Yan Li
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Publication
Journal: Microvascular research
October/26/2019
Abstract
Pathological angiogenesis is a hallmark of many diseases. Previously, we reported that orphan nuclear receptor TR3/Nur77 was a critical mediator of angiogenesis to regulate tumor growth, sepsis and skin wound healing. However, none of the TR3/Nur77 targeting molecule has been in clinical trial so far. Here, we designed and generated novel TR3 shRNAs and two minigenes that had therapeutic potential for cancer treatment. In addition to extend our previous findings that tumor growth was inhibited in Nur77 knockout mice, we found that metastasis of colorectal tumor was completely inhibited in Nur77-/- mice. Tumor masses were increased ~70% and decreased ~40% in our transgenic EC-Nur77-S mice and EC-Nur77-DN mice, in which the full-length cDNA and the dominant negative mutant of TR3/Nur77 were inducibly and specifically expressed in mouse endothelium, respectively. TR3 was highly expressed in the vasculature and tumor cells of human melanoma and colorectal cancer tissues, but not in normal tissues. The novel TR3 shRNAs and two minigenes almost completely inhibited the proliferation and migration of HUVECs and human melanoma A375sm cells. Angiogenesis induced by adenoviruses expressing VEGF and melanoma growth in mice were greatly and significantly inhibited by systemically administration of adenoviruses expressing TR3 shRNAs and two minigenes. Tumor angiogenesis and the expressions of genes associated with angiogenesis were greatly regulated in tumor tissues treated with TR3 shRNAs and minigenes. Taken together, these studies demonstrated that TR3/Nur77 was a specific therapeutic target for several human cancers by targeting both tumor cells and tumor microenvironment. These TR3/Nur77 biologics inhibit angiogenesis and tumor growth, and have translational potential.
Publication
Journal: Stem cells international
October/22/2019
Abstract
Our previous studies confirmed that human Wharton's Jelly stem cell (hWJSC) transplantation improved motor function in children with spastic cerebral palsy (CP). This study investigated the dose-effect relationship between the transplanted cell dosage and efficacy in CP children.

Methods
CP children who received one- or two-course (four or eight times lumbar puncture, 4 or 8 × 107 hWJSCs) cell therapy were recruited into this study. Assessments of motor function were performed according to scales for gross motor function measurement (GMFM) and fine motor function measurement (FMFM). The measurement data obtained in the two different groups were analyzed by t-test. Univariate repeated measures analysis of variance was used to compare the data obtained at baseline and 6 or 12 months posttransplantation and met the conditions for Mauchly's sphericity test.

The results for fifty-seven pediatric CP patients (including 35 male and 22 female patients) who completed follow-up showed that gross and fine motor functions improved after cell therapy. Interestingly, the GMFM and FMFM scores in patients who received one course of transplantation were significantly increased at 6 months after treatment. Moreover, another course of transplantation further improved gross and fine motor function in children. The scores for GMFM and FMFM were significantly higher at 6 months posttransplantation than at baseline and showed a linear upward trend. There was no gender difference in GMFM. Interestingly, there was a significant difference between male and female patients in the B and C dimensions of FMFM. These results reveal a gender-related susceptibility to stem cell therapy, especially for movement capability of the upper extremity joint and grasping ability. Similarly, in the group aged ≤3 years old, the improvement observed in dimension A (lying and rolling) of GMFM was nearly exponential and showed a quadratic trend. The results for FMFM were similar to those for GMFM. Moreover, the improvement in motor function was not age dependent.In this study, our data collectively reveal that CP children display sex- or age-dependent responses to hWJSC therapy; these results shed light on the clinical utility of this approach in specific populations.
Publication
Journal: Microorganisms
October/18/2019
Abstract
Colistin is considered to be an antimicrobial of last-resort for the treatment of multidrug-resistant Gram-negative bacterial infections. The recent global dissemination of mobilized colistin resistance (mcr) genes is an urgent public health threat. An accurate estimate of the global prevalence of mcr genes, their reservoirs and the potential pathways for human transmission are required to implement control and prevention strategies, yet such data are lacking. Publications from four English (PubMed, Scopus, the Cochrane Database of Systematic Reviews and Web of Science) and two Chinese (CNKI and WANFANG) databases published between 18 November 2015 and 30 December 2018 were identified. In this systematic review and meta-analysis, the prevalence of mcr genes in bacteria isolated from humans, animals, the environment and food products were investigated. A total of 974 publications were identified. 202 observational studies were included in the systematic review and 71 in the meta-analysis. mcr genes were reported from 47 countries across six continents and the overall average prevalence was 4.7% (0.1-9.3%). China reported the highest number of mcr-positive strains. Pathogenic Escherichia coli (54%), isolated from animals (52%) and harboring an IncI2 plasmid (34%) were the bacteria with highest prevalence of mcr genes. The estimated prevalence of mcr-1 pathogenic E. coli was higher in food-animals than in humans and food products, which suggests a role for foodborne transmission. This study provides a comprehensive assessment of prevalence of the mcr gene by source, organism, genotype and type of plasmid.
Publication
Journal: Journal of physics. Condensed matter : an Institute of Physics journal
October/10/2019
Abstract
The coupling of lattice vibrations with macroscopic electric fields in ionic crystals is examined from first principles based on density functional theory and density functional perturbation theory. Our analyses show that the coupled optical phonon-photon modes are well represented by using the pure phonon modes evaluated at $\bq=0$ as a basis. In addition, we find that apparent ``discontinuities'' and mode ``disappearances'' in the phonon dispersion curves of ionic materials for $\bq \rightarrow 0$ in hexagonal and other anisotropic materials are caused by the directional dependence of the Born effective charge tensor which is responsible for this coupling. The full dispersion curves, including the phonon-photon transverse modes are shown to be continuous functions of wavevector. Our work in this report provides a promising tool for first principles evaluation of phonon polaritons that may be accessible to experiment. Explicit examples are explored for cubic and hexagonal BN; the calculated results are in good agreement with previous computational values and available experimental measurements.
Publication
Journal: Journal of clinical anesthesia
September/16/2019
Publication
Journal: Optics express
September/12/2019
Abstract
Helically twisted microstructured optical fibers have a wide application prospect in the field of optical vortex communications. In this paper, a helically twisted single-ring photonic crystal fiber (HS-PCF) is proposed for orbital angular momentum (OAM) vortex modes selective filtering. And the theoretical framework of OAMs filtering is also constructed. Positive and negative OAM vortexes have different transmission losses in HS-PCF, and the loss difference between them increases significantly after the twist rate reaches a certain value. Such fibers can filter out OAMs with a certain sign of the topological charge (depending on the handedness of the thread), while dissipating oppositely charged OAMs. In addition to the general OAMs, i.e., zero-order radial vortex modes, the helically twisted fiber also performs a good selective filtering for the first-order radial vortex modes. Remarkably, the filtering bandwidth of HS-PCF is very broad, covering four communication bands from O- to C-band. This kind of fiber can be used as a broadband OAMs filter.
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Publication
Journal: Mathematical biosciences and engineering : MBE
September/10/2019
Abstract
In this paper, a low distortion reversible database watermarking method based on histogram gap is proposed in view of the large gap in histogram of database integer data. By using the method, the tolerance of the attribute column containing all integer data is firstly calculated and the prediction error is obtained according to the tolerance. Then according to the watermark bits to be embedded, the database tuples will be randomly grouped and the histogram can be constructed by using the prediction error. Finally, the histogram correction rule is used to find the histogram peak bin, the number of consecutive non-zero prediction errors on the left and right sides of the peak is obtained, and the histogram shift is performed on the side with a smaller number of non-zero prediction errors, and then the watermark embedding will be realized. The results of the experiments based on the published dataset of FCTD (Forest Cover Type Dataset) show that compared with the existing GAHSW which also considers distortion, the proposed method significantly reduces the number of histogram column shift while embedding the watermarks, greatly reduces the changes to the carrier data, and effectively reduces the database's data distortion caused by watermark embedding.
Publication
Journal: Technology and health care : official journal of the European Society for Engineering and Medicine
July/8/2019
Abstract
Quality control system is one of the hospital information systems. The adoption of quality control system increases the work efficiency; however, to some extent, it also increases the workload for physicians.The purpose of this study is to investigate the impacts of the quality control system on quality of care (e.g., process and outcome performance).Our study collected physicians' behavior information from a large urban hospital in China. We constructed the fixed-effect model to examine the relationship between the quality control system adoption and quality of care.The quality control system has a significant (p< 0.001) and negative effect on patients' stay length in the hospital (process performance). Further, the quality control system has a significant (p< 0.001) and positive effect on the trends of cure rate in the hospital (outcome performance). The coefficient of the dependent variable from the patients' stay length (process performance) is lower than the trends of cure rate (outcome performance).The controlling system can improve medical quality even though it limits physician behavior to some extent. The controlling system improves both the process performance and outcome performance, and it brings more benefits to outcome performance rather than process performance which means the reflection of the new technology may have more evident on outcome variables.
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Publication
Journal: The American journal of gastroenterology
July/1/2019
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Publication
Journal: Optics express
June/29/2019
Abstract
An analogous model system for high-dimensional quantum entanglement is proposed, based on the angular and radial degrees of freedom of the improved Laguerre Gaussian mode. Experimentally, we observed strong violations of the Bell-CGLMP inequality for maximally non-separable states of dimension 2 through 10. The results for violations in classical non-separable state are in very good agreement with quantum instance, which illustrates that our scheme can be a useful platform to simulate high-dimensional non-local entanglement. Additionally, we found that the Bell measurements provide sufficient criteria for identifying mode separability in a high-dimensional space. Similar to the two-dimensional spin-orbit non-separable state, the proposed high-dimensional angular-radial non-separable state may provide promising applications for classical and quantum information processing.
Publication
Journal: Plant biotechnology journal
June/29/2019
Abstract
Trichomes are storage compartments for specialized metabolites in many plant species. In trichome, plant primary metabolism is significantly changed, providing substrates for downstream secondary metabolism. However, little is known of how plants coordinate trichome formation and primary metabolism regulation. In this report, tomato (Solanum lycopersicum) trichome regulator SlMIXTA-like is indicated as a metabolic regulation gene by mGWAS analysis. Overexpression of SlMIXTA-like in tomato fruit enhances trichome formation. In addition, SlMIXTA-like can directly bind to the promoter region of gene encoding 3-deoxy-7-phosphoheptulonate synthase (SlDAHPS) to activate its expression. Induction of SlDAHPS expression enhances shikimate pathway activities and provides substrates for downstream secondary metabolism. Our data provide direct evidence that trichome regulator can directly manipulate primary metabolism, in which way plants can coordinate metabolic regulation and the formation of storage compartments for specialized metabolites. The newly identified SlMIXTA-like can be used for future metabolic engineering.
Authors
Publication
Journal: BMC pediatrics
April/25/2019
Abstract
Former evidence regarding reference values of abdominal fat percentage (AFP) and optimal anthropometric indicators in predicting abdominal obesity measured by dual-energy X-ray absorptiometry (DXA) scan in Chinese children were scarce.A total of 452 Chinese children aged 6-9 years were included in this cross-sectional study. Abdominal fat and lean mass were measured by a DXA scan, and AFP were calculated. Anthropometric indicators including body mass index (BMI), chest circumference (CC), waist circumference (WC) and hip circumference (HC) were measured, waist-to-hip ratio (WHR), waist-to-height ratio (WHtR) was also calculated.By defining abdominal obesity as those with an AFP ≥ 85th percentile, the cutoffs values are 24.80, 30.29, 31.58, 31.86% in boys, and 25.02, 30.32, 31.66, 31.79% in girls, for children aged 6, 7, 8, and 9 years old, respectively. All anthropometric indicators were independently and positively associated with AFP (P all < 0.01). In girls, BMI was found to be the optimal predictors of childhood abdominal obesity. The values of area under curves (AUCs) were significantly higher (P all < 0.05) than other anthropometric indicators, except for WHtR (AUCs value: 0.886). However, in boys, WHtR instead of BMI, provided the largest AUCs value (0.922) in predicting abdominal obesity, followed by BMI ((AUCs value: 0.913).This study provides reference values of AFP measured by DXA in Chinese children aged 6-9 years. BMI and WHtR tend to be the optimal anthropometric indicators in predicting abdominal obesity in Chinese girls and boys, respectively.
Publication
Journal: Environmental pollution (Barking, Essex : 1987)
January/31/2019
Abstract
To better understand the toxicological activities of perfluorooctanoic acid (PFOA), we examined the effects of PFOA on apoptosis and its molecular mechanism in SMMC-7721 hepatoma cells. Cell viability was evaluated by MTT assay and apoptosis was determined by flow cytometry. Western blot and quantitative real-time PCR were used to examine the protein and gene expressions of Bax and Bcl-2. Our results showed that PFOA inhibited SMMC-7721 cell growth and induced apoptosis. PFOA treatment increased Bax expression and increased Bcl-2 expression at both gene and protein levels. Our study demonstrated that PFOA had toxic effects on SMMC-7721 cells, such as inhibiting cell proliferation and inducing apoptosis. Furthermore, we showed that PFOA-mediated induction of apoptosis involved inducing Bax and decreasing Bcl-2 expression as a molecular mechanism of its toxicological effects.
Publication
Journal: Journal of human hypertension
January/11/2019
Abstract
Although previous data showed that remote ischemic preconditioning (RIPC) has beneficial effect on blood pressure (BP) reduction, the efficacy of RIPC-induced decline in BP and the favorable humoral factors in hypertension is elusive. This present study is performed to evaluate whether RIPC reduces BP, improves microvascular endothelial function and increases circulating hSDF-1α generation in hypertension. Fifteen hypertensive patients received 3 periods of 5-min inflation/deflation of the forearm with a cuff on the upper arm daily for 30 days. Clinic and 24-h ambulatory blood pressure monitoring (ABPM) were examined before and after the end of this procedure. Microvascular endothelial function was measured by finger reactive hyperemia index (RHI) using the Endo-PAT 2000 device. The circulating hSDF-1α level was tested by ELISA. RIPC significantly decreased systolic BP (139.13 ± 6.68 versus 131.45 ± 7.45 mmHg) and diastolic BP (89.67 ± 4.98 versus 83.83 ± 6.65 mmHg), meanwhile 24-h ambulatory systolic and diastolic BP dropped from 136.33 ± 9.10 mmHg to 131.33 ± 7.12 mmHg and 87.60 ± 6.22 mmHg to 82.47 ± 4.47 mmHg respectively. RHI was improved (1.95 ± 0.34 versus 2.47 ± 0.44). Plasma hSDF-1α level was markedly increased after RIPC (1585.86 ± 167.17 versus 1719.54 ± 211.17 pg/ml). The increase in hSDF-1α level was associated with the fall in clinic and 24-h ABPM and rise in RHI. The present data suggests that RIPC may be a novel alternative or complementary intervention means to treat hypertension and protect endothelial function.
Publication
Journal: Autism research : official journal of the International Society for Autism Research
January/10/2019
Abstract
Autism spectrum disorder (ASD) is a serious lifelong neurodevelopmental disorder. ASD is diagnosed for children at the age of two. ASD diagnosis, as early as possible, lays the foundation for treatment and much better prognosis. Notably, gene-based test is an inherent method to recognize the potential infants with ASD before the age of two. To investigate whether SHANK family contributes to ASD prediction, on the basis of our previous studies of SHANK2 and SHANK3, we further investigated associations between SHANK1 polymorphisms and ASD risk as well as SNP-SNP interactions among SHANK family. We enrolled 470 subjects (229 cases and 241 healthy controls) who were northeast Chinese Han. Four tag SNPs (rs73042561, rs3745521, rs4801846, and rs12461427) of SHANK1 were selected and genotyped. We used the SNPStats online analysis program to assess the associations between the four SNPs and ASD risk. The SNP-SNP interactions among SHANK family were analyzed using multifactor dimensionality reduction method. We found that the four SHANK1 SNPs were not associated with ASD risk in northeast Chinese Han population. There existed a strong synergistic interaction between rs11236697 [SHANK2] and rs74336682 [SHANK2], and moderate synergistic interactions (rs74336682 [SHANK2]-rs73042561 [SHANK1], rs11236697 [SHANK2]-rs77716438 [SHANK2], and rs11236697 [SHANK2]-rs75357229 [SHANK2]). These SHANK1 variants may not affect the susceptibility to ASD in Chinese Han population. SNP-SNP interactions in SHANK family may confer ASD risk. Autism Res 2019, 12: 375-383 © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: ASD is a serious lifelong neurodevelopmental disorder with strong genetic components. We investigated associations between SHANK1 polymorphisms and ASD risk as well as SNP-SNP interactions among SHANK family. Our results indicated that there exists no association between SHANK1 SNPs and ASD, and SNP-SNP interactions in SHANK family may confer ASD risk in the Northeast Han Chinese population. Future studies are needed to test more SHANK family SNPs in a large sample to demonstrate the associations.
Publication
Journal: Cancer management and research
December/27/2018
Abstract
To develop nomogram models to predict individualized estimates of overall survival (OS) and cancer-specific survival (CSS) in patients with adrenocortical carcinoma (ACC).A total of 751 patients with ACC were identified within the Surveillance Epidemiology, and End Results (SEER) database between 1973 and 2015. The predictors comprised marital status, sex, age at diagnosis, year of diagnosis, laterality, histologic grade, ethnicity, historic stage, radiation therapy, chemotherapy, and surgery of primary site. Based on the results of the multivariate logistic regression analyses, the nomogram models were used for predicting OS and CSS in patients with ACC. The nomograms were tested using concordance index (C-index) and calibration curves.In univariate and multivariate analyses of OS, OS was significantly associated with age at diagnosis, year of diagnosis, histologic grade, historic stage, and chemotherapy. In univariate and multivariate analyses of CSS, age at diagnosis, year of diagnosis, historic stage, and chemotherapy were the independent risk factors with CSS. These characteristics were included in the nomograms predicting OS and CSS. The nomograms demonstrated good accuracy in predicting OS and CSS, with the C-index of 0.677 and 0.672.These clinically useful tools predicted OS and CSS in patients with ACC using readily available clinicopathologic factors and could aid individualized clinical decision making.
Publication
Journal: Organic & biomolecular chemistry
December/5/2018
Abstract
The mechanism and origin of stereoselectivities in N-heterocyclic carbine (NHC)-catalyzed [3 + 2] cycloaddition of 3-bromoenals and isatin N-Boc ketimines have been studied using density functional theory (DFT) calculations. Various possible reaction pathways were examined and analyzed. Our calculation results reveal that the catalytic cycle can be characterized by six steps: nucleophilic attack of a catalyst on 3-bromoenal (step I); [1,2]-proton transfer (step II); addition to the other reactant isatin N-Boc ketimine (step III); debromination (step IV); intramolecular cycloaddition concerted with hydrogen-elimination (step V) and elimination of the NHC catalyst (step VI). For step II, besides the direct [1,2]-proton transfer, the mediator (base and water)-assisted proton transfer has been investigated, and the DFT results show that the 2H2O cluster-mediated proton transfer is most energy favorable. The carbon-carbon bond formation step (step III) is calculated to be the stereoselectivity-determining step and the S-configuration product is the predominant product, which are in good agreement with the experimental observations. The mechanistic insights gained in this work should be helpful for other NHC-catalyzed reactions.
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Publication
Journal: International journal of systematic and evolutionary microbiology
December/4/2018
Abstract
A Gram-stain-positive, rod-shaped bacterial strain, 22-7T, was isolated from ocean sediment of Laizhou Bay, China, and was characterized by using a polyphasic approach. Optimal growth was observed at 33 °C on a 2216E agar plate of pH 7.5 and with 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences identified it as a member of the genus Jeotgalibacillus, most similar to Jeotgalibacillus campisalis SF-57T (98.7 % similarity), Jeotgalibacillus marinus DSM 1297T (98.2 %) and Jeotgalibacillus soli P9T (97.1 %). Average nucleotide identity values and digital DNA-DNA hybridization values were less than 74.2 and 18.1 %, respectively, between strain 22-7T and the type strains of closely related species. The major polar lipids were aminophospholipid, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; the major fatty acids (>10 %) were anteiso-C15 : 0 and iso-C15 : 0; and the major menaquinone was MK-7. The peptidoglycan type of the cell wall was A1α linked through l-lysine as the diamino acid. Combined data from phenotypic, chemotaxonomic and genotypic characterizations demonstrated that strain 22-7T represents a novel Jeotgalibacillus species, for which the name Jeotgalibacillus proteolyticus sp. nov. is proposed. The type strain is 22-7T(=MCCC 1H00228T=KCTC 33930T).
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Publication
Journal: Journal of neuroscience methods
December/3/2018
Abstract
BACKGROUND
Electroencephalogram (EEG) signals are important for brain health monitoring applications. Characteristics of EEG signals are complex, being non-stationarity, aperiodic and nonlinear in nature. EEG signals are a combination of sustained oscillation and non-oscillation transients that are challenging to deal with using linear approaches.
METHODS
This research proposes a new scheme based on a tunable Q-factor wavelet transform (TQWT) and a statistical approach to analyse various EEG recordings. Firstly, the proposed method decompose EEG signals into different sub-bands using the TQWT method, which is parameterized by its Q-factor and redundancy. This method depends on the resonance of a signal, instead of frequency or scaling as in the Fourier and wavelet transforms. Secondly, using a statistical feature extraction on the sub-bands to divide each sub-band into n windows, and then extract several statistical features from each window. Finally, the extracted features are forwarded to a bagging tree (BT), k nearest neighbor (k-NN), and support vector machine (SVM) as classifiers to evaluate the performance of the proposed feature extraction technique.
RESULTS
The proposed method is tested on two different EEG databases: Bonn University database and Born University database. The experimental results demonstrate that the proposed feature extraction algorithm with thek-NN classifier produces the best performance compared with the other two classifiers. Comparison with existing methods: In order to further evaluate the performances, the proposed scheme is compared with the other existing methods in terms of accuracy. The results prove that the proposed TQWT based feature extraction method has great potential to extract discriminative information from brain signals.
CONCLUSIONS
The outcomes of the proposed technique can assist doctors and other health experts to identify diversified EEG categories.
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Publication
Journal: Bioorganic chemistry
December/3/2018
Abstract
Agonism of S1P1 receptor has been proven to be responsible for peripheral blood lymphopenia and elicts the identification of various S1P1 modulators. In this paper we described a series of oxadiazole-based S1P1 direct-acting agonists disubstituted on terminal benzene ring, with high potency for S1P1 receptor and favorable selectivity against S1P3 receptor. In addition, two representative agents named 16-3b and 16-3g demonstrated impressive efficacy in lymphocyte reduction along with reduced effect on heart rate when orally administered. Furthermore, these compounds have been shown to possess desired pharmacokinetic (PK) and physicochemical profiles. The binding mode between 16-3b and the activated S1P1 model was also studied.
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Publication
Journal: Development (Cambridge, England)
December/2/2018
Abstract
In vivo genomic engineering is instrumental for studying developmental biology and regenerative medicine. Development of novel systems with more site-specific recombinases (SSRs) that complement with the commonly used Cre-loxP would be valuable for more precise lineage tracing and genome editing. Here, we introduce a new SSR system via Nigri-nox. By generating tissue-specific Nigri knock-in and its responding nox reporter mice, we show that the Nigri-nox system works efficiently in vivo by targeting specific tissues. As a new orthogonal system to Cre-loxP, Nigri-nox provides an additional control of genetic manipulation. We also demonstrate how the two orthogonal systems Nigri-nox and Cre-loxP could be used simultaneously to map the cell fate of two distinct developmental origins of cardiac valve mesenchyme in the mouse heart, providing dynamics of cellular contribution from different origins for cardiac valve mesenchyme during development. This work provides a proof-of-principle application of the Nigri-nox system for in vivo mouse genomic engineering. Coupled with other SSR systems, Nigri-nox would be valuable for more precise delineation of origins and cell fates during development, diseases and regeneration.
Publication
Journal: Nature communications
November/30/2018
Abstract
Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression and plant development. Here, we identified 6,510 lncRNAs in Arabidopsis under normal or stress conditions. We found that the expression of natural antisense transcripts (NATs) that are transcribed in the opposite direction of protein-coding genes often positively correlates with and is required for the expression of their cognate sense genes. We further characterized MAS, a NAT-lncRNA produced from the MADS AFFECTING FLOWERING4 (MAF4) locus. MAS is induced by cold and indispensable for the activation of MAF4 transcription and suppression of precocious flowering. MAS activates MAF4 by interacting with WDR5a, one core component of the COMPASS-like complexes, and recruiting WDR5a to MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3). Our study greatly extends the repertoire of lncRNAs in Arabidopsis and reveals a role for NAT-lncRNAs in regulating gene expression in vernalization response and likely in other biological processes.
Publication
Journal: Bioprocess and biosystems engineering
November/26/2018
Abstract
Start-up of membrane bioreactor under different NaCl stress was investigated in this study. Results showed that nearly 90% chemical oxygen demands and ammonia nitrogen ([Formula: see text]-N) was oxidized in none and 0.5% NaCl condition during the start-up stage. While 1% NaCl dramatically depressed the utilization of [Formula: see text]-N and about 4 weeks were required for adaption of sludge biomass to saline condition. In addition, the accumulation of nitrite high to 11.84 mg/L was observed in 1% NaCl stress, indicating the more inhibition on the activity of nitrite oxidizing bacteria. Microbial community responded to the different salinity levels. The phylum Proteobacteria and Bacteroidetes occupied over 60% in all the three MBRs. Salinity enriched the relative abundance of Maribacter, Methyloversatilis, Aeromonas and Curvibacter, while reducing the proportion of Nitrospira and Haliscomenobacter. Nitrospirae decreased sharply at 1% NaCl accounting for the accumulation of nitrite. Higher content of soluble microbial products (SMP) under saliferous MBR were released, which deteriorated the permeability of membrane module. Protein-like substances and humic substances were the main ingredients of SMP, of which the former contributed more to membrane flux decline. This study provided better understanding on the impact of salinity on the start-up of MBR.
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Journal: Journal of chemical information and modeling
November/26/2018
Abstract
In structure-based drug design, scoring functions are often employed to evaluate protein-ligand interactions. A variety of scoring functions have been developed so far, and thus some objective benchmarks are desired for assessing their strength and weakness. The comparative assessment of scoring functions (CASF) benchmark developed by us provides an answer to this demand. CASF is designed as a "scoring benchmark", where the scoring process is decoupled from the docking process to depict the performance of scoring function more precisely. Here, we describe the latest update of this benchmark, i.e. CASF-2016. Each scoring function is still evaluated by four metrics, including "scoring power", "ranking power", "docking power", and "screening power". Nevertheless, the evaluation methods have been improved considerably in several aspects. A new test set is compiled, which consists of 285 protein-ligand complexes with high-quality crystal structures and reliable binding constants. A panel of 25 scoring functions are tested on CASF-2016 as demonstration. Our results reveal that the performance of current scoring functions is more promising in terms of docking power than scoring, ranking, and screening power. Scoring power is somewhat correlated with ranking power, so are docking power and screening power. The results obtained on CASF-2016 may provide valuable guidance for the end users to make smart choices among available scoring functions. Moreover, CASF is created as an open-access benchmark so that other researchers can utilize it to test a wider range of scoring functions. The complete CASF-2016 benchmark will be released on the PDBbind-CN web server (http://www.pdbbind-cn.org/casf.asp/) once this article is published.
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