, inefficiency, and limited to single signal types. We developed Modtector, an unified tool for extracting mutation and reverse-transcription stop signals from aligned sequencing reads. By using a "count-then-correct" strategy, Modtector reduces computational complexity and enables efficient dual-signal analysis. It achieves multi-fold speedups on large-genome and high-coverage datasets, including completing HEK293 22G data analysis in 5 minutes, and show strong scalability on single-cell datasets with speedups exceeding 50-fold. AVAILABILITY: The source code is available at GitHub (https://github.com/TongZhou2017/modtector) and Crates.io (https://crates.io/crates/modtector). The archived source-code snapshot used in this study is available at Zenodo (DOI: 10.5281/zenodo.20967747), corresponding to GitHub commit 7c60e9d. Workflow examples, datasets, and analysis scripts are available at Zenodo (DOI: 10.5281/zenodo.17316476 and 10.5281/zenodo.18523297).

Humans↗
PubMed2026

Plasma Proteomic Profiling Identifies Candidate Biomarkers for Pancreatic Ductal Adenocarcinoma.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy that is often diagnosed after curative treatment is no longer feasible. Existing biomarkers, particularly CA19-9, have limited sensitivity and specificity. Plasma proteins that capture tumor-associated biological alterations may therefore provide useful signals for earlier detection. METHODS: Plasma samples from 99 patients with PDAC and 30 healthy controls were analyzed using data-independent acquisition (DIA) proteomics. Differentially expressed proteins were identified using predefined statistical thresholds and further examined by functional enrichment analysis. Selected candidate biomarkers were validated by ELISA in an independent subset. RESULTS: Among 565 quantified plasma proteins, 52 were differentially expressed between PDAC and controls. These proteins were enriched in extracellular processes, cholesterol metabolism, complement and coagulation cascades, and pancreatic secretion pathways. ELISA validation confirmed higher plasma levels of Cathepsin S, CTRB2, MARCO, PIGR, PRDX6, REG1A, Trypsin-2, and PEP-FAP in patients with PDAC compared with healthy controls. ROC analyses showed moderate-to-good discriminatory performance for several candidates, and the MARCO + PEP-FAP model improved classification compared with either marker alone. CONCLUSION: These findings reveal circulating proteins linked to key PDAC-related biological processes and identify eight candidates for further evaluation in multi-protein diagnostic panels. Larger validation studies incorporating clinically relevant disease control groups are warranted to determine their diagnostic specificity and clinical utility.

Humans↗
PubMed2025

Genome-wide profiling the integration patterns with T7-PCR.

Integration of exogenous gene fragments into the host genomes is a widely used and powerful method for studying gene functions, advancing molecular breeding, and conducting gene therapy. Accurately identifying the integration sites is essential for ensuring both the safety and efficacy of genome engineering efforts. However, current mapping techniques are constrained by high costs and a low signal-to-noise ratio. In this study, we developed an innovative tool for mapping integration sites, leveraging T7 polymerase-mediated in vitro transcription (T7-IVT) to capture the junction fragments surrounding integration loci. This approach converts genomic flanking sequences into RNA, enabling the simultaneous enrichment of junction fragments and the elimination of background genomic DNA, thereby significantly enhancing the signal-to-noise ratio. We have validated the efficiency of this method, named T7-PCR, across yeast, plant, and human cells under diverse integration scenarios. T7-PCR outperforms current next-generation sequencing (NGS)-based mapping strategies in terms of efficiency and accuracy, with minimal positional effects. This method is highly applicable for high-throughput transgene screening and also supports the development of next-generation tools for targeted integration of large fragments.

Humans↗
PubMed2006

All-trans retinoic acid negatively regulates cytotoxic activities of nature killer cell line 92.

NK cells are key components of innate immune systems and their activities are regulated by cytokines and hormones. All-trans retinoic acid (ATRA), as a metabolite of vitamin A and an immunomodulatory hormone, plays an important role in regulating immune responses. In the present study, we investigated the effect of ATRA on human NK cell line NK92. We found that ATRA dose-dependently suppressed cytotoxic activities of NK92 cells without affecting their proliferation. To explore the mechanisms underlying the ATRA influence on NK92 cells, we examined the production of cytokines (TNF-alpha, IFN-gamma), gene expression of cytotoxic-associated molecules (perforin, granzyme B, nature killer receptors (NCRs), and NKG2D), and the activation of NF-kappaB pathways related with immune response. Our results demonstrated that ATRA suppressed NF-kappaB activity and prevented IkappaBalpha degradation in a dose-dependent way, inhibited IFN-gamma production and gene expression of granzyme B and NKp46. Our findings suggest that ATRA is a negative regulator of NK92 cell activation and may act as a potential regulator of anti-inflammatory functions in vivo.

Cell Line↗
PubMed2006

Genetic variation in Hippophae rhamnoides ssp. sinensis (Elaeagnaceae) revealed by RAPD markers.

Hippophae rhamnoides ssp. sinensis is endemic to China, and it is a dioecious, outcrossing plant. Although many studies have been undertaken mainly on its agricultural, nutritional, medical, and ornamental value, little is known about its population genetics. This study uses random amplified polymorphic DNA to investigate the genetic diversity and population genetic structure of 13 natural populations of the subspecies sinensis. Fifteen primers amplified 107 reproducible bands, with 95 (88.79%) being polymorphic. The gene diversity within population was 0.168, considerably lower than that of tree species and most perennial, outcrossing species, but higher than that of annual or short-lived, selfing species. The Gst value showed that 18.3% of the total genetic variation resided among populations, a little lower than that of outcrossing species. The present results are quite similar to those previously reported in another subspecies, H ssp. . rhamnoides rhamnoides. The low genetic differentiation among populations in ssp. sinensis may be attributed to the long-distance dispersal of seeds facilitated by birds, in addition to its characteristics of outcrossing, wind pollination, and widespread distribution. No association between genetic distance and geographical distribution was found. The population relationships revealed by the UPGMA dendrogram parallel this result, in that genetic distance did not increase with geographic separation. This pattern of population differentiation may imply the adaptation of ssp. s populations to the local environment, given that its habitats vary greatly across its distribution.

China↗
PubMed2006

Hypoxia can contribute to the induction of the Epstein-Barr virus (EBV) lytic cycle.

BACKGROUND: Like other herpes viruses, latent Epstein-Barr virus (EBV) infection can be reactivated to lytic replication. Reactivation can be achieved by treatment with various reagents, including tetradecanoyl phorbol acetate (TPA) and Ca2+ ionophores. Relatively little is known about the physiological factors related to reactivation of EBV. Previous studies have demonstrated that G0/G1 cell cycle arrest is associated with EBV activation, and that hypoxic conditions can induce cell cycle arrest. In the present study we investigated the effect of hypoxia on reactivation of EBV. OBJECTIVE AND METHODS: Hypoxic culture conditions were established and the expression of Zta protein and the number of EBV DNA copies were measured in B95-8 cells maintained under these conditions. RESULTS: Hypoxia treatment not only increased the expression of the EBV immediate-early protein Zta (which mediates the switch between the latent and lytic form of infection), but also increased the number of EBV DNA copies in B95-8 cells. CONCLUSIONS: EBV in latent infection can be activated to lytic infection by hypoxia treatment.

Animals↗
PubMed2006

Down-regulation of survivin expression by small interfering RNA induces pancreatic cancer cell apoptosis and enhances its radiosensitivity.

AIM: To investigate the inhibitory effect of small interfering RNA (siRNA) on the expression of survivin in pancreatic cancer cell line PC-2 and the role of siRNA in inducing PC-2 cell apoptosis and enhancing its radiosensitivity. METHODS: A siRNA plasmid expression vector against survivin was constructed and transfected into PC-2 cells with Lipofectamine 2000. The down regulation of survivin expression was detected by semi-quantitative RT-PCR and immunohistochemical SP method and the role of siRNA in inducing PC-2 cell apoptosis and enhancing its radiosensitivity was detected by flow cytometry. RESULTS: The sequence-specific siRNA efficiently and specifically down-regulated the expression of survivin at both mRNA and protein levels. The expression inhibition ratio was 81.25% at mRNA level detected by semi-quantitative RT-PCR and 74.24% at protein level detected by immunohistochemical method. Forty-eight hours after transfection,apoptosis was induced in 7.03% cells by siRNA and in 14.58% cells by siRNA combined with radiation. CONCLUSION: The siRNA plasmid expression vector against survivin can inhibit the expression of survivin in PC-2 cells efficiently and specifically. Inhibiting the expression of survivin can induce apoptosis of PC-2 cells and enhance its radiosensitivity significantly. RNAi against survivin is of potential value in gene therapy of pancreatic cancer.

Apoptosis↗
PubMed2006

Charge migration in dicationic electrophiles and its application to the synthesis of aza-polycyclic aromatic compounds.

[reaction: see text] Superacid-promoted reactions of dicationic electrophiles have been studied, and the positive charge centers are found to migrate apart in a predictable manner. Using isotopic labeling the charge migration is found in one system to occur through successive deprotonation-reprotonation steps. The charge migration chemistry is the basis for new general synthetic route to aza-polycyclic aromatic compounds.

Aza Compounds↗
PubMed2006

Treatment of severe post-kidney-transplant lung infection by integrative Chinese and Western medicine.

OBJECTIVE: To explore treatments of severe post-kidney-transplant lung infection by integrative Chinese and Western medicine (ICWM), in order to elevate the curing rate as well as to lower the death rate. METHODS: Based on conventional ways of Western medical treatments of 18 cases of severe post-kidney-transplant lung infection, such as putting the patients in single individual ward, antibiotics to prevent infection, respiratory machines, blood filtration, nutritional support, steroids, and maintaining electrolytes balance, we applied integrated Chinese medicinal treatments, like altering conventional prescription "pneumonia III", and conducted clinical observation of effectiveness, and indexes including white blood cell (WBC), neutrophilic granulocyte, blood urea nitrogen (BUN), blood creatinine (Cr), etc. RESULTS: Of the 18 cases studied, 7 were already cured, 8 proved the treatment effective, 3 died. All clinical indexes had statistically significant changes compared with those of before treatment (P < 0.01). CONCLUSION: ICWM can increase curing rate and lower death rate.

Adult↗
PubMed2006

Heterogeneous inclusions in neurofilament inclusion disease.

Neurofilament inclusion disease (NFID) is a rare disease, whose pathogenesis remains to be elucidated. Immunoreactivity of ubiquitin-binding protein p62 has been reported in various neurodegenerative diseases, but it has not been studied in NFID. In this report we show p62 immunoreactivity in neuronal perikaryon of three cases of NFID. We found inclusions in NFID to be heterogenous based on immunoreactivity for alpha-internexin, phosphorylated neurofilament-H, p62 and ubiquitin. Moreover, we showed both p62- and alpha-internexin-immunoreactive inclusions within the perikarya of the same neuron. Electron microscopy findings support the notion that inclusions in NFID are heterogenous. The present study extends the list of proteins that have been identified as components of neuronal inclusions in NFID, and may help account for the pathogenesis of NFID.

Adaptor Proteins, Signal Transducing↗
PubMed2006

[siRNA targeted against survivin induces apoptosis of pancreatic cancer cells].

OBJECTIVE: To investigate the effect of a sequence-specific small interfering RNA (siRNA) in suppressing survivin expression and cell proliferation and inducing apoptosis of PC-2 cells. METHODS: The plasmid expression vector of siRNA targeted against survivin was constructed and transfected into PC-2 cells with Lipofectamine 2000. The changes of survivin expression were detected by semi-quantitative RT-PCR and immunohistochemical SP methods. The effect of siRNA in suppressing the proliferation of PC-2 cells was detected by MTT assay, and its role in inducing PC-2 cell apoptosis evaluated by flow cytometry. RESULTS: The sequence-specific siRNA effectively suppressed survivin expression at both mRNA and protein levels with inhibition rate of 81.25% at mRNA level and 74.24% at protein level. Survivin expression suppression significantly inhibited the proliferation of PC-2 cells, and at 24 and 48 h after cell seeding, the proliferation inhibition rate was 28.00% and 33.38% respectively; 24, 48 h after the transfection, apoptosis occurred in 8.46% and 7.53% of the cells, respectively. CONCLUSIONS: The plasmid expression vector for the siRNA against survivin constructed in the study can effectively and specifically suppress survivin expression in PC-2 cells, and blocking survivin expression suppresses PC-2 cell proliferation and induces cell apoptosis. siRNA targeted against survivin has a potential value in gene therapy for pancreatic cancer.

Apoptosis↗
PubMed2006

[Effects of peroxisome proliferators PFOA on immune system of mice].

AIM: To examine the effects of peroxisome proliferators (PP), perfluorooctanoic acid (PFOA), on mouse immune system. METHODS: Male C57B/6 mice were received the diet containing PFOA and the following parameters were examined, including weight and cell number of thymus and spleen, cell cycle of thymocytes by PI staining, cell phenotype in thymus and spleen by flow cyto metry (FCM) analysis, IgM and IgG production by the protein-A plaque and ELISA assay, and proliferation of splenocytes in response to ConA or LPS by (3)H-TdR labeling. RESULTS: Severe thymic and splenic atrophy was observed in mice administrated with potent PP, e.g., PFOA. Number of both T and B cells in spleen was decreased upon treatment. Thymocytes were decreased over 90% by treatment, among which the immature CD4(+) CD8(+) population was decreased most dramatically. The most obvious change in thymocytes occurred in the S and G2/M phases. PFOA also prevented the increase both in plaque formation by anti-IgM and -IgG and in serum level of IgM and IgG that normally evoked by immunization with horse red blood cells. Following withdrawal of PFOA from diet, the above parameters rapidly returned to normal. CONCLUSION: Potent PP significantly inhibits mouse immune system.

Animals↗
PubMed2006

[siRNA against survivin coupling with epirubicin enhances to induce breast cancer cell MCF-7 to apoptosis].

OBJECTIVE: To use the sequence-specific siRNA knocking down the expressions of Survivin gene and inducing breast cancer MCF-7 cell line to apoptosis, and to couple the siRNA with Survivin for investigating the effects of MCF-7 cell induced to apoptosis and the chemotherapy sensitivity of breast cancer cell treated to epirubicin. METHODS: The molecular cloning technique was applied to construct the eukaryotic expression vector of siRNA against Survivin, and lipofectamine 2000 was used to transfect MCF-7 cell. Survivin expressions were detected by semi-quantitive RT-PCR and immunohistochemical SABC methods. The effects of inducing MCF-7 cell apoptosis and enhanced chemotherapy sensitivity to epirubicin were assessed by TUNEL method. RESULTS: The sequence-specific siRNA can, effectively and specifically, knock the expressions of Survivin gene down at both mRNA and protein levels, in which the expression inhibition rates were 64.91 and 79.72% respectively. After 48 h, 8.75% cells transfected with siRNA expression vector were induced to apoptosis; Coupling siRNA against Survivin with epirubicin can induce the cell apoptosis rate up to 24.21%. CONCLUSIONS: In the study, the siRNA against Survivin can, effectively and specifically, decrease the expressions of Survivin gene in MCF-7 cell; blocking the expressions of Survivin can, in certain degree, induce MCF-7 cell to apoptosis and enhance cell chemotherapy sensitivity to epirubicin significantly; Survivin RNAi has a great potential value in the gene therapy of breast cancer.

Antibiotics, Antineoplastic↗
PubMed2006

[Influence of the peroxisome proliferator-activated receptor alpha on the development of T and B cells in mice].

AIM: To investigate the role of peroxisome proliferator-activated receptor a (PPARa) in the function and development of murine immune system. METHODS: Wild-type and PPARa-null C57B/6 mice were sacrificed after 7-day dietary treatment of with peroxisome proliferator (PP). The changes in the weight of the thymus and spleen and cell numbers from the thymus and spleen were observed. The alterations of the cell phenotypes in bone marrow, thymus and spleen were determined by immunofluorescent staining using anti-mouse CD3, CD4, CD8a, CD19, IgM or CD45R/220 mAb through FACS analysis. The proliferation of T or B cells in response to ConA or LPS, respectively, was analyzed by 3H-TdR labeling. The PPARa mRNA expression in the bone marrow, thymus and spleen was examined by RT-PCR. RESULTS: PP treatment caused significant decreases in the weight and cell numbers of thymus and spleen and proliferative responsiveness of lymphocytes to ConA and LPS in wild-type mice, whereas these effects were significantly weaker in PPARalpha-null mice. The significant decreases of the CD4+ CD8+ population existed in the thymus and pro/pre-B cells and total B220+ cells in the bone marrow of wild-type mice with PP treatment, but not in PPARa-null mice. Interestingly, PPARalpha expression was detected in mouse thymus and spleen, rather than bone marrow. CONCLUSION: PPARalpha plays a major role in the PP-induced immunomodulation, indirectly affecting the development of T and B cells.

Animals↗
PubMed2006

[Cloning of A73 gene and its coding sequence analysis].

OBJECTIVE: To clone A73 gene of Epstein-Barr virus (EBV) and examine the variation of its coding sequence. METHODS: A73 coding sequence (CDS) amplified from 7 patients in nasophryngeal carcinoma (NPC) biopsies by RT-PCR was cloned into pGEM-T-Easy vector to construct the recombinant plasmid, which was subjected to sequence analysis in Gen Bank database using Blast software. RESULTS: A73 gene from nasophryngeal carcinoma was successfully cloned into pGEM-T Easy vector. A locus with conversion of A-->C in A73 was found at CDS 45 nt, located in the exonVB157154 nt, which did not result in an amino acid replacement, and the variation frequency was 7/7. CONCLUSION: There is a point mutation in A73 CDS of EBV isolated from NPC tissue, which might produce NPC-associated polymorphism with possible involvement in the composition of some subtype of EB virus.

Cloning, Molecular↗