Publications by authors named "Xinjie Wang"

68 Publications

A Systematic Review of Tissue Engineering Scaffold in Tendon Bone Healing .

Front Bioeng Biotechnol 2021 15;9:621483. Epub 2021 Mar 15.

Sports Medicine Department, Beijing Key Laboratory of Sports Injuries, Peking University Third Hospital, Beijing, China.

Tendon-bone healing is an important factor in determining the success of ligament reconstruction. With the development of biomaterials science, the tissue engineering scaffold plays an extremely important role in tendon-bone healing and bone tissue engineering. Electronic databases (PubMed, Embase, and the Web of Science) were systematically searched for relevant and qualitative studies published from 1 January 1990 to 31 December 2019. Only original articles that met eligibility criteria and evaluated the use of issue engineering scaffold especially biomaterials in tendon bone healing were selected for analysis. The search strategy identified 506 articles, and 27 studies were included for full review including two human trials and 25 animal studies. Fifteen studies only used biomaterials like PLGA, collage, PCL, PLA, and PET as scaffolds to repair the tendon-bone defect, on this basis, the rest of the 11 studies using biological interventions like cells or cell factors to enhance the healing. The adverse events hardly ever occurred, and the tendon bone healing with tissue engineering scaffold was effective and superior, which could be enhanced by biological interventions. Although a number of tissue engineering scaffolds have been developed and applied in tendon bone healing, the researches are mainly focused on animal models which are with limitations in clinical application. Since the efficacy and safety of tissue engineering scaffold has been proved, and can be enhanced by biological interventions, substantial clinical trials remain to be done, continued progress in overcoming current tissue engineering challenges should allow for successful clinical practice.
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http://dx.doi.org/10.3389/fbioe.2021.621483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8005599PMC
March 2021

Computational Modeling of Structural Synaptic Plasticity in Echo State Networks.

IEEE Trans Cybern 2021 Mar 24;PP. Epub 2021 Mar 24.

Most existing studies on computational modeling of neural plasticity have focused on synaptic plasticity. However, regulation of the internal weights in the reservoir based on synaptic plasticity often results in unstable learning dynamics. In this article, a structural synaptic plasticity learning rule is proposed to train the weights and add or remove neurons within the reservoir, which is shown to be able to alleviate the instability of the synaptic plasticity, and to contribute to increase the memory capacity of the network as well. Our experimental results also reveal that a few stronger connections may last for a longer period of time in a constantly changing network structure, and are relatively resistant to decay or disruptions in the learning process. These results are consistent with the evidence observed in biological systems. Finally, we show that an echo state network (ESN) using the proposed structural plasticity rule outperforms an ESN using synaptic plasticity and three state-of-the-art ESNs on four benchmark tasks.
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http://dx.doi.org/10.1109/TCYB.2021.3060466DOI Listing
March 2021

Ionic-strength-dependent effect of suspended sediment on the aggregation, dissolution and settling of silver nanoparticles.

Environ Pollut 2021 Jun 15;279:116926. Epub 2021 Mar 15.

Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China.

Suspended sediment (SS) is ubiquitous in natural waters and plays a key role in the fate of engineered nanomaterials. In this study, the effect of SS on the aggregation, settling, and dissolution of polyvinylpyrrolidone-coated silver nanoparticles (PVP-AgNPs) was investigated under environmentally relevant conditions. The heteroaggregation of AgNPs with SS was not observed at low ionic strength (≤0.01 M) due to high electrostatic repulsion and steric forces. At higher NaCl concentrations (0.1 and 0.3 M), PVP-AgNPs were found to attach onto the SS surface, and the formation of AgNP-SS heteroaggregates strongly promoted settling of PVP-AgNPs due to the overwhelming gravity force. PVP-AgNP dissolution was reduced after the addition of sediment to ultrapure water because the presence of sediment-associated dissolved organic matter (SS-DOM). The formation of an AgCl layer on PVP-AgNP surface in 0.01 M NaCl solution resulted in the minor effect of SS on AgNP dissolution. After addition of SS, the dissolved silver concentrations of PVP-AgNP increased in 0.1 and 0.3 M NaCl solution. The interactions of SS-DOM with AgNPs under different NaCl concentrations interfered the dissolution of AgNPs in sediment-laden water. This study provides new insight into the fate of AgNPs in sediment-laden water under various environmental conditions.
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http://dx.doi.org/10.1016/j.envpol.2021.116926DOI Listing
June 2021

Value of 3D preoperative planning for primary total hip arthroplasty based on artificial intelligence technology.

J Orthop Surg Res 2021 Feb 24;16(1):156. Epub 2021 Feb 24.

Department of Orthopedics, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, No. 183, Zhongshan Rd West, Guangzhou, 510630, China.

Background: Accurate preoperative planning is an important step for accurate reconstruction in total hip arthroplasty (THA). Presently, preoperative planning is completed using either a two-dimensional (2D) template or three-dimensional (3D) mimics software. With the development of artificial intelligence (AI) technology, AI HIP, a planning software based on AI technology, can quickly and automatically identify acetabular and femur morphology, and automatically match the optimal prosthesis size. However, the accuracy and feasibility of its clinical application still needs to be further verified. The purposes of this study were to investigate the accuracy and time efficiency of AI HIP in preoperative planning for primary THA, compared with 3D mimics software and 2D digital template, and further analyze the factors that influence the accuracy of AI HIP.

Methods: A prospective study was conducted on 53 consecutive patients (59 hips) undergoing primary THA with cementless prostheses in our department. All preoperative planning was completed using AI HIP as well as 3D mimics and 2D digital template. The predicted component size and the actual implantation results were compared to determine the accuracy. The templating time was compared to determine the efficiency. Furthermore, the potential factors influencing the accuracy of AI HIP were analyzed including sex, body mass index (BMI), and hip dysplasia.

Results: The accuracy of predicting the size of acetabular cup and femoral stem was 74.58% and 71.19%, respectively, for AI HIP; 71.19% (P = 0.743) and 76.27% (P = 0.468), respectively, for 3D mimics; and 40.68% (P < 0.001) and 49.15% (P = 0.021), respectively, for 2D digital templating. The templating time using AI HIP was 3.91 ± 0.64 min, which was equivalent to 2D digital templates (2.96 ± 0.48 min, P < 0.001), but shorter than 3D mimics (32.07 ± 2.41 min, P < 0.001). Acetabular dysplasia (P = 0.021), rather than sex and BMI, was an influential factor in the accuracy of AI HIP templating. Compared to patients with developmental dysplasia of the hip (DDH), the accuracy of acetabular cup in the non-DDH group was better (P = 0.021), but the difference in the accuracy of the femoral stem between the two groups was statistically insignificant (P = 0.062).

Conclusion: AI HIP showed excellent reliability for component size in THA. Acetabular dysplasia may affect the accuracy of AI HIP templating.
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http://dx.doi.org/10.1186/s13018-021-02294-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7903792PMC
February 2021

Detection of the SARS-CoV-2 D614G mutation using engineered Cas12a guide RNA.

Biotechnol J 2021 Jun 9;16(6):e2100040. Epub 2021 Mar 9.

Guangzhou Laboratory, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.

Detection of pathogens with single-nucleotide variations is indispensable for the disease tracing, but remains technically challenging. The D614G mutation in the SARS-CoV-2 spike protein is known to markedly enhance viral infectivity but is difficult to detect. Here, we report an effective approach called "synthetic mismatch integrated crRNA guided Cas12a detection" (symRNA-Cas12a) to detect the D614 and G614 variants effectively. Using this method, we systemically screened a pool of crRNAs that contain all the possible nucleotide substitutions covering the -2 to +2 positions around the mutation and identify one crRNA that can efficiently increase the detection specificity by 13-fold over the ancestral crRNA. With this selected crRNA, the symRNA-Cas12a assay can detect as low as 10 copies of synthetic mutant RNA and the results are confirmed to be accurate by Sanger sequencing. Overall, we have developed the symRNA-Cas12a method to specifically, sensitively and rapidly detect the SARS-CoV-2 D614G mutation.
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http://dx.doi.org/10.1002/biot.202100040DOI Listing
June 2021

Development of a Broadly Applicable Cas12a-Linked Beam Unlocking Reaction for Sensitive and Specific Detection of Respiratory Pathogens Including SARS-CoV-2.

ACS Chem Biol 2021 03 15;16(3):491-500. Epub 2021 Feb 15.

Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.

The outbreak of novel coronavirus SARS-CoV-2 has caused a worldwide threat to public health. COVID-19 patients with SARS-CoV-2 infection can develop clinical symptoms that are often confused with the infections of other respiratory pathogens. Sensitive and specific detection of SARS-CoV-2 with the ability to discriminate from other viruses is urgently needed for COVID-19 diagnosis. Herein, we streamlined a highly efficient CRISPR-Cas12a-based nucleic acid detection platform, termed s12a-nked eam nlocking eactio (CALIBURN). We show that CALIBURN could detect SARS-CoV-2 and other coronaviruses and influenza viruses with little cross-reactivity. Importantly, CALIBURN allowed accurate diagnosis of clinical samples with extremely low viral loads, which is a major obstacle for the clinical applications of existing CRISPR diagnostic platforms. When tested on the specimens from SARS-CoV-2-positive and negative donors, CALIBURN exhibited 73.0% positive and 19.0% presumptive positive rates and 100% specificity. Moreover, unlike existing CRISPR detection methods that were mainly restricted to respiratory specimens, CALIBURN displayed consistent performance across both respiratory and nonrespiratory specimens, suggesting its broad specimen compatibility. Finally, using a mouse model of SARS-CoV-2 infection, we demonstrated that CALIBURN allowed detection of coexisting pathogens without cross-reactivity from a single tissue specimen. Our results suggest that CALIBURN can serve as a versatile platform for the diagnosis of COVID-19 and other respiratory infectious diseases.
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http://dx.doi.org/10.1021/acschembio.0c00840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901234PMC
March 2021

Advances in Female Germ Cell Induction from Pluripotent Stem Cells.

Stem Cells Int 2021 13;2021:8849230. Epub 2021 Jan 13.

Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, 1400 Beijing Road West, Shanghai 200040, China.

Germ cells are capable of maintaining species continuity through passing genetic and epigenetic information across generations. Female germ cells mainly develop during the embryonic stage and pass through subsequent developmental stages including primordial germ cells, oogonia, and oocyte. However, due to the limitation of using early human embryos as research model, research models are needed to reveal the early developmental process and related mechanisms of female germ cells. After birth, the number of follicles gradually decreases with age. Various conditions which damage ovarian functions would cause premature ovarian failure. Alternative treatments to solve these problems need to be investigated. Germ cell differentiation from pluripotent stem cells can simulate early embryonic development of female germ cells and clarify unresolved issues during the development process. In addition, pluripotent stem cells could potentially provide promising applications for female fertility preservation after proper differentiation. Mouse female germ cells have been successfully reconstructed and delivered to live offspring. However, the derivation of functional human female germ cells has not been fully achieved due to technical limitations and ethical issues. To provide an updated and comprehensive information, this review centers on the major studies on the differentiation of mouse and human female germ cells from pluripotent stem cells and provides references to further studies of developmental mechanisms and potential therapeutic applications of female germ cells.
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http://dx.doi.org/10.1155/2021/8849230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7822693PMC
January 2021

Simulation Analysis of the Aerodynamic Performance of a Bionic Aircraft with Foldable Beetle Wings in Gliding Flight.

Appl Bionics Biomech 2020 24;2020:8843360. Epub 2020 Dec 24.

College of Mechanical and Electrical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China.

Beetles have excellent flight performance. Based on the four-plate mechanism theory, a novel bionic flapping aircraft with foldable beetle wings was designed. It can perform flapping, gliding, wing folding, and abduction/adduction movements with a self-locking function. In order to study the flight characteristics of beetles and improve their gliding performance, this paper used a two-way Fluid-Structure Interaction (FSI) numerical simulation method to focus on the gliding performance of the bionic flapping aircraft. The effects of elastic model, rigid and flexible wing, angle of attack, and velocity on the aerodynamic characteristics of the aircraft in gliding flight are analyzed. It was found that the elastic modulus of the flexible hinges has little effect on the aerodynamic performance of the aircraft. Both the rigid and the flexible wings have a maximum lift-to-drag ratio when the attack angle is 10°. The lift increased with the increase of the gliding speed, and it was found that the lift cannot support the gliding movement at low speeds. In order to achieve gliding, considering the weight and flight performance, the weight of the microair vehicle is controlled at about 3 g, and the gliding speed is guaranteed to be greater than 6.5 m/s. The results of this study are of great significance for the design of bionic flapping aircrafts.
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http://dx.doi.org/10.1155/2020/8843360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775174PMC
December 2020

In situ decorated Au NPs on chitosan-encapsulated FeO-NH NPs as magnetic nanocomposite: Investigation of its anti-colon carcinoma, anti-gastric cancer and anti-pancreatic cancer.

Int J Biol Macromol 2021 Feb 10;171:198-207. Epub 2020 Dec 10.

Department of Gastroenterology, Shandong Provincial Qianfoshan Hospital, The First Affiliated Hospital of Shandong First Medical University, No. 16766, Jingshi Road, Lixia District, Jinan, Shandong Province 250014, China. Electronic address:

Chitosan is a linear polysaccharide and non-toxic bioactive polymer with a wide variety of applications due to its functional properties such as ease of modification, and biodegradability. In this investigation, magnetic cores (FeO) were synthesized using a fabrication method involving coprecipitation of Fe and Fe. Then the magnetic nanoparticles were encapsulated by chitosan layers. In the next step, magnetite-gold composite nanoparticles were synthesized with spherical shapes and sizes ranging from 20 to 30 nm, using sodium citrate as a natural reducing agent. The morphological and physicochemical features of the material were determined using several advanced techniques like FT-IR, ICP analysis, FESEM, EDS, XRD, TEM, XPS and VSM. In the biological part of the present study, the cell viability of FeO, HAuCl, and [email protected]/AuNPs was very low against human colorectal carcinoma cell lines i.e. Ramos.2G6.4C10, HCT-8 [HRT-18], HCT 116, and HT-29, human gastric cancer cell lines i.e. MKN45, AGS, and KATO III, and human pancreatic cancer cell lines i.e. PANC-1, AsPC-1, and MIA PaCa-2. The IC50 of [email protected]/AuNPs against Ramos.2G6.4C10, HCT-8 [HRT-18], HCT 116, HT-29, MKN45, AGS, KATO III, PANC-1, AsPC-1, and MIA PaCa-2 cell lines were 385, 429, 264, 286, 442, 498, 561, 513, 528, and 425 μg/mL, respectively. Thereby, the best cytotoxicity results of our [email protected]/AuNPs were observed in the case of the HCT 116 cell line. Seemingly, the present nanoparticles may be used for the treatment of several types of gastro-duodenal cancers especially colon, gastric, and pancreatic cancers in near future.
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http://dx.doi.org/10.1016/j.ijbiomac.2020.12.037DOI Listing
February 2021

Targeting MDM2 for Neuroblastoma Therapy: In Vitro and In Vivo Anticancer Activity and Mechanism of Action.

Cancers (Basel) 2020 Dec 5;12(12). Epub 2020 Dec 5.

Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA.

Background: Neuroblastoma is an aggressive pediatric solid tumor with an overall survival rate of <50% for patients with high-risk disease. The majority (>98%) of pathologically-diagnosed neuroblastomas have wild-type p53 with intact functional activity. However, the mouse double minute 2 (MDM2) homolog, an E3 ubiquitin ligase, is overexpressed in neuroblastoma and leads to inhibition of p53. MDM2 also exerts p53-independent oncogenic functions. Thus, MDM2 seems to be an attractive target for the reactivation of p53 and attenuation of oncogenic activity in neuroblastoma.

Methods: In this study, we evaluated the anticancer activities and underlying mechanisms of action of SP141, a first-in-class MDM2 inhibitor, in neuroblastoma cell lines with different p53 backgrounds. The findings were confirmed in mouse xenograft models of neuroblastoma.

Results: We demonstrate that SP141 reduces neuroblastoma cell viability, induces apoptosis, arrests cells at the G2/M phase, and prevents cell migration, independent of p53. In addition, in neuroblastoma xenograft models, SP141 inhibited MDM2 expression and suppressed tumor growth without any host toxicity at the effective dose.

Conclusions: MDM2 inhibition by SP141 results in the inhibition of neuroblastoma growth and metastasis, regardless of the p53 status of the cells and tumors. These findings provide proof-of-concept that SP141 represents a novel treatment option for both p53 wild-type and p53 null neuroblastoma.
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http://dx.doi.org/10.3390/cancers12123651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7762001PMC
December 2020

Inhibitory effects of everolimus in combination with paclitaxel on adriamycin-resistant breast cancer cell line MDA-MB-231.

Taiwan J Obstet Gynecol 2020 Nov;59(6):828-834

Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China.

Objective: We aimed to evaluate the therapeutic effects of paclitaxel in combination with mTOR inhibitor everolimus on adriamycin-resistant breast cancer cell line MDA-MB-231 (MDA-MB-231/ADR).

Materials And Methods: MDA-MB-231/ADR cells were treated with different concentrations of paclitaxel and everolimus. The IC values after 48 h of treatment were measured by the MTT assay. The apoptosis rate and cell cycle were detected by flow cytometry. The protein expressions of Akt, PI3K, mTOR, p-pI3K, p-AKT and p-mTOR were detected by Western blot.

Results: When paclitaxel at ≥1.56 μg/ml was used, the growth of MDA-MB-231/ADR cells was inhibited more significantly than that of control group (P < 0.05). After treatment with ≥6.25 μg/ml everolimus, the cell growth was also suppressed more significantly (P < 0.05). The IC values of everolimus and paclitaxel were 32.50 μg/ml and 7.80 μg/ml, respectively. The inhibition rate of paclitaxel plus everolimus was significantly enhanced with increasing paclitaxel concentration (P < 0.001). After treatment with 7.80 μg/ml paclitaxel, the two drugs had best synergistic inhibitory effects on proliferation. Compared with drugs alone, the combination significantly promoted apoptosis (P < 0.001). The paclitaxel + everolimus group had significantly more cells in the G0-G1 phase than those of control and individual drug groups (P < 0.001). Everolimus significantly decreased mTOR and p-mTOR expressions compared with those of control group (P < 0.001). Compared with everolimus alone, the combination reduced the expressions more significantly (P < 0.05). Paclitaxel decreased the expression levels of PI3K, p-PI3K and p-AKT. Compared with paclitaxel alone, the combination significantly promoted the reduction of PI3K, p-PI3K and p-AKT expressions (P < 0.05).

Conclusion: Everolimus can enhance the effect of paclitaxel on MDA-MB-231/ADR cells, inhibit cell proliferation, induce apoptosis and arrest cell cycle in the G1 phase mainly by down-regulating the expressions of key proteins in the mTOR signaling pathway.
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http://dx.doi.org/10.1016/j.tjog.2020.09.008DOI Listing
November 2020

Double-bundle anterior cruciate ligament reconstruction technique has advantages in chondroprotection and knee laxity control compared with single-bundle technique : A long-term follow-up with a minimum of 12 years.

Knee Surg Sports Traumatol Arthrosc 2020 Nov 20. Epub 2020 Nov 20.

Department of Sports Medicine, Peking University Third Hospital, Beijing, China.

Purpose: To compare the long-term clinical outcomes of single-bundle anterior cruciate ligament reconstruction (SBR) and double-bundle anterior cruciate ligament reconstruction (DBR) in patients with isolated anterior cruciate ligament (ACL) rupture, presenting no meniscus injury and no obvious preoperative cartilage degeneration.

Methods: One hundred and three patients (38.6 ± 9.5 years) with a median follow-up of 151.6 months (range, 144-189 months) completed the retrospective study (SBR group: n = 51; DBR group: n = 52). Clinical outcomes were evaluated with physical examinations, KT-2000 anterior and posterior stability measurement with the knee in 30º of flexion, International Knee Documentation Committee (IKDC) subjective score, Tegner score, Lysholm score; magnetic resonance imaging (MRI) (3.0 T) was performed, and International Cartilage Repair Society (ICRS) cartilage degeneration grades were determined. Multivariate analysis was performed to identify factors associated with cartilage degeneration.

Results: There were significant differences in the pre- and postoperative IKDC, Lysholm and Tegner scores between the SBR and DBR groups. The SBR group had over double the rate of positive pressure/rub patellar test results (SBR vs DBR, 43.1% vs. 19.2%, p < 0.011). The KT-2000, pivot-shift and Lachman test results were stratified and analyzed, and significant differences between the SBR and DBR groups were found (p < 0.05, respectively). The distribution of ICRS grades differed significantly between the groups at the last follow-up (p = 0.013). A multivariate analysis found that age and operation procedures were significant predictors of 0 and non-0 ICRS grades (odds ratio, 6.077 [95% CI 2.117-17.447] and 0.210 [95% CI 0.068-0.654], respectively) (p < 0.05).

Conclusion: Both SBR and DBR achieved overall good long-term results. DBR had advantages in objective outcome measures and was superior in preventing the occurrence of cartilage degeneration. Age was identified as a preoperative risk factor for significant postoperative cartilage degeneration.

Level Of Evidence: III. ClinicalTrials.gov: NCT03984474.
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http://dx.doi.org/10.1007/s00167-020-06350-5DOI Listing
November 2020

Molecular targeting therapies for neuroblastoma: Progress and challenges.

Med Res Rev 2021 03 6;41(2):961-1021. Epub 2020 Nov 6.

Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas, USA.

There is an urgent need to identify novel therapies for childhood cancers. Neuroblastoma is the most common pediatric solid tumor, and accounts for ~15% of childhood cancer-related mortality. Neuroblastomas exhibit genetic, morphological and clinical heterogeneity, which limits the efficacy of existing treatment modalities. Gaining detailed knowledge of the molecular signatures and genetic variations involved in the pathogenesis of neuroblastoma is necessary to develop safer and more effective treatments for this devastating disease. Recent studies with advanced high-throughput "omics" techniques have revealed numerous genetic/genomic alterations and dysfunctional pathways that drive the onset, growth, progression, and resistance of neuroblastoma to therapy. A variety of molecular signatures are being evaluated to better understand the disease, with many of them being used as targets to develop new treatments for neuroblastoma patients. In this review, we have summarized the contemporary understanding of the molecular pathways and genetic aberrations, such as those in MYCN, BIRC5, PHOX2B, and LIN28B, involved in the pathogenesis of neuroblastoma, and provide a comprehensive overview of the molecular targeted therapies under preclinical and clinical investigations, particularly those targeting ALK signaling, MDM2, PI3K/Akt/mTOR and RAS-MAPK pathways, as well as epigenetic regulators. We also give insights on the use of combination therapies involving novel agents that target various pathways. Further, we discuss the future directions that would help identify novel targets and therapeutics and improve the currently available therapies, enhancing the treatment outcomes and survival of patients with neuroblastoma.
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http://dx.doi.org/10.1002/med.21750DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7906923PMC
March 2021

MeCas12a, a Highly Sensitive and Specific System for COVID-19 Detection.

Adv Sci (Weinh) 2020 Sep 23:2001300. Epub 2020 Sep 23.

Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China.

Cas12a-based systems, which detect specific nucleic acids via collateral cleavage of reporter DNA, display huge potentials for rapid diagnosis of infectious diseases. Here, the Manganese-enhanced Cas12a (MeCas12a) system is described, where manganese is used to increase the detection sensitivity up to 13-fold, enabling the detection of target RNAs as low as five copies. MeCas12a is also highly specific, and is able to distinguish between single nucleotide polymorphisms (SNPs) differing by a single nucleotide. MeCas12a can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples and distinguish between SARS-CoV-2 and Middle East respiratory syndrome coronavirus (MERS-CoV) RNA in simulated samples, thus offering an attractive alternative to other methods for the diagnosis of infectious diseases including COVID-19 and MERS.
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http://dx.doi.org/10.1002/advs.202001300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536916PMC
September 2020

Picroside II alleviates liver injury induced by alpha-naphthylisothiocyanate through AMPK-FXR pathway.

Toxicol Appl Pharmacol 2020 12 22;408:115248. Epub 2020 Sep 22.

School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, Jiangsu, China. Electronic address:

Alpha-naphthylisothiocyanate (ANIT) is a typical hepatotoxicant that causes cholestasis, which causes toxic bile acid accumulation in the liver and leads to liver injury. Picroside II (PIC), one of the dominant effective components extracted from Picrorhiza scrophulariiflora Pennell, exhibits many pharmacological effects. However, the role of AMP-activated protein kinase (AMPK)-Farnesoid X receptor (FXR) pathway in the hepatoprotective effect of PIC against ANIT-induced cholestasis remains largely unknown. This study aimed to investigate the mechanisms of PIC on ANIT-induced cholestasis in vivo and in vitro. Our results showed that PIC protected against ANIT-induced liver injury in primary mouse hepatocytes, and decreased serum biochemical markers and lessened histological injuries in mice. ANIT inhibited FXR and its target genes of bile acid synthesis enzymes sterol-12α-hydroxylase (CYP8B1), and increase bile acid uptake transporter Na + -dependent taurocholate transporter (NTCP), efflux transporter bile salt export pump (BSEP) and bile acid metabolizing enzymes UDP-glucuronosyltransferase 1a1 (UGT1A1) expressions. PIC prevented its downregulation of FXR, NTCP, BSEP and UGT1A1, and further reduced CYP8B1 by ANIT. Furthermore, ANIT activated AMPK via ERK1/2-LKB1 pathway. PIC inhibited ERK1/2, LKB1 and AMPK phosphorylation in ANIT-induced cholestasis in vivo and in vitro. AICAR, an AMPK agonist, blocked PIC-mediated changes in FXR, CYP8B1 and BSEP expression in vitro. Meanwhile, U0126, an ERK1/2 inhibitor, further repressed ERK1/2-LKB1-AMPK pathway phosphorylation. In conclusion, PIC regulated bile acid-related transporters and enzymes to protect against ANIT-induced liver injury, which related to ERK1/2-LKB1-AMPK pathway. Thus, this study extends the understanding of the anti-cholestasis effect of PIC and provides new therapeutic targets for cholestasis treatment.
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http://dx.doi.org/10.1016/j.taap.2020.115248DOI Listing
December 2020

A review of microplastics aggregation in aquatic environment: Influence factors, analytical methods, and environmental implications.

J Hazard Mater 2021 01 16;402:123496. Epub 2020 Jul 16.

Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China. Electronic address:

A large amount of plastic waste released into natural waters and their demonstrated toxicity have made the transformation of microplastics (MPs; < 5 mm) and nanoplastics (NPs; < 100 nm) an emerging environmental concern. Aggregation is one of the most important environmental behaviors of MPs, especially in aquatic environments, which determines the mobility, distribution and bioavailability of MPs. In this paper, the sources and inputs of MPs in aquatic environments were first summarized followed by the analytical methods for investigating MP aggregation, including the sampling, visualization, and quantification procedures of MP' particle sizes. We critically evaluated the sampling methods that still remains a methodological gap. Identification and quantification of MPs were mostly carried out by visual, spectroscopic and spectrometric techniques, and modeling analysis. Important factors affecting MP aggregation in natural waters and environmental implications of the aggregation process were also reviewed. Finally, recommendations for future research were discussed, including (1) conducting more field studies; (2) using MPs in laboratory works representing those in the environment; and (3) standardizing methods of identification and quantification. The review gives a comprehensive overview of current knowledge for MP aggregation in natural waters, identifies knowledge gaps, and provides suggestions for future research.
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http://dx.doi.org/10.1016/j.jhazmat.2020.123496DOI Listing
January 2021

Next-generation pathogen diagnosis with CRISPR/Cas-based detection methods.

Emerg Microbes Infect 2020 Dec;9(1):1682-1691

School of Life Science and Technology, ShanghaiTech University, Shanghai, People's Republic of China.

Ideal methods for detecting pathogens should be sensitive, specific, rapid, cost-effective and instrument-free. Conventional nucleic acid pathogen detection strategies, mostly PCR-based techniques, have various limitations, such as expensive equipment, reagents and skilled performance. Recently, CRISPR/Cas-based methods have burst onto the scene, with the potential to power the pathogen detection field. Here we introduce these unique methods and discuss its hurdles and promises.
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http://dx.doi.org/10.1080/22221751.2020.1793689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7473117PMC
December 2020

miR-301a Suppression within Fibroblasts Limits the Progression of Fibrosis through the TSC1/mTOR Pathway.

Mol Ther Nucleic Acids 2020 Sep 26;21:217-228. Epub 2020 May 26.

National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China. Electronic address:

Pulmonary fibrosis has been characterized by abnormal proliferation of fibroblasts and massive deposition of the extracellular matrix, which results from a complex interplay of chronic injury and inflammatory responses. MicroRNA-301a (miR-301a) is activated by multiple inflammatory stimulators, contributing to multiple tumorigenesis and autoimmune diseases. This study showed that miR-301a was overexpressed in a bleomycin-induced murine model of pulmonary fibrosis and patients with idiopathic pulmonary fibrosis (IPF). In addition, miR-301a was activated by transforming growth factor β (TGF-β) and interleukin 6 (IL-6) in normal and IPF fibroblasts, which was markedly reversed by the signal transducer and activator of transcription 3 (STAT3) inhibitor. The genetic ablation of miR-301a in mice reduced bleomycin-induced lung fibrosis, and the downregulation of miR-301a restrained proliferation and activation of fibroblasts. Furthermore, this study demonstrated that TSC1 was a functional target of miR-301a in fibroblasts, and the negative regulation of TSC1 by miR-301a promoted the severity of pulmonary fibrosis through the mammalian target of rapamycin (mTOR) signaling pathway. The blocking of miR-301a by the intravenous injection of antagomiR-301a inhibited the proliferation of fibroblasts and the structural destruction of lung tissues in the bleomycin-induced lung fibrosis mouse model. The findings revealed the crucial role of the miR-301a/TSC1/mTOR axis in the pathogenesis of pulmonary fibrosis, suggesting that miR-301a might serve as a potential therapeutic target.
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http://dx.doi.org/10.1016/j.omtn.2020.05.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7321782PMC
September 2020

Rapid and sensitive detection of COVID-19 using CRISPR/Cas12a-based detection with naked eye readout, CRISPR/Cas12a-NER.

Sci Bull (Beijing) 2020 Sep 5;65(17):1436-1439. Epub 2020 May 5.

State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou 510120, China.

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http://dx.doi.org/10.1016/j.scib.2020.04.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7198415PMC
September 2020

Comparison of gene disruption induced by cytosine base editing-mediated iSTOP with CRISPR/Cas9-mediated frameshift.

Cell Prolif 2020 May 29;53(5):e12820. Epub 2020 Apr 29.

Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.

Objectives: Recently developed CRISPR-dependent cytosine base editor (CBE), converting four codons (CAA, CAG, CGA and TGG) into stop codons without DNA double-strand breaks (DSB), serves as an efficient gene disruption strategy besides uncontrollable CRISPR-mediated frameshift. However, the detailed difference of gene knockout between the two systems has not been clarified.

Materials And Methods: Here, we selected some sgRNAs with different position background, then HEK293T cells were transfected with CBE/Cas9 plasmids together with sgRNAs. GFP-positive cells were harvested by fluorescence-activated cell sorting (FACS) 48 hours after transfection. Genomic DNA was collected for deep sequencing to analyse editing efficiency and genotype. RNA and protein were extracted to analyse gene mRNA level using qPCR analysis and Western blot.

Results: Here, we compared the gene disruption by CBE-mediated iSTOP with CRISPR/Cas9-mediated frameshift. We found BE-mediated gene knockout yielded fewer genotypes. BE-mediated gene editing precisely achieved silencing of two neighbouring genes, while CRISPR/Cas9 may delete the large fragment between two target sites. All of three stop codons could efficiently disrupt the target genes. It is worth notifying, Cas9-mediated gene knockout showed a more impact on neighbouring genes mRNA level than the BE editor.

Conclusions: Our results reveal the differences between the two gene knockout strategies and provide useful information for choosing the appropriate gene disruption strategy.
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http://dx.doi.org/10.1111/cpr.12820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7260061PMC
May 2020

WITHDRAWN: Porcine reproductive and respiratory syndrome virus (PRRSV) inhibition with engineered Cas13d.

J Genet Genomics 2020 Mar 17. Epub 2020 Mar 17.

State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100093, China; College of Biological Sciences, China Agricultural University, Beijing, 100093, China. Electronic address:

This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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http://dx.doi.org/10.1016/j.jgg.2020.02.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118647PMC
March 2020

Climate-zone-dependent effect mechanism of humic acid and fulvic acid extracted from river sediments on aggregation behavior of graphene oxide.

Sci Total Environ 2020 Jun 5;721:137682. Epub 2020 Mar 5.

State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, People's Republic of China.

Climate factors could affect the physicochemical properties of dissolved organic matter (DOM) in river sediments, which potentially influence the stability of nanoparticles in natural waters. In this study, we extracted humic acid (HA) and fulvic acid (FA) from river sediments in different climate zones of China. Their effect with different concentrations (0.2 and 1 mg·C·L) on the aggregation kinetics of large (589 nm) and small graphene oxide (GO, 200 nm) in NaCl solutions was investigated. Both concentrations of HA/FA significantly inhibited the aggregation of small GO because of the steric forces rendered by DOM. For large GO, the inhibition effect of HA on aggregation was higher than FA because of the higher molecular weight, longer carbon chain length, and more structure complexity of HA. Interestingly, with 0.2 mg·C·L HA and large GO, Makou in Subtropical monsoon climate zone decreased the aggregation rate more significantly due to its larger molecular weight, while, Maqin in the Plateau and mountain (PM) climate zone with smaller molecular weight and greater hydrophobicity showed lower inhibition effect on the aggregation. One mg·C·L FA with high polarity from Tangke in PM climate zone and Panjin from Temperate monsoon climate zone showed more stability ability towards large GO. Derjaguin-landau-verwey-overbeek (DLVO) theory indicated that the interaction energy barrier between GO particles dependent on physicochemical characteristics of DOM and GO size. Understanding the climate-zone-dependent effect of sediment DOM on stability of GO is essential for anticipating its fate in natural systems.
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http://dx.doi.org/10.1016/j.scitotenv.2020.137682DOI Listing
June 2020

Short-term effects of thinning on the development and communities of understory vegetation of Chinese fir plantations in Southeastern China.

PeerJ 2020 11;8:e8536. Epub 2020 Feb 11.

State Forestry Administration Key Laboratory of Forest Resources & Environmental Management, College of Forestry, Beijing Forestry University, Beijing, China.

Background: High-density conditions are global issues that threaten the sustainable management of plantations throughout the world. Monocultures and untimely management practices have identically resulted in the simplex of community structures, decreases in biodiversity, and long-term productivity losses in plantations China. The most popular measure which is commonly used to address these issues is thinning, which potentially results in increases in the development of understory plants in plantations. However, there is limited information currently available regarding the community composition of understory vegetation and the associated environmental factors, which has limited the sustainable management of China's fir plantation ecosystems.

Method: In the present study, a thinning experiment was implemented which included a control check (CK: no thinning), as well as low intensity thinning (LIT: 20%), moderate intensity thinning (MIT: 33%), and high intensity thinning (HIT: 50%) in Chinese fir plantations located in the Southeastern China. During the investigation process, the understory vegetation examined three years after thinning measures were completed, in order to analyze the impacts of different thinning intensities on the growth and community composition of the understory plants. At the same time, the associated environmental factors in the fir plantations were also investigated.

Results: The species richness, total coverage, and biomass of the understory vegetation were observed to be apparently increased with increasing thinning intensity. In addition, it was found that the thinning measures had prominently influenced the soil nutrients. The community compositions of the understory vegetation were significantly different among the four thinning intensity levels, especially between the CK and the HIT. Furthermore, the development of the understory vegetation was found to be significantly correlated with the soil nutrient contents, and the community compositions of the understory vegetation were prominently driven by the tree densities, slope positions, and soil nutrient contents.
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http://dx.doi.org/10.7717/peerj.8536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7020821PMC
February 2020

CRISPR/Cas12a technology combined with immunochromatographic strips for portable detection of African swine fever virus.

Commun Biol 2020 02 11;3(1):62. Epub 2020 Feb 11.

Animal Infectious Diseases Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510631, China.

African swine fever virus (ASFV), the aetiological agent of African swine fever (ASF), causes lethal haemorrhagic fever in domestic pigs with high mortality and morbidity and has devastating consequences on the global swine industry. On-site rapid and sensitive detection of ASFV is key to the timely implementation of control. In this study, we developed a rapid, sensitive and instrument-free ASFV detection method based on CRISPR/Cas12a technology and lateral flow detection (named CRISPR/Cas12a-LFD). The limit of detection of CRISPR/Cas12a-LFD is 20 copies of ASFV genomic DNA per reaction, and the detection process can be completed in an hour. The assay showed no cross-reactivity with other swine DNA viruses, and has 100% agreement with real-time PCR detection of ASFV in 149 clinical samples. Overall, the CRISPR/Cas12a-LFD method provides a novel alternative for the portable, simple, sensitive, and specific detection of ASFV and may contribute to the prevention and control of ASF outbreaks.
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http://dx.doi.org/10.1038/s42003-020-0796-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012833PMC
February 2020

Picroside II protects against cholestatic liver injury possibly through activation of farnesoid X receptor.

Phytomedicine 2020 Mar 16;68:153153. Epub 2019 Dec 16.

State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China; School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China. Electronic address:

Backgroud: Cholestasis, accompanied by the accumulation of bile acids in body, may ultimately cause liver failure and cirrhosis. There have been limited therapies for cholesteric disorders. Therefore, development of appropriate therapeutic drugs for cholestasis is required. Picroside II is a bioactive component isolated from Picrorhiza scrophulariiflora Pennell, its mechanistic contributions to the anti-cholestasis effect have not been fully elucidated, especially the role of picroside II on bile acid homeostasis via nuclear receptors remains unclear.

Purpose: This study was designed to investigate the hepatoprotective effect of picroside II against alpha-naphthylisothiocyanate (ANIT)-induced cholestatic liver injury and elucidate the mechanisms in vivo and in vitro.

Methods: The ANIT-induced cholestatic mouse model was used with or without picroside II treatment. Serum and bile biochemical indicators, as well as liver histopathological changes were examined. siRNA, Dual-luciferase reporter, quantitative real-time PCR and Western blot assay were used to demonstrate the farnesoid X receptor (FXR) pathway in the anti-cholestasis effects of picroside II in vivo and in vitro.

Results: Picroside II exerted hepatoprotective effect against ANIT-induced cholestasis by impaired hepatic function and tissue damage. Picroside II increased bile acid efflux transporter bile salt export pump (Bsep), uptake transporter sodium taurocholate cotransporting polypeptide (Ntcp), and bile acid metabolizing enzymes sulfate transferase 2a1 (Sult2a1) and UDP-glucuronosyltransferase 1a1 (Ugt1a1), whereas decreased the bile acid synthesis enzymes cholesterol 7α-hydroxylase (Cyp7a1) and oxysterol 12α-hydroxylase (Cyp8b1). In addition, expression of FXR and the target gene Bsep was increased, whereas aryl hydrocarbon receptor (AhR), pregnane X receptor (PXR), peroxisome proliferator-activated receptor alpha (PPARα) and their corresponding target genes were not significantly influenced by picroside II under cholestatic conditions. Furthermore, regulation of transporters and enzymes involved in bile acid homeostasis by picroside II were abrogated by FXR silencing in mouse primary cultured hepatocytes. Dual-luciferase reporter assay performed in HepG2 cells demonstrated FXR activation by picroside II.

Conclusion: Our findings demonstrate that picroside II exerts protective effect on ANIT-induced cholestasis possibly through FXR activation that regulates the transporters and enzymes involved in bile acid homeostasis. Picroside II might be an effective approach for the prevention and treatment of cholestatic liver diseases.
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http://dx.doi.org/10.1016/j.phymed.2019.153153DOI Listing
March 2020

Efficient Gene Silencing by Adenine Base Editor-Mediated Start Codon Mutation.

Mol Ther 2020 02 29;28(2):431-440. Epub 2019 Nov 29.

Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, Center for Studies of Psychological Application, South China Normal University, Guangzhou 510631, China. Electronic address:

Traditional CRISPR/Cas9-based gene knockouts are generated by introducing DNA double-strand breaks (DSBs), but this may cause excessive DNA damage or cell death. CRISPR-based cytosine base editors (CBEs) and adenine base editors (ABEs) can facilitate C-to-T or A-to-G exchanges, respectively, without DSBs. CBEs have been employed in a gene knockout strategy: CRISPR-STOP or i-STOP changes single nucleotides to induce in-frame stop codons. However, this strategy is not applicable for some genes, and the unwanted mutations in CBE systems have recently been reported to be surprisingly significant. As a variant, the ABE systems mediate precise editing and have only rare unwanted mutations. In this study, we implemented a new strategy to induce gene silencing (i-Silence) with an ABE-mediated start codon mutation from ATG to GTG or ACG. Using both in vitro and in vivo model systems, we showed that the i-Silence approach is efficient and precise for producing a gene knockout. In addition, the i-Silence strategy can be employed to analyze ~17,804 human genes and can be used to mimic 147 kinds of pathogenic diseases caused by start codon mutations. Altogether, compared to other methods, the ABE-based i-Silence method is a safer gene knockout strategy, and it has promising application potential.
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http://dx.doi.org/10.1016/j.ymthe.2019.11.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001054PMC
February 2020

Succession in arbuscular mycorrhizal fungi can be attributed to a chronosequence of Cunninghamia lanceolata.

Sci Rep 2019 12 2;9(1):18057. Epub 2019 Dec 2.

College of Forestry, Beijing Forestry University, Beijing, 100083, China.

Arbuscular mycorrhizal (AM) fungi play an important role in plant-fungi communities. It remains a central question of how the AM fungal community changes as plants grow. To establish an understanding of AM fungal community dynamics associated with Chinese fir, Chinese fir with five different growth stages were studied and 60 root samples were collected at the Jiangle National Forestry Farm, Fujian Province. A total of 76 AM fungal operational taxonomic units (OTUs) were identified by high-throughput sequencing on an Illumina Miseq platform. The genera covered by OTUs were Glomus, Archaeospora, Acaulospora, Gigaspora and Diversispora. Glomus dominated the community in the whole stage. The number and composition of OTUs varied along with the host plant growth. The number of OTUs showed an inverted V-shaped change with the host plant age, and the maximum occurred in 23-year. Overall, the basic species diversity and richness in this study were stable. Non-metric multi-dimensional scaling (NMDS) analysis based on bray-curtis distance revealed that there were remarkable differentiations between the 9-year and other stages. Besides, AM fungal community in 32-year had a significant difference with that of 23-year, while no significant difference with that of 45-year, suggesting that 32-year may be a steady stage for AM fungi associated with Chinese fir. The cutting age in 32-year may be the most favorable for microbial community. The pH, total N, total P, total K, available N, available P, available K, organic matter and Mg varied as the Chinese fir grows. According to Mantel test and redundancy analysis, available N, available P, K and Mg could exert significant influence on AM fungal communities, and these variables explained 31% of variance in the composition of AM fungal communities.
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http://dx.doi.org/10.1038/s41598-019-54452-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889488PMC
December 2019

Aggregation kinetics and mechanisms of silver nanoparticles in simulated pollution water under UV light irradiation.

Water Environ Res 2020 Jun 5;92(6):840-849. Epub 2019 Dec 5.

State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China.

This paper investigated the effect mechanism of complex components (fulvic acid [FA], sodium dodecylbenzene sulfonate [SDBS], and sodium nitrate [NaNO ]) on the aggregation kinetics of polyvinylpyrrolidone-modified silver nanoparticles (PVP-AgNPs) under UV irradiation. The results showed that FA and NaNO alone did not cause aggregation due to the high steric hindrance and/or electrostatic repulsive forces. In high concentration of SDBS solution (20-50 mM), the stability of PVP-AgNPs was reduced by adsorbing SDBS on nanoparticle surface and replacing their PVP coatings. A mixed system of two pollutants had a synergistic effect on PVP-AgNPs aggregation. In the mixed system of SDBS and FA, the interaction of SDBS and PVP-AgNPs dominated the aggregation of PVP-AgNPs. NaNO significantly improved the aggregation rate of PVP-AgNPs in SDBS solution due to the charge neutralization effect of electrolyte. In 20 mg/L FA solution, the aggregation rate increased slightly with increasing NaNO concentration from 50 to 200 mM due to the charge neutralization effect, while the hydrodynamic diameters of PVP-AgNPs increased linearly and rapidly to micrometer size because the spatial conformation of adsorbed FA became compact in high-salinity solution. The calculation results of eDLVO theory were basically consistent with most of the experimental results. PRACTITIONER POINTS: PVP-AgNPs was uniformly dispersed in NaNO or FA solution under UV irradiation. PVP-AgNPs formed aggregates in SDBS solutions under UV irradiation. A system with two mixed pollutants had a synergistic effect on promoting aggregation of PVP-AgNPs. eDLVO theory could explain the aggregation results in different chemical conditions except in NaNO solution.
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http://dx.doi.org/10.1002/wer.1276DOI Listing
June 2020

Development and validation of a novel 29-plex Y-STR typing system for forensic application.

Forensic Sci Int Genet 2020 01 1;44:102169. Epub 2019 Oct 1.

Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai 200063, China. Electronic address:

Short tandem repeat within the male-specific part of the human Y chromosome (Y-STR) is an effective forensic tool in mixture identification, patrilineal relationship evaluation, and familial searches. Despite their usefulness, current Y-STR-based genotyping systems often lack the discriminatory power to resolve genetic relationships between distant relatives or within patrilocal populations. In this study, we developed a novel Y-STR 29-plex typing system, which combined the 17 Y-STR loci used in the AmpFLSTR® Yfiler® PCR Amplification Kit (Yfiler), eight Y-STR loci with a low-medium mutation rate, and four rapidly mutating Y-STR loci. The system was generated to achieve greater discriminatory power between male subjects and improved ability to infer haplogroup classifications. The system was extensively tested on data from 752 individuals for its sensitivity, male specificity, species specificity, mixture resolution, reproducibility, concordance, stutter and size accuracy, precision, and population genetics, following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The results demonstrated that the Y-STR 29-plex typing system was time-efficient, reproducible, accurate, sensitive, and robust to familial searching and paternal biogeographic ancestry inference.
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http://dx.doi.org/10.1016/j.fsigen.2019.102169DOI Listing
January 2020

Transcriptome sequencing of a toxic dinoflagellate, Karenia mikimotoi subjected to stress from solar ultraviolet radiation.

Harmful Algae 2019 09 24;88:101640. Epub 2019 Jul 24.

Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China. Electronic address:

Solar ultraviolet radiation (UVR) is a stress factor in aquatic environments and may act directly or indirectly on orgnisms in the upper layers of the water column. However, UVR effects are usually species-specific and difficult to extrapolate. Here we use the HAB-forming, toxic dinoflagellate Karenia mikimotoi (which was found to be relatively resistant in previous studies) to investigate its transcriptional responses to a one-week UVR exposure. For this, batch cultures of K. mikimotoi were grown with and without UVR, and their transcriptomes (generated via RNAseq technology) were compared. RNA-seq generated 45.31 million reads, which were further assembled to 202600 unigenes (>300bp). Among these, ca. 61% were annotated with NCBI, NR, GO, KOG, PFAM, Swiss-Prot, and KEGG database. Transcriptomic analysis revealed 722 differentially expressed unigenes (DEGs, defined as being within a |log2 fold change| ≥ 2 and padj < 0.05) responding to solar UVR, which were only 0.36% of all unigenes. 716 unigenes were down-regulated, and only 6 unigenes were up-regulated in the UVR compared to non-UVR treatment. KEGG pathway further analysis revealed DEGs were involved in the different pathway; genes involved in the ribosome, endocytosis and steroid biosynthesis pathways were highly down-regulated, but this was not the case for those involved in the energy metabolisms (including photosynthesis, oxidative phosphorylation) which may contribute to the sustainable growth observed in UVR treatment. The up-regulated expression of both zinc-finger proteins (ZFPs) and ribosomal protein L11 (RPL11) may be one of the acclimated mechanisms against UVR. In addition, this work identified down-regulated genes involved in fatty acid degradation and the hydrophobic branched chain amino acids (e.g., Valine, leucine, and isoleucine), which act as structural components of cell membranes modulating lipid homeostasis or turnover. In conclusion, the present study suggests that the toxic dinoflagellate K. mikimotoi has limited transcriptomic regulation but confirms that it appears as a tolerant species in response to solar UVR. These findings expand current knowledge of gene expression in HAB-forming species in response to natural environment factors such as solar radiation.
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http://dx.doi.org/10.1016/j.hal.2019.101640DOI Listing
September 2019
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