Publications by authors named "Ji Huang"

189 Publications

Fabrication of microlenses with continuously variable numerical aperture through a temporally shaped femtosecond laser.

Opt Express 2021 Feb;29(3):4596-4606

We developed a novel method for fabricating microlenses and microlens arrays by controlling numerical aperture (NA) through temporally shaped femtosecond laser on fused silica. The modification area was controlled through the pulse delay of temporally shaped femtosecond laser. The final radius and sag height were obtained through subsequent hydrofluoric acid etching. Electron density was controlled by the temporally shaped femtosecond laser, and the maximum NA value (0.65) of a microlens was obtained in the relevant studies with femtosecond laser fabrication. Furthermore, the NA can be continuously adjusted from 0.1 to 0.65 by this method. Compared with the traditional methods, this method exhibited high flexibility and yielded microlenses with various NAs and microlens arrays to meet the different demands for microlens applications.
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http://dx.doi.org/10.1364/OE.411511DOI Listing
February 2021

Functionalization of freeform curved surfaces by shaped femtosecond laser pulses in the propagation axis.

Opt Express 2021 Feb;29(4):5487-5496

With ultrashort pulse durations and ultrahigh peak intensities, ultrafast lasers can create different types of micro/nano-structures to functionalize the processed surface with new properties. However, the applications of this method on freeform surfaces are still limited by the short length of a laser focusing spot and complex control of the 3D moving trajectory in the fabrication process. In this paper, we overcome this problem by shaping the on-axis intensity along the propagation axis using the spatial light modulator. By designing the phase mask, we increased the length of the stable-intensity zone (intensity fluctuation < 10%) by more than 3 times compared to that of an unshaped Bessel beam. The energy deposition was also optimized to be less than 2% fluctuation based on simulations. Using this method, we fabricated micro/nano structures on 3D surfaces at different fluences and demonstrated various properties including colorization, anti-reflection, and hydrophobicity in large height range. We demonstrated the applications of the proposed method in creating hydrophobicity on complex freeform syringe tip surfaces. This improved the minimum manipulatable volume of a liquid droplet to 2 times smaller compared with untreated syringe, thus greatly extending its performance for micro-droplet manipulation. This method offers an alternative approach for reliable and affordable freeform curved-surface processing.
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http://dx.doi.org/10.1364/OE.418663DOI Listing
February 2021

Role of tubular epithelial arginase-II in renal inflammaging.

NPJ Aging Mech Dis 2021 Mar 2;7(1). Epub 2021 Mar 2.

Cardiovascular and Aging Research, Department of Endocrinology, Metabolism, and Cardiovascular System, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.

The aging kidney undergoes complex changes and is vulnerable to injury and development of chronic kidney disease (CKD) with preponderance affecting more women than men. Evidence has been presented that the type-II L-arginine:ureohydrolase, arginase-II (Arg-II) plays a role in the acceleration of aging. Arg-II is highly expressed in the kidney. However, the role of Arg-II in renal aging is not known. This study is to investigate whether Arg-II is involved in the kidney aging process dependently on sex. Arg-II level in the kidney of wild type (WT) mice is significantly elevated with aging, which is accompanied by an increase in expression of the inflammatory cytokines/chemokines, tissue macrophages, factors involved in fibrosis, and tubulointestitial fibrosis in both males and females. This renal aging phenotype is significantly suppressed in arg-II mice, mainly in the females in which Arg-II level is higher than in the males. Importantly, numerous factors such as IL-1β, MCP1, VCAM-1, and TGFβ1 are mainly localized in the proximal tubular S3 segment cells expressing Arg-II in the aging kidney. In human proximal tubular cells (HK-2), TNF-α enhances adhesion molecule expression dependently on Arg-II upregulation. Overexpression of Arg-II in the cells enhances TGFβ1 levels which is prevented by mitochondrial ROS inhibition. In summary, our study reveals that renal proximal tubular Arg-II plays an important role in the kidney aging process in females. Arg-II could be a promising therapeutic target for the treatment and prevention of aging-associated kidney diseases.
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http://dx.doi.org/10.1038/s41514-021-00057-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7925687PMC
March 2021

Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase.

Acta Crystallogr D Struct Biol 2021 Mar 19;77(Pt 3):357-368. Epub 2021 Feb 19.

Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.

Succinyl-CoA synthetase (SCS) catalyzes a reversible reaction that is the only substrate-level phosphorylation in the citric acid cycle. One of the essential steps for the transfer of the phosphoryl group involves the movement of the phosphohistidine loop between active site I, where CoA, succinate and phosphate bind, and active site II, where the nucleotide binds. Here, the first crystal structure of SCS revealing the conformation of the phosphohistidine loop in site II of the porcine GTP-specific enzyme is presented. The phosphoryl transfer bridges a distance of 29 Å between the binding sites for phosphohistidine in site I and site II, so these crystal structures support the proposed mechanism of catalysis by SCS. In addition, a second succinate-binding site was discovered at the interface between the α- and β-subunits of SCS, and another magnesium ion was found that interacts with the side chains of Glu141β and Glu204β via water-mediated interactions. These glutamate residues interact with the active-site histidine residue when it is bound in site II.
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http://dx.doi.org/10.1107/S2059798321000334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919408PMC
March 2021

ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks.

Plant Physiol 2021 Feb;185(1):49-66

Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA.

Deciphering gene regulatory networks (GRNs) is both a promise and challenge of systems biology. The promise lies in identifying key transcription factors (TFs) that enable an organism to react to changes in its environment. The challenge lies in validating GRNs that involve hundreds of TFs with hundreds of thousands of interactions with their genome-wide targets experimentally determined by high-throughput sequencing. To address this challenge, we developed ConnecTF, a species-independent, web-based platform that integrates genome-wide studies of TF-target binding, TF-target regulation, and other TF-centric omic datasets and uses these to build and refine validated or inferred GRNs. We demonstrate the functionality of ConnecTF by showing how integration within and across TF-target datasets uncovers biological insights. Case study 1 uses integration of TF-target gene regulation and binding datasets to uncover TF mode-of-action and identify potential TF partners for 14 TFs in abscisic acid signaling. Case study 2 demonstrates how genome-wide TF-target data and automated functions in ConnecTF are used in precision/recall analysis and pruning of an inferred GRN for nitrogen signaling. Case study 3 uses ConnecTF to chart a network path from NLP7, a master TF in nitrogen signaling, to direct secondary TF2s and to its indirect targets in a Network Walking approach. The public version of ConnecTF (https://ConnecTF.org) contains 3,738,278 TF-target interactions for 423 TFs in Arabidopsis, 839,210 TF-target interactions for 139 TFs in maize (Zea mays), and 293,094 TF-target interactions for 26 TFs in rice (Oryza sativa). The database and tools in ConnecTF will advance the exploration of GRNs in plant systems biology applications for model and crop species.
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http://dx.doi.org/10.1093/plphys/kiaa012DOI Listing
February 2021

Detrimental Effects of Chronic L-Arginine Rich Food on Aging Kidney.

Front Pharmacol 2020 19;11:582155. Epub 2021 Jan 19.

Department of Endocrinology, Metabolism, and Cardiovascular System, Laboratory of Cardiovascular and Aging Research, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.

The impaired L-arginine/nitric oxide pathway is a well-recognized mechanism for cardiovascular and renal diseases with aging. Therefore, supplementation of L-arginine is widely proposed to boost health or as adjunct therapy for the patients. However, clinical data, show adverse effects and even enhanced mortality in patients receiving long-term L-arginine supplementation. The effects of long-term L-arginine supplementation on kidney aging and the underlying mechanisms remain elusive. Moreover, high protein and high amino acid diet has been thought detrimental for kidney. We therefore investigated effects of chronic dietary L-arginine supplementation on kidney aging. In both young (4 months) and old (18-24 months) mice, animals either receive standard chow containing 0.65% L-arginine or diet supplemented with L-arginine to 2.46% for 16 weeks. Inflammation and fibrosis markers and albuminuria are then analyzed. Age-associated increases in , , , , , , , and macrophage infiltration, collagen expression, and S6K1 activation are observed, which is not favorably affected, but rather further enhanced, by L-arginine supplementation. Importantly, L-arginine supplementation further enhances age-associated albuminuria and mortality particularly in females, accompanied by elevated renal arginase-II (Arg-II) levels. The enhanced albuminuria by L-arginine supplementation in aging is not protected in Arg-II mice. In contrast, L-arginine supplementation increases ROS and decreases nitric oxide production in old mouse aortas, which is reduced in Arg-II mice. The results do not support benefits of long-term L-arginine supplementation. It rather accelerates functional decline of kidney and vasculature in aging. Thus, the long-term dietary L-arginine supplementation should be avoided particularly in elderly population.
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http://dx.doi.org/10.3389/fphar.2020.582155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7851093PMC
January 2021

PhasiRNAnalyzer: an integrated analyser for plant phased siRNAs.

RNA Biol 2021 Feb 4:1-8. Epub 2021 Feb 4.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University , Nanjing, China.

Phased siRNAs (phasiRNAs) are a class of small interfering RNAs (siRNAs) which play essential roles in plant development and defence. However, only a few phasiRNAs have been extensively studied due to the difficulties in identifying and characterizing plant phasiRNAs by plant biologists. Herein, we describe a comprehensive and multi-functional web server termed PhasiRNAnalyzer, which is able to identify all crucial components in plant phasiRNA's regulatory pathway (phase-initiator→ gene→phasiRNA cluster→target gene). Currently, PhasiRNAnalyzer exhibits the following advantages: It is the most comprehensive platform which hosts 170 plant species with 256 genome data, 438 cDNA data and 271 degradome data. It can identify all crucial components in phasiRNA's regulatory pathway, and verify the interactions between phasiRNAs and their target genes based on degradome data. It can perform differential expression analysis of phasiRNAs on each gene locus between different samples conveniently. It provides the user-friendly interfaces and introduces several improvements, primarily by making more accurate and efficient analysis when dealing with deep sequencing data. In summary, PhasiRNAnalyzer is a comprehensive and systemic phasiRNA analysis server with high sensitivity and efficiency. It can be freely accessed at https://cbi.njau.edu.cn/PPSA/.
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http://dx.doi.org/10.1080/15476286.2021.1879543DOI Listing
February 2021

Pre-existing Health Conditions and Epicardial Adipose Tissue Volume: Potential Risk Factors for Myocardial Injury in COVID-19 Patients.

Front Cardiovasc Med 2020 11;7:585220. Epub 2021 Jan 11.

Division of Cardiology, Department of Internal Medicine, The Center for Cardiovascular Biology and Atherosclerosis Research, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States.

Myocardial injury is a life-threatening complication of coronavirus disease 2019 (COVID-19). Pre-existing health conditions and early morphological alterations may precipitate cardiac injury and dysfunction after contracting the virus. The current study aimed at assessing potential risk factors for COVID-19 cardiac complications in patients with pre-existing conditions and imaging predictors. The multi-center, retrospective cohort study consecutively enrolled 400 patients with lab-confirmed COVID-19 in six Chinese hospitals remote to the Wuhan epicenter. Patients were diagnosed with or without the complication of myocardial injury by history and cardiac biomarker Troponin I/T (TnI/T) elevation above the 99th percentile upper reference limit. The majority of COVID-19 patients with myocardial injury exhibited pre-existing health conditions, such as hypertension, diabetes, hypercholesterolemia, and coronary disease. They had increased levels of the inflammatory cytokine interleukin-6 and more in-hospital adverse events (admission to an intensive care unit, invasive mechanical ventilation, or death). Chest CT scan on admission demonstrated that COVID-19 patients with myocardial injury had higher epicardial adipose tissue volume ([EATV] 139.1 (83.8-195.9) vs. 92.6 (76.2-134.4) cm; = 0.036). The optimal EATV cut-off value (137.1 cm) served as a useful factor for assessing myocardial injury, which yielded sensitivity and specificity of 55.0% (95%CI, 32.0-76.2%) and 77.4% (95%CI, 71.6-82.3%) in adverse cardiac events, respectively. Multivariate logistic regression analysis showed that EATV over 137.1 cm was a strong independent predictor for myocardial injury in patients with COVID-19 [OR 3.058, (95%CI, 1.032-9.063); = 0.044]. Augmented EATV on admission chest CT scan, together with the pre-existing health conditions (hypertension, diabetes, and hyperlipidemia) and inflammatory cytokine production, is associated with increased myocardial injury and mortality in COVID-19 patients. Assessment of pre-existing conditions and chest CT scan EATV on admission may provide a threshold point potentially useful for predicting cardiovascular complications of COVID-19.
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http://dx.doi.org/10.3389/fcvm.2020.585220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7829196PMC
January 2021

The influence of pre-existing hypertension on coronavirus disease 2019 patients.

Epidemiol Infect 2021 01 5;149:e4. Epub 2021 Jan 5.

Division of Cardiology, Department of Internal Medicine, The Center for Cardiovascular Biology and Atherosclerosis Research, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA.

Hypertension represents one of the most common pre-existing conditions and comorbidities in Coronavirus disease 2019 (COVID-19) patients. To explore whether hypertension serves as a risk factor for disease severity, a multi-centre, retrospective study was conducted in COVID-19 patients. A total of 498 consecutively hospitalised patients with lab-confirmed COVID-19 in China were enrolled in this cohort. Using logistic regression, we assessed the association between hypertension and the likelihood of severe illness with adjustment for confounders. We observed that more than 16% of the enrolled patients exhibited pre-existing hypertension on admission. More severe COVID-19 cases occurred in individuals with hypertension than those without hypertension (21% vs. 10%, P = 0.007). Hypertension associated with the increased risk of severe illness, which was not modified by other demographic factors, such as age, sex, hospital geological location and blood pressure levels on admission. More attention and treatment should be offered to patients with underlying hypertension, who usually are older, have more comorbidities and more susceptible to cardiac complications.
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http://dx.doi.org/10.1017/S0950268820003118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7804074PMC
January 2021

Screening and Discovery of New Potential Biomarkers and Small Molecule Drugs for Cervical Cancer: A Bioinformatics Analysis.

Technol Cancer Res Treat 2020 Jan-Dec;19:1533033820980112

Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People's Hospital of Taicang), Jiangsu, China.

Background: Cervical cancer (CC) is the second most common type of malignant tumor survival rate is low in advanced stage, metastatic, and recurrent CC patients. This study aimed at identifying potential genes and drugs for CC diagnosis and targeting therapies.

Methods: Three GEO mRNA microarray datasets of CC tissues and non-cancerous tissues were analyzed for differentially expressed genes (DEGs) by limma package. GO (Gene Ontologies) and KEGG (Kyoto Encyclopedia of Genes and Genomes) were used to explore the relationships between the DEGs. Protein-protein interaction (PPI) of these genes was established by the STRING database. MCODE was used for screening significant modules in the PPI networks to select hub genes. Biochemical mechanisms of the hub genes were investigated with Metascape. GEPIA database was used for validating the core genes. According to these DEGs, molecular candidates for CC were recognized from the CMAP database.

Results: We identified 309 overlapping DEGs in the 2 tissue-types. Pathway analysis revealed that the DEGs were involved in cell cycle, DNA replication, and p53 signaling. PPI networks between overlapping DEGs showed 68 high-connectivity DEGs that were chosen as hub genes. The GEPIA database showed that the expression levels of RRM2, CDC45, GINS2, HELLS, KNTC1, MCM2, MYBL2, PCNA, RAD54 L, RFC4, RFC5, TK1, TOP2A, and TYMS in CC tissues were significantly different from those in the healthy tissues and were significantly relevant to the OS of CC. We found 10 small molecules from the CMAP database that could change the trend of gene expression in CC tissues, including piperlongumine and chrysin.

Conclusions: The 14 DEGs identified in this study could serve as novel prognosis biomarkers for the detection and forecasting of CC. Small molecule drugs like piperlongumine and chrysin could be potential therapeutic drugs for CC treatment.
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http://dx.doi.org/10.1177/1533033820980112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7734488PMC
December 2020

Comparison of Pathogenicity of Different Infectious Doses of H3N2 Canine Influenza Virus in Dogs.

Front Vet Sci 2020 13;7:580301. Epub 2020 Nov 13.

College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.

The canine influenza virus (CIV) outbreaks have raised concerns as they pose a threat to the health of dogs. The successful construction of a canine influenza (CI) infection model is essential to study the CIV. Here we investigated the pathogenicity of different infectious doses of H3N2 CIV in Beagle dogs. Thirty-seven healthy Beagle dogs were used in the experiment and were infected with 10, 10, 10, and 10 50% egg-infectious doses (EID). Compared to the dogs in the other three groups, those in the 10 EID group presented with obvious clinical symptoms, high virus titer, and typical pathological changes. Considering the ensemble of clinical scores, body temperature, virus shedding, lung lesions, pathological section scores, and visceral virus titers, we determined that 10 EID is the minimum infectious dose for the Beagle infection model. The other three infectious doses had almost no clinical symptoms. These results indicate that 10 EID is the minimum infectious dose of H3N2 CIV that can cause obvious clinical manifestations and pathological changes associated with CI in Beagle dogs. The theoretical framework developed in this research will guide the establishment of an infection model of CIV for future research.
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http://dx.doi.org/10.3389/fvets.2020.580301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7691240PMC
November 2020

A Cys2/His2 Zinc Finger Protein Acts as a Repressor of the Green Revolution Gene SD1/OsGA20ox2 in Rice (Oryza sativa L.).

Plant Cell Physiol 2021 Feb;61(12):2055-2066

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.

Gibberellins (GAs) play important roles in the regulation of plant growth and development. The green revolution gene SD1 encoding gibberellin 20-oxidase 2 (GA20ox2) has been widely used in modern rice breeding. However, the molecular mechanism of how SD1/OsGA20ox2 expression is regulated remains unclear. Here, we report a Cys2/His2 zinc finger protein ZFP207 acting as a transcriptional repressor of OsGA20ox2. ZFP207 was mainly accumulated in young tissues and more specifically in culm nodes. ZFP207-overexpression (ZFP207OE) plants displayed semidwarfism phenotype and small grains by modulating cell length. RNA interference of ZFP207 caused increased plant height and grain length. The application of exogenous GA3 could rescue the semidwarf phenotype of ZFP207OE rice seedlings. Moreover, ZFP207 repressed the expression of OsGA20ox2 via binding to its promoter region. Taken together, ZFP207 acts as a transcriptional repressor of SD1/OsGA20ox2 and it may play a critical role in plant growth and development in rice through the fine-tuning of GA biosynthesis .
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http://dx.doi.org/10.1093/pcp/pcaa120DOI Listing
February 2021

Pathogenesis and management of myocardial injury in coronavirus disease 2019.

Eur J Heart Fail 2020 11 22;22(11):1994-2006. Epub 2020 Aug 22.

Center for Coronary Heart Disease, Department of Cardiology, Fu Wai Hospital, National Center for Cardiovascular Diseases of China, State Key Laboratory of Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

The outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has become a major health crisis and a worldwide pandemic. COVID-19 is characterized by high infectivity, long incubation period, diverse clinical presentations, and strong transmission intensity. COVID-19 can cause myocardial injury as well as other cardiovascular complications, particularly in senior patients with pre-existing medical conditions. The current review summarizes the epidemiological characteristics, potential mechanisms, clinical manifestations, and recent progress in the management of COVID-19 cardiovascular complications.
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http://dx.doi.org/10.1002/ejhf.1967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7405025PMC
November 2020

Tartryl-CoA inhibits succinyl-CoA synthetase.

Acta Crystallogr F Struct Biol Commun 2020 Jul 1;76(Pt 7):302-308. Epub 2020 Jul 1.

Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.

Succinyl-CoA synthetase (SCS) catalyzes the only substrate-level phosphorylation step in the tricarboxylic acid cycle. Human GTP-specific SCS (GTPSCS), an αβ-heterodimer, was produced in Escherichia coli. The purified protein crystallized from a solution containing tartrate, CoA and magnesium chloride, and a crystal diffracted to 1.52 Å resolution. Tartryl-CoA was discovered to be bound to GTPSCS. The CoA portion lies in the amino-terminal domain of the α-subunit and the tartryl end extends towards the catalytic histidine residue. The terminal carboxylate binds to the phosphate-binding site of GTPSCS.
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http://dx.doi.org/10.1107/S2053230X20008201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7336359PMC
July 2020

Natural variation in OsGASR7 regulates grain length in rice.

Plant Biotechnol J 2021 Jan 6;19(1):14-16. Epub 2020 Jul 6.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China.

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http://dx.doi.org/10.1111/pbi.13436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7769224PMC
January 2021

Inhibition of p38mapk Reduces Adipose Tissue Inflammation in Aging Mediated by Arginase-II.

Pharmacology 2020 26;105(9-10):491-504. Epub 2020 May 26.

Cardiovascular and Aging Research, Department of Endocrinology, Metabolism, and Cardiovascular System, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland,

Background: Adipose tissue inflammation occurs not only in obesity but also in aging and is mechanistically linked with age-associated diseases. Studies show that ablation of the l-arginine-metabolizing enzyme arginase-II (Arg-II) reduces adipose tissue inflammation and improves glucose tolerance in obesity. However, the role of Arg-II in aging adipose tissue inflammation is not clear.

Objective: This study investigated the role of Arg-II in age-associated adipose tissue inflammation.

Methods: Visceral adipose tissues of young (3-6 months) and old (20-24 months) wild-type (WT) and Arg-II-/- mice were investigated. Immunofluorescence confocal microscopy was performed for analysis of macrophage accumulation and cellular localization of arginase and cytokines; expression of arginase and cytokines was analyzed by qRT-PCR or immunoblotting or ELISA; activation of mitogen-activated protein kinases in adipose tissues was analyzed by immunoblotting; and arginase activity was measured by colorimetric determination of urea production.

Results: In the old WT mice, there is more macrophage accumulation in the visceral adipose tissues than in Arg-II knockout animals. An age-associated increase in arginase activity and Arg-II expression in adipose tissues of WT mice is observed. Arg-II knockout enhances Arg-I expression and activity, but inhibits interleukin (IL)-6 expression and secretion and reduces active p38mapk in aging adipose tissue macrophages and stromal cells. Treatment of aging adipose tissues of WT mice with a specific p38mapk inhibitor SB203580 reduces IL-6 secretion.

Conclusions: Arg-II promotes IL-6 production in aging adipose tissues through p38mapk. The results suggest that targeting Arg-II or inhibiting p38mapk could be beneficial in reducing age-associated adipose tissue inflammation.
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http://dx.doi.org/10.1159/000507635DOI Listing
February 2021

LncRNA SNHG17 aggravated prostate cancer progression through regulating its homolog SNORA71B via a positive feedback loop.

Cell Death Dis 2020 05 23;11(5):393. Epub 2020 May 23.

Urology, Jiangxi cancer hospital, Nanchang, 330029, Jiangxi, China.

Prostate cancer (PC) is a prevalent male malignancy with high occurrence rate. Recent studies have showed that small nucleolar host genes (SNHGs) and their homolog small nucleolar RNAs (snoRNAs) elicit regulatory functions in carcinogenesis. Present study aimed to investigate the role of SNHG17 and its homolog SNORA71B in PC. Function of SNHG17 and SNORA71B in PC is detected by CCK-8, colony formation, flow cytometry analysis of apoptosis, and transwell migration assay. The mechanism whereby SNHG17 regulated SNORA71B was detected by RIP, pulldown, ChIP, and luciferase reporter assays. Results depicted that transcript 6 of SNHG17 and SNORA71B were upregulated in PC. Knockdown of SNHG17 or SNORA71B weakened proliferation, invasion, migration, and epithelial-to-mesenchymal transition (EMT) and strengthened apoptosis. Mechanistically, SNHG17 and SNORA71B were transcriptionally activated by signal transducer and activator of transcription 5A (STAT5A). SNHG17 positively regulated SNORA71B in PC cell lines and other cell lines. SNHG17 sponged miR-339-5p to upregulate STAT5A and therefore to cause transactivation of SNORA71B. Rescue experiments delineated that SNORA71B was required for the regulation of SNHG17 on PC. Moreover, SNHG17 silence hindered tumorigenesis of PC in vivo. In conclusion, current study first revealed that lncRNA SNHG17 aggravated prostate cancer progression through regulating its homolog SNORA71B via a positive feedback loop, which might do help to the pursuit of better PC treatment.
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http://dx.doi.org/10.1038/s41419-020-2569-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245601PMC
May 2020

Comparative Transcriptome and Proteome Analysis of Heat Acclimation in Predatory Mite .

Front Physiol 2020 29;11:426. Epub 2020 Apr 29.

Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.

In our previous study, we reported a high temperature adapted strain (HTAS) of the predatory mite was artificially selected via a long-term heat acclimation (35°C) and frequent heat hardenings. To understand the molecular basis of heat acclimation, 'omics' analyses were performed to compare the differences between HTAS female adults to conventional strain (CS) at transcriptional and translational levels. We obtained a total of 5,374 differentially expressed genes and 500 differentially expressed proteins. Among them, 119 transcripts had concurrent transcription and translation profiles. It's conserved that some processes, such as high expression of heat shock protein (HSP) genes, involved in heat tolerance of transcriptome analyses, while many protective enzymes including glutathione S-transferase, superoxide dismutase, peroxidase, and cytochrome P450 displayed down-regulated expression. KEGG analysis mapped 4,979 and 348 differentially expressed genes and proteins, to 299 and 253 pathways, respectively. The mitogen-activated protein kinases (MAPK) signaling pathway may provide new insights for the investigation of the molecular mechanisms of heat tolerance. Correlation enriched pathways indicated that there were four pathways associated with heat acclimation involving in energy metabolism and immunity. In addition, the expression patterns of ten randomly selected genes including HSP were consistent with the transcriptome results obtained through quantitative real-time PCR. Comparisons between transcriptome and proteome results indicated the upregulation of HSPs and genes participated in ATP production, immunity and energy metabolism process. A majority of antioxidant-related genes and detoxication-related genes were down-regulated suggesting a fitness cost of heat acclimation. Our results demonstrated that heat tolerance during a long-time acclimation of is a fairly complicated process of physiological regulations. These findings also contribute to a better understanding of the mechanisms of thermal responses of phytoseiid mites which could provide useful information for biological control through natural enemies.
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http://dx.doi.org/10.3389/fphys.2020.00426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7201100PMC
April 2020

Strengthening effects of bone marrow mononuclear cells with intensive atorvastatin in acute myocardial infarction.

Open Heart 2020 05;7(1)

Department of Cardiology, Center for Coronary Heart Disease, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

Objective: To test whether intensive atorvastatin (ATV) increases the efficacy of transplantation with autologous bone marrow mononuclear cells (MNCs) in patients suffering from anterior ST-elevated myocardial infarction (STEMI).

Methods: This clinical trial was under a 2×2 factorial design, enrolling 100 STEMI patients, randomly into four groups of regular (RA) or intensive ATV (IA) with MNCs or placebo. The primary endpoint was the change of left ventricular ejection fraction (LVEF) at 1-year follow-up from baseline, primarily assessed by MRI. The secondary endpoints included other parameters of cardiac function, remodelling and regeneration determined by MRI, echocardiography, positron emission tomography (PET) and biomarkers.

Results: All the STEMI patients with transplantation of MNCs showed significantly increased LVEF change values than those with placebo (p=0.01) with only in the IA+MNCs patients group demonstrating significantly elevation of LVEF than in the IA+placebo group (+12.6% (95%CI 10.4 to 19.3) vs +5.0% (95%CI 4.0 to 10.0), p=0.001), pointing to a better synergy between ATV and MNCs (p=0.019). PET analysis revealed significantly increased viable areas of myocardium (p=0.015), while the scar sizes (p=0.026) and blood aminoterminal pro-B-type natriuretic peptide (p<0.034) reduced. All these above benefits of MNCs were also attributed to IA+MNCs instead of RA+MNCs group of patients with STEMI.

Conclusions: Intensive ATV treatment augments the therapeutic efficacy of MNCs in patients with anterior STEMI at the convalescent stage. The treatment with the protocol of intensive ATV and MNC combination offers a clinically essential approach for myocardial infarction.

Trial Registration Number: NCT00979758.
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http://dx.doi.org/10.1136/openhrt-2019-001139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223465PMC
May 2020

Pathophysiological characteristics and therapeutic approaches for pulmonary injury and cardiovascular complications of coronavirus disease 2019.

Cardiovasc Pathol 2020 Jul - Aug;47:107228. Epub 2020 Apr 17.

Department of Internal Medicine, McGovern School of Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA; Division of Pulmonary, Critical and Sleep Medicine, University of South California Keck School of Medicine, Los Angeles, CA, USA.

The pandemic of coronavirus disease 2019 (COVID-19) has emerged as a major health crisis, with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) having infected over a million people around the world within a few months of its identification as a human pathogen. Initially, SARS-CoV-2 infects cells in the respiratory system and causes inflammation and cell death. Subsequently, the virus spreads out and damages other vital organs and tissues, triggering a complicated spectrum of pathophysiological changes and symptoms, including cardiovascular complications. Acting as the receptor for SARS-CoV entering mammalian cells, angiotensin converting enzyme-2 (ACE2) plays a pivotal role in the regulation of cardiovascular cell function. Diverse clinical manifestations and laboratory abnormalities occur in patients with cardiovascular injury in COVID-19, characterizing the development of this complication, as well as providing clues to diagnosis and treatment. This review provides a summary of the rapidly appearing laboratory and clinical evidence for the pathophysiology and therapeutic approaches to COVID-19 pulmonary and cardiovascular complications.
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http://dx.doi.org/10.1016/j.carpath.2020.107228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162778PMC
June 2020

An ultrasensitive electrochemical biosensor for Pseudomonas aeruginosa assay based on a rolling circle amplification-assisted multipedal DNA walker.

Chem Commun (Camb) 2020 Jun 6;56(46):6273-6276. Epub 2020 May 6.

State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China.

Herein, we developed an ultrasensitive electrochemical biosensor for Pseudomonas aeruginosa detection based on a rolling circle amplification-assisted multipedal DNA walking strategy. The cascade signal amplification method can improve the sensitivity, showing promising applications in food security, environmental monitoring, and disease diagnosis.
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http://dx.doi.org/10.1039/d0cc01619eDOI Listing
June 2020

Circular RNA hsa_circ_0001380 in peripheral blood as a potential diagnostic biomarker for active pulmonary tuberculosis.

Mol Med Rep 2020 Apr 20;21(4):1890-1896. Epub 2020 Feb 20.

Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China.

Numerous studies have suggested that circular RNAs (circRNAs), a type of non‑coding RNA lacking 5'‑caps and 3'‑poly(A) tails, are involved in the biological processes of various human diseases. However, little is known about their functions and diagnostic value in active pulmonary tuberculosis (APTB). The aim of the present study was to examine whether hsa_circ_0001380 is able to serve as a diagnostic biomarker for patients with APTB. The expression level of hsa_circ_0001380 was detected in the peripheral blood of 32 patients with APTB and 31 healthy volunteers by reverse transcription‑quantitative PCR. The functional prediction of hsa_circ_0001380 was performed in silico. RNase R was used to detect the stability of hsa_circ_0001380. Finally, the diagnostic value of hsa_circ_0001380 was evaluated by receiver operating characteristic (ROC) curve analysis. The results showed that hsa_circ_0001380 was significantly downregulated in the peripheral blood of patients with APTB. In addition, hsa_circ_0001380 was found to be resistant to RNase R treatment. Moreover, four N6‑adenosine methylation modification sites and two potential microRNA binding sites were predicted in silico. Importantly, the area under the ROC curve was 0.9502, which suggested that hsa_circ_0001380 may act as a diagnostic biomarker for APTB. Taken together, the results indicated that circRNA hsa_circ_0001380 was downregulated in the peripheral blood of patients with APTB, and could serve as a diagnostic biomarker.
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http://dx.doi.org/10.3892/mmr.2020.10992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7057807PMC
April 2020

Epigenetic Regulation of ABA-Induced Transcriptional Responses in Maize.

G3 (Bethesda) 2020 05 4;10(5):1727-1743. Epub 2020 May 4.

Department of Biological Science, Florida State University, Tallahassee, Florida 32306

Plants are subjected to extreme environmental conditions and must adapt rapidly. The phytohormone abscisic acid (ABA) accumulates during abiotic stress, signaling transcriptional changes that trigger physiological responses. Epigenetic modifications often facilitate transcription, particularly at genes exhibiting temporal, tissue-specific and environmentally-induced expression. In maize (), MEDIATOR OF PARAMUTATION 1 (MOP1) is required for progression of an RNA-dependent epigenetic pathway that regulates transcriptional silencing of loci genomewide. MOP1 function has been previously correlated with genomic regions adjoining particular types of transposable elements and genic regions, suggesting that this regulatory pathway functions to maintain distinct transcriptional activities within genomic spaces, and that loss of MOP1 may modify the responsiveness of some loci to other regulatory pathways. As critical regulators of gene expression, MOP1 and ABA pathways each regulate specific genes. To determine whether loss of MOP1 impacts ABA-responsive gene expression in maize, and homozygous seedlings were subjected to exogenous ABA and RNA-sequencing. A total of 3,242 differentially expressed genes (DEGs) were identified in four pairwise comparisons. Overall, ABA-induced changes in gene expression were enhanced in homozygous plants. The highest number of DEGs were identified in ABA-induced mutants, including many transcription factors; this suggests combinatorial regulatory scenarios including direct and indirect transcriptional responses to genetic disruption () and/or stimulus-induction of a hierarchical, cascading network of responsive genes. Additionally, a modest increase in CHH methylation at putative MOP1-RdDM loci in response to ABA was observed in some genotypes, suggesting that epigenetic variation might influence environmentally-induced transcriptional responses in maize.
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http://dx.doi.org/10.1534/g3.119.400993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7202028PMC
May 2020

Comparative analysis of salt responsive gene regulatory networks in rice and Arabidopsis.

Comput Biol Chem 2020 Apr 28;85:107188. Epub 2019 Dec 28.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address:

By using the available expression datasets of mRNAs and small RNAs, we constructed and compared the salt-responsive gene regulatory networks (GRNs) involving both transcriptional and post-transcriptional regulations between model plants rice and Arabidopsis. The salt-responsive GRNs involve the transcription factors (TFs), microRNAs (miRNAs) and their target genes. Here we describe 552 miRNA-target interactions (MTIs), 95 up-regulated TF-target interactions (TTIs) and 56 down-regulated TTIs in rice, while 332 MTIs, 138 up-regulated and 4 down-regulated TTIs in Arabidopsis. Interestingly, we observed the networks in rice are more complicated where target genes were enriched in rice development and growth, while more stress-related genes were detected in Arabidopsis networks. With the construction and comparison of GRNs between rice and Arabidopsis in response to salt stress, we can basically describe the differences of salt responsive mechanisms in two species: rice tends to respond slower and chooses to manipulate its development and growth to avoid salt stress, while Arabidopsis prefers to trigger a serious salt-defending genes to protect itself from stress. Our work provides the foundation for further exploring the molecular basis of plant salt response and the potential breeding practice by engineering the critical components in the networks in improving plant salt tolerance.
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http://dx.doi.org/10.1016/j.compbiolchem.2019.107188DOI Listing
April 2020

HY5 Contributes to Light-Regulated Root System Architecture Under a Root-Covered Culture System.

Front Plant Sci 2019 28;10:1490. Epub 2019 Nov 28.

Laboratory of Medicinal Plant, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China.

Light is essential for plant organogenesis and development. Light-regulated shoot morphogenesis has been extensively studied; however, the mechanisms by which plant roots perceive and respond to aboveground light are largely unknown, particularly because the roots of most terrestrial plants are usually located underground in darkness. To mimic natural root growth conditions, we developed a root-covered system (RCS) in which the shoots were illuminated and the plant roots could be either exposed to light or cultivated in darkness. Using the RCS, we observed that root growth of wild-type plants was significantly promoted when the roots were in darkness, whereas it was inhibited by direct light exposure. This growth change seems to be regulated by ELONGATED HYPOCOTYL 5 (HY5), a master regulator of photomorphogenesis. Light was found to regulate expression in the roots, while a HY5 deficiency partially abolished the inhibition of growth in roots directly exposed to light, suggesting that expression is induced by direct light exposure and inhibits root growth. However, no differences in expression were observed between illuminated and dark-grown roots, indicating that HY5 may be regulated by COP1-mediated proteasome degradation. We confirmed the crucial role of HY5 in regulating root development in response to light under soil-grown conditions. A transcriptomic analysis revealed that light controls the expression of numerous genes involved in phytohormone signaling, stress adaptation, and metabolic processes in a HY5-dependent manner. In combination with the results of the flavonol quantification and exogenous quercetin application, these findings suggested that HY5 regulates the root response to light through a complex network that integrates flavonol biosynthesis and reactive oxygen species signaling. Collectively, our results indicate that HY5 is a master regulator of root photomorphogenesis.
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http://dx.doi.org/10.3389/fpls.2019.01490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892842PMC
November 2019

Response to Multiple Stressors: Enhanced Tolerance of Hughes (Acari: Phytoseiidae) to Heat and Desiccation Stress through Acclimation.

Insects 2019 Dec 13;10(12). Epub 2019 Dec 13.

Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China.

Organisms are always confronted with multiple stressors simultaneously. Combinations of stressors, rather than single stressor, may be more appropriate in evaluating the stress they experience. is one of predatory mite species that are commercialized for controlling spider mites. However, their biological control efficiency was often reduced because of high temperature and desiccation in summer. To understand how to improve the tolerance of to combined heat and desiccation stress, we pre-exposed the adult female of to high temperature, desiccation and high temperature × desiccation stress for acclimation. After proper recovery time, mites were subjected to high temperature × desiccation stress again to detect the acclimation effects. The results are as follows: (1) No decrease in mortality rate were observed under high temperature × desiccation stress after heat acclimation. Instead, it increased significantly with acclimation temperature and time. (2) Dehydration acclimation both at 25 °C and high temperatures reduced mortality rate under high temperature × desiccation stress. Mortality rate was only significantly correlated with the amount of water loss, but not with temperature or water loss rate in acclimation, suggesting the increased tolerance is related to dehydration stress rather than heat stress. Among all acclimations, chronic dehydration at 25 °C, 50% relative humidity were the most effective treatment. This study indicated dehydration acclimation is effective to enhance tolerance of to combined heat and desiccation stress, which can improve the efficiency of biological control under multiple stressors.
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http://dx.doi.org/10.3390/insects10120449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6956224PMC
December 2019

Novel 2D hybrids composed of SnInS nanoplates on BiOBr nanosheets for enhanced photocatalytic applications.

Nanotechnology 2019 Nov 21;31(10):105202. Epub 2019 Nov 21.

Low Carbon Energy Institute, China University of Mining and Technology, Xuzhou 221008, People's Republic of China. School of Materials Science and Engineering, China University of Mining and Technology, Xuzhou 221116, People's Republic of China.

In the last ten years, bismuth oxybromide (BiOBr) has attracted wide attention due to its superior optoelectronic property. However, its practical application still suffers from slow carrier transport and high carrier recombination. Here we report a kind of novel tannum indium sulfide (SnInS)/BiOBr hybrid prepared by a two-step hydrothermal method. The results showed that small amount of SnInS had no influence on the crystal phase of BiOBr, but the morphology could be regulated from nanosheet to nanoflower. Specially, SnInS exerted a slight effect on the light absorption and band gap of BiOBr. Importantly, SnInS/BiOBr hybrids exhibited remarkable enhancement of the photocatalytic activity towards the degradation of rhodamin B (RhB) dye molecules. SnInS/BiOBr-0.20 with 99.8% degradation efficiency had the highest photocatalytic activity within 40 min, while it was only 71.1% for pure BiOBr. The enhanced photocatalytic activity was mainly attributed to efficient interfacial transfer and low carrier recombination. This work will help us understand the photocatalytic mechanism of bismuth oxyhalide hybrids.
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http://dx.doi.org/10.1088/1361-6528/ab5a1fDOI Listing
November 2019

A pre-catalytic non-covalent step governs DNA polymerase β fidelity.

Nucleic Acids Res 2019 12;47(22):11839-11849

Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA.

DNA polymerase β (pol β) selects the correct deoxyribonucleoside triphosphate for incorporation into the DNA polymer. Mistakes made by pol β lead to mutations, some of which occur within specific sequence contexts to generate mutation hotspots. The adenomatous polyposis coli (APC) gene is mutated within specific sequence contexts in colorectal carcinomas but the underlying mechanism is not fully understood. In previous work, we demonstrated that a somatic colon cancer variant of pol β, K289M, misincorporates deoxynucleotides at significantly increased frequencies over wild-type pol β within a mutation hotspot that is present several times within the APC gene. Kinetic studies provide evidence that the rate-determining step of pol β catalysis is phosphodiester bond formation and suggest that substrate selection is governed at this step. Remarkably, we show that, unlike WT, a pre-catalytic step in the K289M pol β kinetic pathway becomes slower than phosphodiester bond formation with the APC DNA sequence but not with a different DNA substrate. Based on our studies, we propose that pre-catalytic conformational changes are of critical importance for DNA polymerase fidelity within specific DNA sequence contexts.
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http://dx.doi.org/10.1093/nar/gkz1076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145665PMC
December 2019

Lagged settlement in sandy cobble strata and earth pressure on shield tunnel.

Math Biosci Eng 2019 07;16(6):6209-6230

School of Civil Engineering & Transportation, South China University of Technology, Guangzhou, Guangdong 510641, China.

Lagged settlement is a typical accident induced by shield construction in sandy cobble strata. This paper analyzed the process and mechanism of lagged settlement, results show that all phases are in accord with the characteristics of ellipsoid theory of particle flows. Based on this theory, a method for calculating coefficient of lateral earth pressure and loosened earth pressure is proposed in this research. For the coefficient of lateral earth pressure, the boundary of loosened ellipsoid is divided into two parts, the arch zone and the excavation zone, and the lateral pressure coefficients are derived respectively according to the stress state. For loosened earth pressure on tunnel, the Terzaghi earth pressure theory and Protodyakonov earth pressure theory are adapted in different conditions according to the state of loosened cobble soil. Theories developed in this study can be applied on determination of shield excavation parameters, as well as calculation of loosened earth pressure and control of tunnel support.
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http://dx.doi.org/10.3934/mbe.2019309DOI Listing
July 2019

WPMIAS: Whole-degradome-based Plant MicroRNA-Target Interaction Analysis Server.

Bioinformatics 2019 Nov 6. Epub 2019 Nov 6.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China.

A critical aspect for exploring the biological function of a microRNA (miRNA) lies on exact detection and validation of its target mRNAs. However, no convenient and efficient web-based server is available for plant biologists to identify the experimentally verified target mRNAs of miRNAs. In this work, we built a comprehensive web-based platform for miRNA-target analysis, named as Whole-degradome-based Plant MiRNA-target Interaction Analysis Server (WPMIAS), for validation of predicted interactions of miRNAs and their target mRNAs (MTIs) by user-submitted data or all available pre-loaded degradome data. Besides, the server can construct degradome-based miRNA regulatory networks (MRNs) based on the validated MTIs to help study the functions and relations among miRNAs and target mRNAs. WPMIAS is also suitable for other small RNAs (sRNAs), such as 21-nt phased siRNAs (phasiRNAs) and natural antisense siRNAs (nat-siRNAs), which direct cleavage of target mRNAs. Currently, WPMIAS supports 64 plant species with ∼200 cDNA libraries and 274 pre-loaded plant degradome datasets. The user can identify all validated MTIs by analyzing all degradome data at a time and understand when and where MTIs take place and their cleavage levels. With the data obtained from WPMIAS, the user can build a plant miRNA-target map, where it is convenient to find interesting research ideas on miRNAs. In summary, WPMIAS is able to support a comprehensive web-based plant miRNA-target analysis and expected to greatly promote future research on plant miRNAs.

Availability: It can be freely accessed at https://cbi.njau.edu.cn/WPMIAS/.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btz820DOI Listing
November 2019