Publications by authors named "Min Lin"

835 Publications

Potential of Antibody Pair Targeting Conserved Antigenic Sites in Diagnosis of SARS-CoV-2 Variants Infection.

J Virol Methods 2022 Aug 3:114597. Epub 2022 Aug 3.

State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, 361102 Xiamen, Fujian, PR China. Electronic address:

Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has become disaster for human society. As the pandemic becomes more regular, we should develop more rapid and accurate detection methods to achieve early diagnosis and treatment. Antigen detection methods based on spike protein has great potential, however, it has not been effectively developed, probably due to the torturing conformational complexity. By utilizing cross-blocking data, we clustered SARS-CoV-2 receptor binding domain (RBD)-specific monoclonal antibodies (mAbs) into 6 clusters. Subsequently, the antigenic sites for representative mAbs were identified by RBDs with designed residue substitutions. The sensitivity and specificity of selected antibody pairs was demonstrated using serial diluted samples of SARS-CoV-2 S protein and SARS-CoV S protein. Furthermore, pseudovirus system was constructed to determine the detection capability against SARS-CoV-2 and SARS-CoV. 6 RBD-specific mAbs, recognizing different antigenic sites, were identified as potential candidates for optimal antibody pairs for detection of SARS-CoV-2 S protein. By considering relative spatial position, accessibility and conservation of corresponding antigenic sites, affinity and the presence of competitive antibodies in clinical samples, 6H7-6G3 was rationally identified as optimal antibody pair for detection of both SARS-CoV-2 and SARS-CoV. Furthermore, our results showed that 6H7 and 6G3 effectively bind to SARS-CoV-2 variants of concern (VOCs). Taken together, we identified 6H7-6G3 antibody pair as a promising rapid antigen diagnostic tool in containing COVID-19 pandemic caused by multiple VOCs. Moreover, our results also provide an important reference in screening of antibody pairs detecting antigens with complex conformation.
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http://dx.doi.org/10.1016/j.jviromet.2022.114597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9347178PMC
August 2022

The functions of long noncoding RNAs on regulation of F-box proteins in tumorigenesis and progression.

Front Oncol 2022 19;12:963617. Epub 2022 Jul 19.

Center for Uterine Cancer Diagnosis and Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.

Accumulated evidence has revealed that F-box protein, a subunit of SCF E3 ubiquitin ligase complexes, participates in carcinogenesis and tumor progression targeting its substrates for ubiquitination and degradation. F-box proteins could be regulated by cellular signaling pathways and noncoding RNAs in tumorigenesis. Long noncoding RNA (lncRNA), one type of noncoding RNAs, has been identified to modulate the expression of F-box proteins and contribute to oncogenesis. In this review, we summarize the role and mechanisms of multiple lncRNAs in regulating F-box proteins in tumorigenesis, including lncRNAs SLC7A11-AS1, MT1JP, TUG1, FER1L4, TTN-AS1, CASC2, MALAT1, TINCR, PCGEM1, linc01436, linc00494, GATA6-AS1, and ODIR1. Moreover, we discuss that targeting these lncRNAs could be helpful for treating cancer modulating F-box protein expression. We hope our review can stimulate the research on exploration of molecular insight into how F-box proteins are governed in carcinogenesis. Therefore, modulation of lncRNAs is a potential therapeutic strategy for cancer therapy regulation of F-box proteins.
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http://dx.doi.org/10.3389/fonc.2022.963617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9343830PMC
July 2022

Chemometrics and genome mining reveal an unprecedented family of sugar acid-containing fungal nonribosomal cyclodepsipeptides.

Proc Natl Acad Sci U S A 2022 Aug 1;119(32):e2123379119. Epub 2022 Aug 1.

Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China.

Xylomyrocins, a unique group of nonribosomal peptide secondary metabolites, were discovered in and spp. fungi by employing a combination of high-resolution tandem mass spectrometry (HRMS/MS)-based chemometrics, comparative genome mining, gene disruption, stable isotope feeding, and chemical complementation techniques. These polyol cyclodepsipeptides all feature an unprecedented d-xylonic acid moiety as part of their macrocyclic scaffold. This biosynthon is derived from d-xylose supplied by xylooligosaccharide catabolic enzymes encoded in the xylomyrocin biosynthetic gene cluster, revealing a novel link between carbohydrate catabolism and nonribosomal peptide biosynthesis. Xylomyrocins from different fungal isolates differ in the number and nature of their amino acid building blocks that are nevertheless incorporated by orthologous nonribosomal peptide synthetase (NRPS) enzymes. Another source of structural diversity is the variable choice of the nucleophile for intramolecular macrocyclic ester formation during xylomyrocin chain termination. This nucleophile is selected from the multiple available alcohol functionalities of the polyol moiety, revealing a surprising polyspecificity for the NRPS terminal condensation domain. Some xylomyrocin congeners also feature methylated amino acid residues in positions where the corresponding NRPS modules lack methyltransferase (M) domains, providing a rare example of promiscuous methylation in the context of an NRPS with an otherwise canonical, collinear biosynthetic program.
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http://dx.doi.org/10.1073/pnas.2123379119DOI Listing
August 2022

Novel perspective on the regulation of food allergy by probiotic: The potential of its structural components.

Crit Rev Food Sci Nutr 2022 Aug 1:1-15. Epub 2022 Aug 1.

State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China.

Food allergy (FA) is a global public health issue with growing prevalence. Increasing evidence supports the strong correlation between intestinal microbiota dysbiosis and food allergies. Probiotic intervention as a microbiota-based therapy could alleviate FA effectively. In addition to improving the intestinal microbiota disturbance and affecting microbial metabolites to regulate immune system, immune responses induced by the recognition of pattern recognition receptors to probiotic components may also be one of the mechanisms of probiotics protecting against FA. In this review, it is highlighted in detail about the regulatory effects on the immune system and anti-allergic potential of probiotic components including the flagellin, pili, peptidoglycan, lipoteichoic acid, exopolysaccharides, surface (S)-layer proteins and DNA. Probiotic components could enhance the function of intestinal epithelial barrier as well as regulate the balance of cytokines and T helper (Th) 1/Th2/regulatory T cell (Treg) responses. These evidences suggest that probiotic components could be used as nutritional or therapeutic agents for maintaining immune homeostasis to prevent FA, which will contribute to providing new insights into the resolution of FA and better guidance for the development of probiotic products.
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http://dx.doi.org/10.1080/10408398.2022.2105304DOI Listing
August 2022

Five-Year Outcomes After Endovascular Treatment for Large Vessel Occlusion Stroke.

Front Neurosci 2022 13;16:920731. Epub 2022 Jul 13.

Department of Neurology, The Third People's Hospital of Zigong, Zigong, China.

Background: The long-term outcomes of acute large vessel occlusion (LVO) in anterior circulation treated by endovascular treatment (EVT) remains to be determined. The aim of this study was to assess the 5-year outcomes of patients with LVO who underwent EVT.

Methods: This study was an observational, nationwide registry of consecutive patients with acute LVO who received EVT in 28 comprehensive stroke centers in China. The primary outcome was the proportion of favorable outcome [modified Rankin Scale score (mRS) 0-2] at 5 years. Secondary outcomes included proportions of patients with excellent outcome (mRS 0-1), all-cause mortality and risk of stroke recurrence at 5 years.

Results: A total of 807 patients were included into the study and had 90-day follow-up data, 657 patients had 5-year follow-up data. At 90 days, 218 patients (27.0%) had an excellent outcome, 349 patients (43.2%) had a favorable functional outcome. 199 patients (24.7%) died. At 5 years, 190 patients (28.9%) had an excellent outcome, 261 patients (39.7%) had a favorable functional outcome, 317 patients (48.2%) died and 129 (28.2%) had stroke recurrence. Because of missing 5-year follow-up data, among available 269 patients who achieved functional independence at 90 days, 208 (77.3%) maintained favorable outcome, 19 (7.1%) had disability (mRS 3-5) and 42 (15.6%) died at 5 years. Furthermore, among available 189 patients with mRS 3-5 at 90 days, 53 (28.0%) patients achieved favorable functional outcome, 60 (31.7%) patients maintained unfavorable functional outcome and 76 (40.2%) patients died within 5 years. Multivariate analyses identified that younger age [odds ratio (OR): 0.96; 95% CI, 0.93-0.99; = 0.009], lower mRS at 90 days (OR: 0.15; 95% CI, 0.10-0.23; < 0.001) and absence of stroke recurrence (OR: 0.001; 95% CI, 0.000-0.006; < 0.001) were significantly associated with favorable outcome at 5 years. Advanced age (OR: 1.06, 95% CI, 1.04-1.08; < 0.001), higher mRS at 90 days (OR: 0.84; 95% CI, 0.73-0.98; = 0.021) and atrial fibrillation (OR: 1.63; 95% CI, 1.02-2.60; = 0.04) were independent factors for stroke recurrence.

Conclusion: Our results indicated that the beneficial effect of EVT in patients with acute LVO can be sustained during the course of at least 5 years. Reducing the risk of stroke recurrence by anticoagulation for atrial fibrillation may be a crucial strategy to improve long-term outcome.
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http://dx.doi.org/10.3389/fnins.2022.920731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326078PMC
July 2022

Clinical practice of Helicobacter pylori infection management by gastroenterologists in secondary and tertiary hospitals: A stratified sampling cross-sectional survey.

J Dig Dis 2022 Jul 26. Epub 2022 Jul 26.

Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China.

Aim: To investigate the management of Helicobacter pylori infection by gastroenterologists in secondary and tertiary hospitals in Shandong, a region with high Helicobacter pylori prevalence and gastric cancer incidence.

Methods: A questionnaire-based, stratified sampling survey was conducted from June 1 to August 30, 2021. The ratio of secondary to tertiary hospitals was set as 2:1. An electronic questionnaire was sent to all gastroenterologists via the WeChat platform.

Results: A total of 1053 (89.09%, 1053/1182) gastroenterologists were included. Overall, 34.19% and 60.59% of gastroenterologists supported universal screening for and treating Helicobacter pylori infection, respectively. The most preferred testing method in secondary and tertiary hospitals was the C-urea breath test (53.92% and 80.48%, respectively), but the reconfirmation rate of results close to the cut-off value was low (55.10% and 59.48%, respectively). Gastroenterologists in secondary and tertiary hospitals preferred bismuth-containing quadruple therapy (96.67% and 98.53%, respectively), but the antibiotic combination prescribed for patients with a penicillin allergy was suboptimal in secondary hospitals. The overall follow-up rate was 64.58%, and gastroenterologists in secondary hospitals were more proactive than those in tertiary hospitals (69.14% vs. 60.04%, P= 0.001). Less than 80% of gastroenterologist emphasized the importance of post-treatment confirmation to their patients. Only a minority of gastroenterologists in secondary and tertiary hospitals (30.79% and 34.36%, respectively) could achieve acceptable eradication rates (exceeding 80%).

Conclusions: Deficiencies exist in both secondary and tertiary hospitals, and the eradication rate is unacceptably low. Additional training programs for gastroenterologists are warranted to strengthen their comprehension of the guidelines.
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http://dx.doi.org/10.1111/1751-2980.13119DOI Listing
July 2022

Deep Learning of Liver Contrast-Enhanced Ultrasound to Predict Microvascular Invasion and Prognosis in Hepatocellular Carcinoma.

Front Oncol 2022 7;12:878061. Epub 2022 Jul 7.

Department of Ultrasound, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.

Background And Aims: Microvascular invasion (MVI) is a well-known risk factor for poor prognosis in hepatocellular carcinoma (HCC). This study aimed to develop a deep convolutional neural network (DCNN) model based on contrast-enhanced ultrasound (CEUS) to predict MVI, and thus to predict prognosis in patients with HCC.

Methods: A total of 436 patients with surgically resected HCC who underwent preoperative CEUS were retrospectively enrolled. Patients were divided into training ( = 301), validation ( = 102), and test ( = 33) sets. A clinical model (Clinical model), a CEUS video-based DCNN model (CEUS-DCNN model), and a fusion model based on CEUS video and clinical variables (CECL-DCNN model) were built to predict MVI. Survival analysis was used to evaluate the clinical performance of the predicted MVI.

Results: Compared with the Clinical model, the CEUS-DCNN model exhibited similar sensitivity, but higher specificity (71.4% vs. 38.1%, = 0.03) in the test group. The CECL-DCNN model showed significantly higher specificity (81.0% vs. 38.1%, = 0.005) and accuracy (78.8% vs. 51.5%, = 0.009) than the Clinical model, with an AUC of 0.865. The Clinical predicted MVI could not significantly distinguish OS or RFS (both > 0.05), while the CEUS-DCNN predicted MVI could only predict the earlier recurrence (hazard ratio [HR] with 95% confidence interval [CI 2.92 [1.1-7.75], = 0.024). However, the CECL-DCNN predicted MVI was a significant prognostic factor for both OS (HR with 95% CI: 6.03 [1.7-21.39], = 0.009) and RFS (HR with 95% CI: 3.3 [1.23-8.91], = 0.011) in the test group.

Conclusions: The proposed CECL-DCNN model based on preoperative CEUS video can serve as a noninvasive tool to predict MVI status in HCC, thereby predicting poor prognosis.
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http://dx.doi.org/10.3389/fonc.2022.878061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9300962PMC
July 2022

Microscopic Proof of Photoluminescence from Mechanochemically Synthesized 1-Octene-Capped Quantum-Confined Silicon Nanoparticles: Implications for Light-Emission Applications.

ACS Omega 2022 Jul 8;7(28):24881-24887. Epub 2022 Jul 8.

Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.

Silicon nanoparticles (SiNPs) have been explored intensively for their use in applications requiring efficient fluorescence for LEDs, lasers, displays, photovoltaic spectral-shifting filters, and biomedical applications. High radiative rates are essential for such applications, and theoretically these could be achieved via quantum confinement and/or straining. Wet-chemical methods used to synthesize SiNPs are under scrutiny because of reported contamination by fluorescent carbon species. To develop a cleaner method, we utilize a specially designed attritor type high-energy ball-mill and use a high-purity (99.999%) Si microparticle precursor. The mechanochemical process is used under a continuous nitrogen gas atmosphere to avoid oxidation of the particles. We confirm the presence of quantum-confined NPs (<5 nm) using atomic force microscopy (AFM). Microphotoluminescence (PL) spectroscopy coupled to AFM confirms quantum-confined tunable red/near-infrared PL emission in SiNPs capped with an organic ligand (1-octene). Using micro-Raman-PL spectroscopy, we confirm SiNPs as the origin of the emission. These results demonstrate a facile and potentially scalable mechanochemical method of synthesis for contamination-free SiNPs.
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http://dx.doi.org/10.1021/acsomega.2c03396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9301942PMC
July 2022

Lithium treatment promotes the activation of primordial follicles through PI3K/Akt signaling.

Biol Reprod 2022 Jul 24. Epub 2022 Jul 24.

Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China.

In mammals, dormant primordial follicles represent the ovarian reserve throughout reproductive life. In vitro activation of dormant primordial follicles has been used to treat patients with premature ovarian insufficiency (POI). However, there remains a lack of effective strategies to stimulate follicle activation in vivo. In this study, we used an in vitro ovarian culture system and intraperitoneal injection to study the effect of lithium treatment on primordial follicle activation. Lithium increased the number of growing follicles in cultured mouse ovaries and promoted pre-granulosa cell proliferation. Furthermore, lithium significantly increased the levels of phosphorylated protein kinase B (Akt) and the number of oocytes with forkhead Box O3a (FOXO3a) nuclear export. Inhibition of the phosphatidylinositol 3 kinase (PI3K)/Akt pathway by LY294002 reversed lithium-promoted mouse primordial follicle activation. These results suggest that lithium promotes mouse primordial follicle activation by the PI3K/Akt signaling. Lithium also promoted primordial follicle activation and increased the levels of p-Akt in mouse ovaries in vivo and in human ovarian tissue cultured in vitro. Taken together, lithium promotes primordial follicle activation in mice and humans by the PI3K/Akt signaling. Lithium might be a potential oral drug for treating infertility in POI patients with residual dormant primordial follicles.
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http://dx.doi.org/10.1093/biolre/ioac150DOI Listing
July 2022

A machine learning protocol for revealing ion transport mechanisms from dynamic NMR shifts in paramagnetic battery materials.

Chem Sci 2022 Jul 13;13(26):7863-7872. Epub 2022 Jun 13.

Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory for Physical Chemistry of Solid Surface, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China

Solid-state nuclear magnetic resonance (ssNMR) provides local environments and dynamic fingerprints of alkali ions in paramagnetic battery materials. Linking the local ionic environments and NMR signals requires expensive first-principles computational tools that have been developed for over a decade. Nevertheless, the assignment of the dynamic NMR spectra of high-rate battery materials is still challenging because the local structures and dynamic information of alkali ions are highly correlated and difficult to acquire. Herein, we develop a novel machine learning (ML) protocol that could not only quickly sample atomic configurations but also predict chemical shifts efficiently, which enables us to calculate dynamic NMR shifts with the accuracy of density functional theory (DFT). Using structurally well-defined P2-type Na(MgMn)O as an example, we validate the ML protocol and show the significance of dynamic effects on chemical shifts. Moreover, with the protocol, it is demonstrated that the two experimental Na shifts (1406 and 1493 ppm) of P2-type Na(NiMn)O originate from two stacking sequences of transition metal (TM) layers for the first time, which correspond to space groups 6/ and 622, respectively. This ML protocol could help to correlate dynamic ssNMR spectra with the local structures and fast transport of alkali ions and is expected to be applicable to a wide range of fast dynamic systems.
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http://dx.doi.org/10.1039/d2sc01306aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9258323PMC
July 2022

Xiao-Chai-Hu Decoction Ameliorates Poly (I:C)-Induced Viral Pneumonia through Inhibiting Inflammatory Response and Modulating Serum Metabolism.

Evid Based Complement Alternat Med 2022 12;2022:1240242. Epub 2022 Jul 12.

The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.

Viral pneumonia is widespread, progresses rapidly, and has a high mortality rate. Developing safe and effective therapies to treat viral pneumonia can minimize risks to public health and alleviate pressures on the associated health systems. Xiao-Chai-Hu (XCH) decoction can be used in the treatment of viral pneumonia. However, the mechanisms of XCH on viral pneumonia remain unclear. In this study, poly (I:C) was used to establish a mouse model of viral pneumonia, and the therapeutic effects of XCH on viral pneumonia were assessed. Furthermore, we evaluated the effects of XCH on inflammatory response. Lastly, untargeted metabolomics were used to study the metabolic regulatory mechanisms of XCH on viral pneumonia model mice. Our results showed that XCH treatment decreased the wet/dry ratio in lung tissue, total protein concentration, and total cell count in bronchoalveolar lavage fluid (BALF). H&E staining indicated that XCH treatment alleviated the pathological changes in lung. Moreover, XCH treatment decreased the levels of proinflammatory cytokines (IL-1, IL-6, and TNF-) and lowered the ratio of CD86/CD206 macrophages and CD11bLY6G neutrophils in BALF. XCH treatment also decreased the myeloperoxidase (MPO) and reduced the phosphorylations of PI3K, AKT, and NF-B p65 in lung. Serum untargeted metabolomics analysis showed that XCH treatment could affect 18 metabolites in serum such as creatine, hydroxyproline, cortisone, hydrocortisone, corticosterone, hypotaurine, and taurine. These metabolites were associated with arginine and proline metabolism, steroid hormone biosynthesis, and taurine and hypotaurine metabolism processes. In conclusion, our study demonstrated that treatment with XCH can ameliorate viral pneumonia and reduce inflammatory response in viral pneumonia. The mechanism of action of XCH in the treatment of viral pneumonia may be associated with inhibiting the activation of PI3K/AKT/NF-B signaling pathway in lung and regulating arginine and proline metabolism, steroid hormone biosynthesis, and taurine and hypotaurine metabolism in serum.
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http://dx.doi.org/10.1155/2022/1240242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9296287PMC
July 2022

Evaluation of RT-LAMP Assay for Rapid Detection of SARS-CoV-2.

Lab Med 2022 Jul 16. Epub 2022 Jul 16.

Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.

Objective: To evaluate the accuracy of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in community or primary-care settings.

Method: We systematically searched the Web of Science, Embase, PubMed, and Cochrane Library databases. We conducted quality evaluation using ReviewManager software (version 5.0). We then used MetaDisc software (version 1.4) and Stata software (version 12.0) to build forest plots, along with a Deeks funnel plot and a bivariate boxplot for analysis.

Result: Overall, the sensitivity, specificity, and diagnostic odds ratio were 0.79, 0.97, and 328.18, respectively. The sensitivity for the subgroup with RNA extraction appeared to be higher, at 0.88 (0.86-0.90), compared to the subgroup without RNA extraction, at 0.50 (0.45-0.55), with no significant difference in specificity.

Conclusion: RT-LAMP assay exhibited high specificity regarding current SARS-CoV-2 infection. However, its overall sensitivity was relatively moderate. Extracting RNA was found to be beneficial in improving sensitivity.
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http://dx.doi.org/10.1093/labmed/lmac030DOI Listing
July 2022

Directed cell migration towards softer environments.

Nat Mater 2022 Jul 11. Epub 2022 Jul 11.

Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA.

How cells sense tissue stiffness to guide cell migration is a fundamental question in development, fibrosis and cancer. Although durotaxis-cell migration towards increasing substrate stiffness-is well established, it remains unknown whether individual cells can migrate towards softer environments. Here, using microfabricated stiffness gradients, we describe the directed migration of U-251MG glioma cells towards less stiff regions. This 'negative durotaxis' does not coincide with changes in canonical mechanosensitive signalling or actomyosin contractility. Instead, as predicted by the motor-clutch-based model, migration occurs towards areas of 'optimal stiffness', where cells can generate maximal traction. In agreement with this model, negative durotaxis is selectively disrupted and even reversed by the partial inhibition of actomyosin contractility. Conversely, positive durotaxis can be switched to negative by lowering the optimal stiffness by the downregulation of talin-a key clutch component. Our results identify the molecular mechanism driving context-dependent positive or negative durotaxis, determined by a cell's contractile and adhesive machinery.
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http://dx.doi.org/10.1038/s41563-022-01294-2DOI Listing
July 2022

Systematic evaluation of line probe assays for the diagnosis of tuberculosis and drug-resistant tuberculosis.

Clin Chim Acta 2022 Aug 2;533:183-218. Epub 2022 Jul 2.

Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China; Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou 511436, China; Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China; Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China; Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou 511436, China. Electronic address:

Background: Line probe assays (LPAs) are PCR-based assays used for the rapid diagnosis of Mycobacterium tuberculosis (MTB) and drug-resistant tuberculosis (DR-TB). But studies on its performance are insufficient. Thus, in this study, we conducted a systematic review and meta-analysis to evaluate the effect of LPAs in the detection of MTB and drug-resistant TB in comparison with the traditional culture and DST methods.

Methods: A systemic literature search was conducted on the Web of Science, Embase, PubMed, the Cochrane Library, Scopus, and OVID databases. All the included studies were classified according to different detecting objects. Sensitivity, specificity, Positive Likely Ratio (PLR), Negative Likely Ratio (NLR), Diagnostic Odds Ratio (DOR), corresponding 95% confidence interval, Area Under Curve (AUC), Deeks' funnel plot, and Bivariate Boxplot was used to do the evaluation.

Results: 147 studies included 491 datasets, with 182,448 samples, were incorporated into our analysis. The sensitivity (95% CI), specificity (95% CI), PLR, NLR, DOR and AUC for MTB were 0.89 (0.86 to 0.92), 0.94 (0.90 to 0.97), 15.70, 0.11, 139 and 0.96, respectively; for rifampicin-resistant TB were 0.96 (0.95 to 0.97), 0.99 (0.98 to 0.99), 82.9, 0.04, 1994 and 1.00, respectively; for isoniazid-resistant TB were 0.91 (0.89 to 0.93), 0.99 (0.98 to 0.99), 83.4, 0.09, (0.99 to 1.00), 195.7, 0.07, 2783 and 1.00, respectively; for Multi-drug resistant TB (MDR-TB) were 0.93 (0.90 to 0.95), 1.00 (0.99 to 1.00), 195.7, 0.07, 2783 and 1.00, respectively; for extensively drug-resistant TB (XDR-TB) were 0.60 (0.33 to 0.82), 1.00 (0.95 to 1.00), 291.3, 0.4, 726 and 0.95, respectively; for (second-line drug-resistant TB) SLID-TB were 0.83 (0.78 to 0.87), 0.98 (0.97 to 0.99), 44.6, 0.17, 262 and 0.98, respectively. Sensitivity in pre-extensively drug-resistant TB (Pre-XDR-TB) was 0.67, specificity was 0.91. No publication bias existed according to Deeks' funnel plot.

Conclusion: High diagnosis performance was confirmed in LPAs for the diagnosis of MTB and drug-resistant TB. LPAs might be a good alternative to culture and DST in detecting MTB, RR-TB, INH-TB, XDR-TB, SLID-TB, and MDR-TB. While more studies were still needed to explore the diagnosis performance of LPAs for Pre-XDR TB.
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http://dx.doi.org/10.1016/j.cca.2022.06.020DOI Listing
August 2022

Insight rifampicin-resistant (rpoB) mutation in Pseudomonas stutzeri leads to enhance the biosynthesis of secondary metabolites to survive against harsh environments.

Arch Microbiol 2022 Jun 29;204(7):437. Epub 2022 Jun 29.

Department of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur, 5200, Bangladesh.

In this study, a wild-type and five distinct rifampicin-resistant (Rif) rpoB mutants of Pseudomonas stutzeri (i.e., Q518R, D521Y, D521V, H531R and I614T) ability were investigated against harsh environments (particularly nutritional complexity). Among these, the robust Rif phenotype of P. Stutzeri was associated only with base replacements of the amino deposits. The use of carboxylic and amino acids significantly increased in various Rif mutants than that of wild type of P. stutzeri. The assimilation of carbon and nitrogen (N) sources of Rif mutants' confirmed that the organism maintains the adaptation in nutritionally complex environments. Acetylene reduction assay at different times also found the variability for N-fixation in all strains. Among them, the highest nitrogenase activity was determined in mutant 'D521V'. The assimilation of carbon and nitrogen sources of P. stutzeri and its Rif mutants ensures that the organism maintains the adaptability in nutritionally complex environments through fixing more nitrogen.
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http://dx.doi.org/10.1007/s00203-022-03064-9DOI Listing
June 2022

Evaluation of the loop-mediated isothermal amplification assay for Staphylococcus aureus detection: a systematic review and meta-analysis.

Ann Clin Microbiol Antimicrob 2022 Jun 24;21(1):27. Epub 2022 Jun 24.

Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.

Background: Staphylococcus aureus can cause many diseases and even death. It's important to detect Staphylococcus aureus rapidly and reliably. The accuracy of a novel test named LAMP in detecting Staphylococcus aureus is unclear. Therefore, a systematic review and meta-analysis were conducted to evaluate the accuracy of the LAMP assay for Staphylococcus aureus detection.

Methods: Four databases were searched for relevant studies. Meta-DiSc 1.4.0 and Stata 12.0 were used for statistical analysis. At the same time, we used QUADAS-2 to assess the studies we included. Two groups of subgroup analysis were done to differentiate the diagnostic effects of various LAMP tests and in cases of different gold standards.

Results: 11 studies were identified and 19 2 × 2 contingency tables were extracted in our study. The results showed that both pooled sensitivity and specificity of the LAMP assay were 99% (95% CI 99-100).

Conclusion: The LAMP assay demonstrated high sensitivity and specificity in diagnosing Staphylococcus aureus.
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http://dx.doi.org/10.1186/s12941-022-00522-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9233341PMC
June 2022

Design of the Threshold-Controllable Memristor Emulator Based on NDR Characteristics.

Micromachines (Basel) 2022 May 26;13(6). Epub 2022 May 26.

School of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China.

Due to the high manufacturing cost of memristors, an equivalent emulator has been employed as one of the mainstream approaches of memristor research. A threshold-type memristor emulator based on negative differential resistance (NDR) characteristics is proposed, with the core part being the R-HBT network composed of transistors. The advantage of the NDR-based memristor emulator is the controllable threshold, where the state of the memristor can be changed by setting the control voltage, which makes the memristor circuit design more flexible. The operation frequency of the memristor emulator is about 250 kHz. The experimental results prove the feasibility and correctness of the threshold-controllable memristor emulator circuit.
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http://dx.doi.org/10.3390/mi13060829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9227755PMC
May 2022

Erratum: Tumor Theranostics of Transition Metal Ions Loaded Polyaminopyrrole Nanoparticles: Erratum.

Nanotheranostics 2022 18;6(3):322-324. Epub 2022 Feb 18.

State Key Supramolecular Structure and Materials Laboratory, College of Chemistry, Jilin University, Changchun 130012, P. R. China.

[This corrects the article DOI: 10.7150/ntno.25119.].
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http://dx.doi.org/10.7150/ntno.67620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9194588PMC
February 2022

Case Report: Successful Treatment of Kaposi's Sarcoma With Anlotinib in an HIV-Negative Patient After the Treatment of Drug Reaction With Eosinophilia and Systemic Symptoms Accessory Tragus.

Front Med (Lausanne) 2022 25;9:907345. Epub 2022 May 25.

Department of Dermatology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.

Kaposi's Sarcoma (KS) is a neoplasm derived from endothelial cells and is associated with human herpesvirus-8 (HHV-8) infection. It is mostly seen in patients suffering from AIDS and/or chronic immunosuppression. Currently, systemic chemotherapy is the primary treatment option for the advanced KS. However, there is no consensus on the treatment of KS. In this case, an 84-year-old man with a history of psoriasis developed multiple painful dark purple nodules on the trunk and extremities during the treatment of drug reaction with eosinophilia and systemic symptoms (DRESS). KS was confirmed by the skin biopsy, and the immunohistochemical staining demonstrated the positivity for HHV-8 while the anti-HIV test was negative. The patient then received anlotinib treatment, a tyrosine kinase inhibitor, for 5 months, and his skin lesions subsided. This case indicates that anlotinib may be a potential treatment option for KS.
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http://dx.doi.org/10.3389/fmed.2022.907345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9174420PMC
May 2022

Evaluation of GeneXpert EV assay for the rapid diagnosis of enteroviral meningitis: a systematic review and meta-analysis.

Ann Clin Microbiol Antimicrob 2022 Jun 9;21(1):25. Epub 2022 Jun 9.

Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.

Background: GeneXpert enterovirus Assay is a PCR-based assay for Enterovirus meningitis diagnosis. However, there is currently no research about the performance of GeneXpert enterovirus assay in the diagnosis of enterovirus meningitis. Thus, a systematic review and meta-analysis is significant on the topic.

Methods: Embase, Cochrane Library, Web of Science, and PubMed were systematically reviewed with retrieval types. Some criteria were used to filter the studies. Only studies published in English, that made a comparison between GeneXpert enterovirus assay and RT-PCR, and could be formulated in a 2*2 table, were included. The quality of the included studies was evaluated by QUADAS-2. The effect of the GeneXpert enterovirus assay was assessed by the Sensitivity, Specificity, Positive Likelihood Ratio, Negative Likelihood Ratio, Diagnosis Odds Ratio, and summary receiver operating characteristic (SROC) curve. Publication bias and heterogeneity were evaluated by the Deeks' funnel test and Bivariate Box plot respectively.

Results: 7 studies were recruited in the analysis. The Pooled Sensitivity was 0.96 [95% CI (0.94-0.97)], Pooled Specificity was 0.99 [95% CI (0.98-0.99)], Positive Likelihood Ratio was 130.46 [95% CI (35.79-475.58)], Negative Likelihood Ratio was 0.04 [95% CI (0.02-0.10)], and Diagnostic Odds Ratio was 3648.23 (95% CI [963.99-13,806.72)]. In SROC Curve, Area Under Curve (AUC) was 0.9980, and Q*= 0.9849. In Deeks' funnel test, the P-value was 0.807 (P > 0.05), indicating no publication bias. The Bivariate Box plot indicated no evident heterogeneity.

Conclusions: The GeneXpert enterovirus assay demonstrated high diagnostic accuracy in diagnosing enterovirus meningitis.
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http://dx.doi.org/10.1186/s12941-022-00517-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9185958PMC
June 2022

Molecular Surveillance of Artemisinin-Based Combination Therapies Resistance in Plasmodium falciparum Parasites from Bioko Island, Equatorial Guinea.

Microbiol Spectr 2022 06 7;10(3):e0041322. Epub 2022 Jun 7.

School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong, People's Republic of China.

Artemisinin-based combination therapies (ACTs) resistance has emerged and could be diffusing in Africa. As an offshore island on the African continent, the island of Bioko in Equatorial Guinea is considered severely affected and resistant to drug-resistant Plasmodium falciparum malaria. However, the spatial and temporal distribution remain unclear. Molecular monitoring targeting the , , , and genes was conducted to provide insight into the impact of current antimalarial drug resistance on the island. Furthermore, polymorphic characteristics, haplotype network, and the effect of natural selection of the gene were evaluated. A total of 152 Plasmodium falciparum samples (collected from 2017 to 2019) were analyzed for copy number variation of the gene and , , and mutations. Statistical analysis of sequences was performed following different evolutionary models using 96 Bioko sequences and 1322 global sequences. The results showed that the prevalence of and mutations was 73.68%, 78.29%, and 75.66%, respectively. Large proportions of isolates with multiple copies of were observed (67.86%). In Bioko parasites, the genetic diversity of was low, and purifying selection was suggested by Tajima's D test (-1.644, > 0.05) and the dN/dS test (-0.0004438, > 0.05). The extended haplotype homozygosity analysis revealed that _K189T, although most frequent in Africa, has not yet conferred a selective advantage for parasitic survival. The results suggested that the implementation of continuous drug monitoring on Bioko Island is an essential measure. Malaria, one of the tropical parasitic diseases with a high transmission rate in Bioko Island, Equatorial Guinea, especially caused by P. falciparum is highly prevalent in this region and is commonly treated locally with ACTs. The declining antimalarial susceptibility of artemisinin-based drugs suggested that resistance to artemisinin and its derivatives is developing in P. falciparum. Copy number variants in and genetic polymorphisms in , , and can be used as risk assessment indicators to track the development and spread of drug resistance. This study reported for the first time the molecular surveillance of , , and genes in Bioko Island from 2017 to 2019 to assess the possible risk of local drug-resistant P. falciparum.
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http://dx.doi.org/10.1128/spectrum.00413-22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9241599PMC
June 2022

Prevalence and molecular characterization of common thalassemia among people of reproductive age in the border area of Guangxi-Yunnan-Guizhou province in Southwestern China.

Hematology 2022 Dec;27(1):672-683

Department of Laboratory Center, The First Affiliated Hospital of Jinan University, Guangzhou, People's Republic of China.

Thalassemia, the most common global monogenetic disorder, is highly prevalent in southern China. Epidemiological and molecular characterization of thalassemia is important for designing appropriate prevention strategies in high-risk areas, especially the border area of Guangxi-Yunnan-Guizhou province in southwestern China. We recruited 38812 reproductive age couples and screened them for thalassemia. Routine blood tests as well as hemoglobin components and levels were evaluated. In addition, suspected thalassemia were identified by gap polymerase chain reaction (Gap-PCR) and PCR-based reverse dot blot (PCR-RDB). The overall prevalence of thalassemia was 26.76%. Specifically, incidences of α-thalassemia, β-thalassemia, and concurrent α- and β-thalassemia were 17.52%, 6.92%, and 2.32%, respectively. The diagnosed α-thalassemia anomalies were associated with six gene mutations and 25 genotypes. The β-thalassemia anomalies were associated with 12 gene mutations and 15 genotypes. Moreover, among the 1799 concurrent mutated α- and β-thalassemia genes, 95 different genotypes were identified. Couples in which both partners were positive for α-thalassemia and β-thalassemia isotypes were 8.80% and 2.08%, respectively. The proportion of couples at a risk of having children with thalassemia major or intermedia was high. This study elucidates on the prevalence and molecular characterization of thalassemia in the border area of Guangxi-Yunnan-Guizhou provinces. These findings provide valuable baseline data for genetic counseling and prenatal diagnosis, with the overarching goal of preventing and controlling severe thalassemia.
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http://dx.doi.org/10.1080/16078454.2022.2080427DOI Listing
December 2022

Post-transcriptional control of bacterial nitrogen metabolism by regulatory noncoding RNAs.

World J Microbiol Biotechnol 2022 Jun 6;38(7):126. Epub 2022 Jun 6.

Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.

Nitrogen metabolism is the most basic process of material and energy metabolism in living organisms, and processes involving the uptake and use of different nitrogen sources are usually tightly regulated at the transcriptional and post-transcriptional levels. Bacterial regulatory noncoding RNAs are novel post-transcriptional regulators that repress or activate the expression of target genes through complementarily pairing with target mRNAs; therefore, these noncoding RNAs play an important regulatory role in many physiological processes, such as bacterial substance metabolism and stress response. In recent years, a study found that noncoding RNAs play a vital role in the post-transcriptional regulation of nitrogen metabolism, which is currently a hot topic in the study of bacterial nitrogen metabolism regulation. In this review, we present an overview of recent advances that increase our understanding on the regulatory roles of bacterial noncoding RNAs and describe in detail how noncoding RNAs regulate biological nitrogen fixation and nitrogen metabolic engineering. Furthermore, our goal is to lay a theoretical foundation for better understanding the molecular mechanisms in bacteria that are involved in environmental adaptations and metabolically-engineered genetic modifications.
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http://dx.doi.org/10.1007/s11274-022-03287-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9170634PMC
June 2022

Peptide Aptamer PA3 Attenuates the Viability of by Hindering of Small Protein B-Outer Membrane Protein A Signal Pathway.

Front Microbiol 2022 19;13:900234. Epub 2022 May 19.

School of Life Sciences, Hainan University, Haikou, China.

The small protein B (SmpB), previously acting as a ribosome rescue factor for translation quality control, is required for cell viability in bacteria. Here, our study reveals that SmpB possesses new function which regulates the expression of outer membrane protein A () gene as a transcription factor in . The deletion of SmpB caused the lower transcription expression of by Quantitative Real-Time PCR (qPCR). Electrophoretic mobility shift assay (EMSA) and DNase I Footprinting verified that the SmpB bound at the regions of -46 to -28 bp, -18 to +4 bp, +21 to +31 bp, and +48 to +59 bp of the predicted promoter (P). The key sites CAT was further identified to interact with SmpB when P was fused with enhanced green fluorescent protein (EGFP) and co-transformed with SmpB expression vector for the fluorescence detection, and the result was further confirmed in microscale thermophoresis (MST) assays. Besides, the amino acid sites G11S, F26I, and K152 in SmpB were the key sites for binding to P. In order to further develop peptide antimicrobial agents, the peptide aptamer PA3 was screened from the peptide aptamer (PA) library by bacterial two-hybrid method. The drug sensitivity test showed that PA3 effectively inhibited the growth of . In summary, these results demonstrated that OmpA was a good drug target for , which was regulated by the SmpB protein and the selected peptide aptamer PA3 interacted with OmpA protein to disable SmpB-OmpA signal pathway and inhibited , suggesting that it could be used as an antimicrobial agent for the prevention and treatment of pathogens.
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http://dx.doi.org/10.3389/fmicb.2022.900234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9159911PMC
May 2022

Chromosome-level genome of Entada phaseoloides provides insights into genome evolution and biosynthesis of triterpenoid saponins.

Mol Ecol Resour 2022 Jun 4. Epub 2022 Jun 4.

School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.

As a medicinal herbal plant, Entada phaseoloides has high levels of secondary metabolites, particularly triterpenoid saponins, which are important resources for scientific research and medical applications. However, the lack of a reference genome for this genus has limited research on its evolution and utilization of its medicinal potential. In this study, we report a chromosome-scale genome assembly for E. phaseoloides using Illumina, Nanopore long reads and high-throughput chromosome conformation capture technology. The assembled reference genome is 456.18 Mb (scaffold N50 = 30.9 Mb; contig N50 = 6.34 Mb) with 95.71% of the sequences anchored onto 14 pseudochromosomes. E. phaseoloides was estimated to have diverged from the Leguminosae lineage at ~72.0 million years ago. With the integration of transcriptomic and metabolomic data, gene expression patterns and metabolite profiling of E. phaseoloides were determined in different tissues. The pattern of gene expression and metabolic profile of the kernel were distinct from those of other tissues. Furthermore, the evolution of certain gene families involved in the biosynthesis of triterpenoid saponins and terpenes was analysed and offers new insights into the formation of these two metabolites. Four CYP genes, one UGT gene and related transcription factors were identified as candidate genes contributing to regulation of triterpenoid saponin biosynthesis. As the first high-quality assembled reference genome in the genus Entada, it will not only provide new information for the evolutionary study of this genus and conservation biology of E. phaseoloides but also lay a foundation for the formation and utilization of secondary metabolites in medicinal plants.
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http://dx.doi.org/10.1111/1755-0998.13662DOI Listing
June 2022

The Sigma Factor AlgU Regulates Exopolysaccharide Production and Nitrogen-Fixing Biofilm Formation by Directly Activating the Transcription of in A1501.

Genes (Basel) 2022 05 12;13(5). Epub 2022 May 12.

Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

A1501, a plant-associated diazotrophic bacterium, prefers to conform to a nitrogen-fixing biofilm state under nitrogen-deficient conditions. The extracytoplasmic function (ECF) sigma factor AlgU is reported to play key roles in exopolysaccharide (EPS) production and biofilm formation in the genus; however, the function of AlgU in A1501 is still unclear. In this work, we mainly investigated the role of in EPS production, biofilm formation and nitrogenase activity in A1501. The mutant Δ showed a dramatic decrease both in the EPS production and the biofilm formation capabilities. In addition, the biofilm-based nitrogenase activity was reduced by 81.4% in the Δ mutant. The transcriptional level of , a key Psl-like (a major EPS in A1501) synthesis-related gene, was almost completely inhibited in the mutant and was upregulated by 2.8-fold in the -overexpressing strain. A predicted AlgU-binding site was identified in the promoter region of . The DNase I footprinting assays indicated that AlgU could directly bind to the promoter, and β-galactosidase activity analysis further revealed mutations of the AlgU-binding boxes drastically reduced the transcriptional activity of the promoter; moreover, we also demonstrated that AlgU was positively regulated by RpoN at the transcriptional level and negatively regulated by the RNA-binding protein RsmA at the posttranscriptional level. Taken together, these data suggest that AlgU promotes EPS production and nitrogen-fixing biofilm formation by directly activating the transcription of , and the expression of AlgU is controlled by RpoN and RsmA at different regulatory levels.
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http://dx.doi.org/10.3390/genes13050867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9141998PMC
May 2022

Integrative Analysis of Metabolome and Transcriptome Identifies Potential Genes Involved in the Flavonoid Biosynthesis in Stem.

Front Plant Sci 2022 10;13:792674. Epub 2022 May 10.

School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.

stem is known for its high medicinal benefits and value. Flavonoids are one of the in stem. However, the regulatory mechanism of flavonoids accumulation in is lacking. Here, phytochemical compounds and transcripts from stems at different developmental stages in were investigated by metabolome and transcriptome analysis. The metabolite profiling of the oldest stem was obviously different from young and older stem tissues. A total of 198 flavonoids were detected, and flavones, flavonols, anthocyanins, isoflavones, and flavanones were the main subclasses. The metabolome data showed that the content of acacetin was significantly higher in the young stem and older stem than the oldest stem. Rutin and myricitrin showed significantly higher levels in the oldest stem. A total of 143 MYBs and 143 bHLHs were identified and classified in the RNA-seq data. Meanwhile, 34 flavonoid biosynthesis structural genes were identified. Based on the expression pattern of structural genes involved in flavonoid biosynthesis, it indicated that flavonol, anthocyanin, and proanthocyanin biosynthesis were first active during the development of stem, and the anthocyanin or proanthocyanin biosynthesis branch was dominant; the flavone biosynthesis branch was active at the late developmental stage of the stem. Through the correlation analysis of transcriptome and metabolome data, the potential candidate genes related to regulating flavonoid synthesis and transport were identified. Among them, the MYBs, bHLH, and TTG1 are coregulated biosynthesis of flavonols and structural genes, bHLH and transporter genes are coregulated biosynthesis of anthocyanins. In addition, the WDR gene TTG1-like (AN11) may regulate dihydrochalcones and flavonol biosynthesis in specific combinations with IIIb bHLH and R2R3-MYB proteins. Furthermore, the transport gene protein TRANSPARENT TESTA 12-like gene is positively regulated the accumulation of rutin, and the homolog of ABC transporter B family member gene is positively correlated with the content of flavone acacetin. This study offered candidate genes involved in flavonoid biosynthesis, information of flavonoid composition and characteristics of flavonoids accumulation, improved our understanding of the MYBs and bHLHs-related regulation networks of flavonoid biosynthesis in stem, and provided references for the metabolic engineering of flavonoid biosynthesis in stem.
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http://dx.doi.org/10.3389/fpls.2022.792674DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9127681PMC
May 2022

A study on aviation supply chain network controllability and control effect based on the topological structure.

Math Biosci Eng 2022 04;19(6):6276-6295

College of Civil Aviation, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China.

The present paper focuses on the controllability of the aviation supply chain network and establishes the judgment criterion for structural controllability of the aviation supply chain network. We determine the control effect by applying the control input to different nodes in the aviation supply chain network. These control nodes include the core enterprises of the aviation supply chain network, the upstream suppliers, and the downstream distributors. It is observed that the control effect is better when the control input is applied to the upstream suppliers of the aviation supply chain network than to the core enterprises of the aviation supply chain network. It is also more desirable to apply the control input to the core enterprises than to the distributors. That is, the control effect is the weakest when the control input is applied to the distributors, whereas the effect is best on application of the control to the upstream suppliers in the supply chain (that is, by choosing the upstream suppliers as the controlled nodes in the aviation supply chain network).
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http://dx.doi.org/10.3934/mbe.2022293DOI Listing
April 2022

A Novel Small RNA, DsrO, in Deinococcus radiodurans Promotes Methionine Sulfoxide Reductase () Expression for Oxidative Stress Adaptation.

Appl Environ Microbiol 2022 06 16;88(11):e0003822. Epub 2022 May 16.

Single Cell Research Center, School of Agriculture and Life Sciences, Shanghai Jiao Tong Universitygrid.16821.3c, Shanghai, China.

Reactive oxygen species (ROS) can cause destructive damage to biological macromolecules and protein dysfunction in bacteria. Methionine sulfoxide reductase (Msr) with redox-active Cys and/or seleno-cysteine (Sec) residues can restore physiological functions of the proteome, which is essential for oxidative stress tolerance of the extremophile Deinococcus radiodurans. However, the underlying mechanism regulating MsrA enzyme activity in D. radiodurans under oxidative stress has remained elusive. Here, we identified the function of MsrA in response to oxidative stress. expression in D. radiodurans was significantly upregulated under oxidative stress. The mutant showed a deficiency in antioxidative capacity and an increased level of dabsyl-Met-S-SO, indicating increased sensitivity to oxidative stress. Moreover, mRNA was posttranscriptionally regulated by a small RNA, DsrO. Analysis of the molecular interaction between DsrO and mRNA demonstrated that DsrO increased the half-life of mRNA and then upregulated MsrA enzyme activity under oxidative stress compared to the wild type. expression was also transcriptionally regulated by the DNA-repairing regulator DrRRA, providing a connection for further analysis of protein restoration during DNA repair. Overall, our results provide direct evidence that DsrO and DrRRA regulate expression at two levels to stabilize mRNA and increase MsrA protein levels, revealing the protective roles of DsrO signaling in D. radiodurans against oxidative stress. The repair of oxidized proteins is an indispensable function allowing the extremophile D. radiodurans to grow in adverse environments. Msr proteins and various oxidoreductases can reduce oxidized Cys and Met amino acid residues of damaged proteins to recover protein function. Consequently, it is important to investigate the molecular mechanism maintaining the high reducing activity of MsrA protein in D. radiodurans during stresses. Here, we showed the protective roles of an sRNA, DsrO, in D. radiodurans against oxidative stress. DsrO interacts with mRNA to improve mRNA stability, and this increases the amount of MsrA protein. In addition, we also showed that DrRRA transcriptionally regulated gene expression. Due to the importance of DrRRA in regulating DNA repair, this study provides a clue for further analysis of MsrA activity during DNA repair. This study indicates that protecting proteins from oxidation is an effective strategy for extremophiles to adapt to stress conditions.
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http://dx.doi.org/10.1128/aem.00038-22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9195949PMC
June 2022
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