Publications by authors named "Jing Tu"

93 Publications

Cardiac Troponin I association with critical illness and death risk in 726 seriously ill COVID-19 patients: A retrospective cohort study.

Int J Med Sci 2021 29;18(6):1474-1483. Epub 2021 Jan 29.

Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University, Beijing 100191, China.

For coronavirus disease 2019 (COVID-19), early identification of patients with serious symptoms at risk of critical illness and death is important for personalized treatment and balancing medical resources. Demographics, clinical characteristics, and laboratory tests data from 726 patients with serious COVID-19 at Tongji Hospital (Wuhan, China) were analyzed. Patients were classified into critical group (n = 174) and severe group (n= 552), the critical group was sub-divided into survivors (n = 47) and non-survivors (n = 127). Multivariable analyses revealed the risk factors associated with critical illness in serious patients were: Advanced age, high respiratory rate (RR), high lactate dehydrogenase (LDH) level, high hypersensitive cardiac troponin I (hs-cTnI) level, and thrombocytopenia on admission. High hs-cTnI level was the independent risk factor of mortality among critically ill patients in the unadjusted and adjusted models. ROC curves demonstrated that hs-cTnI and LDH were predictive factors for critical illness in patients with serious COVID-19 whereas procalcitonin and D-Dimer with hs-cTnI and LDH were predictive parameters in mortality risk. Advanced age, high RR, LDH, hs-cTnI, and thrombocytopenia, constitute risk factors for critical illness among patients with serious COVID-19, and the hs-cTnI level helps predict fatal outcomes in critically ill patients.
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http://dx.doi.org/10.7150/ijms.53641DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893554PMC
January 2021

Magnesium Calcium Phosphate Cement Incorporating Citrate for Vascularized Bone Regeneration.

ACS Biomater Sci Eng 2020 Nov 13;6(11):6299-6308. Epub 2020 Oct 13.

State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Biomedical Materials and Engineering Research Center of Hubei Province, Wuhan University of Technology, Wuhan 430070, China.

The development of bioactive bone cement is still a challenge for vascularized bone regeneration. Citrate participated in multiple biological processes, such as energy metabolism, osteogenesis, and angiogenesis. However, it is difficult to obtain a thorough and comprehensive understanding on osteogenic effects of exogenous citrate from different experimental conditions and treatment methods. In this study, by using a magnesium calcium phosphate cement (MCPC) matrix, we investigated the dual effect of exogenous citrate on osteogenesis and angiogenesis. Our studies show that citrate elevates the osteogenic function of osteoblasts under low doses and the angiogenic function of vascular endothelial cells under a broader dose range. These findings furnish a new strategy for regulating angiogenesis and osteogenic differentiation by administration of citrate in MCPC, driving the development of bioactive bone repair materials.
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http://dx.doi.org/10.1021/acsbiomaterials.0c00929DOI Listing
November 2020

Magnesium Calcium Phosphate Cement Incorporating Citrate for Vascularized Bone Regeneration.

ACS Biomater Sci Eng 2020 Nov 13;6(11):6299-6308. Epub 2020 Oct 13.

State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Biomedical Materials and Engineering Research Center of Hubei Province, Wuhan University of Technology, Wuhan 430070, China.

The development of bioactive bone cement is still a challenge for vascularized bone regeneration. Citrate participated in multiple biological processes, such as energy metabolism, osteogenesis, and angiogenesis. However, it is difficult to obtain a thorough and comprehensive understanding on osteogenic effects of exogenous citrate from different experimental conditions and treatment methods. In this study, by using a magnesium calcium phosphate cement (MCPC) matrix, we investigated the dual effect of exogenous citrate on osteogenesis and angiogenesis. Our studies show that citrate elevates the osteogenic function of osteoblasts under low doses and the angiogenic function of vascular endothelial cells under a broader dose range. These findings furnish a new strategy for regulating angiogenesis and osteogenic differentiation by administration of citrate in MCPC, driving the development of bioactive bone repair materials.
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http://dx.doi.org/10.1021/acsbiomaterials.0c00929DOI Listing
November 2020

Rapid droplet multiple displacement amplification based on the droplet regeneration strategy.

Anal Chim Acta 2021 Jan 19;1141:173-179. Epub 2020 Oct 19.

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China. Electronic address:

Multiple displacement amplification (MDA) is a popular whole genome amplification method for its simplicity and high coverage on whole genome DNA. Yet it suffers from uneven magnification and long reaction time. Here we present the cyclical concentration adjusting concept to speed up MDA and realize the droplet dilution steps with a novel droplet re-generation strategy. The increased initial concentration shortened inefficient time and the repeated high-speed period maintained the reaction efficient for long. This rapid droplet MDA method could save more than 1/2 of the total reaction time and exhibited higher accuracy than the conventional method. The cyclical concentration adjusting method alters nothing but the concentration of reactants in different periods of reaction. Therefore, it may be widely utilized to accelerating MDA-like time-consuming reactions without concerns of compatibility.
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http://dx.doi.org/10.1016/j.aca.2020.10.031DOI Listing
January 2021

Citrate regulates extracellular matrix mineralization during osteoblast differentiation in vitro.

J Inorg Biochem 2021 Jan 8;214:111269. Epub 2020 Oct 8.

State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Biomedical Materials and Engineering Research Center of Hubei Province, Wuhan University of Technology, Wuhan 430070, China.

The extremely high levels of citrate in bone highlight its important role, which must be involved in some essential functional or structural role that is required for the development and maintenance of normal bone. However, biomineralization researches have emphasized the interaction between the citrate and inorganic minerals during crystallization in cell-free systems. It is difficult to obtain a thorough and comprehensive understanding from cell-free experimental conditions and treatment methods. In this study, by proposing an osteoblast mineralization experimental model, we explored the regulation of citrate on bone apatite crystal structure. Our studies show that citrate stabilizes two precursors and then inhibits their transformation into hydroxyapatite. Concomitantly, the smaller size and lower crystallinity mineral deposition emerge during citrate-mediated osteogenic mineralization. These findings may provide a new perspective for the mechanism of osteogenic mineralization and a basis for further understanding of bone metabolism.
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http://dx.doi.org/10.1016/j.jinorgbio.2020.111269DOI Listing
January 2021

Predictive indicators of severe COVID-19 independent of comorbidities and advanced age: a nested case-control study.

Epidemiol Infect 2020 10 14;148:e255. Epub 2020 Oct 14.

Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China.

To determine what exacerbate severity of the COVID-19 among patients without comorbidities and advanced age and investigate potential clinical indicators for early surveillance, we adopted a nested case-control study, design in which severe cases (case group, n = 67) and moderate cases (control group, n = 67) of patients diagnosed with COVID-19 without comorbidities, with ages ranging from 18 to 50 years who admitted to Wuhan Tongji Hospital were matched based on age, sex and BMI. Demographic and clinical characteristics, and risk factors associated with severe symptoms were analysed. Percutaneous oxygen saturation (SpO2), lymphocyte counts, C-reactive protein (CRP) and IL-10 were found closely associated with severe COVID-19. The adjusted multivariable logistic regression analyses revealed that the independent risk factors associated with severe COVID-19 were CRP (OR 2.037, 95% CI 1.078-3.847, P = 0.028), SpO2 (OR 1.639, 95% CI 0.943-2.850, P = 0.080) and lymphocyte (OR 1.530, 95% CI 0.850-2.723, P = 0.148), whereas the changes exhibited by indicators influenced incidence of disease severity. Males exhibited higher levels of indicators associated with inflammation, myocardial injury and kidney injury than the females. This study reveals that increased CRP levels and decreased SpO2 and lymphocyte counts could serve as potential indicators of severe COVID-19, independent of comorbidities, advanced age and sex. Males could at higher risk of developing severe symptoms of COVID-19 than females.
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http://dx.doi.org/10.1017/S0950268820002502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642916PMC
October 2020

The psychological status of 8817 hospital workers during COVID-19 Epidemic: A cross-sectional study in Chongqing.

J Affect Disord 2020 Nov 19;276:555-561. Epub 2020 Jul 19.

Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, China; Mental Health Center, University-Town Hospital of Chongqing Medical University, China. Electronic address:

Background: There was an outbreak of COVID-19 towards the end of 2019 in China, which spread all over the world rapidly. The Chinese healthcare system is facing a big challenge where hospital workers are experiencing enormous psychological pressure. This study aimed to (1) investigate the psychological status of hospital workers and (2) provide references for psychological crisis intervention in the future.

Method: An online survey was conducted to collect sociodemographic features, epidemic-related factors, results of PHQ-9, GAD-7, PHQ-15, suicidal and self-harm ideation (SSI), and the score of stress and support scales. Chi-square test, t-test, non-parametric, and logistic regression analysis were used to detect the risk factors to psychological effect and SSI.

Results: 8817 hospital workers participated in this online survey. The prevalence of depression, anxiety, somatic symptoms, and SSI were 30.2%, 20.7%, 46.2%, and 6.5%, respectively. Logistic regression analysis showed that female, single, Tujia minority, educational background of junior or below, designated or county hospital, need for psychological assistance before or during the epidemic, unconfident about defeating COVID-19, ignorance about the epidemic, willingness of attending parties, and poor self-rated health condition were independent factors associated with high-level depression, somatic symptom, and SSI among hospital workers (P<0.05).

Limitations: This cross-sectional study cannot reveal the causality, and voluntary participation could be prone to selection bias. A modified epidemic-related stress and support scale without standardization was used. The number of hospital workers in each hospital was unavailable.

Conclusion: There were a high level of psychological impact and SSI among hospital workers, which needed to be addressed. County hospital workers were more severe and easier to be neglected. More studies on cognitive and behavioral subsequence after a public health disaster among hospital workers are needed.
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http://dx.doi.org/10.1016/j.jad.2020.07.092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7369013PMC
November 2020

Molecular dynamics discrimination of the conformational states of calmodulin through solid-state nanopores.

Phys Chem Chem Phys 2020 Sep 19;22(34):19188-19194. Epub 2020 Aug 19.

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.

As a type of biological macromolecule, the conformation of proteins dynamically changes in a solution, which often results in a change in their function. However, traditional biological assays have significant drawbacks in detecting the conformation properties of proteins. Alternatively, nanopores have potential advantages in this area, which can detect protein in high throughput and without labelling. Herein, we investigated the translocation of calmodulins through silicon nitride nanopores using molecular dynamics (MD) simulation. Initially, the calmodulins were fixed in the nanopore. Distinguished blocked ionic currents were obtained between the two forms of calmodulin. Next, in the translocation simulations, a prominent difference in time resolution was easily found between the two states of calmodulin by using the appropriate voltage and comparable size of pore to protein, r/r→ 1, 4.5 nm (where r is the protein radius and r is the gyration radius). These simulations on the nanoscale are helpful for developing Ca-sensitive ion channels and nanodevices.
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http://dx.doi.org/10.1039/d0cp02500cDOI Listing
September 2020

Application of Solid-State Nanopore in Protein Detection.

Int J Mol Sci 2020 Apr 17;21(8). Epub 2020 Apr 17.

State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.

A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks.
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http://dx.doi.org/10.3390/ijms21082808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7215903PMC
April 2020

Microfluidic Systems Applied in Solid-State Nanopore Sensors.

Micromachines (Basel) 2020 Mar 23;11(3). Epub 2020 Mar 23.

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.

Microfluidic system, as a kind of miniature integrated operating platform, has been applied to solid-state nanopore sensors after many years of experimental study. In the process of introducing microfluidic into solid-state nanopore sensors, many novel device structures are designed due to the abundance of analytes and the diversity of detection methods. Here we review the fundamental setup of nanopore-based microfluidic systems and the developments and advancements that have been taking place in the field. The microfluidic systems with a multichannel strategy to elevate the throughput and efficiency of nanopore sensors are then presented. Multifunctional detection represented by optical-electrical detection, which is realized by microfluidic integration, is also described. A high integration microfluidic system with nanopore is further discussed, which shows the prototype of commercialization.
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http://dx.doi.org/10.3390/mi11030332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142662PMC
March 2020

Microfluidic Technologies for cfDNA Isolation and Analysis.

Micromachines (Basel) 2019 Oct 3;10(10). Epub 2019 Oct 3.

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.

Cell-free DNA (cfDNA), which promotes precision oncology, has received extensive concern because of its abilities to inform genomic mutations, tumor burden and drug resistance. The absolute quantification of cfDNA concentration has been proved as an independent prognostic biomarker of overall survival. However, the properties of low abundance and high fragmentation hinder the isolation and further analysis of cfDNA. Microfluidic technologies and lab-on-a-chip (LOC) devices provide an opportunity to deal with cfDNA sample at a micrometer scale, which reduces required sample volume and makes rapid isolation possible. Microfluidic platform also allow for high degree of automation and high-throughput screening without liquid transfer, where rapid and precise examination and quantification could be performed at the same time. Microfluidic technologies applied in cfDNA isolation and analysis are limited and remains to be further explored. This paper reviewed the existing and potential applications of microfluidic technologies in collection and enrichment of cfDNA, quantification, mutation detection and sequencing library construction, followed by discussion of future perspectives.
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http://dx.doi.org/10.3390/mi10100672DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6843514PMC
October 2019

Obtaining Genome Sequences of Mutualistic Bacteria in Single Colonies.

Int J Mol Sci 2019 Oct 11;20(20). Epub 2019 Oct 11.

State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.

Cells of are associated with heterotrophic bacteria and organized in colonies in natural environment, which are basic elements in the mass occurrence of cyanobacterial species. Analyzing these colonies by using metagenomics is helpful to understand species composition and relationship. Meanwhile, the difference in population abundance among colonies could be used to recover genome bins from metagenome assemblies. Herein, we designed a pipeline to obtain high-quality genomes of mutualistic bacteria from single natural colonies. Single colonies were lysed, and then amplified by using multiple displacement amplification to overcome the DNA quantity limit. A two-step assembly was performed after sequencing and scaffolds were grouped into putative bins based on their differential-coverage among species. We analyzed six natural colonies of three prevailing species from Lake Taihu. Clustering results proved that colonies of the same species were similar in the microbial community composition. Eight putative population genome bins with wide bacterial diversity and different GC content were identified based on coverage difference among colonies. At the phylum level, proteobacteria was the most abundant besides cyanobacteria. Six of the population bins were further refined into nearly complete genomes (completeness > 90%).
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http://dx.doi.org/10.3390/ijms20205047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829522PMC
October 2019

Deficient IL-2 Produced by Activated CD56 T Cells Contributes to Impaired NK Cell-Mediated ADCC Function in Chronic HIV-1 Infection.

Front Immunol 2019 16;10:1647. Epub 2019 Jul 16.

Department of Microbiology and Infectious Disease Center School of Basic Medical Sciences, Peking University, Beijing, China.

Antibody-dependent cellular cytotoxicity (ADCC), which mainly mediated by natural killer (NK) cells, may play a critical role in human immunodeficiency virus type-1 (HIV-1) disease progression. However, the potential mechanisms that affecting NK-mediated ADCC response are still not well-elucidated. Antigen-antibody complex model of Ab-opsonized P815 cells was adopted to induce a typical non-specific ADCC response. The capacities of HIV-1 specific NK-ADCC were measured by using the combination model of gp120 protein and plasma of HIV-1 elite controllers. The levels of plasma cytokine were measured by ELISA. Anti-IL-2 blocking antibody was used to analyze the impact of activated CD56 T cells on NK-ADCC response. IL-2, IL-15, IFN-α, and IFN-β could effectively enhance the non-specific and HIV-1-specific NK-ADCC responses. Compared with healthy controls, HIV-1-infected patients showed decreased plasma IL-2 levels, while no differences of plasma IFN-α, IL-15, and IFN-β were presented. IL-2 production was detected from CD56 T cells activated through antibody-dependent manner. The capability of NK-ADCC could be weakened by blocking IL-2 secretion from activated CD56 T cells. Although no difference of frequencies of CD56 T cells was found between HIV-1-infected patients and healthy controls, deficient IL-2 secretion from activated CD56 T were found in chronic HIV-1 infection. The impaired ability of activated CD56 T cells to secreting IL-2 might contribute to the attenuated NK cell-mediated ADCC function in HIV-1 infection.
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http://dx.doi.org/10.3389/fimmu.2019.01647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6648879PMC
October 2020

ChimeraMiner: An Improved Chimeric Read Detection Pipeline and Its Application in Single Cell Sequencing.

Int J Mol Sci 2019 Apr 21;20(8). Epub 2019 Apr 21.

State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.

As the most widely-used single cell whole genome amplification (WGA) approach, multiple displacement amplification (MDA) has a superior performance, due to the high-fidelity and processivity of phi29 DNA polymerase. However, chimeric reads, generated in MDA, cause severe disruption in many single-cell studies. Herein, we constructed ChimeraMiner, an improved chimeric read detection pipeline for analyzing the sequencing data of MDA and classified the chimeric sequences. Two datasets (MDA1 and MDA2) were used for evaluating and comparing the efficiency of ChimeraMiner and previous pipeline. Under the same hardware condition, ChimeraMiner spent only 43.4% (43.8% for MDA1 and 43.0% for MDA2) processing time. Respectively, 24.4 million (6.31%) read pairs out of 773 million reads, and 17.5 million (6.62%) read pairs out of 528 million reads were accurately classified as chimeras by ChimeraMiner. In addition to finding 83.60% (17,639,371) chimeras, which were detected by previous pipelines, ChimeraMiner screened 6,736,168 novel chimeras, most of which were missed by the previous pipeline. Applying in single-cell datasets, all three types of chimera were discovered in each dataset, which introduced plenty of false positives in structural variation (SV) detection. The identification and filtration of chimeras by ChimeraMiner removed most of the false positive SVs (83.8%). ChimeraMiner revealed improved efficiency in discovering chimeric reads, and is promising to be widely used in single-cell sequencing.
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http://dx.doi.org/10.3390/ijms20081953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6515389PMC
April 2019

Nanoscale Observation of Conformational Transformation of DNA Polymerase via Liquid-Cell Transmission Electron Microscopy.

J Biomed Nanotechnol 2019 May;15(5):1106-1111

In recent years, liquid-cell transmission electron microscopy (LC-TEM) has been developed as , dynamic characterization of nanoscale materials in the liquid, although the state-of-art focus is heavy materials such as metals, and alloys. Herein we present a practical and stable liquid cell fabricated with standard micro-electro-mechanical (MEM) processes on silicon wafers. The liquid cell is universal for commonly used TEM holder, which may not only keep the liquid available for several weeks, and it has been also proven protective factor from electron beam damage when characterizing biomolecules such as proteins and DNAs, which are typical light-element molecules. DNA polymerase has been successfully characterized in the physiological state (unlabeled in PBS buffer), providing single molecular resolution, the dynamic structural evolution of the molecules and the complex interactions. Although more understandings of this technique has to be explored in the future, as we have pointed out in the manuscript, this work has illustrated that the LC-TEM can also become a potential and promising strategy, besides to the cryo-TEM technique, in the high-resolution characterization of biomolecules, which may benefit relative researches and industry, such as molecular and structural biology, ecology, pharmacology and environmental sciences.
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http://dx.doi.org/10.1166/jbn.2019.2740DOI Listing
May 2019

Evaluating heteroplasmic variations of the mitochondrial genome from whole genome sequencing data.

Gene 2019 May 13;699:145-154. Epub 2019 Mar 13.

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. Electronic address:

Background: Detecting heteroplasmic variations in the mitochondrial genome can help identify potential pathogenic possibilities, which is significant for disease prevention. The development of next-generation sequencing changed the quantification of mitochondrial DNA (mtDNA) heteroplasmy from scanning limited recorded points to the entire mitochondrial genome. However, due to the presence of nuclear mtDNA homologous sequences (nuMTs), maximally retaining real variations while excluding falsest heteroplasmic variations from nuMTs and sequencing errors presents a dilemma.

Results: Herein, we used an improved method for detecting low-frequency mtDNA heteroplasmic variations from whole genome sequencing data, including point variations and short-fragment length alterations, and evaluated the effect of this method. A two-step alignment was designed and performed to accelerate data processing, to obtain and retain the true mtDNA reads and to eliminate most nuMTs reads. After analyzing whole genome sequencing data of K562 and GM12878 cells, ~90% of heteroplasmic point variations were identified in MitoMap. The results were consistent with the results of an amplification refractory mutation system qPCR. Many linkages of the detected heteroplasmy variations were also discovered.

Conclusions: Our improved method is a simple, efficient and accurate way to mine mitochondrial low-frequency heteroplasmic variations from whole genome sequencing data. By evaluating the highest misalignment possibility caused by the remaining nuMTs-like reads and sequencing errors, our procedure can detect mtDNA heteroplasmic variations whose heteroplasmy frequencies are as low as 0.2%.
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http://dx.doi.org/10.1016/j.gene.2019.03.016DOI Listing
May 2019

Advanced transferring of large-area freestanding graphene films by using fullerenes.

Nanotechnology 2019 Jun 5;30(26):26LT01. Epub 2019 Mar 5.

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, People's Republic of China.

Freestanding graphene films are desired to be widely applied in biosensor fabrication due to their distinctive physical properties and improved performance. Chemical vapor deposition has been developed to efficiently fabricate large-area graphene. However, some of the fabricated graphene films might break or be contaminated in the current transferring step using polymers. A stable and high-quality transfer method is needed. Herein, we report on an advanced transfer method of large-area graphene film which uses fullerene as a supporting substrate. Unlike polymers, which are commonly eliminated by being dissolved in an organic solution, fullerene can be easily removed by evaporation in a vacuum because it has a different heat stability to graphene. By using the improved transferring method, the percentage of integrated freestanding films after transferring was increased from 60.7% to 93.4%. The vacuum is beneficial in terms of keeping the brittle freestanding films intact. Graphene films transferred using fullerene showed an advanced flatness and a simplicial elementary composition in comparison to those transferred using polymers. Even through there is trace residue, this stable allotrope of graphene is considered to have almost no impact on biomolecule sensing. These advantages make the fullerene transferring method an attractive candidate for fabricating large-area freestanding graphene films, especially for using in the field of biochemistry analysis and biosensors.
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http://dx.doi.org/10.1088/1361-6528/ab0cabDOI Listing
June 2019

Landscape of somatic mutations in gastric cancer assessed using next-generation sequencing analysis.

Oncol Lett 2018 Oct 16;16(4):4863-4870. Epub 2018 Aug 16.

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, P.R. China.

Gastric cancer is a highly heterogeneous disease and the second leading cause of cancer-associated mortality. However, the genomic basis of gastric cancer is not completely understood and the underlying genetic heterogeneity has not been well studied. In the present study, 1,021 genes were sequenced and the somatic mutations of 45 formalin-fixed, paraffin-embedded gastric adenocarcinoma samples were assessed using next-generation sequencing technologies. In the present study, a median sequencing coverage depth of 708-fold was achieved. Somatic genomic alterations were detected in 37/45 patients (82.4%) and the most frequent genetic alterations identified were tumor protein P53 (TP53) gene mutations. Mutations in MLL4, ERBB3, FBXW7, MLL3, MTOR, NOTCH1, PIK3CA, KRAS, ERBB4 and EGFR were also detected. Patients with TP53 mutations had a higher number of somatic mutations, and the total number of somatic mutations was weakly correlated with patient age. These results provided data on the intratumoral heterogeneity of gastric cancer and may be used in order to develop personalized cancer therapy.
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http://dx.doi.org/10.3892/ol.2018.9314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6144630PMC
October 2018

Accurate and sensitive single-cell-level detection of copy number variations by micro-channel multiple displacement amplification (μcMDA).

Nanoscale 2018 Sep;10(37):17933-17941

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.

Whole genome amplification (WGA) has laid the foundation for investigating complex genomic alteration with single-cell or even single-molecule resolution. Coupled with sequencing-based copy number variation (CNV) analysis, it promotes understanding of the nature of commonly existing genetic heterogeneity by constructing the sequencing profiles for every single cell. However, prevailing methods only provide insights into limited aspects due to their intrinsic technical challenges. Their output data, as a result, fails to render comprehensive information (which is) concerned. Here, we describe the CNV detection analysis based on micro-channel multiple displacement amplification (μcMDA), a protocol able to provide optimized amplification uniformity while inheriting the advantages of MDA chemistry. We demonstrate the analysis of both the normal diploid YH-1 cell line and the aneuploid K562 cancer cell line. In the detection of simulated CNVs ranging from 300 kb to 2 Mb, μcMDA can respectively increase the detection rates of copy number loss and gain by 28.8% and 40.2% on average, using only 0.2× sequencing data. When detecting the inherent CNVs in tumor cells, the resolution of CNV recognition can be improved to 250 kb. Starting from either superabundant template copies or minute single-cell-level input, this easily accessible approach is capable of providing quantitatively reliable coverage as well as more robust GC-content regression for CNV detection.
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http://dx.doi.org/10.1039/c8nr04917cDOI Listing
September 2018

Molecular inhibitory mechanism study on the potent inhibitor brigatinib against four crizotinib-resistant ALK mutations.

J Cell Biochem 2019 01 6;120(1):562-574. Epub 2018 Sep 6.

College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, China.

As a potent and selective drug, brigatinib exhibits high efficacy against wild-type and mutant anaplastic lymphoma kinase (ALK) proteins to treat non-small cell lung cancer. In this work, the mechanisms of brigatinib binding to wild type and four mutant ALKs were investigated to gain insight into the dynamic energetic and structural information with respect to the design of novel inhibitors. Comparison between ALK-brigatinib and ALK-crizotinib suggests that the scaffold of brigatinib is well anchored to the residue Met1199 of hinge region by two hydrogen bonds, and the residue Lys1150 has the strong electrostatic interaction with the dimethylphosphine oxide moiety in brigatinib. These ALK mutations have significant influences on the flexibility of P-loop region and DFG sequences, but do not impair the hydrogen bonds between brigatinib and the residue Met1199 of hinge region. And mutations (L1196M, G1269A, F1174L, and R1275Q) induce diverse conformational changes of brigatinib and the obvious energy variation of residues Glu1167, Arg1209, Asp1270, and Asp1203. Together, the detailed explanation of mechanisms of those mutations with brigatinib further provide several guidelines for the development of more effective ALK inhibitors.
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http://dx.doi.org/10.1002/jcb.27412DOI Listing
January 2019

The complete mitochondrial genome sequence of .

Mitochondrial DNA B Resour 2018 Aug 9;3(2):896-897. Epub 2018 Aug 9.

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing,China.

() is a wild relative of Arabidopsis, occurring in mostly montane regions of western North America. In this article, we assembled the complete mitochondrial (mt) DNA sequence of into a circular genome of length 271,601 bp, including 31 protein-coding genes, 21 tRNA genes, and 3 rRNA genes. From the neighbour-joining phylogenetic tree was constructed, based on the 23 conserved protein-coding genes of and other 23 plant species, and the phylogenic relationship and evolution position of were determined. The complete mt genome would be useful for further investigation of the genotype-by-environment interactions in mitochondria of .
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http://dx.doi.org/10.1080/23802359.2018.1501323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800680PMC
August 2018

Molecular mechanism study of several inhibitors binding to BRD9 bromodomain based on molecular simulations.

J Biomol Struct Dyn 2019 Jul 13;37(11):2970-2979. Epub 2018 Nov 13.

a College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou , P. R. China.

Bromodomain-containing protein 9 (BRD9) has been employed as a potential target for anticancer drugs in recent years. In this work, molecular docking, molecular dynamics (MD) simulations, binding free energy calculations, and per residue energy decomposition approaches were performed to elucidate the different binding modes between four pyridinone-like scaffold inhibitors and BRD9 bromodomain. Analysis results indicate that non-polar contribution mainly deriving from van der Waals energy is a critical impact on binding affinity of inhibitors against BRD9. Some key residues Phe44, Phe47, Val49, and Ile53 (at ZA loop) enhance the binding energy of inhibitors in BRD9 by means of providing hydrophobic interactions. Moreover, it is observed that BRD9 is anchored by the formation of a stable hydrogen bond between the carbonyl of the inhibitors and the residue Asn100 (at BC loop), and a strong π-π stacking interaction formed between the residue Tyr106 (at BC loop) and the inhibitors. The existence of dimethoxyphenyl structure and the aromatic ring merged to pyridinone scaffold are useful to enhance the BRD9 binding affinity. These findings should guide the rational design of more prospective inhibitors targeting BRD9. Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2018.1502097DOI Listing
July 2019

Design of novel quinoline-aminopiperidine derivatives as (MTB) GyrB inhibitors: an study.

J Biomol Struct Dyn 2019 Jul 28;37(11):2913-2925. Epub 2018 Dec 28.

a College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou , PR China.

Tuberculosis (TB) is an infectious disease that causes a number of deaths, and the development of new, safer and more adequate TB inhibitors/drugs has become a necessity as well as a great challenge. Mycobacterial DNA gyrase B subunit has been identified to be one of the potentially underexploited drug targets in the field of anti-tubercular drug discovery. To design the novel and potent (MTB) inhibitors, we performed molecular modeling studies that combined the 3D-QSAR, molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations. Forty eight quinoline-aminopiperidine inhibitors which act on DNA gyrase B subunit were used for constructing 3D-QSAR models. The results showed that the best CoMFA model had the high performance with   0.643, , while the best CoMSIA model yielded   0.536, 0.948. The contour map was in good agreement with the docking and MD simulations which strongly demonstrated that the molecular modeling was reliable. Based on this information, several potential compounds were designed and their inhibitory activities were also verified by the accomplished models and ADME/T predictions. We hope that our research could bring new ideas to facilitate the development of novel inhibitors with higher inhibitory activity for TB. Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2018.1498806DOI Listing
July 2019

Selective mechanisms and molecular design of 2,4 Diarylaminopyrimidines as ALK inhibitors.

Int J Biol Macromol 2018 Oct 2;118(Pt A):1149-1156. Epub 2018 Jul 2.

College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China.

As an attractive therapeutic target for non-small-cell lung cancer (NSCLC), anaplastic lymphoma kinase (ALK) has got increased attention, and the selectivity of ALK inhibitors is an enormous challenge. Recently, 2,4-Diarylaminopyrimidines with high inhibitory activity over InsR/IGF1R were reported as ALK inhibitors, which harboring phosphine oxide moiety. In this work, it is the first time to reveal that the incorporation of dimethylphosphine oxide moiety and the smaller active pocket of ALK is key factor in the selectivity of inhibitor 11q toward ALK over IGF1R/InsR. The results of molecular simulation indicate that the subtle change in the binding pocket of ALK is mainly associated with the flexibility of P-loop and the own residues K1150 and D1270. The replacement of the dimethylphosphine oxide and methylpiperazine of inhibitor 11q would alter the major inhibitory effects of binding and activation. The results further combined 3D-QSAR can not only profile the binding mechanism between the 2,4-Diarylaminopyrimidines inhibitors and ALK, but also supply the useful information for the rational design of a more potential small molecule inhibitor bound to ALK receptor.
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http://dx.doi.org/10.1016/j.ijbiomac.2018.06.192DOI Listing
October 2018

Singlicate analysis: should this be the default for biomarker measurements using ligand-binding assays?

Bioanalysis 2018 06 20;10(12):909-912. Epub 2018 Jun 20.

Biomarker Services, PPD Laboratories, 2244 Dabney Road, Richmond, VA 23230, USA.

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http://dx.doi.org/10.4155/bio-2018-0067DOI Listing
June 2018

11th GCC Closed Forum: cumulative stability; matrix stability; immunogenicity assays; laboratory manuals; biosimilars; chiral methods; hybrid LBA/LCMS assays; fit-for-purpose validation; China Food and Drug Administration bioanalytical method validation.

Bioanalysis 2018 Apr 27;10(7):433-444. Epub 2018 Apr 27.

Worldwide Clinical Trials, Austin, TX, USA.

The 11th Global CRO Council Closed Forum was held in Universal City, CA, USA on 3 April 2017. Representatives from international CRO members offering bioanalytical services were in attendance in order to discuss scientific and regulatory issues specific to bioanalysis. The second CRO-Pharma Scientific Interchange Meeting was held on 7 April 2017, which included Pharma representatives' sharing perspectives on the topics discussed earlier in the week with the CRO members. The issues discussed at the meetings included cumulative stability evaluations, matrix stability evaluations, the 2016 US FDA Immunogenicity Guidance and recent and unexpected FDA Form 483s on immunogenicity assays, the bioanalytical laboratory's role in writing PK sample collection instructions, biosimilars, CRO perspectives on the use of chiral versus achiral methods, hybrid LBA/LCMS assays, applications of fit-for-purpose validation and, at the Global CRO Council Closed Forum only, the status and trend of current regulated bioanalytical practice in China under CFDA's new BMV policy. Conclusions from discussions of these topics at both meetings are included in this report.
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http://dx.doi.org/10.4155/bio-2018-0014DOI Listing
April 2018

Lipid bilayer-coated mesoporous silica nanoparticles carrying bovine hemoglobin towards an erythrocyte mimic.

Int J Pharm 2018 May 19;543(1-2):169-178. Epub 2018 Mar 19.

Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands. Electronic address:

Hemoglobin (Hb)-loaded mesoporous silica nanoparticles (MSNs) coated with a lipid bilayer (LB-MSNs) were investigated as an erythrocyte mimic. MSNs with a large average pore size (10 nm) act as a rigid core and provide a protective environment for Hb encapsulated inside the pores. The colloidal stability of Hb-loaded MSNs was enhanced upon the application of a lipid bilayer, through fusion of PEGylated liposomes onto the exterior surface of Hb-loaded MSNs. The morphology and mesostructure of the MSNs were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and surface area analysis. The Hb loading capacity (mg/g) in MSNs was studied by thermogravimetric analysis (TGA). UV-Vis absorption spectroscopy revealed that Hb inside MSNs had an identical, but slightly broadened peak in the Soret region compared to free Hb. Furthermore the encapsulated Hb exhibits similar peroxidase-like activity in catalyzing the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) with hydrogen peroxide. The introduction of a supported lipid bilayer (LB) demonstrated the potential to prevent premature Hb release (the burst release decreased from 25.50 ± 0.33% to 6.73 ± 0.83%) and increased the colloidal stability of the Hb-loaded MSNs (hydrodynamic diameter remained ∼250 nm for at least one week). The in vivo systemic circulation and biodistribution of LB-MSNs were studied in optically transparent zebrafish embryos, revealing that LB-MSNs have the potential to act as an erythrocyte mimic in transfusion therapy.
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http://dx.doi.org/10.1016/j.ijpharm.2018.03.037DOI Listing
May 2018

Recent Advances in Detecting Mitochondrial DNA Heteroplasmic Variations.

Molecules 2018 Feb 3;23(2). Epub 2018 Feb 3.

State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.

The co-existence of wild-type and mutated mitochondrial DNA (mtDNA) molecules termed heteroplasmy becomes a research hot point of mitochondria. In this review, we listed several methods of mtDNA heteroplasmy research, including the enrichment of mtDNA and the way of calling heteroplasmic variations. At the present, while calling the novel ultra-low level heteroplasmy, high-throughput sequencing method is dominant while the detection limit of recorded mutations is accurate to 0.01% using the other quantitative approaches. In the future, the studies of mtDNA heteroplasmy may pay more attention to the single-cell level and focus on the linkage of mutations.
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http://dx.doi.org/10.3390/molecules23020323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6017848PMC
February 2018

Programmable and Multifunctional DNA-Based Materials for Biomedical Applications.

Adv Mater 2018 Jun 1;30(24):e1703658. Epub 2018 Feb 1.

Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland.

DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
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http://dx.doi.org/10.1002/adma.201703658DOI Listing
June 2018