Publications by authors named "Yanfang Wu"

82 Publications

NF-κB-Dependent Snail Expression Promotes Epithelial-Mesenchymal Transition in Mastitis.

Animals (Basel) 2021 Dec 1;11(12). Epub 2021 Dec 1.

College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang 712100, China.

Mastitis is a common and important clinical disease in ruminants. This may be associated with inflammatory fibrosis if not treated promptly. Inflammation-derived fibrosis is usually accompanied by epithelial-mesenchymal transition (EMT) in epithelial cells. However, the precise molecular mechanism underlying mastitis-induced fibrosis remains unclear. Nuclear factor kappa-B (NF-κB) and Snail are key regulators of EMT. In this study, primary goat mammary epithelial cells (GMECs) were treated with 10 μg/mL lipopolysaccharide (LPS) for 14 d to mimic the in vivo mastitis environment. After LPS treatment, the GMECs underwent mesenchymal morphological transformation and expressed mesenchymal cell markers. Snail expression was induced by LPS and was inhibited by suppression of the TLR4/NF-κB signaling pathway. Snail knockdown alleviated LPS-induced EMT and altered the expression of inflammatory cytokines. Finally, we found that the expression of key molecules of the TLR4/NF-κB/Snail signaling pathway was increased in mastitis tissues. These results suggest that Snail plays a vital role in LPS-induced EMT in GMECs and that the mechanism is dependent on the activation of the TLR4/NF-κB signaling pathway.
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http://dx.doi.org/10.3390/ani11123422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8698035PMC
December 2021

Identification of a Pyroptosis-Related Gene Signature for Predicting Overall Survival and Response to Immunotherapy in Hepatocellular Carcinoma.

Front Genet 2021 3;12:789296. Epub 2021 Dec 3.

Department of Hepatic Oncology, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China.

Pyroptosis is a novel kind of cellular necrosis and shown to be involved in cancer progression. However, the diverse expression, prognosis and associations with immune status of pyroptosis-related genes in Hepatocellular carcinoma (HCC) have yet to be analyzed. Herein, the expression profiles and corresponding clinical characteristics of HCC samples were collected from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Then a pyroptosis-related gene signature was built by applying the least absolute shrinkage and selection operator (LASSO) Cox regression model from the TCGA cohort, while the GEO datasets were applied for verification. Twenty-four pyroptosis-related genes were found to be differentially expressed between HCC and normal samples. A five pyroptosis-related gene signature (GSDME, CASP8, SCAF11, NOD2, CASP6) was constructed according to LASSO Cox regression model. Patients in the low-risk group had better survival rates than those in the high-risk group. The risk score was proved to be an independent prognostic factor for overall survival (OS). The risk score correlated with immune infiltrations and immunotherapy responses. GSEA indicated that endocytosis, ubiquitin mediated proteolysis and regulation of autophagy were enriched in the high-risk group, while drug metabolism cytochrome P450 and tryptophan metabolism were enriched in the low-risk group. In conclusion, our pyroptosis-related gene signature can be used for survival prediction and may also predict the response of immunotherapy.
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http://dx.doi.org/10.3389/fgene.2021.789296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8678488PMC
December 2021

Spiers Memorial Lecture. Next generation nanoelectrochemistry: the fundamental advances needed for applications.

Faraday Discuss 2021 Dec 7. Epub 2021 Dec 7.

School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.

Nanoelectrochemistry, where electrochemical processes are controlled and investigated with nanoscale resolution, is gaining more and more attention because of the many potential applications in energy and sensing and the fact that there is much to learn about fundamental electrochemical processes when we explore them at the nanoscale. The development of instrumental methods that can explore the heterogeneity of electrochemistry occurring across an electrode surface, monitoring single molecules or many single nanoparticles on a surface simultaneously, have been pivotal in giving us new insights into nanoscale electrochemistry. Equally important has been the ability to synthesise or fabricate nanoscale entities with a high degree of control that allows us to develop nanoscale devices. Central to the latter has been the incredible advances in nanomaterial synthesis where electrode materials with atomic control over electrochemically active sites can be achieved. After introducing nanoelectrochemistry, this paper focuses on recent developments in two major application areas of nanoelectrochemistry; electrocatalysis and using single entities in sensing. Discussion of the developments in these two application fields highlights some of the advances in the fundamental understanding of nanoelectrochemical systems really driving these applications forward. Looking into our nanocrystal ball, this paper then highlights: the need to understand the impact of nanoconfinement on electrochemical processes, the need to measure many single entities, the need to develop more sophisticated ways of treating the potentially large data sets from measuring such many single entities, the need for more new methods for characterising nanoelectrochemical systems as they operate and the need for material synthesis to become more reproducible as well as possess more nanoscale control.
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http://dx.doi.org/10.1039/d1fd00088hDOI Listing
December 2021

Mitral valve regurgitation is associated with left atrial fibrosis in patients with atrial fibrillation.

J Electrocardiol 2022 Jan-Feb;70:24-29. Epub 2021 Nov 23.

Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

Background: Low voltage zones (LVZ) are associated with poor outcomes in patients with atrial fibrillation (AF). The APPLE and DR-FLASH scores predict LVZ in patients undergoing catheter ablation. This study aimed to assess the relationship of mitral valve regurgitation (MR) and LVZ after adjusting for APPLE or DR-FLASH scores.

Methods: This was a retrospective study on patients with AF who underwent their first catheter ablation. All patients underwent a transthoracic echocardiographic examination before ablation. The APPLE and DR-FLASH scores were calculated at baseline. LVZ determined by high-density mapping was defined as bipolar voltage amplitude <0.5 mV. LVZ presence was defined as LVZ covering >5% of the left atrial surface area.

Results: Altogether, 152 patients (mean age 62.0 ± 10.8 years, 65.8% men, and 36.2% with persistent AF) were included. Of the 152 patients, 47 (30.9%) had LVZ. The patients with LVZ had more moderate-to-severe MR (17.0% vs. 3.8%, P = 0.014) and higher APPLE scores (1.7 ± 1.1 vs. 1.2 ± 1.1, P = 0.009) and DR-FLASH scores (3.0 ± 1.5 vs. 2.4 ± 1.4, P = 0.010). Using multivariate logistic regression analysis, we found moderate-to-severe MR was related to LVZ presence after adjusting for the APPLE (OR 4.040, P = 0.034) or DR-FLASH (OR 4.487, P = 0.020) scores. Furthermore, moderate-to-severe MR had an incremental predictive value for LVZ presence in addition to the APPLE (P = 0.03) or DR-FLASH (P = 0.02) scores.

Conclusion: In patients with AF, MR severity was related to LVZ after adjusting the APPLE score or DR-FLASH score.
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http://dx.doi.org/10.1016/j.jelectrocard.2021.11.031DOI Listing
November 2021

[Effects of fine particulate matter on cognitive function and gut microbiota in adult male mice].

Wei Sheng Yan Jiu 2021 Sep;50(5):821-826

School of Public Health, North China of Science and Technology, Tangshan 063210, China.

Objective: To study the effects of fine particulate matter(PM_(2.5))exposure to cognitive function and intestinal flora abundance and diversity in adult male mice.

Methods: The SPF grade male C57 BL/6 J mice with 8 weeks old were randomly divided into control group(NS group), PM_(2.5) exposure group(PM_(2.5) group), probiotic group(VSL#3 group) and PM_(2.5) + VSL#3 group(PMV group), with 8 mice in each group. The PM_(2.5) group and PMV group mice were exposed to PM_(2.5) using animal exposure system equipped with real-time PM_(2.5) concentration, and concentrated 6 times the outdoor PM_(2.5) concentration, 8 h every day, 5 d every week for 4 weeks. The VSL#3 group and PMV group mice were given VSL#3, 0.5 mL, 2×10~9 CFU/mL. After four weeks of exposure, feces from mice were collected for 16 s rRNA high-throughput sequencing, and the cognitive function was evaluated using Morris water maze and object recognition experiments.

Results: The escape latency of PM_(2.5) group in four-day training [(54.99±6.77) s, (41.21±9.98) s, (36.27±13.11) s, (30.01±14.80) s] were higher than that of NS group [(32.19±4.59) s, (20.50±6.77) s, (19.93±7.30) s, (16.94±9.91) s], and the difference were statistically significant(P<0.05). The escape latency of PMV group on the first and second day of training [(39.02±6.23) s, (28.83±9.53) s] were lower than that of PM_(2.5) group(P<0.05). The target quadrant residence time of mice in PM_(2.5) group [(18.30± 8.88) s] was lower than that in NS group and PMV group [(30.53±9.10) s, (30.00±10.61) s]. Compared with NS group(6.09±0.40), the shannon index of PM_(2.5) group and PMV group(5.05±0.65 and 5.46±0.52) were significantly reduced(P<0.05). The target quadrant time was positively correlated with the relative abundance of Actinomyces(r=0.576, P<0.05), and the recognition index was positively correlated with the relative abundance of Firmicutes(r=0.612, P<0.05).

Conclusion: PM_(2.5) could lead to cognitive dysfunction in mice, which is related to diversity and abundance of the intestinal flora. Probiotic can improve cognitive function.
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http://dx.doi.org/10.19813/j.cnki.weishengyanjiu.2021.05.019DOI Listing
September 2021

Key Parameters That Determine the Magnitude of the Decrease in Current in Nanopore Blockade Sensors.

Nano Lett 2021 Nov 2;21(22):9374-9380. Epub 2021 Nov 2.

School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.

Nanopore blockade sensors were developed to address the challenges of sensitivity and selectivity for conventional nanopore sensors. To date, the parameters affecting the current of the sensor have not been elucidated. Herein, the impacts of nanopore size and charge and the shape, size, surface charge, and aggregation state of magnetic nanoparticles were assessed. The sensor was tolerant to all parameters contrary to predictions from electronic or geometric arguments on the current change. Theoretical models showed the greater importance of the polymers around nanoparticles and the access resistance of nanopores to the current, when compared with translocation-based nanopore sensors. The signal magnitude was dominated by the change in access resistance of ∼4.25 MΩ for all parameters, resulting in a robust system. The findings provide understandings of changes in current when nanopores are blocked, like in RNA trapping or nanopore blockade sensors, and are important for designing sensors based on nanopore blockades.
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http://dx.doi.org/10.1021/acs.nanolett.1c01855DOI Listing
November 2021

Response to ibutilide and the long-term outcome after catheter ablation for non-paroxysmal atrial fibrillation.

Cardiovasc J Afr 2021 Oct 15;32:1-6. Epub 2021 Oct 15.

Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. Email:

Purpose: This study aimed to assess the relationship between the cardiac rhythm response to ibutilide infusion after pulmonary vein isolation and the recurrence of long-term atrial arrhythmias.

Methods: One hundred and thirty-eight patients with non-paroxysmal atrial fibrillation who had had their first catheter ablation were retrospectively included. All patients whose atrial fibrillation did not terminate after pulmonary vein isolation were administered intravenous ibutilide (1.0 mg). Those with termination of atrial fibrillation after ibutilide administration were defined as responders ( = 86); those without termination of atrial fibrillation, as non-responders ( = 52). The primary endpoint was any documented recurrence of atrial arrhythmia lasting more than 30 seconds after the initial catheter ablation.

Results: Conversion of atrial fibrillation to sinus rhythm, directly or via atrial flutter, with ibutilide administration was achieved in 62.3% of patients. A longer duration of atrial fibrillation was associated with failed termination of atrial fibrillation (odds ratio 1.009, 95% confidence interval 1.002-1.017, = 0.011). During a median follow-up period of 610 days (interquartile range 475-1 106) post ablation, non-responders ( = 24, 46.2%) had a higher recurrence rate of atrial arrhythmia than the responders ( = 26, 30.2%; log-rank, = 0.011) after the initial catheter ablation. Multivariate Cox regression analysis revealed that non-responders (hazard ratio 1.994, 95% confidence interval 1.117-3.561, = 0.020) was significantly correlated with recurrence of atrial arrhythmias.

Conclusions: In patients whose atrial fibrillation persisted after pulmonary vein isolation, the response to ibutilide administration could predict the recurrence of atrial arrhythmias after catheter ablation, which may be useful for risk stratification for recurrence of atrial fibrillation and individualised management of atrial fibrillation.
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http://dx.doi.org/10.5830/CVJA-2021-044DOI Listing
October 2021

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms.

BMC Genomics 2021 Sep 22;22(1):690. Epub 2021 Sep 22.

Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, 212013, Zhenjiang, Jiangsu, China.

Background: Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources of this species is relatively limited, which considerably hampers further work on its biology and genetic improvement.

Results: In this study, through analyzing the transcriptome of mixed samples of leaves and stems using the latest PacBio Iso-Seq sequencing technology combined with Illumina HiSeq, we report the first full-length transcriptome dataset of M. sinensis with a total of 58.21 Gb clean data. An average of 15.75 Gb clean reads of each sample were obtained from the PacBio Iso-Seq system, which doubled the data size (6.68 Gb) obtained from the Illumina HiSeq platform. The integrated analyses of PacBio- and Illumina-based transcriptomic data uncovered 408,801 non-redundant transcripts with an average length of 1,685 bp. Of those, 189,406 transcripts were commonly identified by both methods, 169,149 transcripts with an average length of 619 bp were uniquely identified by Illumina HiSeq, and 51,246 transcripts with an average length of 2,535 bp were uniquely identified by PacBio Iso-Seq. Approximately 96 % of the final combined transcripts were mapped back to the Miscanthus genome, reflecting the high quality and coverage of our sequencing results. When comparing our data with genomes of four species of Andropogoneae, M. sinensis showed the closest relationship with sugarcane with up to 93 % mapping ratios, followed by sorghum with up to 80 % mapping ratios, indicating a high conservation of orthologs in these three genomes. Furthermore, 306,228 transcripts were successfully annotated against public databases including cell wall related genes and transcript factor families, thus providing many new insights into gene functions. The PacBio Iso-Seq data also helped identify 3,898 alternative splicing events and 2,963 annotated AS isoforms within 10 function categories.

Conclusions: Taken together, the present study provides a rich data set of full-length transcripts that greatly enriches our understanding of M. sinensis transcriptomic resources, thus facilitating further genetic improvement and molecular studies of the Miscanthus species.
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http://dx.doi.org/10.1186/s12864-021-07971-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8459517PMC
September 2021

Unraveling the metabolic network of organic acids in solid-state fermentation of Chinese cereal vinegar.

Food Sci Nutr 2021 Aug 18;9(8):4375-4384. Epub 2021 Jun 18.

State Key Laboratory of Food Nutrition and Safety Key Laboratory of Industrial Fermentation Microbiology Ministry of Education College of Biotechnology Tianjin University of Science & Technology Tianjin China.

Shanxi aged vinegar (SAV) is fermented by multispecies microorganism with solid-state fermentation (SSF) technology, which contains a variety of organic acids. However, the metabolic network of them in SSF is still unclear. In this study, metagenomics technology was used to reveal the microbial community and functional genes in SAV fermentation. The metabolic network of key organic acids with taste active value higher than 1 was reconstructed for the first time, including acetate, lactate, malate, citrate, succinate, and tartrate. The results show pyruvate is the core compound in the metabolic network of organic acids. Metabolic pathway of acetate plays a pivotal role in this network, and acetate has regulatory function on metabolism of other organic acids. and are the predominant genera for organic acid metabolism in SSF of SAV. This is also the first report on metabolic network of organic acids in cereal vinegar, adding new knowledge on the flavor substance metabolism during multispecies fermentation of traditional fermented food.
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http://dx.doi.org/10.1002/fsn3.2409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8358386PMC
August 2021

Rapid and ultrasensitive electrochemical detection of circulating tumor DNA by hybridization on the network of gold-coated magnetic nanoparticles.

Chem Sci 2021 Mar 3;12(14):5196-5201. Epub 2021 Mar 3.

School of Chemistry, The University of New South Wales Sydney NSW 2052 Australia

An accurate and robust method for quantifying the levels of circulating tumor DNA (ctDNA) is vital if this potential biomarker is to be used for the early diagnosis of cancer. The analysis of ctDNA presents unique challenges because of its short half-life and ultralow abundance in early stage cancers. Here we develop an ultrasensitive electrochemical biosensor for rapid detection of ctDNA in whole blood. The sensing of ctDNA is based on hybridization on a network of probe DNA modified gold-coated magnetic nanoparticles ([email protected]). This [email protected] biosensor can selectively detect short- and long-strand DNA targets. It has a broad dynamic range (2 aM to 20 nM) for 22 nucleotide DNA target with an ultralow detection limit of 3.3 aM. For 101 nucleotide ctDNA target, a dynamic range from 200 aM to 20 nM was achieved with a detection limit of 5 fM. This [email protected] based sensor provides a promising method to achieve 20 min response time and minimally invasive cancer early diagnosis.
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http://dx.doi.org/10.1039/d1sc01044aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8179593PMC
March 2021

The complete chloroplast genome sequence of W. W. Smith (Lauraceae) from Jiangxi Province, China.

Mitochondrial DNA B Resour 2021 Jun 7;6(7):1890-1892. Epub 2021 Jun 7.

Camphor Engineering Technology Research Center for National Forestry and Grassland Administration, Jiangxi Academy of Forestry, Nanchang, China.

W. W. Smith is an evergreen plant distributed in the Yangtze River Basin and the south regions of China. Here we analyzed the complete chloroplast (cp) genome sequence of to determine its structure and evolutionary relationship to other Lauraceae. The cp genome is 152,737 bp in length and has an overall GC content of 39.2% The genome includes a large single-copy (LSC) region of 93,706 bp and a small single-copy (SSC) region of 18,885 bp, and these are separated by a pair of inverted repeats (IRs) of 20,073 bp. The cp genome contains 128 genes, including 83 protein-coding, 37 tRNAs, and 8 rRNAs. Phylogenetic analysis based on complete cp genome sequences fully resolved in a clade with This work provides new molecular data for evolutionary studies of the Lauraceae.
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http://dx.doi.org/10.1080/23802359.2021.1934160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8189048PMC
June 2021

Metabolic profile of main organic acids and its regulatory mechanism in solid-state fermentation of Chinese cereal vinegar.

Food Res Int 2021 07 11;145:110400. Epub 2021 May 11.

State Key Laboratory of Food Nutrition and Safety. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China. Electronic address:

Shanxi aged vinegar (SAV), a traditional Chinese cereal vinegar, is produced using solid-state fermentation (SSF) technology. Organic acids are the key flavor compounds of vinegar. However, the metabolic mechanism of organic acids during SSF process is still unclear. In this study, metatranscriptomics was used to explore the metabolic profile of main organic acids in SSF. The results show that carbon metabolism is the dominant pathway during fermentation, among which pyruvate metabolism, glycolysis and starch and sucrose metabolism associated with organic acids were the most abundant. The metabolic pathways of acetic acid and lactic acid shift from acetyl-P and pyruvate pathways at early and middle-early stages of fermentation to acetaldehyde and L-lactaldehyde pathways at later stages, respectively, and Lactobacillus and Acetobacter are the predominant microorganisms contributed to them. Temperature and acetic acid are proven to be the environmental factors that regulate the metabolic activity during SSF. This study sheds new lights on metabolism of flavor substances in the spontaneous ecosystems of traditional fermented food.
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http://dx.doi.org/10.1016/j.foodres.2021.110400DOI Listing
July 2021

Selectively detecting attomolar concentrations of proteins using gold lined nanopores in a nanopore blockade sensor.

Chem Sci 2020 Oct 26;11(46):12570-12579. Epub 2020 Oct 26.

School of Chemistry, Australian Centre for NanoMedicine, Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales Sydney New South Wales 2052 Australia

Disease diagnosis at earlier stages requires the development of ultrasensitive biosensors for detecting low-abundance biomarkers in complex biological fluids within a reasonable time frame. Here, we demonstrate the development of an ultrasensitive nanopore blockade biosensor that can rapidly diagnose a model protein biomarker, prostate-specific antigen (PSA) with high selectivity. The solid-state nanopores have gold located only along the length of the nanopore whilst the rest of the membrane is silicon nitride. The orthogonal use of materials allows nanopore arrays with a different surface chemistry inside the nanopore relative to the rest of the membrane to be fabricated. The importance of this differential surface chemistry is it can improve the detection limit of nanopore blockade sensors in quantitative analysis. Based on such functionalized nanopore devices, nanopore blockade sensors lower the limit of detection by an order of magnitude and enable ultrasensitive detection of PSA as low as 80 aM. The findings from this study open new opportunities for nanopore sensors in further developments including optical detection and ultralow detection limit biosensing at complex biological fluids.
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http://dx.doi.org/10.1039/d0sc04552gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8163308PMC
October 2020

IL-1β promotes cervical cancer through activating NF-κB/CCL-2.

Int J Clin Exp Pathol 2021 15;14(4):426-433. Epub 2021 Apr 15.

Department of Geriatrics, The First Affiliated Hospital of Nanchang University No. 17, Yong Wai Zheng Road, Nangchang 330006, China.

Cervical cancer is a malignancy with high morbidity and mortality among women. Interleukin (IL)-1β, chemokine (C-C motif) ligand 2 (CCL-2), and activation of NF-κB have been proven to be closely related to the progression of various tumors. However, their role in cervical cancer remains unclear. Cell proliferation, migration, and invasion were detected using MTT, wound healing, and transwell assays. Western blotting and qRT-PCR were used to measure expression of target genes. IL-1β greatly promoted the release of CCL-2 from HeLa cells. Activation of NF-κB and phosphorylated NF-κB (p65) nuclear translocation were accelerated by IL-1β. TPCA-1, a blocker of NF-κB, significantly inhibited the release of CCL-2 from HeLa cells. TPCA-1 markedly reversed the promotional effect of IL-1β on viability of HeLa cells. IL-1β increased the cell migration, proliferation, and invasion of HeLa cells through targeting the NF-κB/CCL-2 pathway. IL-1β/NF-κB/CCL-2 might be a promising treatment target for cervical cancer treatment and prevention.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085834PMC
April 2021

FIT2 organizes lipid droplet biogenesis with ER tubule-forming proteins and septins.

J Cell Biol 2021 05;220(5)

National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Lipid droplets (LDs) are critical for lipid storage and energy metabolism. LDs form in the endoplasmic reticulum (ER). However, the molecular basis for LD biogenesis remains elusive. Here, we show that fat storage-inducing transmembrane protein 2 (FIT2) interacts with ER tubule-forming proteins Rtn4 and REEP5. The association is mainly transmembrane domain based and stimulated by oleic acid. Depletion of ER tubule-forming proteins decreases the number and size of LDs in cells and Caenorhabditis elegans, mimicking loss of FIT2. Through cytosolic loops, FIT2 binds to cytoskeletal protein septin 7, an interaction that is also required for normal LD biogenesis. Depletion of ER tubule-forming proteins or septins delays nascent LD formation. In addition, FIT2-interacting proteins are up-regulated during adipocyte differentiation, and ER tubule-forming proteins, septin 7, and FIT2 are transiently enriched at LD formation sites. Thus, FIT2-mediated nascent LD biogenesis is facilitated by ER tubule-forming proteins and septins.
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http://dx.doi.org/10.1083/jcb.201907183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8056755PMC
May 2021

Response surface methodology optimised solvothermal system enables an efficient extraction of echinacoside and oleuropein from Syringa pubescens Turcz.

Phytochem Anal 2021 Nov 9;32(6):1074-1081. Epub 2021 Apr 9.

Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, China.

Introduction: Syringa pubescens Turcz. was reported to be abundant in the Funiu Mountains of Henan Province and can be used to treat hepatitis and cirrhosis. In order to develop and utilise the resource, a fast and simple technique to extract bioactive compounds is needed.

Objectives: Our aims were to provide an extraction technique of glycosides from S. pubescens and study the antioxidant activity of this material.

Methods: Box-Behnken design (BBD) was employed with three factors at three levels. The process parameters such as ethanol concentration (X ), temperature (X ), and solvent-solid ratio (X ) could significantly influence efficiency and yield of target compounds. High-performance liquid chromatography (HPLC) was used to determine the content of glycosides. DPPH (α,α-diphenyl-β-picrylhydrazyl), ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) and reducing power were used to evaluate the antioxidant activity of S. pubescens extract.

Results: The optimal parameters for the maximal extraction yield were obtained with ethanol concentration of 68%, temperature of 89°C, solvent-solid ratio of 46 mL/g, and time of 20 min. The S. pubescens extract showed strong antioxidant properties in vitro.

Conclusion: The findings indicated the potential application of solvothermal extraction method to extract bioactive compounds from S. pubescens Turcz. Furthermore, the S. pubescens extract could be used as an important resource of antioxidant activity.
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http://dx.doi.org/10.1002/pca.3049DOI Listing
November 2021

Comprehensive Analysis of the Prognosis and Correlations With Immune Infiltration of S100 Protein Family Members in Hepatocellular Carcinoma.

Front Genet 2021 18;12:648156. Epub 2021 Mar 18.

Xiamen Branch, Department of Hepatic Oncology, Zhongshan Hospital, Fudan University, Xiamen, China.

S100 protein family members (S100s) are commonly dysregulated in various tumors including hepatocellular carcinoma (HCC). However, the diverse expression, mutation, prognosis and associations with immune infiltration of S100s in HCC have yet to be analyzed. Herein we investigated the roles of S100s in HCC from the Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), Human Protein Atlas, Kaplan-Meier Plotter, cBioPortal and TIMER databases. Compared with para-cancer tissues, the expression levels of S100A4/S100A6/S100A10/S100A11/S100A13/S100A14/S100P were higher in HCC tissues, while the expression levels of S100A8/S100A9/S100A12 were decreased in tumor tissues. The mRNA levels of S100A2/S100A7/S100A7A/S100A8/S100A9/S100A11 were correlated with advanced tumor stage. Besides, higher mRNA expressions of S100A6/S100A10/S100A11/S100A13/S100A14/S100P were shown to have shorter overall survival (OS), while higher expression of S100A12 was associated with favorable OS. Further, the mutation rate of S100s was investigated, and the high mutation rate (53%) was associated with shorter OS. Additionally, the expressions of S100s were found to be significantly associated with various immune infiltrating cells. Hence, our results showed that S100A6/S100A10/S100A11/S10012/S100A13/S100A14/S100P may be regarded as new prognostic or therapeutic markers and S100s inhibitors may be helpful in the combination of immunotherapies.
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http://dx.doi.org/10.3389/fgene.2021.648156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8013731PMC
March 2021

Efficacy and safety of thalidomide on psychological symptoms and sleep disturbances in the patient with refractory ankylosing spondylitis.

Ann Palliat Med 2021 Mar 15;10(3):2512-2519. Epub 2021 Jan 15.

Department of Rheumatology, Fujian Provincial Hospital, Fuzhou, China; Department of Rheumatology, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China.

Background: Thalidomide has been used to treat ankylosing spondylitis (AS) patients, but the efficacy and safety of thalidomide on psychological symptoms and sleep disturbances in the patient with refractory AS has not been evaluated.

Methods: In this 6-month open study, 35 cases of patients with refractory AS were recruited, using thalidomide at a dose of 150 mg/d before sleep. Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Bath Ankylosing Spondylitis Functional Index (BASFI), Bath Ankylosing Spondylitis Metrology Index (BASMI), fingertip-to-floor distance, nocturnal pain, total back pain, psychological symptoms, and sleep were assessed at baseline, 3 months and 6 months respectively.

Results: Clinical parameters, included BASDAI, BASFI, fingertip-to-floor distance, nocturnal pain, total back pain, ESR, CRP, SAS, SDS and PSQI lower levels of month 3 were found when compared to initial levels (P<0.05). In the 6th month, the levels of BASDAI, fingertip-to-floor, nocturnal pain, total back pain, SDS were further lower than those in the 3rd month (P<0.05). The levels of BASMI were lower than this at baseline (P<0.05). The most tolerable common adverse reactions were drowsiness (10/35), dry mouth (8/35), constipation (8/35), dandruff (7/35), dizziness (4/35).

Conclusions: Thalidomide can improve effectiveness and safety in the treatment of physical, as well as psychological symptoms and sleep disturbances accompanying refractory AS.
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http://dx.doi.org/10.21037/apm-19-409DOI Listing
March 2021

[Advancement of imaging technology for coronary microcirculation dysfunction assessment].

Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2020 Oct;37(5):892-896

Center for Biomedical Imaging Research (CBIR), Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, P.R.China.

Coronary microcirculation dysfunction (CMVD) is an important risk factor for the prognosis of re-perfused ischemic heart. Recent studies showed that the evaluation of CMVD has significant impact on both the early diagnosis of heart diseases relevant to blood supply and prognosis after myocardial reperfusion. In this review, the definition of CMVD from the perspective of pathophysiology was clarified, the principles and features of the state-of-the-art imaging technologies for CMVD assessment were reviewed from the perspective of engineering and the further research direction was promoted.
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http://dx.doi.org/10.7507/1001-5515.202005003DOI Listing
October 2020

Corrigendum: The Extracts of and Its Hairy Roots Attenuate Dextran Sodium Sulfate-Induced Chronic Ulcerative Colitis in Mice by Regulating Inflammation and Lymphocyte Apoptosis.

Front Immunol 2020 11;11:2092. Epub 2020 Sep 11.

Guangdong Provincial Key Laboratory of New Chinese Medicinals Development and Research, Guangzhou University of Chinese Medicine, Guangzhou, China.

[This corrects the article DOI: 10.3389/fimmu.2017.00905.].
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http://dx.doi.org/10.3389/fimmu.2020.02092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7518505PMC
September 2020

Modulation of gut mucosal microbiota as a mechanism of probiotics-based adjunctive therapy for ulcerative colitis.

Microb Biotechnol 2020 11 23;13(6):2032-2043. Epub 2020 Sep 23.

Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education P. R. C., Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs P. R. C., Inner Mongolia Agricultural University, Hohhot, 010018, China.

This was a pilot study aiming to evaluate the effects of probiotics as adjunctive treatment for ulcerative colitis (UC). Twenty-five active patients with UC were assigned to the probiotic (n = 12) and placebo (n = 13) groups. The probiotic group received mesalazine (60 mg kg  day ) and oral probiotics (containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8 and Bifidobacterium animalis subsp. lactis V9) twice daily for 12 weeks, while the placebo group received the same amounts of mesalazine and placebo. The clinical outcomes were assessed. The gut mucosal microbiota was profiled by PacBio single-molecule, real-time (SMRT) sequencing of the full-length 16S rRNA of biopsy samples obtained by colonoscopy. A significantly greater magnitude of reduction was observed in the UC disease activity index (UCDAI) in the probiotic group compared with the placebo group (P = 0.043), accompanying by a higher remission rate (91.67% for probiotic-receivers versus 69.23% for placebo-receivers, P = 0.034). The probiotics could protect from diminishing of the microbiota diversity and richness. Moreover, the gut mucosal microbiota of the probiotic-receivers had significantly more beneficial bacteria like Eubacterium ramulus (P < 0.05), Pediococcus pentosaceus (P < 0.05), Bacteroides fragilis (P = 0.02) and Weissella cibaria (P = 0.04). Additionally, the relative abundances of the beneficial bacteria correlated significantly but negatively with the UCDAI score, suggesting that the probiotics might alleviate UC symptoms by modulating the gut mucosal microbiota. Our research has provided new insights into the mechanism of symptom alleviation in UC by applying probiotic-based adjunctive treatment.
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http://dx.doi.org/10.1111/1751-7915.13661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7533322PMC
November 2020

Evaluating the sensing performance of nanopore blockade sensors: A case study of prostate-specific antigen assay.

Biosens Bioelectron 2020 Oct 8;165:112434. Epub 2020 Jul 8.

School of Chemistry, Australian Centre for NanoMedicine, Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales, 2052, Australia. Electronic address:

The detection principle of nanopore sensors relies on measuring changes in electrical signal as analyte molecules translocate through a nanoscale pore. There are two challenges with this experimental construct when using nanopores for quantitative sensing with low detection limits in complex samples. The first is getting the analyte to the nanopore in a reasonable time frame and the second is other species in the sample also translocating through the nanopore and generating erroneous signals. We have developed a nanopore blockade sensor that alleviates the limitations of diffusion-limited mass transport and non-specific signals. Antibody-modified magnetic nanoparticles are utilized to deliver analytes of interest extracted from sample to an array of antibody-modified nanopores under a controlled electromagnet, resulting in long-term nanopore blocking events due to the formation of sandwiched immunocomplexes. Herein, this study reports on understanding some of important parameters in determining the performance of nanopore blockade sensing system, where prostate-specific antigen (PSA) is used as a model analyte. We describe the characterization of nanopore blockade sensing of PSA by (1) tuning on/off the electromagnet, (2) varying nanopore number in a nanopore chip, and (3) deploying the sensor in human plasma. Results show that magnetophoresis effectively facilitates active delivery and selective sensing of PSA to the nanopore. Nanopore chips with a larger number of nanopores are shown to receive more nanopore blockades for a given concentration of analyte. Furthermore, identifiable blockade events accounted for successful detection of PSA in plasma, indicate the high specificity of the sensing system.
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http://dx.doi.org/10.1016/j.bios.2020.112434DOI Listing
October 2020

Amorphous/low-crystalline core/shell-type nanoparticles as highly efficient and self-stabilizing catalysts for alkaline hydrogen evolution.

Chem Commun (Camb) 2020 Aug 8;56(63):8984-8987. Epub 2020 Jul 8.

Key Laboratory of Coal Processing and Efficient Utilization (Ministry of Education), China University of Mining & Technology, Xuzhou 221116, P. R. China.

Amorphous/low-crystalline core/shell-type nanoparticles (Pd-P/Pt-Ni NPs) were prepared via a facile seed-mediated method. After acid treatment, the NPs exhibited self-improved catalysis for hydrogen evolution during electrolysis in an alkaline medium.
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http://dx.doi.org/10.1039/d0cc03016cDOI Listing
August 2020

CRISPR Mediated Biosensing Toward Understanding Cellular Biology and Point-of-Care Diagnosis.

Angew Chem Int Ed Engl 2020 11 25;59(47):20754-20766. Epub 2020 Aug 25.

School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, NSW, 2052, Australia.

Recent advances in CRISPR based biotechnologies have greatly expanded our capabilities to repurpose CRISPR for the development of biomolecular sensors for diagnosing diseases and understanding cellular pathways. The key attribute that allows CRISPR to be widely utilized is the programmable and highly selective mechanism. In this Minireview, we first illustrate the molecular principle of CRISPR functioning process from sensing to actuating. Next, the CRISPR based biosensing strategies for nucleic acids, proteins and small molecules are summarized. We highlight some of recent advances in applications for in vitro detection of biomolecules and in vivo imaging of cellular networks. Finally, the challenges with, and exciting prospects of, CRISPR based biosensing developments are discussed.
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http://dx.doi.org/10.1002/anie.202005398DOI Listing
November 2020

Patterned Molecular Films of Alkanethiol and PLL-PEG on Gold-Silicate Interfaces: How to Add Functionalities while Retaining Effective Antifouling.

Langmuir 2020 05 5;36(19):5243-5250. Epub 2020 May 5.

School of Chemistry, Australian Centre for NanoMedicine, University of New South Wales, Sydney, New South Wales 2052, Australia.

Spatial control of surface functionalization and interactions is essential for microarray-based analysis. This study reports the fabrication of two-dimensional molecular films with site-specific functionalities, forming microarrays at discrete locations. Arrays of microsized gold disks were produced on a silicate membrane using microfabrication. On these arrays, orthogonal self-assembly of molecules was performed that can specifically bind to gold or silicate. The gold array elements were functionalized with a range of alkanethiols and the silicate with polymeric poly-l-lysine-grafted-poly(ethylene glycol) (PLL-PEG). The surface functionalization on the gold disk array and the surrounding substrate was characterized at each step using X-ray photoelectron spectroscopy (XPS) to show that alkanethiols are specifically attached to the gold. PLL-PEG was used to provide resistance against nonspecific protein and cell adsorption and attached exclusively to the silicate. The effectiveness of the surface chemistry was validated by the selective self-assembly of a gold nanoparticle monolayer array on the gold regions. In a more sophisticated example, selective adhesion of MCF-7 cells to anti-EpCAM antibody modified gold areas of the gold-silicate surface was demonstrated to give a cell microarray. This study provides a general approach to fabricate chemical patterns on silicon-based devices with the convergence of microfabrication and material-specific surface modification, which may be useful to expand the functionalities and potential applications for patterned biomolecular films. Importantly, the ability to pattern surfaces with different surface chemistries is not limited to planar surfaces using this orthogonal surface-coupling approach.
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http://dx.doi.org/10.1021/acs.langmuir.0c00586DOI Listing
May 2020

IRF1 association with tumor immune microenvironment and use as a diagnostic biomarker for colorectal cancer recurrence.

Oncol Lett 2020 Mar 10;19(3):1759-1770. Epub 2020 Jan 10.

Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Beijing 102218, P.R. China.

Colorectal cancer (CRC) is considered to be one of the most lethal cancer types globally, and its recurrence is a major treatment challenge. Identifying the factors involved when determining the risk of CRC recurrence is required to improve personalized therapy for patients with CRC. Based on the GSE39582 dataset, the present study demonstrated that a higher ratio of M1 macrophages and activated memory CD4 T cells indicated a better recurrence-free survival (RFS) time for CRC, using CIBERSORT and Pearson's correlation analysis. Through weighted correlation network analysis (WGCNA), an immune-associated module was identified that was significantly positively correlated with the ratio of M1 macrophages and activated memory CD4 T cells. In this module, using WGCNA and a protein-protein interaction network, interferon regulatory factor 1 (IRF1), chemokine ligand 5, ubiquitin/ISG15-conjugating enzyme E2 L6, guanylate binding protein 1 and interleukin 2 receptor subunit beta were identified as hub genes. Among these genes, univariate Cox and multivariate Cox analysis revealed that IRF1 may be a potential diagnostic biomarker for RFS in patients with CRC. This was further validated using The Cancer Genome Atlas data. Gene set enrichment analysis demonstrated that IRF1 influenced the genes and pathways that are associated with immune cell recruitment and activation. Additionally, the DNA methylation of cg27587780 and cg15375424 CpG sites in the IRF1 gene region was indicated to be negatively correlated with IRF1 mRNA expression and positively correlated with the recurrence of CRC. Collectively, the results of the present study demonstrated that IRF1 may be a potential diagnostic biomarker for RFS in patients with CRC.
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http://dx.doi.org/10.3892/ol.2020.11289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7039159PMC
March 2020

Optimization of polysaccharide process from Fructus corni with box-behnken design and antioxidant capacity.

Pak J Pharm Sci 2019 Jul;32(4):1537-1544

Chemical Engineering and Pharmaceutical College, Henan University of Science and Technology, Luoyang, PR China.

In the present study, the ultrasound-assisted extraction (UAE) process of polysaccharide from Fructus corni (FCP) was opitimized using the Box-Behnken design (BBD). The main parameters including ultrasound time (min), temperature (oC) and solvent to raw material ratio (mL/g) were chosen as the process variables for the optimization of UAE process. The results of analysis of variance indicated that the equation obtained from the experiments could represent the data and the predicted responses satisfactorily. The optimum conditons obtained by BBD were ultrasonic time (51min), temperature (69oC) and solvent to solid ratio (20mL/g) with actual yield (12.68±0.16%), which was good agreement with value predicted by the model. The antioxidant properties of FCP were assessed in vitro based on scavenging effect of the DPPH radical, hydroxyl radical and super oxide radical tests. The FCP possessed strong antioxidant abilities on DPPH and super oxide radical at the high concentration. The results on hydroxyl radical demonstrated that FCP exhibited high scavenging effect when the concentration was over 3000μg/mL. The findings suggested that the FCP had antioxidant capacities and could be developed as a source of natural antioxidants and functional food material.
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July 2019

How Nanoparticles Transform Single Molecule Measurements into Quantitative Sensors.

Adv Mater 2020 May 30;32(18):e1904339. Epub 2019 Sep 30.

School of Chemistry, The University of New South Wales, Sydney, NSW, 2052, Australia.

Single molecule measurements are revolutionizing the understanding of the stochastics of behavior of single molecules. There is a common theme referred to as a near-field approach, in how many single molecule measurements are being performed in assays. The term near field is used because the measurement volume is typically very small such that a single molecule, or a single molecule binding pair, within that volume is of an appreciable concentration. The next development in detection will be performing many single molecule measurements at one time such that single molecule measurements can be used as the basis for quantitative analysis. There have already been some notable developments in this direction. Again, all have a common theme in that nanoparticles are used to create many near-field volumes that can be measured simultaneously. Herein, the coupled developments in nanoparticles and measurement strategies that allow nanoparticles to be the backbone of the next generation of sensing technologies are discussed.
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http://dx.doi.org/10.1002/adma.201904339DOI Listing
May 2020

Intrinsic and well-defined second generation hot spots in gold nanobipyramids versus gold nanorods.

Chem Commun (Camb) 2019 Jun;55(53):7707-7710

School of Chemistry, University of New South Wales Sydney, NSW 2052, Australia.

An effective strategy for regioselective modification and directional assembly of anisotropic nanoparticles is demonstrated to explore the electric field enhancement in assembled gold nanobipyramids compared with gold nanorods. The well-defined secondary plasmonic hot spots between the coupled gold nanobipyramids exhibit the capability for single molecule detection.
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http://dx.doi.org/10.1039/c9cc02730kDOI Listing
June 2019

Nanopore blockade sensors for ultrasensitive detection of proteins in complex biological samples.

Nat Commun 2019 05 8;10(1):2109. Epub 2019 May 8.

School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, NSW, 2052, Australia.

Nanopore sensors detect individual species passing through a nanoscale pore. This experimental paradigm suffers from long analysis times at low analyte concentration and non-specific signals in complex media. These limit effectiveness of nanopore sensors for quantitative analysis. Here, we address these challenges using antibody-modified magnetic nanoparticles ((anti-PSA)-MNPs) that diffuse at zero magnetic field to capture the analyte, prostate-specific antigen (PSA). The (anti-PSA)-MNPs are magnetically driven to block an array of nanopores rather than translocate through the nanopore. Specificity is obtained by modifying nanopores with anti-PSA antibodies such that PSA molecules captured by (anti-PSA)-MNPs form an immunosandwich in the nanopore. Reversing the magnetic field removes (anti-PSA)-MNPs that have not captured PSA, limiting non-specific effects. The combined features allow detecting PSA in whole blood with a 0.8 fM detection limit. Our 'magnetic nanoparticle, nanopore blockade' concept points towards a strategy to improving nanopore biosensors for quantitative analysis of various protein and nucleic acid species.
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http://dx.doi.org/10.1038/s41467-019-10147-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506515PMC
May 2019
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