Publications by authors named "Si Wu"

339 Publications

Identification of Proteomic Signatures in Chronic Obstructive Pulmonary Disease Emphysematous Phenotype.

Front Mol Biosci 2021 1;8:650604. Epub 2021 Jul 1.

Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China.

Chronic obstructive pulmonary disease (COPD) is a highly heterogeneous disease. Emphysematous phenotype is the most common and critical phenotype, which is characterized by progressive lung destruction and poor prognosis. However, the underlying mechanism of this structural damage has not been completely elucidated. A total of 12 patients with COPD emphysematous phenotype (COPD-E) and nine patients with COPD non-emphysematous phenotype (COPD-NE) were enrolled to determine differences in differential abundant protein (DAP) expression between both groups. Quantitative tandem mass tag-based proteomics was performed on lung tissue samples of all patients. A total of 29 and 15 lung tissue samples from patients in COPD-E and COPD-NE groups, respectively, were used as the validation cohort to verify the proteomic analysis results using western blotting. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted for DAPs. A total of 4,343 proteins were identified, of which 25 were upregulated and 11 were downregulated in the COPD-E group. GO and KEGG analyses showed that wound repair and retinol metabolism-related pathways play an essential role in the molecular mechanism of COPD emphysematous phenotype. Three proteins, namely, KRT17, DHRS9, and FMO3, were selected for validation. While KRT17 and DHRS9 were highly expressed in the lung tissue samples of the COPD-E group, FMO3 expression was not significantly different between both groups. In conclusion, KRT17 and DHRS9 are highly expressed in the lung tissue of patients with COPD emphysematous phenotype. Therefore, these proteins might involve in wound healing and retinol metabolism in patients with emphysematous phenotype and can be used as phenotype-specific markers.
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http://dx.doi.org/10.3389/fmolb.2021.650604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8280333PMC
July 2021

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices.

Nat Methods 2021 Jul 8;18(7):747-756. Epub 2021 Jul 8.

CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.

Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.
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http://dx.doi.org/10.1038/s41592-021-01197-1DOI Listing
July 2021

Silencing of RSPO1 mitigates obesity-related renal fibrosis in mice by deactivating Wnt/β-catenin pathway.

Exp Cell Res 2021 Jun 25;405(2):112713. Epub 2021 Jun 25.

Department of Nephrology, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China. Electronic address:

Obesity, a global epidemic, is one of the critical causes of chronic kidney disease (CKD). R-spondin1 (RSPO1) possessing the potential to activate Wnt/β-catenin pathway was reported to be elevated in circulation of obesity objects. However, the function of RSPO1 and the latent mechanism in obesity-related CKD are still left to be revealed. In the present study, renal RSPO1 expression was increased in mice fed on high-fat diet (HFD) for 12 weeks. Lentivirus-mediated RSPO1 knockdown partly recovered obesity-related metabolic symptoms, while distinctly remitted kidney dysfunction and renal fibrosis in obesity mice. In vitro, recombinant RSPO1 was found to elevate leucine-rich repeat-containing G protein coupled receptor 4 (LGR4) expression, promote Wnt/β-catenin signaling pathway activation, facilitate epithelial-mesenchymal transition (EMT) and increase collagen deposition in HK2 renal tubular cells. Such pro-fibrotic effect of RSPO1 was diminished by LGR4 siRNA in HK2 cells. In summary, we demonstrate that RSPO1/LGR4 axis is involved in obesity-related renal fibrosis at least through activating Wnt/β-catenin signaling pathway, providing a potential therapeutic target for this disease.
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http://dx.doi.org/10.1016/j.yexcr.2021.112713DOI Listing
June 2021

Blood Biomarkers Predict Cardiac Workload Using Machine Learning.

Biomed Res Int 2021 1;2021:6172815. Epub 2021 Jun 1.

Applied Psychology and Human Development, University of Toronto, 252 Bloor St. West, Toronto, Ontario, Canada M5S 1V6.

Introduction: Rate pressure product (the product of heart rate and systolic blood pressure) is a measure of cardiac workload. Resting rate pressure product (rRPP) varies from one individual to the next, but its biochemical/cellular phenotype remains unknown. This study determined the degree to which an individual's biochemical/cellular profile as characterized by a standard blood panel is predictive of rRPP, as well the importance of each blood biomarker in this prediction.

Methods: We included data from 55,730 participants in this study with complete rRPP measurements and concurrently collected blood panel information from the Health Management Centre at the Affiliated Hospital of Hangzhou Normal University. We used the XGBoost machine learning algorithm to train a tree-based model and then assessed its accuracy on an independent portion of the dataset and then compared its performance against a standard linear regression technique. We further determined the predictive importance of each feature in the blood panel.

Results: We found a fair positive correlation (Pearson ) of 0.377 (95% CI: 0.375-0.378) between observed rRPP and rRPP predicted from blood biomarkers. By comparison, the performance for standard linear regression was 0.352 (95% CI: 0.351-0.354). The top three predictors in this model were glucose concentration, total protein concentration, and neutrophil count. /.

Conclusion: Blood biomarkers predict resting RPP when modeled in combination with one another; such models are valuable for studying the complex interrelations between resting cardiac workload and one's biochemical/cellular phenotype.
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http://dx.doi.org/10.1155/2021/6172815DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8187049PMC
June 2021

Knowledge Exchange Between Domain-Adversarial and Private Networks Improves Open Set Image Classification.

IEEE Trans Image Process 2021 23;30:5807-5818. Epub 2021 Jun 23.

Both target-specific and domain-invariant features can facilitate Open Set Domain Adaptation (OSDA). To exploit these features, we propose a Knowledge Exchange (KnowEx) model which jointly trains two complementary constituent networks: (1) a Domain-Adversarial Network (DAdvNet) learning the domain-invariant representation, through which the supervision in source domain can be exploited to infer the class information of unlabeled target data; (2) a Private Network (PrivNet) exclusive for target domain, which is beneficial for discriminating between instances from known and unknown classes. The two constituent networks exchange training experience in the learning process. Toward this end, we exploit an adversarial perturbation process against DAdvNet to regularize PrivNet. This enhances the complementarity between the two networks. At the same time, we incorporate an adaptation layer into DAdvNet to address the unreliability of the PrivNet's experience. Therefore, DAdvNet and PrivNet are able to mutually reinforce each other during training. We have conducted thorough experiments on multiple standard benchmarks to verify the effectiveness and superiority of KnowEx in OSDA.
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http://dx.doi.org/10.1109/TIP.2021.3088642DOI Listing
June 2021

A brain-inspired computational model for spatio-temporal information processing.

Neural Netw 2021 May 16;143:74-87. Epub 2021 May 16.

Center for Neurointelligence, School of Medicine, Chongqing University, No.174 Shazhengjie, Shapingba, Chongqing 400044, PR China; AI Research Center, Peng Cheng Laboratory, No.2, Xingke First Street, Nanshan District, Shenzhen 518005, PR China. Electronic address:

Spatio-temporal information processing is fundamental in both brain functions and AI applications. Current strategies for spatio-temporal pattern recognition usually involve explicit feature extraction followed by feature aggregation, which requires a large amount of labeled data. In the present study, motivated by the subcortical visual pathway and early stages of the auditory pathway for motion and sound processing, we propose a novel brain-inspired computational model for generic spatio-temporal pattern recognition. The model consists of two modules, a reservoir module and a decision-making module. The former projects complex spatio-temporal patterns into spatially separated neural representations via its recurrent dynamics, the latter reads out neural representations via integrating information over time, and the two modules are linked together using known examples. Using synthetic data, we demonstrate that the model can extract the frequency and order information of temporal inputs. We apply the model to reproduce the looming pattern discrimination behavior as observed in experiments successfully. Furthermore, we apply the model to the gait recognition task, and demonstrate that our model accomplishes the recognition in an event-based manner and outperforms deep learning counterparts when training data is limited.
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http://dx.doi.org/10.1016/j.neunet.2021.05.015DOI Listing
May 2021

Grain security assessment in Bangladesh based on supply-demand balance analysis.

PLoS One 2021 26;16(5):e0252187. Epub 2021 May 26.

Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.

Ensuring the grain supply-demand balance and achieving grain security had been the main tasks for the government of Bangladesh. On the supply side, Bangladesh's supply of grain products has increased substantially, with an average annual growth rate of 1.99 million tons in 1998-2018. Domestic grain production, especially rice production, accounted for the largest proportion in its structure. However, under the constraints of resources and environment, imports and international aid were needed to ensure a stable and sustainable grain supply. On the demand side, Bangladesh's demand for grain products continued to grow at an average annual rate of 2.09 million tons and its structure was constantly diversified. In recent years, domestic grain production has fully met the grain demand for food use, but the overall grain supply dependence on foreign gradually increased. From the analysis of the influencing factors, the grain supply, especially the domestic production of rice and maize, had the greatest impact on the balance of grain supply-demand in Bangladesh. Moreover, multiple cropping index, chemical fertilizer application per hectare and irrigation rate were the three main factors affecting grain production. As a typical agricultural country, Bangladesh's grain security was faced with challenges, such as high population density, insufficient cultivated land resources, international grain trade and frequent natural disasters. It is suggested that its government should strengthen scientific and technological research, adjust agricultural structure, improve the efficient utilization of agricultural resources and grain circulation systems, and balance the grain demand between food use and indirect use, so as to achieve complete grain self-sufficiency and overall grain security.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0252187PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8153451PMC
May 2021

Neurotrophic factor levels in the serum and cerebrospinal fluid of neonates infected with human cytomegalovirus.

Microbiol Immunol 2021 May 21. Epub 2021 May 21.

Department of BioBank, Sheng Jing Hospital of China Medical University, Shenyang, China.

Human cytomegalovirus (HCMV) is most likely to damage the central nervous system (CNS) during early embryonic development; however, the early neurodevelopmental abnormalities caused by HCMV infection and the regulation of cytokines remain unclear. Therefore, we investigated neuronal factors in the serum and cerebrospinal fluid (CSF) of newborns infected with HCMV using protein microarray technology with a view to elucidating the changes in specific neuronal factors for use in the development of a reliable index for predicting CNS injury caused by HCMV infection. Serum and CSF were collected from four newborns with HCMV infection and CNS injury (HCMV-infected group) and from four newborns without CNS infection (control group). A protein microarray containing 29 kinds of CNS-related cytokines was used to identify differentially expressed neuronal factors in the serum and CSF of the HCMV-infected and control groups. The levels of the differentially expressed proteins were verified further in 30 CSF samples from an HCMV-infected group using enzyme-linkedimmunosorbent assay (ELISA). Between newborns in the HCMV-infected and control groups, the protein microarray analysis identified three differentially expressed neurotrophic factors in the CSF samples: Acrp30, MMP-3, and interleukin-1 alpha (IL-1α). No differential cytokine expression was seen in the serum. ELISA showed significantly higher expression levels of Acrp30 and MMP-3 in the CSF of the 30 newborns with HCMV infection and CNS injury than in those in the control group, whereas the expression of IL-1α was significantly lower. Our results demonstrate that changes in the expression levels of Acrp30, MMP-3, and IL-1α in the CSF of newborns infected with HCMV may be related to the pathogenesis of CNS infection.
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http://dx.doi.org/10.1111/1348-0421.12918DOI Listing
May 2021

Analysis based on Monte Carlo simulation: How effective is tigecycline in routine antimicrobial therapy?

Int J Clin Pharmacol Ther 2021 Jul;59(7):496-505

Objective: This paper aims to assess the efficacy of tigecycline in the treatment of several different infections from a pharmacokinetic/pharmacodynamic (PK/PD) perspective.

Materials And Methods: The minimum inhibitory concentration (MIC) test strip test was used to determine the MICs of clinical isolates of tigecycline. A 5,000-subjects simulation was performed by Crystal Ball software to calculate the probability of achieving the required PK/PD exposure.

Results: The use of standard tigecycline dosing is predicted to have a good clinical outcome for patients suffering from complicated skin and skin structure infection (cSSSI) with MICs ≤ 0.25 mg×L, patients suffering from complicated intra-abdominal infection (cIAI) with MICs ≤ 1 mg×L, and patients suffering from hospital-acquired pneumonia (HAP) with MICs ≤ 0.5 mg×L. Generally, Gram-positive bacteria are highly sensitive to tigecycline, while Gram-negative bacteria are less sensitive: for patients with HAP and cIAI, the tolerable outcome was achieved using the standard regimen for most Gram-negative pathogens; the desired outcomes could be obtained for the increased-dose treatment; with increasing dose (100 mg every 12 hours), the average cumulative fractions of response (CFRs) markedly increased from 38.18 to 56.21% for cSSSI patients. When tigecycline, a standard regimen, was used to treat carbapenem-resistant (CRKP) and carbapenem-resistant . (CRE) infections, the cumulative response scores were 4.96 - 66.39% and 13.14 - 95.18%, respectively, and the CFRs of the increased dose also increased correspondingly.

Conclusion: Currently, the standard dose of tigecycline is feasible in the treatment of common bacterial infections, and PK/PD indexes are needed to optimize the regimens for refractory carbapenem-resistant bacterial infections.
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http://dx.doi.org/10.5414/CP203903DOI Listing
July 2021

Dual-Functional Aligned and Interconnected Graphite Nanoplatelet Networks for Accelerating Solar Thermal Energy Harvesting and Storage within Phase Change Materials.

ACS Appl Mater Interfaces 2021 Apr 19;13(16):19200-19210. Epub 2021 Apr 19.

Research Center of Solar Power & Refrigeration, School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.

Solar thermal energy conversion and storage within phase change materials (PCMs) can overcome solar radiation intermittency to enable continuous operation of many heating-related processes. However, the energy-harvesting performance of current storage systems is always limited by low efficiencies in either solar thermal energy conversion or thermal transport within PCMs. Although PCM-based nanocomposites can address one or both of these issues, achieving high-performance composites with simultaneously enhanced photothermal performance and thermal transport capacity remains challenging. Here, we demonstrate that dual-functional aligned and interconnected graphite nanoplatelet networks (AIGNNs) yield the synergistic enhancement of interfacial photothermal conversion and thermal transport within PCMs to accelerate the solar thermal energy harvesting and storage. The AIGNNs include the naked part as the three-dimensional optical absorber and the incorporated part as thermally conductive pathways within PCMs. First, a phase change composite composed of the AIGNNs and the solid-solid PCM of polyhydric alcohol is synthesized using a facile three-step method, and shows 400% thermal conductivity enhancement for per 1 wt % graphite loading compared to pristine PCMs. After the elaborate surface treatment, a small part of the graphite networks is in situ exposed as the 3D optical absorber to boost the surface full-spectrum sunlight absorptivity up to 95%. This dual function design takes full advantage of the integrated AIGNNs in terms of both photothermal conversion and thermal transport capacities, superior to the traditional coating-enhanced photothermal conversion. This work offers a promising route to accelerating solar thermal energy harvesting and storage within PCMs.
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http://dx.doi.org/10.1021/acsami.0c22814DOI Listing
April 2021

PES inhibits human-inducible Hsp70 by covalent targeting of cysteine residues in the substrate-binding domain.

J Biol Chem 2021 Jan-Jun;296:100210. Epub 2020 Dec 24.

National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of the Chinese Academy of Sciences, Beijing, China. Electronic address:

Hsp70 proteins are a family of ancient and conserved chaperones. They play important roles in vital cellular processes, such as protein quality control and the stress response. Hsp70 proteins are a potential drug target for treatment of disease, particularly cancer. PES (2-phenylethynesulfonamide or pifithrin-μ) has been reported to be an inhibitor of Hsp70. However, the mechanism of PES inhibition is still unclear. In this study we found that PES can undergo a Michael addition reaction with Cys-574 and Cys-603 in the SBDα of human HspA1A (hHsp70), resulting in covalent attachment of a PES molecule to each Cys residue. We previously showed that glutathionylation of Cys-574 and Cys-603 affects the structure and function of hHsp70. In this study, PES modification showed similar structural and functional effects on hHsp70 to glutathionylation. Further, we found that susceptibility to PES modification is influenced by changes in the conformational dynamics of the SBDα, such as are induced by interaction with adjacent domains, allosteric changes, and mutations. This study provides new avenues for development of covalent inhibitors of hHsp70.
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http://dx.doi.org/10.1074/jbc.RA120.015440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7948744PMC
December 2020

Novel Gene Regulation in Normal and Abnormal Spermatogenesis.

Cells 2021 Mar 17;10(3). Epub 2021 Mar 17.

The NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou 510600, China.

Spermatogenesis is a complex and dynamic process which is precisely controlledby genetic and epigenetic factors. With the development of new technologies (e.g., single-cell RNA sequencing), increasingly more regulatory genes related to spermatogenesis have been identified. In this review, we address the roles and mechanisms of novel genes in regulating the normal and abnormal spermatogenesis. Specifically, we discussed the functions and signaling pathways of key new genes in mediating the proliferation, differentiation, and apoptosis of rodent and human spermatogonial stem cells (SSCs), as well as in controlling the meiosis of spermatocytes and other germ cells. Additionally, we summarized the gene regulation in the abnormal testicular microenvironment or the niche by Sertoli cells, peritubular myoid cells, and Leydig cells. Finally, we pointed out the future directions for investigating the molecular mechanisms underlying human spermatogenesis. This review could offer novel insights into genetic regulation in the normal and abnormal spermatogenesis, and it provides new molecular targets for gene therapy of male infertility.
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http://dx.doi.org/10.3390/cells10030666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8002376PMC
March 2021

[Cupping treatment combined with antibiotics for bacterial pneumonia in children: a randomized controlled trial].

Zhongguo Zhen Jiu 2021 Mar;41(3):283-7

Children's Diagnosis and Treatment Center, Affiliated Hospital of Changchun University of CM, Changchun 130021, Jilin Province.

Objective: To compare the clinical efficacy of cupping treatment combined with antibiotics and antibiotics alone for bacterial pneumonia in children.

Methods: A total of 72 children with bacterial pneumonia were randomly divided into an observation group (36 cases, 1 case dropped off) and a control group (36 cases). The children in the control group were treated with intravenous drip of cefodizine sodium [80 mg/(kg•d)] for 7 days. Based on the treatment of the control group, the children in the observation group were treated with cupping treatment on the bladder meridian of the back on the first day and the fourth day of antibiotic treatment; each cupping treatment was given for 5-10 min; the treatment of observation group was given for 7 days. The days for complete fever reduction, TCM syndrome scores and Canadian acute respiratory illness flu scale (CARIFS) scores before and after treatment were observed, and the clinical efficacy was evaluated.

Results: The days for complete fever reduction in the observation group were shorter than that in the control group (<0.05). After treatment, the TCM syndrome scores and CARIFS scores in the two groups were reduced (<0.05), and the cough score, expectoration score, lung auscultation score of TCM syndrome and cough score, runny nose score and sore throat score of CARIFS in the observation group were lower than those in the control group (<0.05). The cured rate in the observation group was 97.1% (34/35), which had no significant difference with 91.7% (33/36) in the control group (>0.05).

Conclusion: Cupping treatment combined with antibiotics has similar efficacy with antibiotics alone for bacterial pneumonia in children, but shows better effect in shortening the duration of fever and improving pulmonary symptoms.
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http://dx.doi.org/10.13703/j.0255-2930.20200804-k0004DOI Listing
March 2021

Bile reflux is an independent risk factor for precancerous gastric lesions and gastric cancer: An observational cross-sectional study.

J Dig Dis 2021 May 6;22(5):282-290. Epub 2021 May 6.

State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Medical University, Xi'an, Shaanxi Province, China.

Objective: To identify whether bile reflux on endoscopy and other related variables are risk factors for precancerous gastric lesions and gastric cancer (GC).

Methods: A multicenter, cross-sectional and observational study was conducted in five centers in China from June to October 2019, 1162 patients were recruited and divided into the chronic gastritis (CG), the precancerous lesion (low-grade intraepithelial neoplasia and intestinal metaplasia), and GC groups (including high-grade intraepithelial neoplasia). All participants underwent detailed interviews, endoscopy and biopsy, and completed questionnaires. Odds ratio and 95% confidence interval were calculated with multivariate logistic regression models with or without adjustment for Helicobacter pylori infection.

Results: We recruited 668 patients with CG, 411 with precancerous lesions and 83 with GC. By comparing the CG and precancerous lesion groups, independent risk factors for cancerous gastric lesions were the grade of bile reflux, patient's age, dietary habits and family history of GC. Similar results were obtained when comparing the CG and GC groups. In addition, bile reflux was confirmed as an independent risk factor for progression from precancerous lesions to cancer.

Conclusions: Bile reflux on endoscopy as well as age, dietary habits and a family history of GC were independent risk factors for the development of precancerous gastric lesions and GC.
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http://dx.doi.org/10.1111/1751-2980.12986DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8252397PMC
May 2021

TopMSV: A Web-Based Tool for Top-Down Mass Spectrometry Data Visualization.

J Am Soc Mass Spectrom 2021 Jun 29;32(6):1312-1318. Epub 2021 Mar 29.

Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States.

Top-down mass spectrometry (MS) investigates intact proteoforms for proteoform identification, characterization, and quantification. Data visualization plays an essential role in top-down MS data analysis because proteoform identification and characterization often involve manual data inspection to determine the molecular masses of highly charged ions and validate unexpected alterations in identified proteoforms. While many software tools have been developed for MS data visualization, there is still a lack of web-based visualization software designed for top-down MS. Here, we present TopMSV, a web-based tool for top-down MS data processing and visualization. TopMSV provides interactive views of top-down MS data using a web browser. It integrates software tools for spectral deconvolution and proteoform identification and uses analysis results of the tools to annotate top-down MS data.
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http://dx.doi.org/10.1021/jasms.0c00460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8172439PMC
June 2021

Quantitative Top-Down Proteomics in Complex Samples Using Protein-Level Tandem Mass Tag Labeling.

J Am Soc Mass Spectrom 2021 Jun 16;32(6):1336-1344. Epub 2021 Mar 16.

Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.

Labeling approaches using isobaric chemical tags (e.g., isobaric tagging for relative and absolute quantification, iTRAQ and tandem mass tag, TMT) have been widely applied for the quantification of peptides and proteins in bottom-up MS. However, until recently, successful applications of these approaches to top-down proteomics have been limited because proteins tend to precipitate and "crash" out of solution during TMT labeling of complex samples making the quantification of such samples difficult. In this study, we report a top-down TMT MS platform for confidently identifying and quantifying low molecular weight intact proteoforms in complex biological samples. To reduce the sample complexity and remove large proteins from complex samples, we developed a filter-SEC technique that combines a molecular weight cutoff filtration step with high-performance size exclusion chromatography (SEC) separation. No protein precipitation was observed in filtered samples under the intact protein-level TMT labeling conditions. The proposed top-down TMT MS platform enables high-throughput analysis of intact proteoforms, allowing for the identification and quantification of hundreds of intact proteoforms from cell lysates. To our knowledge, this represents the first high-throughput TMT labeling-based, quantitative, top-down MS analysis suitable for complex biological samples.
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http://dx.doi.org/10.1021/jasms.0c00464DOI Listing
June 2021

Single Molecule Characterization of Amyloid Oligomers.

Molecules 2021 Feb 11;26(4). Epub 2021 Feb 11.

National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China.

The misfolding and aggregation of polypeptide chains into β-sheet-rich amyloid fibrils is associated with a wide range of neurodegenerative diseases. Growing evidence indicates that the oligomeric intermediates populated in the early stages of amyloid formation rather than the mature fibrils are responsible for the cytotoxicity and pathology and are potentially therapeutic targets. However, due to the low-populated, transient, and heterogeneous nature of amyloid oligomers, they are hard to characterize by conventional bulk methods. The development of single molecule approaches provides a powerful toolkit for investigating these oligomeric intermediates as well as the complex process of amyloid aggregation at molecular resolution. In this review, we present an overview of recent progress in characterizing the oligomerization of amyloid proteins by single molecule fluorescence techniques, including single-molecule Förster resonance energy transfer (smFRET), fluorescence correlation spectroscopy (FCS), single-molecule photobleaching and super-resolution optical imaging. We discuss how these techniques have been applied to investigate the different aspects of amyloid oligomers and facilitate understanding of the mechanism of amyloid aggregation.
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http://dx.doi.org/10.3390/molecules26040948DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7916856PMC
February 2021

Studying protein folding in health and disease using biophysical approaches.

Emerg Top Life Sci 2021 May;5(1):29-38

National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China.

Protein folding is crucial for normal physiology including development and healthy aging, and failure of this process is related to the pathology of diseases including neurodegeneration and cancer. Early thermodynamic and kinetic studies based on the unfolding and refolding equilibrium of individual proteins in the test tube have provided insight into the fundamental principles of protein folding, although the problem of predicting how any given protein will fold remains unsolved. Protein folding within cells is a more complex issue than folding of purified protein in isolation, due to the complex interactions within the cellular environment, including post-translational modifications of proteins, the presence of macromolecular crowding in cells, and variations in the cellular environment, for example in cancer versus normal cells. Development of biophysical approaches including fluorescence resonance energy transfer (FRET) and nuclear magnetic resonance (NMR) techniques and cellular manipulations including microinjection and insertion of noncanonical amino acids has allowed the study of protein folding in living cells. Furthermore, biophysical techniques such as single-molecule fluorescence spectroscopy and optical tweezers allows studies of simplified systems at the single molecular level. Combining in-cell techniques with the powerful detail that can be achieved from single-molecule studies allows the effects of different cellular components including molecular chaperones to be monitored, providing us with comprehensive understanding of the protein folding process. The application of biophysical techniques to the study of protein folding is arming us with knowledge that is fundamental to the battle against cancer and other diseases related to protein conformation or protein-protein interactions.
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http://dx.doi.org/10.1042/ETLS20200317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8138949PMC
May 2021

Spray-Capillary-Based Capillary Electrophoresis Mass Spectrometry for Metabolite Analysis in Single Cells.

Anal Chem 2021 03 1;93(10):4479-4487. Epub 2021 Mar 1.

Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States.

Single-cell capillary electrophoresis mass spectrometry (CE-MS) is a promising platform to analyze cellular contents and probe cell heterogeneity. However, current single-cell CE-MS methods often rely on offline microsampling processes and may demonstrate low sampling precision and accuracy. We have recently developed an electrospray-assisted device, , for low-volume sample extraction. With the spray-capillary, low-volume samples (pL-nL) are drawn into the sampling end of the device, which can be used directly for CE separation and online MS detection. Here, we redesigned the spray-capillary by utilizing a capillary with a <15 μm tapered tip so that it can be directly inserted into single cells for sample collection and on-capillary CE-MS analysis. We evaluated the performance of the modified spray-capillary by performing single-cell microsampling on single onion cells with varying sample injection times and direct MS analysis or online CE-MS analysis. We have demonstrated, for the first time, online sample collection and CE-MS for the analysis of single cells. This application of the modified spray-capillary device facilitates the characterization and relative quantification of hundreds of metabolites in single cells.
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http://dx.doi.org/10.1021/acs.analchem.0c04624DOI Listing
March 2021

Mechanisms of Manganese(II) Oxidation by Filamentous Ascomycete Fungi Vary With Species and Time as a Function of Secretome Composition.

Front Microbiol 2021 10;12:610497. Epub 2021 Feb 10.

Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States.

Manganese (Mn) oxides are among the strongest oxidants and sorbents in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and manganese peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Here we use a combination of chemical and in-gel assays and bulk mass spectrometry to demonstrate secretome-based Mn(II) oxidation in three phylogenetically diverse Ascomycetes that is mechanistically distinct from hyphal-associated Mn(II) oxidation on solid substrates. We show that Mn(II) oxidative capacity of these fungi is dictated by species-specific secreted enzymes and varies with secretome age, and we reveal the presence of both Cu-based and FAD-based Mn(II) oxidation mechanisms in all 3 species, demonstrating mechanistic redundancy. Specifically, we identify candidate Mn(II)-oxidizing enzymes as tyrosinase and glyoxal oxidase in sp. SRC1lsM3a, bilirubin oxidase in sp. and AP3s5-JAC2a, and GMC oxidoreductase in all 3 species, including sp. DS3sAY3a. The diversity of the candidate Mn(II)-oxidizing enzymes identified in this study suggests that the ability of fungal secretomes to oxidize Mn(II) may be more widespread than previously thought.
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http://dx.doi.org/10.3389/fmicb.2021.610497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7902709PMC
February 2021

Tristetraprolin expression by keratinocytes protects against skin carcinogenesis.

JCI Insight 2021 Mar 8;6(5). Epub 2021 Mar 8.

Institute for Medical Immunology, ULB Center for Research in Immunology, and ULB Center for Cancer Research, Université Libre de Bruxelles, Gosselies, Belgium.

Cancer is caused primarily by genomic alterations resulting in deregulation of gene regulatory circuits in key growth, apoptosis, or DNA repair pathways. Multiple genes associated with the initiation and development of tumors are also regulated at the level of mRNA decay, through the recruitment of RNA-binding proteins to AU-rich elements (AREs) located in their 3'-untranslated regions. One of these ARE-binding proteins, tristetraprolin (TTP; encoded by Zfp36), is consistently dysregulated in many human malignancies. Herein, using regulated overexpression or conditional ablation in the context of cutaneous chemical carcinogenesis, we show that TTP represents a critical regulator of skin tumorigenesis. We provide evidence that TTP controlled both tumor-associated inflammation and key oncogenic pathways in neoplastic epidermal cells. We identify Areg as a direct target of TTP in keratinocytes and show that EGFR signaling potentially contributed to exacerbated tumor formation. Finally, single-cell RNA-Seq analysis indicated that ZFP36 was downregulated in human malignant keratinocytes. We conclude that TTP expression by epidermal cells played a major role in the control of skin tumorigenesis.
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http://dx.doi.org/10.1172/jci.insight.140669DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8021119PMC
March 2021

High-Temperature Synthesis of a Uranyl Peroxo Complex Facilitated by Hydrothermally In Situ Formed Organic Peroxide.

Inorg Chem 2021 Feb 26;60(4):2133-2137. Epub 2021 Jan 26.

Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.

Because HO is thermally unstable, it seems to be difficult to synthesize peroxides at elevated temperatures. We describe here the in situ generation of peroxide that is incorporated in a new uranyl peroxo complex, HT-UPO1, through the hydrothermal treatment of uranyl nitrate at 150 °C in the presence of organic ligands. In this novel process, a highly conjugated aromatic carboxylate linker, ()-4-[2-(pyridin-4-yl)vinyl]benzoic acid (H), plays a crucial role by inducing the reduction of oxygen in air to form peroxide in situ and coordinating with uranyl to promote the preferred formation of thermally stable HT-UPO1. This work expands our knowledge on the speciation and chemistry of uranyl peroxide compounds and also sheds light on the possibility of their synthesis under more harsh conditions.
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http://dx.doi.org/10.1021/acs.inorgchem.0c03661DOI Listing
February 2021

Exosomal miR-186 derived from BMSCs promote osteogenesis through hippo signaling pathway in postmenopausal osteoporosis.

J Orthop Surg Res 2021 Jan 7;16(1):23. Epub 2021 Jan 7.

Department of Acupuncture, Tianjin Nankai Hospital, Tianjin, 300100, People's Republic of China.

Background: Postmenopausal osteoporosis (PMO) that results from estrogen withdrawal is the most common primary osteoporosis among older women. However, little is known about the mechanism of PMO, and effective treatment of PMO is limited.

Methods: We used real-time polymerase chain reaction (qPCR), Western blotting, and RNA pull down to investigate the relationship between miR-186 and MOB Kinase Activator 1A (Mob1). Also, we investigated the effect of exosome in osteogenesis using alkaline phosphatase (ALP) staining. And hematoxylin eosin (HE) staining was used to verify the osteogenesis in PMO model.

Results: Exosomal miR-186 plays an important role in bone formation. The results of miRNA-seq and q-PCR showed that miR-186 was upregulated in a PMO + Exo treatment group. Results of RNA-pull down and luciferase reporter assays verified interactions between miR-186 and Mob1. We also verified the Hippo signaling pathway plays an important role in osteogenesis.

Conclusions: We concluded that exosomes derived from human bone marrow mesenchymal stem cells (hBMSCs) can transfer miR-186 to promote osteogenesis in ovariectomy (OVX) rats through the Hippo signaling pathway.
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http://dx.doi.org/10.1186/s13018-020-02160-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7791800PMC
January 2021

Individual particle investigation on the chloride depletion of inland transported sea spray aerosols during East Asian summer monsoon.

Sci Total Environ 2021 Apr 24;765:144290. Epub 2020 Dec 24.

Guangdong Provincial Engineering Research Center for On-line Source Apportionment System of Air Pollution, Institute of Mass Spectrometry and Atmospheric Environment, Jinan University, Guangzhou 510632, PR China.

Inland transported sea spray aerosol (SSA) particles along with multiphase reactions are essential to drive the regional circulation of nitrogen, sulfur and halogen species in the atmosphere. Specially, the physicochemical properties of SSA will be significantly affected by the displacement reaction of chloride. However, the role of organic species and the mixing state on the chloride depletion of SSA during long-range inland transport remains unclear. Hence, a single particle aerosol mass spectrometer (SPAMS) was employed to investigate the particle size and chemical composition of individual SSA particles over inland southern China during the East Asian summer monsoon. Based on the variation of chemical composition, SSA particles were clustered into SSA-Aged, SSA-Bio and SSA-Ca. SSA-Aged was regarded as the aged Na-rich SSA particles. In comparison to the SSA-Aged, SSA-Bio involved some extra organic species associated with biological origin (i.e., organic nitrogen and phosphate). Each type occupies for approximately 50% of total detected SSA particles. Besides, SSA-Ca may relate to organic shell of Na-rich SSA particles, which is negligible (~3%). Tight correlation between Na and diverse organic acids was exhibited for the SSA-Aged (r = 0.52, p < 0.01) and SSA-Bio (r = 0.61, p < 0.01), reflecting the impact of organic acids to the chloride displacement during inland transport SSA particles. The chloride depletion occupied by organic acids is estimated to be up to 34%. It is noted that distinctly different degree of chloride depletion was observed between SSA-Aged and SSA-Bio. It is more likely to be attributed to the associated organic coatings for the SSA-Bio particles, which inhibits the displacement reactions between acids and chloride. As revealed from the mixing state of SSA-Bio, defined hourly mean peak area ratio of Cl / Na increases with the increasing phosphate and organic nitrogen. This finding provides additional basis for the improvement of modeling simulations in chlorine circulation and a comprehensive understanding of the effects of organics on chloride depletion of SSA particles.
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http://dx.doi.org/10.1016/j.scitotenv.2020.144290DOI Listing
April 2021

High-throughput hydrogen deuterium exchange mass spectrometry (HDX-MS) coupled with subzero-temperature ultrahigh pressure liquid chromatography (UPLC) separation for complex sample analysis.

Anal Chim Acta 2021 Jan 21;1143:65-72. Epub 2020 Nov 21.

Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA. Electronic address:

Hydrogen deuterium exchange coupled with mass spectrometry (HDX-MS) is a powerful technique for the characterization of protein dynamics and protein interactions. Recent technological developments in the HDX-MS field, such as sub-zero LC separations, large-scale data analysis tools, and efficient protein digestion methods, have allowed for the application of HDX-MS to the analysis of multi protein systems in addition to pure protein analysis. Still, high-throughput HDX-MS analysis of complex samples is not widespread because the co-elution of peptides combined with increased peak complexity after labeling makes peak de-convolution extremely difficult. Here, for the first time, we evaluated and optimized long gradient subzero-temperature ultra-high-pressure liquid chromatography (UPLC) separation conditions for the HDX-MS analysis of complex protein samples such as E. coli cell lysate digest. Under the optimized conditions, we identified 1419 deuterated peptides from 320 proteins at -10 °C, which is about 3-fold more when compared with a 15-min gradient separation under the same conditions. Interestingly, our results suggested that the peptides eluted late in the gradient are well-protected by peptide-column interactions at -10 °C so that peptides eluted even at the end of the gradient maintain high levels of deuteration. Overall, our study suggests that the optimized, sub-zero, long-gradient UPLC separation is capable of characterizing thousands of peptides in a single HDX-MS analysis with low back-exchange rates. As a result, this technique holds great potential for characterizing complex samples such as cell lysates using HDX-MS.
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http://dx.doi.org/10.1016/j.aca.2020.11.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8265693PMC
January 2021

Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells.

Viruses 2020 12 8;12(12). Epub 2020 Dec 8.

Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.

T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. Activation significantly altered PTMs following influenza infection, histone maps changed as T cells migrated to the site of infection, and T cells responding to secondary infections had significantly more transcription enhancing modifications. Thus, HiPTMap identified and quantified proteoforms and determined changes in CD8 T cell histone PTMs over the course of infection.
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http://dx.doi.org/10.3390/v12121409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7762524PMC
December 2020

The optimization conditions of establishing an H9c2 cardiomyocyte hypoxia/reoxygenation injury model based on an AnaeroPack System.

Cell Biol Int 2021 Apr 3;45(4):757-765. Epub 2021 Jan 3.

Department of Pharmacy, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.

Ischemia-reperfusion (I/R) injury is a major cause of cardiomyocyte apoptosis after vascular recanalization, which was mimicked by a hypoxia/reoxygenation (H/R) injury model of cardiomyocytes in vitro. In this study, we explored an optimal H/R duration procedure using the AnaeroPack System. To study the H/R procedure, cardiomyocytes were exposed to the AnaeroPack System with sugar and serum-free medium, followed by reoxygenation under normal conditions. Cell injury was detected through lactate dehydrogenase (LDH) and cardiac troponin (c-Tn) release, morphological changes, cell apoptosis, and expression of apoptosis-related proteins. The results showed that the damage to H9c2 cells increased with prolonged hypoxia time, as demonstrated by increased apoptosis rate, LDH and c-Tn release, HIF-1α expression, as well as decreased expression of Bcl-2. Furthermore, hypoxia for 10 h and reoxygenation for 6 h exhibited the highest apoptosis rate and damage and cytokine release; in addition, cells were deformed, small, and visibly round. After 12 h of hypoxia, the majority of the cells were dead. Taken together, this study showed that subjecting H9c2 cells to the AnaeroPack System for 10 h and reoxygenation for 6 h can achieve a practicable and repeatable H/R injury model.
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http://dx.doi.org/10.1002/cbin.11513DOI Listing
April 2021

A Customizable Analysis Flow in Integrative Multi-Omics.

Biomolecules 2020 11 27;10(12). Epub 2020 Nov 27.

Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA.

The number of researchers using multi-omics is growing. Though still expensive, every year it is cheaper to perform multi-omic studies, often exponentially so. In addition to its increasing accessibility, multi-omics reveals a view of systems biology to an unprecedented depth. Thus, multi-omics can be used to answer a broad range of biological questions in finer resolution than previous methods. We used six omic measurements-four nucleic acid (i.e., genomic, epigenomic, transcriptomics, and metagenomic) and two mass spectrometry (proteomics and metabolomics) based-to highlight an analysis workflow on this type of data, which is often vast. This workflow is not exhaustive of all the omic measurements or analysis methods, but it will provide an experienced or even a novice multi-omic researcher with the tools necessary to analyze their data. This review begins with analyzing a single ome and study design, and then synthesizes best practices in data integration techniques that include machine learning. Furthermore, we delineate methods to validate findings from multi-omic integration. Ultimately, multi-omic integration offers a window into the complexity of molecular interactions and a comprehensive view of systems biology.
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http://dx.doi.org/10.3390/biom10121606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7760368PMC
November 2020

Identification of key genes involved in JAK/STAT pathway in colorectal cancer.

Mol Immunol 2020 12 25;128:287-297. Epub 2020 Nov 25.

BioBank, Shengjing Hospital of China Medical University, PR China. Electronic address:

JAK/STAT pathway has been well confirmed in the development of colorectal cancer (CRC), however, the exact mechanism is unclear. Therefore, we aimed to identify key genes involved in JAK/STAT pathway in CRC, as well as the potential mechanism. RT² profiler PCR arrays were performed to identify key genes of the JAK/STAT pathway. GO, KEGG pathway and PPI analyses were performed to screen the main functions of differentially expressed genes (DEGs). Moreover, the expression of DEGs was detected by GEPIA based on TCGA database and verified by qPCR and/or Western blot. Subsequently, the association between the two DEGs (CXCL9 and IL6ST) and clinicopathological features were determined by immunohistochemistry, and survival analysis was also conducted. Finally, the effects of IL6ST overexpression on STAT3 activation and HT29 cell functions were analyzed. A total of 14 DEGs were identified. Among the DEGs, GHR, NR3C1, IL6ST and A2M were confirmed to be statistically decreased, while CXCL9 was significantly increased in the CRC tissues. Furthermore, CXCL9 was significantly associated with differentiation, lymph node metastasis, distant metastasis and invasion, while IL6ST was related with tumor size, differentiation, stage and invasion. Patients with high expression of IL6ST presented significantly lower lifetime, however, CXCL9 showed the opposite results without significance. Additionally, we found that overexpression of IL6ST statistically elevated p-STAT3 level, cell viability, adhesion rate and migration, and decreased apoptosis, but had no effects on cell cycle. Our results suggest that IL6ST is a critical key gene involved in JAK/STAT signaling pathway in CRC.
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http://dx.doi.org/10.1016/j.molimm.2020.10.007DOI Listing
December 2020

Identification of mucins and their expression in the vector mosquito Aedes albopictus.

J Vector Ecol 2020 12;45(2):297-305

Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Science, Hunan Normal University, Changsha, 410081, China.

Mucins, the main structural components of vertebrate respiratory, digestive and reproductive tract mucus, as well as insect peritrophic matrix, play important roles in protecting host cells from invading microbes and difficult external environments. Mucins are characterized by highly glycosylated proteins constituting the mucin domain that is rich in repetitive sequences of threonine, serine, and proline (PTS). Despite potential important roles, mosquito mucins remain largely uncharacterized. Here, we performed bioinformatics analyses to identify proteins with PTS repeat domain and predicted 43 mucins or mucin-related proteins in Aedes albopictus. Gene expression analysis revealed that these mucins are dynamically expressed across different development stages and in different organs of Aedes albopictus. Of note, blood feeding upregulated AALF016448 and AALF013291 expression in the midgut, fat body, and ovary, raising the possibility that these mucins play potential roles in reproduction, digestion, and intestinal defense against invading pathogens upon blood feeding. Our in silico identification, followed by expressional validation, thus established a valuable resource for further dissecting the functions of mucins for vector control.
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http://dx.doi.org/10.1111/jvec.12400DOI Listing
December 2020
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