Publications by authors named "Rong Tang"

388 Publications

Neurotoxicity induced by combined exposure of microcystin-LR and nitrite in male zebrafish (Danio rerio): Effects of oxidant-antioxidant system and neurotransmitter system.

Comp Biochem Physiol C Toxicol Pharmacol 2021 Nov 23:109248. Epub 2021 Nov 23.

College of Fisheries, Huazhong Agricultural University, Wuhan 430070, PR China; Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, PR China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, PR China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, PR China. Electronic address:

With the intensification of water eutrophication around the world, cyanobacterial blooms have been becoming a common environmental pollution problem. The levels of microcystin-LR (MC-LR) and nitrite rise sharply during the cyanobacterial bloom period, which may have potential joint toxicity on aquatic organisms. In this study, adult male zebrafish were immersed into different joint solutions of MC-LR (0, 3, 30 μg/L) and nitrite (0, 2, 20 mg/L) for 30 days to explore the neurotoxic effects and underlying mechanisms. The results showed that single factor MC-LR or nitrite caused a concentration-dependent damage in brain ultrastructure and the effects of their joint exposure were much more intense. Downregulated expression of mbp and bdnf associated with myelination of nerve fibers further confirmed that MC-LR and nitrite could damage the structure and function of neuron. The decreases in dopamine content, acetylcholinesterase activity and related gene mRNA levels indicated that MC-LR and nitrite adversely affected the normal function of the dopaminergic and cholinergic systems in zebrafish brain. In addition, the significant increase in malondialdehyde content suggested the occurrence of oxidative stress caused by MC-LR, nitrite and their joint-exposure, which paralleled a significant decrease in antioxidant enzyme‑manganese superoxide dismutase activity and its transcription level. In conclusion, MC-LR + nitrite joint-exposure has synergistic neurotoxic effects on the structure and neurotransmitter systems of fish brain, and antioxidant capacity disruption caused by these two factors might be one of the underlying synergistic mechanisms. Therefore, there is a risk of being induced neurotoxicity in fish during sustained cyanobacterial bloom events.
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http://dx.doi.org/10.1016/j.cbpc.2021.109248DOI Listing
November 2021

Simultaneous temperature and refractive index sensor based on an L-like Michelson interferometer.

Appl Opt 2021 Nov;60(32):10101-10108

We experimentally demonstrate, to the best of our knowledge, temperature and refractive index (RI) sensing with a novel L-like Michelson interferometer (MI). Two MIs are designed based on single-mode fiber (SMF) and multimode fiber (MMF), respectively, fabricated via an oxyhydrogen flame and a rotatable platform. By comparative experiments on the size and bent degree of the sensor, the corresponding parameters of the sensor with excellent performance are determined for measurement experiments. The RI sensitivity of the SMF L-like MI reaches -131.0/, and the highest temperature sensitivity is 94.17 pm/°C. The highest RI of the MMF L-like MI is 176.5 nm/RIU, and the temperature sensitivity is 104.2 pm/°C. The L-like MI has advantages of low cost and easy fabrication, and is a promising temperature and RI sensor in a wide range of measurements.
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http://dx.doi.org/10.1364/AO.441963DOI Listing
November 2021

Genetic characteristics and ploidy trigger the high inducibility of double haploid (DH) inducer in Brassica napus.

BMC Plant Biol 2021 Nov 16;21(1):538. Epub 2021 Nov 16.

Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, 611130, China.

Background: Our recently reported doubled haploid (DH) induction lines e.g., Y3380 and Y3560 are allo-octoploid (AAAACCCC, 2n = 8× ≈ 76), which can induce the maternal parent to produce DH individuals. Whether this induction process is related to the production of aneuploid gametes form male parent and genetic characteristics of the male parent has not been reported yet.

Results: Somatic chromosome counts of DH inducer parents, female wax-less parent (W1A) and their F hybrid individuals revealed the reliability of flow cytometry analysis. Y3560 has normal chromosome behavior in metaphase I and anaphase I, but chromosome division was not synchronized in the tetrad period. Individual phenotypic identification and flow cytometric fluorescence measurement of F individual and parents revealed that DH individuals can be distinguished on the basis of waxiness trait. The results of phenotypic identification and flow cytometry can identify the homozygotes or heterozygotes of F generation individuals. The data of SNP genotyping coupled with phenotypic waxiness trait revealed that the genetic distance between W1A and F homozygotes were smaller as compared to their heterozygotes. It was found that compared with allo-octoploids, aneuploidy from allo-octoploid segregation did not significantly increase the DH induction rate, but reduced male infiltration rate and heterozygous site rate of induced F generation. The ploidy, SNP genotyping and flow cytometry results cumulatively shows that DH induction is attributed to the key genes regulation from the parents of Y3560 and Y3380, which significantly increase the induction efficiency as compared to ploidy.

Conclusion: Based on our findings, we hypothesize that genetic characteristics and aneuploidy play an important role in the induction of DH individuals in Brassca napus, and the induction process has been explored. It provides an important insight for us to locate and clone the genes that regulate the inducibility in the later stage.
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http://dx.doi.org/10.1186/s12870-021-03311-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594162PMC
November 2021

sp. nov., isolated from hyperthermophilic compost.

Int J Syst Evol Microbiol 2021 Nov;71(11)

Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China.

Two aerobic, Gram-stain-positive, rod-shaped, endospore-forming, thermophilic bacterial strains, designated FJAT-54423 and FJAT-54424, were isolated from hyperthermophilic compost sampled in Shanxi Province, PR China. Growth was observed at 30-60 °C (optimum, 50 °C) and pH 6.0-9.0 (optimum, pH 7.0), with up to 2.0 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence similarity between FJAT-54423 and FJAT-54424 was 99.9%, and the maximum similarity to a valid taxon was observed with (98.3%). Further, in phylogenetic and phylogenomic trees, strains FJAT-54423 and FJAT-54424 branched with members of the genus . The menaquinone was MK-7, and the major fatty acids were iso-C and anteiso-C. The main polar lipids included phosphatidylmethylethanolamine, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The cell-wall peptidoglycan was found to contain -diaminopimelic acid. The DNA G+C content of strains FJAT-54423 and FJAT-54424 were 54.3 and 54.4 mol%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strain FJAT-54423 and its most closely related reference strain DSM 6347 were 77.7 and 21.5 %, respectively, which were lower than the recommended species delineation thresholds of ANI (95%) and dDDH (70%). Based on the observed physiological properties, chemotaxonomic characteristics and ANI and dDDH values, FJAT-54423 and FJAT-54424 belong to a novel species of the genus , for which the name sp. nov. is proposed. The type strain is FJAT-54423 (=GDMCC 1.2054=KCTC 43273).
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http://dx.doi.org/10.1099/ijsem.0.005098DOI Listing
November 2021

Protective Effect of Selenium on the Oxidative Damage of Kidney Cells Induced by Sodium Nitrite in Grass Carp (Ctenopharyngodon idellus).

Biol Trace Elem Res 2021 Nov 2. Epub 2021 Nov 2.

College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.

The present study was conducted to investigate the protective effects of selenium on the oxidative damage of kidney cells (CIK) caused by nitrite exposure in grass carp (Ctenopharyngodon idella). Cells were pre-incubated by NaSeO (10 μmol/L) for 12 h and then exposed to NaNO (25 mg/L) for 24 h, the cell viability, apoptosis, gene expression, and antioxidant enzyme activity were assayed. The results show that nitrite reduced cell viability and induced apoptosis, and the activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) as well as the sod, cat, and gpx genes reduced (p < 0.05), while the intracellular calcium ion concentration increased (p < 0.05). Interestingly, selenium treatment significantly alleviated the nitrite induced changes in cell growth, apoptosis, and calcium influx. The cell viability after low-concentration selenium treatment is higher than that of normal cells (p < 0.05). CIK cells were pre-incubated with NaSeO and then exposed to NaNO, the antioxidant indicators could be maintained at normal levels. And compared with nitrite exposure, intracellular calcium ion concentration and apoptotic rate of selenium-incubated still decreased. The expressions of Nrf2 and Keap1 genes increased significantly in CIK cells treated with sodium selenite for 12 h, and the same trend as the enzyme activities of this group. The results show that the supplement of selenium can enhance the cell's resistance to sodium nitrite exposure to a certain extent, by alleviating the antioxidant imbalance, high apoptosis rate, and intracellular calcium ion disturbance caused by nitrite exposure. And the Nrf2-Keap1 pathway may play an important role in the process.
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http://dx.doi.org/10.1007/s12011-021-02982-xDOI Listing
November 2021

Peripheral blood neutrophil-to-lymphocyte ratio in inflammatory bowel disease and disease activity: A meta-analysis.

Int Immunopharmacol 2021 Oct 19;101(Pt B):108235. Epub 2021 Oct 19.

Sichuan Provincial Center for Gynecology and Breast Diseases (Gynecology), Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, PR China. Electronic address:

Objective: The peripheral blood neutrophil-to-lymphocyte ratio (NLR) is a valuable predictor of clinical disease activity in inflammatory bowel disease (IBD). Therefore, we conducted a meta-analysis to evaluate the clinical significance of peripheral blood NLR in IBD patients.

Methods: A comprehensive literature search was conducted by searching PubMed, Embase, Web of Science, Cochrane Library, and Chinese databases from inception to May 10, 2021. We used the standard mean difference (SMD) with a 95% confidence interval (CI) to estimate the pooled effect and subgroup analysis to investigate heterogeneity.

Results: Sixteen studies including 2185 IBD patients and 993 healthy controls (HCs) were enrolled in this study. The peripheral blood NLR values were significantly higher in 1,092 IBD patients than in 933 HCs (SMD = 1.54, 95% CI = 1.05-2.02, P < 0.001) and in 1,269 patients with active IBD than in 1,056 patients with remissive IBD (SMD = 1.55, 95% CI = 1.06-2.05, P < 0.001). Subgroup analysis of the major subtypes of IBD revealed significantly elevated peripheral blood NLR values in patients with active ulcerative colitis (UC) compared to HCs (SMD = 2.04), remissive UC than HCs (SMD = 0.63), and active UC than in those with remissive UC (SMD = 1.32) (P < 0.05). Both Crohn's disease (CD) patients and active CD patients had significantly elevated peripheral blood NLR values than HCs with the SMD of 0.52 and 3.53 (P < 0.001).

Conclusions: Peripheral blood NLR could serve as a valuable biomarker for predicting disease severity in IBD patients.
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http://dx.doi.org/10.1016/j.intimp.2021.108235DOI Listing
October 2021

Structural and Catalytic Characterization of TsBGL, a β-Glucosidase From sp. ex4484_79.

Front Microbiol 2021 1;12:723678. Epub 2021 Oct 1.

State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China.

Beta-glucosidase is an enzyme that catalyzes the hydrolysis of the glycosidic bonds of cellobiose, resulting in the production of glucose, which is an important step for the effective utilization of cellulose. In the present study, a thermostable β-glucosidase was isolated and purified from the sp. ex4484_79 and subjected to enzymatic and structural characterization. The purified β-glucosidase (TsBGL) exhibited maximum activity at 90°C and pH 5.0 and displayed maximum specific activity of 139.2μmol/min/mg against -nitrophenyl β-D-glucopyranoside (NPGlc) and 24.3μmol/min/mg against cellobiose. Furthermore, TsBGL exhibited a relatively high thermostability, retaining 84 and 47% of its activity after incubation at 85°C for 1.5h and 90°C for 1.5h, respectively. The crystal structure of TsBGL was resolved at a resolution of 2.14Å, which revealed a classical (α/β)-barrel catalytic domain. A structural comparison of TsBGL with other homologous proteins revealed that its catalytic sites included Glu210 and Glu414. We provide the molecular structure of TsBGL and the possibility of improving its characteristics for potential applications in industries.
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http://dx.doi.org/10.3389/fmicb.2021.723678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8517440PMC
October 2021

Stress response mechanisms and description of three novel species Shewanella avicenniae sp. nov., Shewanella sedimentimangrovi sp. nov. and Shewanella yunxiaonensis sp. nov., isolated from mangrove ecosystem.

Antonie Van Leeuwenhoek 2021 Dec 8;114(12):2123-2131. Epub 2021 Oct 8.

State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.

Three Gram-staining negative, facultatively anaerobic, rod-shaped and motile strains, FJAT-51800, FJAT-52962 and FJAT-54481 were isolated from the sediment samples of Zhangjiang Estuary Mangrove National Nature Reserve in Fujian Province, China. The 16S rRNA gene sequencing results indicated they could be novel members of the genus Shewanella. The optimum temperature for growth was 30 °C. The respiratory quinones of the strains were ubiquinone Q-7 or Q-8, and menaquinone MK-7. Polar lipids of the strains FJAT-52962 and FJAT-51800 were phosphatidyl glycerol, phosphatidyl ethanolamine, and unidentified aminophospholipids while strain FJAT-54481 consist of phosphatidylglycerol, phosphatidylethanolamine, unidentified aminophospholipids, two unidentified aminolipids and four unidentified lipids. The major fatty acid of the three strains was iso-C. The genomic DNA G + C contents of strains FJAT-51800, FJAT-52962 and FJAT-54481 were 48.2, 55.3 and 48.1%, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strains FJAT-51800, FJAT-52962 and FJAT-54481 and other closely related Shewanella members were below the cut-off level (95-96%) for species identification. Genome analysis showed that these strains encode genes for osmo-regulation. Based on the results of phenotypic, chemotaxonomic and genome analyses, strains FJAT-51800, FJAT-52962 and FJAT-54481 represent three novel species of the genus Shewanella, for which the names Shewanella avicenniae sp. nov., Shewanella sedimentimangrovi sp. nov., and Shewanella yunxiaonensis sp. nov., are proposed. The type strains are FJAT-51800 (= GDMCC 1.2204 = KCTC 82448), FJAT-52962 (= MCCC 1K05496 = KCTC 82445) and FJAT-54481 (= GDMCC 1.2348 = KCTC 82646).
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http://dx.doi.org/10.1007/s10482-021-01666-9DOI Listing
December 2021

Security strategy of parallel bit interleaved FBMC/OQAM based on four-dimensional chaos.

Opt Express 2021 Jul;29(15):24561-24575

A parallel bit-interleaved filter-bank multicarrier/offset quadrature amplitude modulation (FBMC/OQAM) security strategy based on four-dimensional chaos is proposed in this paper. After the QAM constellation point distribution is disturbed, the modulated FBMC bits and symbols are interleaved and encrypted to realize the improvement of the FBMC/OQAM system physical layer security performance. The chaotic sequence generated by the four-dimensional hyperchaotic system is optimized and calculated to control the disturbance process, which enhances the performance of the system against illegal malicious attacks. The parallel encryption scheme proposed in this scheme increases the encryption efficiency by 1.43 times; can provide a keyspace of 10 size, which effectively resists brute force attacks; and improves the physical layer security of the system. The proposed FBMC/OQAM parallel bit interleaved encryption scheme using a 5 km weakly coupled four-mode fiber achieves a 3×10 Gb/s multiple-input multiple-output-free transmission. The experimental results show that this scheme can effectively improve the security performance of the system, and combines the few-mode multiplexing technology with advanced modulation. It is a candidate for the future large-capacity and high-security optical transmission system.
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http://dx.doi.org/10.1364/OE.433691DOI Listing
July 2021

High-sensitivity transverse-load and high-temperature sensor based on the cascaded Vernier effect.

Appl Opt 2021 Sep;60(25):7714-7720

In this paper, we demonstrate a novel, to the best of our knowledge, transverse-load and high-temperature sensor based on the cascaded Vernier effect. Two Fabry-Perot interferometers fabricated by a piece of hollow-core fiber (HCF) and a piece of polarization-maintaining photonic crystal fiber (PM-PCF) are connected by a long part of single-mode fiber with a length of 1 m, and play the roles of transverse-load sensor and high-temperature sensor, respectively. The sensitivity of not only the transverse load but also that of temperature can be enhanced by the Vernier effect. The sensitivity of the transverse load is raised by 7.7 times to 5.84 nm/N, and the temperature sensitivities increased by 5.5 and 5.9 times to -0.0689/ and -0.1038/ within the temperature range of 50-400°C to 400-900°C. Moreover, both the HCF cavity and PM-PCF cavity can be split and combined flexibly. Hence, such a sensor could have great potential in sensing applications.
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http://dx.doi.org/10.1364/AO.432056DOI Listing
September 2021

Clinical diagnosis and treatment strategy of oral organophosphorus pesticide poisoning.

Panminerva Med 2021 Oct 5. Epub 2021 Oct 5.

Department of Emergency Medicine.

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http://dx.doi.org/10.23736/S0031-0808.21.04462-1DOI Listing
October 2021

Ornidazole-Induced Recurrent Encephalopathy in a Chinese Man: A Rare Case Report and Literature Review.

Front Neurol 2021 9;12:706094. Epub 2021 Sep 9.

Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China.

Ornidazole-induced encephalopathy (OIE) is seldom seen in the clinic. In this study, we report a new case of a patient who had taken 1,000 mg ornidazole daily for nearly 4 years because of suspected diarrhea and proctitis and presented with subacute symptoms such as unsteady gait, slurred speech, and psychiatric disorder. These symptoms were significantly relieved 3 days after the patient stopped taking ornidazole. When he took this medicine again, however, similar symptoms occurred 4 months later, which were again reduced after 4 days of drug discontinuation. After the second onset, abnormal signals were identified around the aqueduct of the midbrain, around the fourth ventricle, and in the dentate nuclei of the cerebellum bilaterally. After 9 days of drug discontinuation, lesions disappeared in the magnetic resonance imaging (MRI) results. According to the clinical manifestations, imaging features, and the reduced symptoms after drug withdrawal, we clinically diagnosed the patient with OIE. This paper also reviews the literature on OIE. Only five cases (including our case) have been reported, all of whom presented with cerebellar ataxia and dysarthria and three with additional mental symptoms such as agitation and irritability. All five patients had abnormal lesions in the dentate nucleus of the cerebellum bilaterally, among whom four also had lesions in the corpus callosum and three around the periaqueduct of the midbrain. After withdrawal of ornidazole, the symptoms in all patients vanished or were alleviated, and three of them showed reduced or disappeared lesions in a head MRI reexamination. Overall, OIE has rarely been reported. Our case report and literature review show that the lesions in the cerebellum, corpus callosum, and brainstem can be reversed. The main manifestations of the lesions-cerebellar ataxia, dysarthria, and mental symptoms-quickly weaken or disappear after drug withdrawal, with good prognosis. Nevertheless, clear pathogenesis has yet to be further investigated.
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http://dx.doi.org/10.3389/fneur.2021.706094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8458754PMC
September 2021

Ezetimibe Improves Rosuvastatin Effects on Inflammation and Vascular Endothelial Function in Acute Coronary Syndrome Patients Undergoing PCI.

J Interv Cardiol 2021 7;2021:2995602. Epub 2021 Sep 7.

Department of Cardiology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China.

Background: Little is known of the acute effects of ezetimibe in patients with acute coronary syndrome (ACS) undergoing PCI. We investigated whether ezetimibe improves inflammation and vascular endothelial function in patients with ACS undergoing PCI.

Methods: We randomized 171 patients with ACS undergoing PCI to receive ezetimibe 10 mg/day plus rosuvastatin 20 mg/day (combination group,  = 81) versus rosuvastatin 20 mg/day (rosuvastatin group,  = 90). Lipid profile, type II secretory phospholipase A2 (sPLA2-IIa), interleukin-1 (IL-1), vascular cell adhesion molecule-1 (VCAM-1), and intercellular cell adhesion molecule-1 (ICAM-1) were measured at baseline and after 7 days. Three months after PCI, clinical outcomes were examined.

Result: The levels of sPLA2-IIa and IL-1 reduced significantly in both groups, but more when ezetimibe and rosuvastatin were coadministered (sPLA2-IIa: 6.16 ± 2.67 vs. 7.42 ± 3.53 ng/ml, =0.01; IL-1: 37.39 ± 26.25 vs. 48.98 ± 32.26 pg/ml, =0.01). A significant rise of VCAM-1 and ICAM-1 was observed on day 7 after PCI in the both groups, but was less in the combination group (VCAM-1: 918.28 ± 235.31 vs. 988.54 ± 194.41 ng/ml, =0.03; ICAM-1: 213.01 ± 100.15 vs. 246.88 ± 105.71 ng/ml, =0.03). Patients in the combination versus rosuvastatin group appeared to suffer from less major adverse events. Periprocedural therapy of ezetimibe improves rosuvastatin effects on proinflammatory responses and endothelial function associated with ACS patients undergoing PCI. This trial is registered with https://clinicaltrials.gov/ct2/show/ChiCTR-IPR-17012219 (Chinese Clinical Trial Registry, http://www.chictr.org.cn on 02/08/2017).
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http://dx.doi.org/10.1155/2021/2995602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8443370PMC
November 2021

Ferroptosis-related lncRNA pairs to predict the clinical outcome and molecular characteristics of pancreatic ductal adenocarcinoma.

Brief Bioinform 2021 Sep 22. Epub 2021 Sep 22.

Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.

Ferroptosis is a form of regulated cell death initiated by oxidative perturbations that can be blocked by iron chelators and lipophilic antioxidants, and ferroptosis may be the silver bullet treatment for multiple cancers, including immunotherapy- and chemotherapy-insensitive cancers such as pancreatic ductal adenocarcinoma (PDAC). Numerous studies have noted that long non-coding RNAs (lncRNAs) regulate the biological behaviour of cancer cells by binding to DNA, RNA and protein. However, few studies have reported the role of lncRNAs in ferroptosis processes and the function of ferroptosis-associated lncRNAs. The primary objective of the present study was to identify ferroptosis-related lncRNAs using bioinformatic approaches combined with experimental validation. The second objective was to construct a prognostic model to predict the overall survival of patients with PDAC. The present study identified ferroptosis-related lncRNAs using a bioinformatic approach and validated them in an independent pancreatic cancer cohort from Fudan University Shanghai Cancer Center. The lncRNA SLCO4A1-AS1 was identified as a novel molecule mediating ferroptosis resistance in vitro. A novel algorithm was used to construct a '0 or 1' matrix-based prognosis model, which showed promising diagnostic accuracy for potential clinical translation (area under the curve = 0.89 for the 2-year survival rate). Notably, molecular subtypes classified by the risk scores of the model did not belong to any previously reported subtypes of PDAC. The immune microenvironment, metabolic activities, mutation landscape and ferroptosis sensitivity were significantly distinct between patients with different risk scores. Sensitivity (IC50) to 30 common anticancer drugs was analysed between patients with different risks, and imatinib and axitinib were found to be potential drugs for the treatment of patients with lower risk scores. Overall, we developed an accurate prognostic model based on the expression patterns of ferroptosis lncRNAs, which may contribute greatly to the evaluation of patient prognosis, molecular characteristics and treatment modalities and could be further translated into clinical applications.
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http://dx.doi.org/10.1093/bib/bbab388DOI Listing
September 2021

Clinical features and outcomes of anti-neutrophil cytoplasmic autoantibody-associated vasculitis in Chinese childhood-onset patients.

Clin Exp Med 2021 Sep 22. Epub 2021 Sep 22.

Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan Province, China.

Data on anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV) are limited in children. This study is to determine the clinical features and outcomes of childhood-onset AAV. A retrospective study was performed on patients who were diagnosed with AAV before 18 years old in Xiangya Hospital. Their medical records were analyzed by retrospective review. Sixteen patients were diagnosed with AAV before 18 years old in the past 9 years, with an average age of 13.3 ± 3.3 years and 13 of them were female. There were 15 patients with microscopic polyangiitis (MPA) and 1 with Wegener's granulomatosis. The interval between onset of disease and diagnosis of AAV was 2 (1.5-3) months. Most patients (15/16, 93.8%) had multi-organ involvement, and all patients had renal involvement with 7 (43.8%) patients requiring dialysis at presentation. Eleven patients underwent a renal biopsy, of which mixed class and sclerotic class were the most two common histological types. All patients received immunosuppressive therapy for induction therapy including intravenous administrations of methylprednisolone (MP) pulse therapy for 8 patients. 8 patients (50%) achieved remission after induction therapy. After a median follow-up of 46.3 ± 36.1 months, nine (56.3%) patients progressed to end-stage renal disease (ESRD) and 5 (31.3%) patients died. Childhood-onset AAV showed similar clinical and pathological features compared to those of adults, except that it usually occurs in girls. The most commonly involved organ was the kidney, and it had a high risk of progression to ESRD. Early diagnosis and initiation of appropriate immunomodulatory therapy would be important to improve outcomes.
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http://dx.doi.org/10.1007/s10238-021-00762-4DOI Listing
September 2021

Rice Ear Counting Based on Image Segmentation and Establishment of a Dataset.

Plants (Basel) 2021 Aug 6;10(8). Epub 2021 Aug 6.

College of Information Engineering, Sichuan Agricultural University, Ya'an 625000, China.

The real-time detection and counting of rice ears in fields is one of the most important methods for estimating rice yield. The traditional manual counting method has many disadvantages: it is time-consuming, inefficient and subjective. Therefore, the use of computer vision technology can improve the accuracy and efficiency of rice ear counting in the field. The contributions of this article are as follows. (1) This paper establishes a dataset containing 3300 rice ear samples, which represent various complex situations, including variable light and complex backgrounds, overlapping rice and overlapping leaves. The collected images were manually labeled, and a data enhancement method was used to increase the sample size. (2) This paper proposes a method that combines the LC-FCN (localization-based counting fully convolutional neural network) model based on transfer learning with the watershed algorithm for the recognition of dense rice images. The results show that the model is superior to traditional machine learning methods and the single-shot multibox detector (SSD) algorithm for target detection. Moreover, it is currently considered an advanced and innovative rice ear counting model. The mean absolute error (MAE) of the model on the 300-size test set is 2.99. The model can be used to calculate the number of rice ears in the field. In addition, it can provide reliable basic data for rice yield estimation and a rice dataset for research.
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http://dx.doi.org/10.3390/plants10081625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8402056PMC
August 2021

Genetic Diversity and Population Differentiation of Kashgarian Loach () in Xinjiang Tarim River Basin.

Biology (Basel) 2021 Aug 1;10(8). Epub 2021 Aug 1.

College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China.

The distribution of is restricted to Xinjiang's Tarim River basin. We collected 119 samples from nine geographic populations in the Tarim River basin and utilized the RAD-seq method for SNP genotyping. In this study, a total of 164.81 Gb bases were generated with the Illumina platform, and 129,873 candidate SNPs were obtained with the Stacks pipeline for population genetic analyses. High levels of genetic diversity were detected among nine populations. The AMOVA results showed that the majority of genetic variations originated from among populations ( = 0.67), and the pairwise values ranged from 0.4579 to 0.8736, indicating high levels of genetic differentiation among these populations. The discriminate analysis of principal components (DAPCs) and neighbor joining (NJ) tree revealed that the nine populations could be separated into two clusters (i.e., south and north populations), and modest genetic differentiation between south and north populations was observed, while the individuals from several populations were not clustered together by geographical location. The evidence of two genetic boundaries between south and north populations (except TTM) was supported by barrier analysis. The Bayesian skyline plotting indicated that populations in the Tarim River basin had not experienced genetic bottlenecks, and the effective population size remained stable. This study first clarified the genetic diversity and differentiation of populations in the Tarim River basin, and it provided valuable molecular data for conservation and management of natural populations.
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http://dx.doi.org/10.3390/biology10080734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8389669PMC
August 2021

Quality Control of DNA Extracted from All-Cell Pellets After Cryopreservation for More Than 10 Years.

Biopreserv Biobank 2021 Aug 25. Epub 2021 Aug 25.

National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China.

Cryopreserved whole blood, all-cell pellets (ACPs), and buffy coats in biobanks are widely used to obtain DNA for genetic testing. However, there are few studies concerning the quality control of DNA extracted from them. Our research aimed to perform quality control of DNA extracted from ACPs after cryopreservation for >10 years. A total of 1377 ACP samples (separated from 3 mL of whole blood) were retrieved from our biobank, where they had been cryopreserved for 10-15 years. Chemagic STAR was used to extract the DNA. Absorbance at A260, A280, and A230 were measured by spectrophotometry, and integrity was analyzed by agarose gel electrophoresis. The quality thresholds for an Illumina Asian Screening Array (ASA) were yields greater than 0.5 μg, concentration of 25-150 ng/μL, A260/280 ratio of 1.6-2.1, and no degradation fragments in the electrophoresis gel. The median yield of genomic DNA was 54.30 μg (interquartile range [IQR] 35.55-74.64). The median A260/280 and A260/230 ratios were 1.90 (IQR 1.87-1.94) and 1.98 (IQR 1.64-2.41), respectively. In total, 1377 samples (100%) had qualified yields, and 1366 samples (99.20%) had qualified integrity results. Finally, 1328 (96.44%) samples were used for ASA. Of the remaining samples, 34 needed to be repurified, 4 were obtained at an insufficient concentration, and 11 were unqualified for integrity. In addition, we analyzed the influence of hemolysis (90 samples) and clots (102 samples) on the quality of DNA samples. Hemolysis and clotting did not influence yield or integrity, but a significant difference was found in A260/230 compared to normal samples ( < 0.05). Furthermore, the samples (14 samples) with both hemolysis and clots had higher A260/280 ( < 0.05). ACP samples stored for >10 years at -80°C produced DNA with high quality for use in genetic analysis. Hemolysis and clots in the ACPs led to lower purity, but did not significantly affect yield or integrity.
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http://dx.doi.org/10.1089/bio.2021.0052DOI Listing
August 2021

Efficacy and tolerability of doxazosin gastro-intestinal therapeutic system versus tamsulosin in patients with lower urinary tract symptoms associated with benign prostatic hyperplasia: A systematic review and meta-analysis.

Medicine (Baltimore) 2021 Aug;100(33):e26955

Viatris Pharmaceuticals Co., Ltd, Shanghai, China.

Background: Alpha1-adrenoceptor antagonists (α1-blockers) are first-line drugs for the treatment of lower urinary tract symptoms associated with benign prostate hyperplasia (BPH). Doxazosin gastrointestinal therapeutic system (GITS) and tamsulosin belong to the 2 most frequently prescribed α1-blockers. This systematic review and meta-analysis was performed to compare the efficacy and tolerability of these 2 α1-blockers.

Methods: A systematic review of published randomized controlled trials in English or Chinese language was performed using the PubMed, EMBASE, Cochrane Library, CNKI, Wanfang, and Vip databases. After data extraction and quality assessment, the meta-analysis was performed to compare clinical parameters (International Prostate Symptom Score [IPSS] total [IPSS-T], storage [IPSS-S], voiding [IPSS-V], maximum urine flow [Qmax], and postvoid residual) and adverse events (AEs) that changed after first drug intake.

Results: After the screening, 8 eligible randomized controlled trials with 1316 patients were identified. Doxazosin-GITS showed a significantly higher efficacy compared with tamsulosin (IPSS-T P < .001, IPSS-S P < .001, and IPSS-V P < .001). There were no significant differences between the 2 drugs for changes in Qmax (P = .477) or postvoid residual (P = .739). The overall AEs were significantly lower in the doxazosin-GITS group (risk ratio: 0.77; 95% CI: 0.54-1.08; P = .036). However, dizziness (P = .387), headache (P = .745), asthenia (P = .693), postural hypotension (P = .114), and retrograde ejaculation (P = .187) were similar between the 2 groups.

Conclusions: This meta-analysis indicates that doxazosin-GITS has significantly higher efficacy and lower AEs than tamsulosin in patients with lower urinary tract symptoms/benign prostate hyperplasia.
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http://dx.doi.org/10.1097/MD.0000000000026955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8376339PMC
August 2021

The unfavorable impact of DR9/DR9 genotype on the frequency and quality of partial remission in type 1 diabetes.

J Clin Endocrinol Metab 2021 Aug 14. Epub 2021 Aug 14.

National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.

Context: Partial remission (PR) is a specific stage in type 1 diabetes (T1D). Although human leukocyte antigen (HLA) class II loci are the strongest genetic determinants in T1D, the relationship between PR and HLA remains unclear.

Objective: To investigate the association between PR status and HLA genotypes in T1D patients.

Methods: A total of 237 T1D patients were included. PR was defined according to C-peptide ≥300 pmol/L. The frequency of PR and peak C-peptide levels during remission phase were compared according to HLA status. Clinical characteristics including age of onset and diabetes autoantibodies were collected. All analyses were duplicated when subjects were divided into childhood- and adult-onset T1D.

Results: The median follow-up time was 24 months, 65.8% (156/237) of T1D patients went into PR. DR9/DR9 carriers had lower PR rate (44.2% vs. 70.6%, P=0.001) and less likely to enter PR (OR=0.218, 95% CI: 0.098-0.487, P<0.001) than the non-DR9/DR9 carriers, observed in both childhood- and adult-onset T1D. Besides, the peak C-peptide during PR phase was also lower in DR9/DR9 carriers, more notable in adult-onset T1D. When compared with non-DR9/DR9 carriers, T1D with DR9/DR9 genotype presented an older age of onset and a lower positivity of zinc transporter 8 antibody (ZnT8A), and the lower trend of ZnT8A was only found in adult-onset T1D (P=0.049).

Conclusions: T1D carrying susceptible DR9/DR9 are less prone to undergo PR. Additionally, the recovery extent of β-cell function during the PR phase tends to be lower in adults carrying DR9/DR9, which might be associated with ZnT8A.
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http://dx.doi.org/10.1210/clinem/dgab589DOI Listing
August 2021

sp. nov., a facultative anaerobic bacterium isolated from mangrove sediment.

Int J Syst Evol Microbiol 2021 Aug;71(8)

State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.

Two Gram-stain-negative, motile, facultatively anaerobic, rod-shaped strains, FJAT-53720 and FJAT-53726, were isolated from rhizosphere sediment of plant . Phylogenetic analysis based on their 16S rRNA gene sequences revealed that strains FJAT-53720 and FJAT-53726 were affiliated to the genus (forming an independent cluster) with the highest sequence similarity to the type strain of . Optimum growth of both strains was observed at 30 °C and pH 7. The respiratory quinones were Q-7, Q-8 and MK-7. The polar lipid profile included phosphatidylmethyl ethanolamine, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified aminophospholipid and four unknown phospholipids. The major fatty acids of strains FJAT-53720 and FJAT-53726 were iso-C C 8 and summed feature 3. The genomic DNA G+C content of strain FJAT-53720 was 55.6 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between FJAT-53720 and FJAT-53726 were 97.4 and 77.9 %, confirming that they were similar species and hence FJAT-53720 was selected for further analysis. The ANI and dDDH values between FJAT-53720 and other members of the genus were below the cut-off level (95-96 %; 70 %) for species delineation. Based on the above results, FJAT-53720 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is FJAT-53720 (=KCTC 82444=GDMCC 1.2207).
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http://dx.doi.org/10.1099/ijsem.0.004940DOI Listing
August 2021

Systemic immune-inflammation index predicts a reduced risk of end-stage renal disease in Chinese patients with myeloperoxidase-anti-neutrophil cytoplasmic antibody-associated vasculitis: A retrospective observational study.

Exp Ther Med 2021 Sep 13;22(3):989. Epub 2021 Jul 13.

Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China.

Chronic inflammation has been indicated to be important in the pathogenesis of anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV). The systemic immune-inflammation index (SII) is a novel marker of inflammation. The present study was thus performed to explore the association between the SII at diagnosis and inflammatory response and disease activity in Chinese patients with myeloperoxidase (MPO)-AAV. Furthermore, it was evaluated whether the SII is able to predict the progression to end-stage renal disease (ESRD) and patient survival. A total of 190 patients with MPO-AAV were included in the present study. The baseline SII was positively correlated with C-reactive protein (CRP; r=0.274, P<0.0001) and the erythrocyte sedimentation rate (ESR; r=0.481, P<0.0001). However, the SII had no obvious correlation with the Birmingham vasculitis activity score. Patients with SII≥2,136.45 exhibited better cumulative renal survival rates than those with SII<2,136.45 (P=0.001). However, no significant difference in patient survival was indicated between patients with SII≥2,136.45 and those with SII<2,136.45 at diagnosis. In conclusion, the SII was positively correlated with CRP and ESR in Chinese patients with MPO-AAV. Furthermore, the SII may be an independent factor associated with a reduced risk of ESRD.
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http://dx.doi.org/10.3892/etm.2021.10421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8311255PMC
September 2021

Association Between Dietary Inflammatory Index and Heart Failure: Results From NHANES (1999-2018).

Front Cardiovasc Med 2021 6;8:702489. Epub 2021 Jul 6.

Department of Cardiology, The First Affiliated Hospital of Xiamen University, Xiamen, China.

To explore the relationship between dietary inflammatory index (DII) and heart failure (HF) in participants with cardiovascular and cerebrovascular diseases. NHANES (1998-2018) data were collected and used to assess the association of HF with DII. Twenty-four-hour dietary consumptions were used to calculate the scores of DII. Demographic characteristics and physical and laboratory examinations were collected for the comparison between HF and non-HF groups. Logistic regression analysis and random forest analysis were performed to calculate the odds rate and determine the potential beneficial dietary components in HF. A total of 19,067 cardiac-cerebral vascular disease participants were categorized as HF ( = 1,382; 7.25%) and non-HF ( = 17,685; 92.75%) groups. Heart failure participants had higher levels of DII score compared with those in the non-HF group (0.239 ± 1.702 vs. -0.145 ± 1.704, < 0.001). Compared with individuals with T1 (DII: -3.884 to -0.570) of DII, those in T3 (DII: 1.019 to 4.598) had a higher level of total cholesterol (4.49 ± 1.16 vs. 4.75 ± 1.28 mmol/L, < 0.01), globulin (29.92 ± 5.37 vs. 31.29 ± 5.84 g/L, < 0.001), and pulse rate (69.90 ± 12.22 vs. 72.22 ± 12.77, < 0.001) and lower levels of albumin (40.76 ± 3.52 vs. 39.86 ± 3.83 g/L, < 0.001), hemoglobin (13.76 ± 1.65 vs. 13.46 ± 1.77 g/dl, < 0.05), and hematocrit (40.83 ± 4.69 vs. 40.17 ± 5.01%, < 0.05). The odds rates of HF for DII from the logistic regression were 1.140, 1.158, and 1.110 in models 1, 2, and 3, respectively. In addition, from the results of random forest analysis, dietary magnesium, fiber, and beta carotene may be essential in HF. Dietary inflammatory index was positively associated with HF in US adults, and dietary intervention might be a promising method in the therapy of HF.
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http://dx.doi.org/10.3389/fcvm.2021.702489DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8292138PMC
July 2021

A case of 15q11-q13 duplication syndrome and literature review.

Brain Behav 2021 08 21;11(8):e2219. Epub 2021 Jul 21.

Department of Pediatric, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China.

Background: The chromosomal 15q11-q13 regions are structurally complex, and their abnormalities are associated with various neuropsychiatric disorders, including autism spectrum disorder (ASD), epilepsy, Angelman syndrome, and Prader-Willi syndrome.

Case Description: A 6-year-old child was admitted to the hospital as a result of an "epileptic status" showing ASD, intractable epilepsy, and total developmental retardation. Chromosome gene detection showed repetitive variation in the 15q11-q13 regions, and the video electroencephalogram was abnormal. Although children are currently given antiepileptic treatment and rehabilitation training, intermittent seizures can still occur.

Conclusion: The clinical phenotypes of 15q11-q13 repetitive syndrome are complex, and vary in severity. Children with intractable epilepsy, ASD, and language and motor retardation should be considered to have this syndrome, which requires confirmation by multiplex ligation-dependent probe amplification and gene detection. These approaches can enable early rehabilitation treatment and improve the patients' quality of life.
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http://dx.doi.org/10.1002/brb3.2219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8413793PMC
August 2021

Dietary selenium promotes the growth performance through growth hormone-insulin-like growth factor and hypothalamic-pituitary-thyroid axes in grass carp (Ctenopharyngodon idella).

Fish Physiol Biochem 2021 Aug 9;47(4):1313-1327. Epub 2021 Jul 9.

College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.

Selenium (Se), an essential component of deiodinases (DIOs), regulates the contents of thyroid hormones and thus improves animal growth. To explore the influences of selenium supplementation on fish growth metabolism, a total of 270 healthy grass carp (Ctenopharyngodon idella) were divided into three groups and feed three graded dietary selenium (0.141, 0.562, and 1.044 mg Se/kg) levels. The results showed that after 60-day feeding, dietary selenium improved the final body weight and specific growth rate (SGR) of grass carp. The hepatic DIO activities in selenium-supplemented groups were higher than those in control group. A significant increase in triiodothyronine (T3), free triiodothyronine (FT3), and thyroid-stimulating hormone (TSH) levels was accompanied by a decrease in the contents of thyroxine (T4) and free thyroxine (FT4) in selenium-supplemented groups. The histopathological observation of thyroid suggested that selenium deficiency resulted in hypertrophy of follicular epithelial cells. Moreover, the gene relative expression levels of dio1, dio2, and dio3 showed an increasing trend with the rising concentration of dietary selenium. The transcription levels of HPT axis-related genes (crh, tsh-β, ttr, tr-s, tpo, nis) and GH/IGF1-related genes (gh, ghr, igf1, igf1r) were significantly upregulated in selenium-supplemented groups. No significant differences in the above indicators were observed between 0.562 and 1.044 mg Se/kg diet group except T3 content and dio1 relative expression ratio. These results indicate that dietary selenium supplementation improves the hepatic DIO activities and thyroid hormone metabolism and regulates the transcription levels of HPT and GH/IGF axis-related genes, which may be responsible for the growth promotion in grass carp.
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http://dx.doi.org/10.1007/s10695-021-00974-1DOI Listing
August 2021

PD-L1/LAG-3 bispecific antibody enhances tumor-specific immunity.

Oncoimmunology 2021 24;10(1):1943180. Epub 2021 Jun 24.

Department of Drug Discovery, Innovent Biologics (Suzhou) Co, Suzhou, China.

Anti-programmed cell death-1 (PD-1)/PD-ligand-1 (PD-L1) treatments are effective in a fraction of patients with advanced malignancies. However, the majority of patients do not respond to it. Resistance to cancer immunotherapy can be mediated by additional immune checkpoints. We hypothesized that co-targeting of PD-L1 and lymphocyte-activation gene 3 (LAG-3) could provide an alternative therapeutic approach. Here, we developed IBI323, a dual blockade bispecific antibody targeting PD-L1 and LAG-3. We assessed the binding affinity, blocking activity, cell bridging effect, and immunomodulation function of IBI323 using in vitro assays. We also evaluated, in two humanized mouse models, anti-tumor effects and antitumor T cell immunity induced by IBI323. IBI323 bound to PD-L1 and LAG-3 with similar potency as its parental antibodies and blocked the interaction of PD-1/PD-L1, CD80/PD-L1, and LAG-3/MHC-II. Moreover, IBI323 mediated the bridging of PD-L1+ cells and LAG-3+ cells and demonstrated superior immune stimulatory activity compared to each parent antibody in mixed leukocyte reaction. In PD-L1/LAG-3 double knock-in mice bearing human PD-L1 knock-in MC38 tumors, IBI323 showed stronger anti-tumor activity compared to each parental antibody. The better antitumor response correlated with increased tumor-specific CD8+ and CD4+ T cells. IBI323 also induced stronger anti-tumor effect against established A375 tumors compared with combination in mice reconstituted with human immune cells. Collectively, these data demonstrated that IBI323 preserved the blockade activities of parental antibodies while processing a novel cell bridging function. Based on the encouraging preclinical results, IBI323 has significant value in further clinical development.
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http://dx.doi.org/10.1080/2162402X.2021.1943180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8237984PMC
August 2021

Construction of a novel risk model based on the random forest algorithm to distinguish pancreatic cancers with different prognoses and immune microenvironment features.

Bioengineered 2021 12;12(1):3593-3602

Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.

Immune-related long noncoding RNAs (irlncRNAs) are actively involved in regulating the immune status. This study aimed to establish a risk model of irlncRNAs and further investigate the roles of irlncRNAs in predicting prognosis and the immune landscape in pancreatic cancer. The transcriptome profiles and clinical information of 176 pancreatic cancer patients were retrieved from The Cancer Genome Atlas (TCGA). Immune-related genes (irgenes) downloaded from ImmPort were used to screen 1903 immune-related lncRNAs (irlncRNAs) using Pearson's correlation analysis (R > 0.5; p < 0.001). Random survival forest (RSF) and survival tree analysis showed that 9 irlncRNAs were highly correlated with overall survival (OS) according to the variable importance (VIMP) and minimal depth. Next, Cox regression analysis was used to establish a risk model with 3 irlncRNAs (LINC00462, LINC01887, RP11-706C16.8) that was evaluated by Kaplan-Meier analysis, the areas under the curve (AUCs) of the receiver operating characteristics and the C-index. Additionally, we performed Cox regression analysis to establish the clinical prognostic model, which showed that the risk score was an independent prognostic factor (p < 0.001). A nomogram and calibration plots were drawn to visualize the clinical features. The Wilcoxon signed-rank test and Pearson's correlation analysis further explored the irlncRNA signatures and immune cell infiltration, as well as the immunotherapy response.
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http://dx.doi.org/10.1080/21655979.2021.1951527DOI Listing
December 2021

Genetic diversity and structure of the endemic and endangered species growing along the Jinsha River.

Plant Divers 2021 Jun 11;43(3):225-233. Epub 2021 Jan 11.

Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.

The traditional medicinal plant, and endangered species (Aristolochiaceae) is an endemic species in China and occurs in the warm and dry areas along the Jinsha river. It is also a specific host of the larvae of , a vulnerable butterfly. In this study, 15 pairs of polymorphic microsatellite primers of were designed and screened based on the Simple Sequence Repeats (SSR) loci found by using the results of genome skimming. Based on these 15 SSR markers, the genetic diversity and structure of 193 individuals from ten natural populations were analyzed in detail. In comparison to other endemic and endangered plants in the region, the population of possess a relatively high genetic diversity (e = 0.550 = 1.112). AMOVA analysis showed that 68.4% of the total genetic diversity was within populations and 31.6% of the variation occurred among populations. There was a significant genetic differentiation among natural populations of detectable, with low gene flow (m = 0.591). This might be attributed to geographical barriers and limited seed dispersal To test the isolation by distance (IBD), we performed Mantel test, which showed a significant correlation between the geographic and genetic distances. In order to cope with the possible biases caused by IBD, we additionally performed Bayesian genetic cluster analyses and principal coordinate analysis (PCoA). The final cluster analysis revealed three groups with distinct geographical distribution. Habitat fragmentation and limited gene flow between these populations may be the main reasons for the current genetic structure. For conservation of this species, we suggest to divide its populations into three protection management units, with subsequent focus on the Yongsheng and Luquan populations which experienced a genetic bottleneck event in the past.
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http://dx.doi.org/10.1016/j.pld.2020.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8233524PMC
June 2021

DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.).

Hortic Res 2021 Jul 1;8(1):142. Epub 2021 Jul 1.

Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.

Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (Brassica napus). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of B. napus. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in B. napus might be partially regulated by MET1. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed Brassica polyploids.
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http://dx.doi.org/10.1038/s41438-021-00576-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245426PMC
July 2021
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