59 results on '"Xinna Li"'
Search Results
2. Prescribed-time synchronization in networks of piecewise smooth systems via a nonlinear dynamic event-triggered control strategy
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Xinna Li, Huaiqin Wu, and Jinde Cao
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Numerical Analysis ,General Computer Science ,Applied Mathematics ,Modeling and Simulation ,Theoretical Computer Science - Published
- 2023
3. Recapitulation of anti-aging phenotypes by global, but not by muscle-specific, deletion of PAPP-A in mice
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Xinna Li, Mary Hager, Madaline McPherson, Michael Lee, Riha Hagalwadi, Mary E. Skinner, David Lombard, and Richard A. Miller
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Aging ,Original Article ,Geriatrics and Gerontology - Abstract
Deletion of pregnancy-associated plasma protein-A (PAPP-A), a protease that cleaves some but not all IGF1 binding proteins, postpones late-life diseases and extends lifespan in mice, but the mechanism of this effect is unknown. Here we show that PAPP-A knockout (PKO) mice display a set of changes, in multiple tissues, that are characteristic of other varieties of slow-aging mice with alterations in GH production or GH responsiveness, including Ames dwarf, Snell dwarf, and GHRKO mice. PKO mice have elevated UCP1 in brown and white adipose tissues (WAT), and a change in fat-associated macrophage subsets that leads to diminished production of inflammatory cytokines. PKO mice also show increased levels of muscle FNDC5 and its cleavage product, the myokine irisin, thought to cause changes in fat cell differentiation. PKO mice have elevated production of hepatic GPLD1 and plasma GPLD1, consistent with their elevation of hippocampal BDNF and DCX, used as indices of neurogenesis. In contrast, disruption of PAPP-A limited to muscle (“muPKO” mice) produces an unexpectedly complex set of changes, in most cases opposite in direction from those seen in PKO mice. These include declines in WAT UCP1, increases in inflammatory macrophages and cytokines in WAT, and a decline in muscle FNDC5 and plasma irisin. muPKO mice do, however, resemble global PKO mice in their elevation of hippocampal BDNF and DCX. The data for the PKO mice support the idea that these changes in fat, macrophages, liver, muscle, plasma, and brain are consistent and biologically significant features of the slow-aging phenotype in mice. The results on the muPKO mice provide a foundation for further investigation of the complex, local, and global circuits by which PAPP-A modulates signals ordinarily controlled by GH and/or IGF1. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11357-022-00692-3.
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- 2022
4. Four anti-aging drugs and calorie-restricted diet produce parallel effects in fat, brain, muscle, macrophages, and plasma of young mice
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Xinna Li, Madaline McPherson, Mary Hager, Michael Lee, Peter Chang, and Richard A. Miller
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Aging ,Geriatrics and Gerontology - Published
- 2023
5. Development and validation of a nomogram for the early prediction of acute kidney injury in hospitalized COVID-19 patients
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Congjie Wang, Huiyuan Sun, Xinna Li, Daoxu Wu, Xiaoqing Chen, Shenchun Zou, Tingshu Jiang, and Changjun Lv
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Nomograms ,Patients ,Public Health, Environmental and Occupational Health ,Humans ,COVID-19 ,Acute Kidney Injury ,Procalcitonin - Abstract
IntroductionAcute kidney injury (AKI) is a prevalent complication of coronavirus disease 2019 (COVID-19) and is closely linked with a poorer prognosis. The aim of this study was to develop and validate an easy-to-use and accurate early prediction model for AKI in hospitalized COVID-19 patients.MethodsData from 480 COVID-19-positive patients (336 in the training set and 144 in the validation set) were obtained from the public database of the Cancer Imaging Archive (TCIA). The least absolute shrinkage and selection operator (LASSO) regression method and multivariate logistic regression were used to screen potential predictive factors to construct the prediction nomogram. Receiver operating curves (ROC), calibration curves, as well as decision curve analysis (DCA) were adopted to assess the effectiveness of the nomogram. The prognostic value of the nomogram was also examined.ResultsA predictive nomogram for AKI was developed based on arterial oxygen saturation, procalcitonin, C-reactive protein, glomerular filtration rate, and the history of coronary artery disease. In the training set, the nomogram produced an AUC of 0.831 (95% confidence interval [CI]: 0.774–0.889) with a sensitivity of 85.2% and a specificity of 69.9%. In the validation set, the nomogram produced an AUC of 0.810 (95% CI: 0.737–0.871) with a sensitivity of 77.4% and a specificity of 78.8%. The calibration curve shows that the nomogram exhibited excellent calibration and fit in both the training and validation sets. DCA suggested that the nomogram has promising clinical effectiveness. In addition, the median length of stay (m-LS) for patients in the high-risk group for AKI (risk score ≥ 0.122) was 14.0 days (95% CI: 11.3–16.7 days), which was significantly longer than 8.0 days (95% CI: 7.1–8.9 days) for patients in the low-risk group (risk score p < 0.001). Moreover, the mortality rate was also significantly higher in the high-risk group than that in the low-risk group (20.6 vs. 2.9%, odd ratio (OR):8.61, 95%CI: 3.45–21.52).ConclusionsThe newly constructed nomogram model could accurately identify potential COVID-19 patients who may experience AKI during hospitalization at the very beginning of their admission and may be useful for informing clinical prognosis.
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- 2022
6. Revisiting adipose thermogenesis for delaying aging and age-related diseases: Opportunities and challenges
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Stefano Tarantini, Madhan Subramanian, Joshua T. Butcher, Andriy Yabluchanskiy, Xinna Li, Richard A. Miller, and Priya Balasubramanian
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Aging ,Neurology ,Molecular Biology ,Biochemistry ,Biotechnology - Published
- 2023
7. <scp>Cap‐independent</scp> translation of <scp>GPLD1</scp> enhances markers of brain health in <scp>long‐lived</scp> mutant and <scp>drug‐treated</scp> mice
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Xinna Li, Xiaofang Shi, Madaline McPherson, Mary Hager, Gonzalo G. Garcia, and Richard A. Miller
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Mice ,Aging ,Liver ,Longevity ,Phospholipase D ,Animals ,Brain ,RNA, Messenger ,Receptors, Somatotropin ,Cell Biology - Abstract
Glycosylphosphatidylinositol-specific phospholipase D1 (GPLD1) hydrolyzes inositol phosphate linkages in proteins anchored to the cell membrane. Mice overexpressing GPLD1 show enhanced neurogenesis and cognition. Snell dwarf (DW) and growth hormone receptor knockout (GKO) mice show delays in age-dependent cognitive decline. We hypothesized that augmented GPLD1 might contribute to retained cognitive function in these mice. We report that DW and GKO show higher GPLD1 levels in the liver and plasma. These mice also have elevated levels of hippocampal brain-derived neurotrophic factor (BDNF) and of doublecortin (DCX), suggesting a mechanism for maintenance of cognitive function at older ages. GPLD1 was not increased in the hippocampus of DW or GKO mice, suggesting that plasma GPLD1 increases elevated these brain proteins. Alteration of the liver and plasma GPLD1 was unaltered in mice with liver-specific GHR deletion, suggesting that the GH effect was not intrinsic to the liver. GPLD1 was also induced by caloric restriction and by each of four drugs that extend lifespan. The proteome of DW and GKO mice is molded by selective translation of mRNAs, involving cap-independent translation (CIT) of mRNAs marked by N
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- 2022
8. Transient early life growth hormone exposure permanently alters brain, muscle, liver, macrophage, and adipocyte status in long‐lived Ames dwarf mice
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Xinna Li, Madaline McPherson, Mary Hager, Yimin Fang, Andrzej Bartke, and Richard A. Miller
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Inflammation ,Human Growth Hormone ,Macrophages ,Muscles ,Brain ,Biochemistry ,Mice, Mutant Strains ,Mice ,Liver ,Growth Hormone ,Adipocytes ,Genetics ,Animals ,Molecular Biology ,Biotechnology - Abstract
The exceptional longevity of Ames dwarf (DF) mice can be abrogated by a brief course of growth hormone (GH) injections started at 2 weeks of age. This transient GH exposure also prevents the increase in cellular stress resistance and decline in hypothalamic inflammation characteristic of DF mice. Here, we show that transient early-life GH treatment leads to permanent alteration of pertinent changes in adipocytes, fat-associated macrophages, liver, muscle, and brain that are seen in DF mice. Ames DF mice, like Snell dwarf and GHRKO mice, show elevation of glycosylphosphatidylinositol specific phospholipase D1 in liver, neurogenesis in brain as indicated by BDNF and DCX proteins, muscle production of fibronectin type III domain-containing protein 5 (a precursor of irisin), uncoupling protein 1 as an index of thermogenic capacity in brown and white fat, and increase in fat-associated anti-inflammatory macrophages. In each case, transient exposure to GH early in life reverts the DF mice to the levels of each protein seen in littermate control animals, in animals evaluated at 15-18 months of age. Thus, many of the traits seen in long-lived mutant mice, pertinent to age-related changes in inflammation, neurogenesis, and metabolic control, are permanently set by early-life GH levels.
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- 2022
9. Muscle-dependent regulation of adipose tissue function in long-lived growth hormone-mutant mice
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Xinna Li, Richard A. Miller, Jacquelyn A. Frazier, Madaline McPherson, and Edward Spahiu
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Male ,Aging ,medicine.medical_specialty ,Longevity ,Adipose tissue ,Inflammation ,Growth hormone receptor ,Biology ,Mice ,chemistry.chemical_compound ,Internal medicine ,Adipocyte ,Adipocytes ,medicine ,Animals ,Muscle, Skeletal ,Uncoupling Protein 1 ,Mice, Knockout ,Thermogenesis ,Cell Biology ,Metabolism ,FNDC5 ,adipose tissue ,Endocrinology ,chemistry ,Growth Hormone ,Female ,Tumor necrosis factor alpha ,medicine.symptom ,uncoupling protein 1 (UCP1) ,hormones, hormone substitutes, and hormone antagonists ,Priority Research Paper - Abstract
Altered adipose tissue may contribute to the longevity of Snell dwarf and growth hormone receptor (GHR) knock-out mice. We report here that white (WAT) and brown (BAT) fat have elevated UCP1 in both kinds of mice, and that adipocytes in WAT depots turn beige/brown. These imply increased thermogenesis and are expected to lead to improved glucose control. Both kinds of long-lived mice show lower levels of inflammatory M1 macrophages and higher levels of anti-inflammatory M2 macrophages in BAT and WAT, with correspondingly lower levels of TNFα, IL-6, and MCP1. Experiments with mice with tissue-specific disruption of GHR showed that these adipocyte and macrophage changes were not due to hepatic IGF1 production nor to direct GH effects on adipocytes, but instead reflect GH effects on muscle. Muscles deprived of GH signals, either globally (GKO) or in muscle only (MKO), produce higher levels of circulating irisin and its precursor FNDC5. The data thus suggest that the changes in adipose tissue differentiation and inflammatory status seen in long-lived mutant mice reflect interruption of GH-dependent irisin inhibition, with consequential effects on metabolism and thermogenesis.
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- 2020
10. Early Life Interventions Can Shape Aging
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Andrzej Bartke, Liou Y. Sun, Xinna Li, and Richard A. Miller
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Mammals ,Aging ,Mice ,Hormone Replacement Therapy ,Endocrinology, Diabetes and Metabolism ,Growth Hormone ,Longevity ,Animals ,Dwarfism - Abstract
It is well documented that the environment of the developing fetus, including availability of nutrients and presence of toxins, can have major impact on adult phenotype, age-related traits and risk of chronic disease. There is also accumulating evidence that postnatal environment can impact adult characteristics related to evolutionary fitness, health, and aging. To determine whether early life hormonal interventions can alter trajectory of aging, we have examined the effects of early life growth hormone (GH) replacement therapy in Prop1df (Ames dwarf) mice which are GH deficient and remarkably long lived. Twice-daily GH injections between the ages of two and eight weeks completely normalized (“rescued”) a number of adult metabolic characteristics believed to contribute to extended longevity of these mutants. Importantly, longevity of Ames dwarf mice was reduced by early life GH treatment. This was associated with histone H3 modifications. We conclude that the trajectory of mammalian aging can be modified by early life interventions. Mechanistic links among interventions during postnatal development, adult metabolic characteristics, aging, and longevity, apparently involve epigenetic phenomena.
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- 2021
11. Clustering and Differentiation of glr-3 Gene Function and Its Homologous Proteins
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Tiantian Guo, Yue Ma, Jingyu Zhang, Yihe Wang, and Xinna Li
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Chemistry ,Nucleic acid sequence ,Protein phosphorylation ,Protein superfamily ,Gene ,Peptide sequence ,Protein secondary structure ,Homology (biology) ,Protein tertiary structure ,Cell biology - Abstract
In order to adapt to the low temperature environment, organisms transmit excitement to the central system through the thermal sensing system, which is a classic reflex reaction. The cold receptor GLR-3 perceives cold and pro duces cold avoidance behavior through peripheral sensory neurons ASER. In order to further understand the gene encoding of the cold sensing glr-3 gene and the evolution of its homologous gene group function and protein function, the nucleotide sequence and amino acid sequence of the glr-3 gene and its homologous gene in 24 species were obtained and compared. By clustering with the GRIK2 gene sequence of Rana chensinensis, the bio informatics method was used to predict and sequence analyze the change of gene, evolution rate, physical and chemical properties of protein, glycosyla tion sites, phosphorylation sites, secondary structure and tertiary structure of protein. The analysis results show that the glr-3 gene and its homologous gene have obvious positive selection effect. The protein prediction analysis showed that the glr-3 gene and its homologous genes encoded proteins in these 25 species were hydrophilic proteins, and the proportion of side chains of aliphatic amino acids was high. The transmembrane helix was widespread and there were more N-glycosylation sites and O-glycosylation sites. The protein phosphorylation sites encoded were serine, threonine and tyrosine phosphorylation sites. Secondary structure prediction showed that the secondary structure units of the encoded protein were α-helix, β-turn, random coil and extended chain, and the proportion of α-helix was the larg est. This study provides useful information on the evolution and function of the cold sensing gene glr-3 and its homologous genes.
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- 2021
12. MiR-223 inhibitor suppresses proliferation and induces apoptosis of thyroid cancer cells by down-regulating aquaporin-1
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Lejun Lin, Xinna Li, Guowei Lu, Weilong Li, and Qiang Zhang
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0301 basic medicine ,Thyroid Gland ,Apoptosis ,Biochemistry ,Flow cytometry ,03 medical and health sciences ,0302 clinical medicine ,Western blot ,Cell Movement ,Cell Line, Tumor ,medicine ,Humans ,Gene silencing ,Gene Silencing ,Thyroid Neoplasms ,RNA, Small Interfering ,Molecular Biology ,Cell Proliferation ,Aquaporin 1 ,medicine.diagnostic_test ,Cell growth ,Chemistry ,Cell Cycle Checkpoints ,Cell Biology ,Transfection ,Cell cycle ,Cell biology ,Gene Expression Regulation, Neoplastic ,MicroRNAs ,030104 developmental biology ,030220 oncology & carcinogenesis - Abstract
To investigate the effect of miR-223 on thyroid cancer cells, further to study its potential mechanisms. The difference in miR-223 expression between normal thyroid Nthy-ori3-l cells and thyroid cancer SW579 cells was detected by PCR. The miR-223 overexpression and silencing vector transfection were verified by qRT-PCR. To further investigate the role of miR-223 in AQP-1, the AQP-1 siRNA vector was transfected on the basis of transfection of miR-223 inhibitor vector. The cell proliferation was detected by plate cloning, MTT, and cellular immunofluorescence assays. Cell cycle and apoptosis were detected by flow cytometry. Western blot was used to detect the expression of AQP-1 protein. The expression of miR-223 in SW579 cells was higher than that in normal cells. After transfection with miR-223 mimic, miR-223 expression was increased in SW579 cells. MiR-223 inhibitor transfection can inhibit SW579 cells proliferation, promote apoptosis, and inhibit cell cycle G0/G1 arrest. The SW579 cells proliferation was decreased, and the apoptosis rate was increased after transfection of AQP-1 silencing vector. Compared with the AQP-1 siRNA group, the SW579 cells proliferation rate was further reduced, and the apoptosis rate was significantly increased after co-transfection of miR-223 silencing vector and AQP-1 silencing vector. AQP-1 protein was highly expressed in SW579 cells, and miR-223 inhibitor can down-regulate the expression of APQ-1 protein. The expression AQP-1 protein was significantly reduced after transfected with AQP-1 silencing vector. Inhibition of miR-223 expression could suppress proliferation and promote apoptosis of SW579, and its mechanism is related to down-regulation of APQ-1 protein expression.
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- 2019
13. Elevated metallothionein expression in long-lived species mediates the influence of cadmium accumulation on aging
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Paolo Garagnani, Marco Malavolta, Claudia Sala, Mauro Provinciali, Kamil Pabis, Robertina Giacconi, Elisabeth Straka, Ylenia Chiari, Xinna Li, Holly M. Brown-Borg, Teresa G. Valencak, Claudia Gundacker, Karin Nowikovsky, Pabis K., Chiari Y., Sala C., Straka E., Giacconi R., Provinciali M., Li X., Brown-Borg H., Nowikovsky K., Valencak T.G., Gundacker C., Garagnani P., and Malavolta M.
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Aging ,media_common.quotation_subject ,Longevity ,chemistry.chemical_element ,Biology ,Kidney ,Mammal ,Mice ,Gene expression ,Metallothionein ,Animals ,Gene ,Maximum life span ,media_common ,Cadmium ,Animal ,Molecular medicine ,Comparative biogerontology ,Cell biology ,chemistry ,Liver ,Original Article ,Geriatrics and Gerontology ,Homeostasis - Abstract
Cadmium (Cd) accumulates with aging and is elevated in long-lived species. Metallothioneins (MTs), small cysteine-rich proteins involved in metal homeostasis and Cd detoxification, are known to be related to longevity. However, the relationship between Cd accumulation, the role of MTs, and aging is currently unclear. Specifically, we do not know if long-lived species evolved an efficient metal stress response by upregulating their MT levels to reduce the toxic effects of environmental pollutants, such as Cd, that accumulate over their longer life span. It is also unknown if the number of MT genes, their expression, or both protect the organisms from potentially damaging effects during aging. To address these questions, we reanalyzed several cross-species studies and obtained data on MT expression and Cd accumulation in long-lived mouse models. We confirmed a relationship between species maximum life span in captive mammals and their Cd content in liver and kidney. We found that although the number of MT genes does not affect longevity, gene expression and protein amount of specific MT paralogs are strongly related to life span in mammals. MT expression rather than gene number may influence the high Cd levels and longevity of some species. In support of this, we found that overexpression of MT-1 accelerated Cd accumulation in mice and that tissue Cd was higher in long-lived mouse strains with high MT expression. We conclude that long-lived species have evolved a more efficient stress response by upregulating the expression of MT genes in presence of Cd, which contributes to elevated tissue Cd levels. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11357-021-00393-3.
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- 2021
14. Unmasking Bayesian RAIM Algorithm for Identifying Simultaneous Two-Faulty Satellites
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Junzheng Li, Ke Chen, and Xinna Li
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Bayes' theorem ,Computer science ,Receiver autonomous integrity monitoring ,GNSS applications ,Monte Carlo method ,Posterior probability ,Bayesian probability ,Statistical theory ,Ephemeris ,Algorithm - Abstract
For the problem of identifying simultaneous two-faulty satellites in global navigation satellite systems (GNSS), an unmasking Bayesian Receiver autonomous integrity monitoring (RAIM) algorithm is proposed. In order to prevent the interaction between the two faults, the posterior distribution of observation error is obtained and the posterior probabilities of the events related to the observation errors of two satellites are calculated based on Bayes statistical theory, The complex posterior probability calculation formula is transformed into sample average by using Monte Carlo method, which meets the real-time requirements of identifying method. The simulation results based on the precise ephemeris products provided by iGMAS show that the proposed algorithm can identify two satellite faults quickly and accurately, and improve the accuracy of navigation and positioning to a certain extent. Compared with the previous RANCO method, it shows that the method is feasible, not only can effectively identify the fault, but also can effectively prevent the interaction between the two faults.
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- 2021
15. The AR Model with Trend Item and the Corresponding Algorithm of AO Detection and Satellite Clock Error Prediction
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Yisong Gong, Guozhong Li, Jianwen Li, Jie Guo, Xinna Li, and Songhui Han
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Correctness ,Autoregressive model ,Computer science ,Physics::Space Physics ,Outlier ,Expectation–maximization algorithm ,Inverse ,Satellite ,Anomaly detection ,Time series ,Algorithm - Abstract
It has a good outlier detection effect and satellite clock error prediction accuracy based on the time series model to eliminate the influence of AO (Additive Outlier) and carry out the satellite clock error prediction. However, there are difference, inverse difference and model order determination operations when a time series model is used. In this paper, the AR model with trend item is combined with the EM algorithm, and an algorithm for AO detection and satellite clock error prediction are proposed to avoid difference, inverse difference and model order determination operations. When the AO in the clock error is successfully detected, the algorithm can obtain an accurate AR model with trend item, and then fit the growth or decline trend of the satellite clock error accurately. The algorithm also has good satellite clock error prediction accuracy. Finally, using the measured data of the BDS satellite clock error to calculate and analyze, the results verify the correctness and effectiveness of the algorithm.
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- 2021
16. Fuzzy subspace clustering noisy image segmentation algorithm with adaptive local variance & non-local information and mean membership linking
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Tongyi Wei, Xiaopeng Wang, Xinna Li, and Shengyang Zhu
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Artificial Intelligence ,Control and Systems Engineering ,Electrical and Electronic Engineering - Published
- 2022
17. Extramedullary melanotic schwannoma recurrence in the cervical vertebral arch: a case report and review of the literature
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Guangrun Li, Zongbin Hou, Lin Tian, Xiaoyang Liu, Xinna Li, and Teng Shi
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Adult ,Medicine (General) ,medicine.medical_specialty ,tumor ,Vertebral Body ,recurrence ,Decompression ,medicine.medical_treatment ,Case Report ,Biochemistry ,Benign tumor ,Metastasis ,03 medical and health sciences ,R5-920 ,0302 clinical medicine ,medicine ,Melanotic schwannoma ,Internal fixation ,Humans ,Pathological ,radiotherapy ,Neck pain ,business.industry ,Biochemistry (medical) ,Laminectomy ,surgical resection ,Cell Biology ,General Medicine ,Neuroma, Acoustic ,medicine.disease ,Radiation therapy ,Nerve sheath tumor ,030220 oncology & carcinogenesis ,Cervical Vertebrae ,Female ,pathological diagnosis ,Radiology ,medicine.symptom ,Neoplasm Recurrence, Local ,business ,030217 neurology & neurosurgery - Abstract
Melanotic schwannoma (MS), a slowly growing nerve sheath tumor, is not a purely benign tumor. MS accounts for less than 1% of all nerve sheath tumors. We herein describe a rare case of MS and present a literature review focusing on the treatment of this disease. Twelve years before presentation at our hospital, a 41-year-old woman was examined because of an 8-month history of neck pain and 6-month history of upper extremity numbness and weakness. She underwent surgery to remove a tumor, and the pathological examination confirmed a diagnosis of MS. Twelve years later, at 53 years of age, the patient presented to our hospital with a 2-year history of neck pain and upper extremity numbness and weakness. Posterior cervical tumor resection was performed along with posterior cervical laminectomy, decompression and intraspinal space-occupying internal fixation, and radiotherapy. MS recurrence was confirmed. No tumor recurrence or metastasis was found after 7 months of follow-up. Recurrence of MS is rare, and its diagnosis depends on pathological features. Radical excision is the primary treatment for MS. Incomplete resection of MS is a risk factor for postoperative recurrence and metastasis. Furthermore, postoperative adjuvant radiotherapy should be performed to prevent recurrence and metastasis of MS.
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- 2020
18. The Role of p53-Mediated Signaling in the Therapeutic Response of Colorectal Cancer to 9F, a Spermine-Modified Naphthalene Diimide Derivative
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Xiaojuan Xu, Yuxia Wang, Songqiang Xie, Xinna Li, Yongli Feng, Chaochao Ge, Lei Gao, Senzhen Wang, Fujun Dai, and Chaojie Wang
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0301 basic medicine ,p53 ,Cancer Research ,Cell cycle checkpoint ,Colorectal cancer ,Angiogenesis ,colorectal cancer ,lcsh:RC254-282 ,Article ,Metastasis ,03 medical and health sciences ,0302 clinical medicine ,polyamine ,medicine ,Chemistry ,Cell growth ,Amonafide ,Cell cycle ,medicine.disease ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,naphthalimide ,digestive system diseases ,030104 developmental biology ,Oncology ,Apoptosis ,030220 oncology & carcinogenesis ,Cancer research - Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers due to its frequency and high rate of mortality. Polyamine-vectorized anticancer drugs possess multiple biological properties. Of these drugs, 9F has been shown to inhibit tumor growth and the metastasis of hepatocellular carcinoma. This current study aims to investigate the effects of 9F on CRC and determine its molecular mechanisms of action. Our findings demonstrate that 9F inhibits CRC cell growth by inducing apoptosis and cell cycle arrest, and suppresses migration, invasion and angiogenesis in vitro, resulting in the inhibition of tumor growth and metastasis in vivo. Based on RNA-seq data, further bioinformatic analyses suggest that 9F exerts its anticancer activities through p53 signaling, which is responsible for the altered expression of key regulators of the cell cycle, apoptosis, the epithelial-to-mesenchymal transition (EMT), and angiogenesis. In addition, 9F is more effective than amonafide against CRC. These results show that 9F can be considered as a potential strategy for CRC treatment.
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- 2020
19. Identification of molecular anti-metastasis mechanisms of lycorine in colorectal cancer by RNA-seq analysis
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Chaojie Wang, Chaochao Ge, Songqiang Xie, Kemeng Zhang, Fujun Dai, Xiaojuan Xu, Lei Gao, Xinna Li, Yongli Feng, and Senzhen Wang
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Male ,Pharmaceutical Science ,Apoptosis ,Biology ,03 medical and health sciences ,chemistry.chemical_compound ,Mice ,Phosphatidylinositol 3-Kinases ,0302 clinical medicine ,Annexin ,Cell Line, Tumor ,Drug Discovery ,Animals ,Humans ,MTT assay ,Propidium iodide ,RNA-Seq ,Neoplasm Metastasis ,Protein kinase B ,PI3K/AKT/mTOR pathway ,030304 developmental biology ,Cell Proliferation ,Pharmacology ,0303 health sciences ,Mice, Inbred BALB C ,Kinase ,Wnt signaling pathway ,Lycorine ,Endoplasmic Reticulum Stress ,Phenanthridines ,Complementary and alternative medicine ,chemistry ,030220 oncology & carcinogenesis ,Cancer research ,Amaryllidaceae Alkaloids ,Molecular Medicine ,Colorectal Neoplasms ,Signal Transduction - Abstract
Background Colorectal cancer (CRC) is one of the most common malignancies worldwide. Metastasis is the major cause of death in patients with CRC. Lycorine, the phenanthridine alkaloid most commonly found in spp of the Amaryllidaceae family, has shown promising anticancer activities with minor side effects. However, the effects and the detailed mechanism of lycorine against metastasis of CRC remains unclear. Study design/methods The purpose of this study was to investigate the effects of lycorine on CRC and characterize the molecular mechanisms observed in lycorine-treated CRC cells using RNA-sequencing. MTT assay, colony formation assay, acridine orange/ethidium bromide (AO/EB) staining and Annexin V-FITC/Propidium iodide (PI) staining were conducted to examine the effects of lycorine on cell proliferation and apoptosis in CRC cells. RNA sequencing, real-time PCR assays and western blot were performed. Migration and invasion abilities of lycorine-treated CRC cells were investigated by wound healing and transwell invasion assays. The mouse CRC lung metastasis model was established and was used to detect the effect of lycorine on CRC in vivo. Results Our results demonstrated that lycorine inhibited the proliferation and colony formation of CRC cells in a concentration-dependent manner. AO/EB staining and Annexin V-FITC/PI staining showed that lycorine induced apoptosis in a concentration-dependent manner. Lycorine also reduced lung metastasis of CRC in vivo. Moreover, transcriptomic analysis suggested that lycorine regulated the expression of 3556 genes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was implicated according to the differentially expressed genes (DEGs), and multiple pathways including those of mitogen-activated protein kinase (MAPK), relaxin, Ras, phosphatidylinositol 3‑kinase (PI3K)-protein kinase B (Akt) and Wnt/β-catenin were selected by functional enrichment analyses. Furthermore, based on transcriptomic analysis, we found that the tumor necrosis factor (TNF) pathway and endoplasmic reticulum stress were responsible for lycorine-induced apoptosis. Conclusions These results obtained in this study demonstrated that lycorine has the potential to suppress CRC in vitro and in vivo through the lycorine-regulated multiple signaling pathways.
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- 2020
20. A probe directed recombinase amplification assay for detection of MTHFR A1298C polymorphism associated with congenital heart disease
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Chen Chen, Fang-zhou Qiu, Le Wang, Xuejun Ma, Su-xia Duan, Meng-chuan Zhao, Guixia Li, Xinna Li, Li Zhao, Teng-fei Yan, and Zhishan Feng
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Heart Defects, Congenital ,0301 basic medicine ,Drug ,Genotype ,Genotyping Techniques ,Heart disease ,media_common.quotation_subject ,Single-nucleotide polymorphism ,Polymorphism, Single Nucleotide ,Proof of Concept Study ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Recombinase ,Humans ,Mthfr c677t ,Genetic Predisposition to Disease ,Methylenetetrahydrofolate Reductase (NADPH2) ,media_common ,Genetics ,biology ,business.industry ,medicine.disease ,Treatment efficacy ,030104 developmental biology ,030220 oncology & carcinogenesis ,Methylenetetrahydrofolate reductase ,biology.protein ,business ,Nucleic Acid Amplification Techniques ,Biotechnology - Abstract
Single nucleotide polymorphisms (SNPs) play an important role in susceptibility to complex diseases, treatment efficacy and adverse drug responses. Conventional methods to detect SNPs are usually based on PCR or DNA sequencing, which are typically time-consuming and require sophisticated equipment. In this proof-of-concept study, a probe-directed recombinase amplification (PDRA) assay was developed to detect the A1298C polymorphism of 5,10-methylenetetrahydrofolate reductase (MTHFR). The PDRA assay included two real-time reactions to detect the A and C nucleotides of A1298C polymorphism. Each reaction contained only one primer and one probe and was finished at 39°C within 35 min. The results of genotyping of 150 clinical samples using PDRA were completely consistent with those by direct sequencing. Additionally, when the 1000 Genomes Project HCB frequencies were used as the control group, MTHFR A1298C was found to be associated with congenital heart disease. In conclusion, the proposed novel PDRA assay is a valuable tool for the detection of SNPs and demonstrates significant potential to be widely applicable in both research and clinical settings.
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- 2018
21. High throughput small molecule screening reveals NRF2-dependent and - independent pathways of cellular stress resistance
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Yang Lyu, Scott D. Pletcher, David B. Lombard, Melissa Han, William Kohler, Christi M. Gendron, Zaneta Nikolovska-Coleska, Ao Lin Hsu, Xiaofang Shi, Thomas Girke, Xinna Li, Yuzhu Duan, Angela H. Guo, Weiqiao Ding, and Richard A. Miller
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Transcriptome ,chemistry.chemical_compound ,chemistry ,Paraquat ,Superoxide ,media_common.quotation_subject ,Longevity ,Stress resistance ,Small molecule ,DNA ,media_common ,Cell biology ,Methyl methanesulfonate - Abstract
Biological aging is the dominant risk factor for most chronic diseases. Development of anti-aging interventions offers the promise of preventing many such illnesses simultaneously. Cellular stress resistance is an evolutionarily conserved feature of longevity. Here, we identify compounds that induced resistance to the superoxide generator paraquat (PQ), the heavy metal cadmium (Cd), and the DNA alkylator methyl methanesulfonate (MMS). Some rescue compounds conferred resistance to a single stressor, while others provoked multiplex resistance. Induction of stress resistance in fibroblasts was predictive of longevity extension in a published large-scale longevity screen in C. elegans. Transcriptomic analysis implicated Nrf2 signaling in stress resistance provided by two protective compounds, cardamonin and AEG 3482. Molecules that conferred stress resistance also induced cellular inflammatory pathways, and other core pathways such as AMPK signaling. Small molecules identified in this work may represent attractive candidates to evaluate for their potential pro-health and pro-longevity effects in mammals.
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- 2019
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22. mTOR regulates the expression of DNA damage response enzymes in long-lived Snell dwarf, GHRKO, and PAPPA-KO mice
- Author
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Graham Dominick, Gonzalo G. Garcia, Jacqueline Bowman, Richard A. Miller, and Xinna Li
- Subjects
Male ,0301 basic medicine ,Aging ,Receptors, CCR4 ,DNA damage ,DNA repair ,Longevity ,Down-Regulation ,Cell Cycle Proteins ,Dwarfism ,mTORC1 ,Biology ,Models, Biological ,03 medical and health sciences ,Downregulation and upregulation ,Gene expression ,medicine ,Animals ,Pregnancy-Associated Plasma Protein-A ,RNA, Messenger ,IGF ,molecular biology of aging ,DNA Modification Methylases ,PI3K/AKT/mTOR pathway ,Mice, Knockout ,Sirolimus ,TOR Serine-Threonine Kinases ,Tumor Suppressor Proteins ,Intracellular Signaling Peptides and Proteins ,Receptors, Somatotropin ,Original Articles ,Cell Biology ,Cell biology ,DNA Repair Enzymes ,030104 developmental biology ,Liver ,gene expression ,Female ,Original Article ,Signal transduction ,signal transduction ,DNA Damage ,Transcription Factors ,medicine.drug - Abstract
Summary Studies of the mTOR pathway have prompted speculation that diminished mTOR complex-1 (mTORC1) function may be involved in controlling the aging process. Our previous studies have shown diminished mTORC1 activity in tissues of three long-lived mutant mice: Snell dwarf mice, growth hormone receptor gene disrupted mice (GHRKO), and in this article, mice deficient in the pregnancy-associated protein-A (PAPPA-KO). The ways in which lower mTOR signals slow aging and age-related diseases are, however, not well characterized. Here, we show that Snell, GHKRO, and PAPPA-KO mice express high levels of two proteins involved in DNA repair, O-6-methylguanine-DNA methyltransferase (MGMT) and N-myc downstream-regulated gene 1 (NDRG1). Furthermore, we report that lowering mTOR enhances MGMT and NDRG1 protein expression via post-transcriptional mechanisms. We show that the CCR4-NOT complex, a post-transcriptional regulator of gene expression, is downstream of the mTORC1 pathway and may be responsible for the upregulation of MGMT and NDRG1 in all three varieties of long-lived mice. Our data thus suggest a novel link between DNA repair and mTOR signaling via post-transcriptional regulation involving specific alteration in the CCR4-NOT complex, whose modulation could control multiple aspects of the aging process.
- Published
- 2016
23. The Optimal Environment Selection Strategy of Risk Model With Perturbed Diffusion
- Author
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Xinna Li, Jie Guo, Lili Zhang, Shumei Guo, and Jiandong Yang
- Subjects
Mathematical optimization ,Risk model ,Computer Science::Information Retrieval ,Selection strategy ,Mathematics::Optimization and Control ,Economics ,Diffusion (business) - Abstract
In this paper, the authors consider the optimal investment of the risk model with perturbed diffusion. Insurance companies invest the surplus in risky asset and risk-free asset. This paper discusses the problem of minimizing the ruin probability of insurance company. By solving the corresponding Hamilton-Jacobi-Bellman equations, the optimal investment portfolio and the upper bound of Lundberg of the minimal ruin probability are obtained. Especially,when the claim distribution is exponential distribution, asymptotic optimality and asymptotic uniqueness of strategy A* and R are obtained.
- Published
- 2020
24. Utilizing Seasonal ARIMA Model for price of live pig in Henan
- Author
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Xinna Li, Shumei Guo, Jie Guo, and Jiandong Yang
- Subjects
History ,Econometrics ,Autoregressive integrated moving average ,Computer Science Applications ,Education ,Mathematics - Abstract
In this paper, the SARIMA model is used to analyze the monthly pig price data of Henan Province from 2005.01 to 2019.10, identify the model, and predict the price in short time. It’s show that the model fits well.
- Published
- 2020
25. Synthesis and biological evaluation of novel asymmetric naphthalene diimide derivatives as anticancer agents depending on ROS generation
- Author
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Songqiang Xie, Xinna Li, Xiaojuan Xu, Chaojie Wang, Yongli Feng, Fujun Dai, Chaochao Ge, Senzhen Wang, Yuan Chang, and Wen Luo
- Subjects
0301 basic medicine ,Pharmacology ,chemistry.chemical_classification ,Reactive oxygen species ,Organic Chemistry ,Autophagy ,Pharmaceutical Science ,Biochemistry ,Hep G2 ,03 medical and health sciences ,chemistry.chemical_compound ,Chemistry ,030104 developmental biology ,chemistry ,Diimide ,Apoptosis ,Drug Discovery ,Biophysics ,Molecular Medicine ,Naphthalene diimide ,IC50 ,Biological evaluation - Abstract
Naphthalenetetracarboxylic diimide (NDI) is widely used as a photoelectric material in the field of medicine. A series of asymmetric naphthalene diimide derivatives were synthesized and evaluated for their anticancer properties by various experimental assays. As the representative compound, 3c exerted significantly greater inhibitory effects on hepatoma cells SMMC-7721 and Hep G2 with an IC(50) value of 1.48 ± 0.43 μM and 1.70 ± 0.53 μM, respectively, than normal hepatocytes QSG-7701 with an IC(50) value of 7.11 ± 0.08 μM. Treatment with compound 3c (3 μM) for 48 h resulted in apoptosis of SMMC-7721 cells and Hep G2 cells with 52.1% and 67.8% apoptotic cells, respectively. Compound 3c induced autophagy and suppressed the migration of hepatoma cells in a concentration-dependent manner, resulting from the generation of reactive oxygen species (ROS). Based on its biological ability, compound 3c was considered as a potent anticancer agent.
- Published
- 2018
26. The Kernel Regression Method Based on the Multiplicative Model to Reduce Speckle for SAR image
- Author
-
Ke Chen and Xinna Li
- Subjects
Speckle pattern ,business.industry ,Maximum likelihood ,Kernel regression ,Pattern recognition ,Artificial intelligence ,business ,Multiplicative model ,Image (mathematics) ,Mathematics - Published
- 2018
27. Use of a rapid reverse-transcription recombinase aided amplification assay for respiratory syncytial virus detection
- Author
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Xuejun Ma, Xinna Li, Li Zhao, Chen Chen, Su-xia Duan, Teng-fei Yan, Guixia Li, and Zhishan Feng
- Subjects
0301 basic medicine ,Microbiology (medical) ,Male ,030106 microbiology ,Respiratory Syncytial Virus Infections ,Biology ,Sensitivity and Specificity ,Virus ,03 medical and health sciences ,Nasopharynx ,Virology ,Recombinase ,Humans ,Respiratory system ,Child ,Reverse Transcriptase Polymerase Chain Reaction ,Infant, Newborn ,Cross reactions ,Infant ,General Medicine ,Molecular biology ,Reverse transcriptase ,Virus detection ,Molecular Typing ,030104 developmental biology ,Infectious Diseases ,Child, Preschool ,Respiratory Syncytial Virus, Human ,RNA, Viral ,Female - Abstract
In this study, a rapid reverse-transcription recombinase aided amplification (RT-RAA) assay was developed to detect respiratory syncytial virus (RSV) subgroups A and B, respectively. The reaction was performed at 39°C in less than 30 min. The analytical sensitivities of RSVA and RSVB at 95% probability by probit regression analysis were 38copies per reaction and 35 copies per reaction, respectively, and no cross reactions with other related respiratory viruses were observed. The RT-RAA assay was further utilized to detect and subgroup 306 clinical specimens and the results showed that 79(25.82%, 79/306) samples were positive for RSV, of those 16(20.25%, 16/79) were identified as RSVA and 63(79.75%, 63/79) were RSVB, which is completely consistent with the results obtained by RSV RT-qPCR assay. In conclusion, the developed RAA assay will be of benefit as a faster, sensitive and specific alternative tool for detection of RSV.
- Published
- 2017
28. Multifocal and Multicentric Breast Carcinoma: A Significantly More Aggressive Tumor than Unifocal Breast Cancer
- Author
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Cuiyan Li, Yanqiu Wu, Zhiqiang Lang, Xuan Wang, Xinna Li, and Guimei Qu
- Subjects
0301 basic medicine ,Oncology ,Adult ,Cancer Research ,medicine.medical_specialty ,Proliferative index ,Breast Neoplasms ,Multicentric breast cancer ,03 medical and health sciences ,Breast cancer ,Internal medicine ,medicine ,Carcinoma ,Biomarkers, Tumor ,Humans ,Lymph node ,In Situ Hybridization, Fluorescence ,Aged ,Neoplasm Staging ,Aged, 80 and over ,Neoplasm Grading ,business.industry ,Carcinoma, Ductal, Breast ,General Medicine ,Middle Aged ,medicine.disease ,Immunohistochemistry ,Tumor Burden ,Axilla ,030104 developmental biology ,medicine.anatomical_structure ,Lymphatic Metastasis ,Disease Progression ,Female ,business - Abstract
BACKGROUND/AIM There are still many questions that surround multifocal or multicentric breast carcinoma (MMBC). The aim of this study was to analyze the clinicopathological characteristics of MMBC and provide feasible suggestions for therapy. PATIENTS AND METHODS A total of 156 cases of MMBC in 3,597 invasive ductal breast carcinomas were collected and reviewed. Some factors related with prognosis such as tumor size, lymph node metastasis and others were assessed in each tumor focus, and mismatches among foci were recorded. RESULTS The majority of MMBC had aggregate dimensions over 2 cm (85.90%). The rate of axillary lymph node metastasis was 56.41% (88/156) compared to unifocal tumors of 33.01% (1,136/3,441). Most cases had higher Ki-67 proliferative indices (91/156). Mismatches in ER status were present in 6 cases, PR in 4 cases, proliferative index (Ki-67) in 9 cases and HER2-positive status in 2 cases. CONCLUSION The larger aggregate dimension of tumor, the higher metastatic rate of axillary lymph node and the high Ki-67 proliferative index seen in most cases, suggest that MMBC is biologically more aggressive than unifocal breast cancer. In addition, every focus should be tested owing to the existence of different expressions of immunostaining between foci.
- Published
- 2017
29. <scp>ATF</scp> 4 activity: a common feature shared by many kinds of slow‐aging mice
- Author
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Weiquan Li, Xinna Li, and Richard A. Miller
- Subjects
Male ,Aging ,medicine.medical_specialty ,Biology ,Activating Transcription Factor 4 ,Mice ,03 medical and health sciences ,0302 clinical medicine ,longevity ,Internal medicine ,medicine ,Animals ,Gene ,030304 developmental biology ,Acarbose ,Mice, Knockout ,chemistry.chemical_classification ,0303 health sciences ,Activating Transcription Factor 3 ,methionine restriction ,rapamycin ,ATF4 ,Original Articles ,Cell Biology ,Ribosomal RNA ,Amino acid ,Disease Models, Animal ,Endocrinology ,Liver ,chemistry ,Knockout mouse ,Female ,caloric restriction ,acarbose ,Transcription Factor CHOP ,030217 neurology & neurosurgery ,Function (biology) ,medicine.drug - Abstract
ATF4, a DNA-binding factor that modulates responses to amino acid availability and ribosomal function, has been shown to be altered in both liver and fibroblasts from two strains of long-lived mice, i.e. Snell dwarf and PAPP-A knockout mice. New data now show elevated ATF4 levels, and elevation of ATF4-dependent proteins and mRNAs, in liver of mice treated with acarbose or rapamycin, calorically restricted mice, methionine-restricted mice, and mice subjected to litter crowding. Elevation of ATF4, at least in liver, thus seems to be a shared feature of diets, drugs, genes, and developmental alterations that extend maximum lifespan in mice.
- Published
- 2014
30. A New Type I Peritrophic Membrane Protein from Larval Holotrichia oblita (Coleoptera: Melolonthidae) Binds to Chitin
- Author
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Dan Zhao, Liu Xiaomin, Xinna Li, Li Ruijun, Wei Guo, and Jie Li
- Subjects
Molecular Sequence Data ,peritrophic membrane ,Chitin ,Sequence alignment ,Plasma protein binding ,Biology ,HoCBP76 ,Article ,Catalysis ,lcsh:Chemistry ,Inorganic Chemistry ,chemistry.chemical_compound ,Western blot ,Chitin binding ,Holotrichia oblita ,medicine ,Animals ,Amino Acid Sequence ,Physical and Theoretical Chemistry ,lcsh:QH301-705.5 ,chitin binding protein ,Molecular Biology ,Peptide sequence ,Spectroscopy ,chemistry.chemical_classification ,Base Sequence ,medicine.diagnostic_test ,cDNA expression library ,fungi ,Organic Chemistry ,Membrane Proteins ,Midgut ,General Medicine ,Molecular biology ,Recombinant Proteins ,Computer Science Applications ,Coleoptera ,lcsh:Biology (General) ,lcsh:QD1-999 ,chemistry ,Biochemistry ,Larva ,Insect Proteins ,Electrophoresis, Polyacrylamide Gel ,Glycoprotein ,Sequence Alignment ,Protein Binding - Abstract
Peritrophic membranes (PMs) are composed of chitin and protein. Chitin and protein play important roles in the structural formation and function of the PM. A new type I PM protein, HoCBP76, was identified from the Holotrichia oblita. HoCBP76 was shown as a 62.3 kDa protein by SDS-PAGE analysis and appeard to be associated with the PM throughout its entire length. In H. oblita larvae, the midgut is the only tissue where HoCBP76 could be detected during the feeding period of the larvae. The predicted amino acid sequence indicates that it contains seven tandem chitin binding domains belonging to the peritrophin-A family. HoCBP76 has chitin binding activity and is strongly associated with the PM. The HoCBP76 was not a mucin-like glycoprotein, and the consensus of conserved cysteines appeared to be CX13–17CX5CX9CX12CX7C. Western blot analysis showed that the abundance of HoCBP76 in the anterior, middle and posterior regions of the midgut was similar, indicating that HoCBP76 was secreted by the whole midgut epithelium, and confirmed the H. oblita PM belonged to the Type I PM. Immunolocalization analysis showed that HoCBP76 was mainly localized in the PM. The HoCBP76 is the first PM protein found in the H. oblita; however, its biochemical and physiological functions require further investigation.
- Published
- 2014
31. Silencing SATB1 Inhibits the Malignant Phenotype and Increases Sensitivity of Human Osteosarcoma U2OS Cells to Arsenic Trioxide
- Author
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Haiying Zhang, Xuejin Su, Li Guo, Yan Mu, Xiaotong Wang, Lingzhi Zhong, Ronggui Li, Zhen Yue, Wenxue Li, Xinna Li, and Zonggui Wang
- Subjects
Programmed cell death ,migration, invasion, apoptosis, arsenic trioxide ,Gene Expression ,Antineoplastic Agents ,Apoptosis ,Bone Neoplasms ,Biology ,Arsenicals ,chemistry.chemical_compound ,SATB1 ,Arsenic Trioxide ,Cell Movement ,Cell Line, Tumor ,medicine ,Humans ,Gene silencing ,Neoplasm Invasiveness ,RNA, Messenger ,RNA, Neoplasm ,RNA, Small Interfering ,Arsenic trioxide ,Osteosarcoma ,TUNEL assay ,Cell growth ,Oxides ,Cell migration ,Matrix Attachment Region Binding Proteins ,General Medicine ,medicine.disease ,Molecular biology ,Phenotype ,chemistry ,Drug Resistance, Neoplasm ,Gene Knockdown Techniques ,Cancer research ,Research Paper - Abstract
In a previous study, we found that the global genome organizer Special AT-rich binding protein 1 (SATB1) is highly expressed in mesenchymal-derived human osteosarcoma U2OS cells and that the knock-down of SATB1 results in the inhibition of cell proliferation. The present study was aimed at investigating the effect of silencing SATB1 on cell migration, invasion, apoptosis and resistance to the chemotherapeutic drug arsenic trioxide. Cell migration and invasion were detected by wound-healing assays and trans-well invasion assays, respectively. Cell apoptosis was analyzed by an in situ Cell Death Detection POD Kit, based on terminal deoxynucleotydyl transferase mediated dUTP nick-end labeling (TUNEL) staining and mRNAs were analyzed by real time qRT-PCR. We found that cell migration and invasion were inhibited and that the proportion of apoptotic cells and sensitivities to the chemotherapeutic drug arsenic trioxide were enhanced by knockdown of SATB1 in U2OS cells. Furthermore, mRNA of ABCC1 and ABCG2 were decreased strikingly after SATB1 silencing. It was concluded that the elevated expression of SATB1 in U2OS cells contributes to maintenance of the malignant phenotype and resistance to chemotherapeutic drugs ATO, suggesting that silencing SATB1 in the cells might improve the effects of arsenic trioxides in the treatment of osteosarcoma in which SATB1 is over-expressed and that ABCC1 and ABCG2 were involved in SATB1 mediated resistance of U2OS cells to ATO.
- Published
- 2014
32. A Reverse Transcription Genome Exponential Amplification Reaction Assay for Visual Detection of Middle East Respiratory Syndrome Coronavirus
- Author
-
Li Guan, Kai Nie, Dan Zhang, Xinna Li, and Xuejun Ma
- Subjects
Isothermal amplification ,Hydroxynaphthol blue dye ,lcsh:RC109-216 ,Middle East respiratory syndrome coronavirus ,lcsh:Infectious and parasitic diseases - Abstract
A simple and rapid reverse-transcription Genome Exponential Amplification Reaction (RT-GEAR) Assay was developed for nucleic acid detection of Middle East respiratory syndrome coronavirus (MERS-CoV) under isothermal conditions at 63℃ for 60 min with good specificity and sensitivity. The products were detected by turbidimeter or through visual inspection by hydroxynaphthol blue dye.
- Published
- 2015
33. Updates on the web-based VIOLIN vaccine database and analysis system
- Author
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Priya Dungarani, Kanika Kochhar, Boyang Zhao, Samantha Sayers, Rebecca Racz, Xinna Li, Joseph Ostrow, Thomas E. Todd, Boris Vidri, Andrew Sylora, Yongqun He, Junguk Hur, Kelsey Strait, George W. Jourdian, Mukti Patel, Zuoshuang Xiang, Yu Lin, Monica Chung, and Guerlain Ulysse
- Subjects
Vaccine research ,Virulence Factors ,Ontology (information science) ,Biology ,computer.software_genre ,Vaccines, Attenuated ,DNA vaccination ,World Wide Web ,Violin ,Vaccine adjuvant ,Adjuvants, Immunologic ,Databases, Genetic ,Genetics ,Vaccines, DNA ,Data Mining ,Humans ,Antigens ,Research data ,Internet ,Vaccines ,Attenuated vaccine ,Database ,Reverse vaccinology ,Proteins ,Genomics ,3. Good health ,Systems Integration ,VI. Genomic variation, diseases and drugs ,Genes ,computer ,Sequence Alignment ,Software ,Plasmids - Abstract
The integrative Vaccine Investigation and Online Information Network (VIOLIN) vaccine research database and analysis system (http://www.violinet.org) curates, stores, analyses and integrates various vaccine-associated research data. Since its first publication in NAR in 2008, significant updates have been made. Starting from 211 vaccines annotated at the end of 2007, VIOLIN now includes over 3240 vaccines for 192 infectious diseases and eight noninfectious diseases (e.g. cancers and allergies). Under the umbrella of VIOLIN, >10 relatively independent programs are developed. For example, Protegen stores over 800 protective antigens experimentally proven valid for vaccine development. VirmugenDB annotated over 200 'virmugens', a term coined by us to represent those virulence factor genes that can be mutated to generate successful live attenuated vaccines. Specific patterns were identified from the genes collected in Protegen and VirmugenDB. VIOLIN also includes Vaxign, the first web-based vaccine candidate prediction program based on reverse vaccinology. VIOLIN collects and analyzes different vaccine components including vaccine adjuvants (Vaxjo) and DNA vaccine plasmids (DNAVaxDB). VIOLIN includes licensed human vaccines (Huvax) and veterinary vaccines (Vevax). The Vaccine Ontology is applied to standardize and integrate various data in VIOLIN. VIOLIN also hosts the Ontology of Vaccine Adverse Events (OVAE) that logically represents adverse events associated with licensed human vaccines.
- Published
- 2013
34. Direct and indirect effects of growth hormone receptor ablation on liver expression of xenobiotic metabolizing genes
- Author
-
Richard A. Miller, Liou Y. Sun, Kevin Funk, John J. Kopchick, Darlene E. Berryman, Edward O. List, Xinna Li, and Andrzej Bartke
- Subjects
Male ,medicine.medical_specialty ,Physiology ,Endocrinology, Diabetes and Metabolism ,Adipose tissue ,Endogeny ,Growth hormone receptor ,Biology ,Gene Expression Regulation, Enzymologic ,Xenobiotics ,Mice ,chemistry.chemical_compound ,Physiology (medical) ,Detoxification ,Internal medicine ,medicine ,Animals ,RNA, Messenger ,Muscle, Skeletal ,Oligonucleotide Array Sequence Analysis ,Mice, Knockout ,chemistry.chemical_classification ,Sex Characteristics ,Messenger RNA ,Skeletal muscle ,Receptors, Somatotropin ,Articles ,Mice, Mutant Strains ,Endocrinology ,Enzyme ,medicine.anatomical_structure ,Adipose Tissue ,Liver ,chemistry ,Organ Specificity ,Mutation ,Female ,Xenobiotic - Abstract
Detoxification of ingested xenobiotic chemicals, and of potentially toxic endogenous metabolites, is carried out largely through a series of enzymes synthesized in the liver, sometimes called “xenobiotic metabolizing enzymes” (XME). Expression of these XME is sexually dimorphic in rodents and humans, with many of the XME expressed at higher levels in females. This expression pattern is thought to be regulated, in part, by the sex differences in circadian growth hormone (GH) pulsatility. We have evaluated mRNA, in the liver, for 52 XME genes in male and female mice of four mutant stocks, with diminished levels of GH receptor (GHR) either globally (GKO), or in liver (LKO), fat (FKO), or muscle (MKO) tissue specifically. The data show complex, sex-specific changes. For some XME, the expression pattern is consistent with direct control of hepatic mRNA by GHR in the liver. In contrast, other XME show evidence for indirect pathways in which hepatic XME expression is altered by GH signals in fat or skeletal muscle. The effects of GHR-null mutations on glucose control, responses to dietary interventions, steroid metabolism, detoxification pathways, and lifespan may depend on a mixture of direct hepatic effects and cross talk between different GH-responsive tissues.
- Published
- 2013
35. Effect Analysis of Fans Activating Time on Smoke Control Mode for Road Tunnel Fire
- Author
-
Tongji Antai, Lili Han, Xin Han, Beihua Cong, and Xinna Li
- Subjects
Fire test ,Smoke ,Control mode ,Engineering ,Effect analysis ,General Computer Science ,business.industry ,General Engineering ,Active fire protection ,Fire damper ,Fire control ,Fire protection ,Forensic engineering ,business ,human activities - Abstract
With the development of economy, more and more road tunnels have been built. Due to the relatively isolated environment of the tunnel, fire protection is the most important factor for the safe management of tunnel operation. During the fire process, many people are killed by the fire smoke. As for preventive measures of road tunnel fire, smoke exhaust system is the most effective way to control the spread of fire smoke. Based on full size tunnel fire test and simulation analysis, this study carries out effect analysis of fans activating time on smoke control mode for road tunnel fire. The corresponding results are useful to establish fire control strategy and personnel evacuation plan for tunnel management system.
- Published
- 2013
36. [Detection of the Zaire Subtype of the Ebola Virus by Isothermal Multiple Self-matching Initiated Amplification]
- Author
-
Xinna, Li, Kai, Nie, Ji, Wang, Dan, Zhang, Li, Guan, Jun, Liu, Yuehua, Ke, Hangyu, Zhou, and Xuejun, Ma
- Subjects
Humans ,Colorimetry ,Hemorrhagic Fever, Ebola ,Ebolavirus ,Nucleic Acid Amplification Techniques ,DNA Primers - Abstract
Given the Ebola outbreak in West Africa and the risks of spread to other regions, a rapid, sensitive and simple method for the detection of the Ebola virus (EBOV) is of great significance for the prevention and control of Ebola. We developed a simple colorimetric isothermal multiple self-matching initiated amplification (IMSA) for rapid detection of the Zaire subtype of the Ebola virus (EBOV-Z). This method employed six primers that recognized seven sites of the EBOV-Z nucleoprotein gene for amplification of nucleic acids under isothermal conditions at 63 degrees C for 1 h. Amplification products were detected through visual inspection of color change by pre-addition of hydroxyl naphthol blue dye. Relative sensitivity was validated by detection of serial tenfold dilutions of virus-like particles containing the partial EBOV-Z nucleoprotein gene and mock clinical sample. Specificity of IMSA was validated by detection of the plasma of 30 healthy volunteers, the dengue virus, and Japanese encephalitis virus. IMSA had comparable sensitivity to Reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and cross-reaction with human plasma or other viruses was not observed. Reverse transcription-isothermal multiple self-matching initiated amplification (RT-IMSA) was also evaluated and compared in parallel with the commercial RT-qPCR kit for detection of EBOV-suspected samples of human blood in Sierra Leone. Sensitivity and specificity of the RT-IMSA was 91.4% and 100%, respectively. These data suggest that RT-IMSA is a valuable tool for the detection of the EBOV with the distinct advantages of simplicity and low cost compared with RT-qPCR.
- Published
- 2016
37. The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology
- Author
-
Yan Xia, Dapeng Wang, Lixia Hou, Xinna Li, and Jun-Hwan Yu
- Subjects
Transcription, Genetic ,Genomics ,Oryza glaberrima ,Genome ,Evolution, Molecular ,User-Computer Interface ,Databases, Genetic ,Genetics ,Plant Proteins ,Repetitive Sequences, Nucleic Acid ,Synteny ,Oryza brachyantha ,Comparative genomics ,Internet ,Polymorphism, Genetic ,Oryza sativa ,biology ,food and beverages ,Molecular Sequence Annotation ,Oryza ,Articles ,biology.organism_classification ,Evolutionary biology ,Protein Biosynthesis ,Genome, Plant ,Software ,Reference genome - Abstract
Over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice (Oryza sativa L.) subspecies, 93-11 (indica) and Nipponbare (japonica). To integrate information from genome assemblies and annotations for better analysis and application, we now introduce a comparative rice genome database, the Rice Genome Knowledgebase (RGKbase, http://rgkbase.big.ac.cn/RGKbase/). RGKbase is built to have three major components: (i) integrated data curation for rice genomics and molecular biology, which includes genome sequence assemblies, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and the relevant literature; (ii) User-friendly viewers, such as Gbrowse, GeneBrowse and Circos, for genome annotations and evolutionary dynamics and (iii) Bioinformatic tools for compositional and synteny analyses, gene family classifications, gene ontology terms and pathways and gene co-expression networks. RGKbase current includes data from five rice cultivars and species: Nipponbare (japonica), 93-11 (indica), PA64s (indica), the African rice (Oryza glaberrima) and a wild rice species (Oryza brachyantha). We are also constantly introducing new datasets from variety of public efforts, such as two recent releases-sequence data from ∼1000 rice varieties, which are mapped into the reference genome, yielding ample high-quality single-nucleotide polymorphisms and insertions-deletions.
- Published
- 2012
38. Reverse transcription genome exponential amplification reaction assay for rapid and universal detection of human rhinoviruses
- Author
-
Hangyu Zhou, Juan Song, Li Guan, Xuejun Ma, Yuan Qian, Kai Nie, Lin-qing Zhao, Dan Zhang, and Xinna Li
- Subjects
0301 basic medicine ,Untranslated region ,medicine.medical_specialty ,Rhinovirus ,Acute otitis media ,030106 microbiology ,Genome, Viral ,Biology ,Genome ,Sensitivity and Specificity ,03 medical and health sciences ,Medical microbiology ,stomatognathic system ,Virology ,Fluorometer ,medicine ,Humans ,Respiratory Tract Infections ,Picornaviridae Infections ,Reverse Transcriptase Polymerase Chain Reaction ,Clinical performance ,virus diseases ,RNA ,General Medicine ,Reverse Transcription ,Molecular biology ,Reverse transcriptase ,RNA, Viral ,circulatory and respiratory physiology - Abstract
Human rhinoviruses (HRVs) have long been recognized as the cause of more than one-half of acute viral upper respiratory illnesses, and they are associated with more-serious diseases in children, such as asthma, acute otitis media and pneumonia. A rapid and universal test for of HRV infection is in high demand. In this study, a reverse transcription genome exponential amplification reaction (RT-GEAR) assay targeting the HRV 5' untranslated region (UTR) was developed for pan-HRV detection. The reaction was performed in a single tube in one step at 65 °C for 60 min using a real-time fluorometer (Genie(®)II; Optigene). The RT-GEAR assay showed no cross-reactivity with common human enteroviruses, including HEV71, CVA16, CVA6, CVA10, CVA24, CVB5, Echo30, and PV1-3 or with other common respiratory viruses including FluA H3, FluB, PIV1-4, ADV3, RSVA, RSVB and HMPV. With in vitro-transcribed RNA containing the amplified regions of HRV-A60, HRV-B06 and HRV-C07 as templates, the sensitivity of the RT-GEAR assay was 5, 50 and 5 copies/reaction, respectively. Experiments to evaluate the clinical performance of the RT-GEAR assay were also carried out with a panel of 143 previously verified samples, and the results were compared with those obtained using a published semi-nested PCR assay followed by sequencing. The tested panel comprised 91 HRV-negative samples and 52 HRV-positive samples (18 HRV-A-positive samples, 3 HRV-B-positive samples and 31 HRV-C-positive samples). The sensitivity and specificity of the pan-HRVs RT-GEAR assay was 98.08 % and 100 %, respectively. The kappa correlation between the two methods was 0.985. The RT-GEAR assay based on a portable Genie(®)II fluorometer is a sensitive, specific and rapid assay for the universal detection of HRV infection.
- Published
- 2015
39. Proinflammatory Caspase-2-Mediated Macrophage Cell Death Induced by a Rough Attenuated Brucella suis Strain
- Author
-
Nammalwar Sriranganathan, Yongqun He, Xicheng Ding, Xinna Li, Fang Chen, Zuoshuang Xiang, Ying Ding, Stephen M. Boyle, Gerhardt G. Schurig, and Debashis Ghosh
- Subjects
Programmed cell death ,Brucella suis ,Interleukin-1beta ,Immunology ,Caspase 2 ,Microbiology ,Brucellosis ,Proinflammatory cytokine ,Mice ,Animals ,Phosphorylation ,Caspase ,Oligonucleotide Array Sequence Analysis ,Host Response and Inflammation ,Cell Death ,biology ,Tumor Necrosis Factor-alpha ,Gene Expression Profiling ,Macrophages ,Pyroptosis ,Gene Expression Regulation, Bacterial ,Infectious Diseases ,Apoptosis ,biology.protein ,Parasitology ,Tumor necrosis factor alpha - Abstract
Brucella spp. are intracellular bacteria that cause an infectious disease called brucellosis in humans and many domestic and wildlife animals. B. suis primarily infects pigs and is pathogenic to humans. The macrophage- Brucella interaction is critical for the establishment of a chronic Brucella infection. Our studies showed that smooth virulent B. suis strain 1330 (S1330) prevented programmed cell death of infected macrophages and rough attenuated B. suis strain VTRS1 (a vaccine candidate) induced strong macrophage cell death. To further investigate the mechanism of VTRS1-induced macrophage cell death, microarrays were used to analyze temporal transcriptional responses of murine macrophage-like J774.A1 cells infected with S1330 or VTRS1. In total 17,685 probe sets were significantly regulated based on the effects of strain, time and their interactions. A miniTUBA dynamic Bayesian network analysis predicted that VTRS1-induced macrophage cell death was mediated by a proinflammatory gene (the tumor necrosis factor alpha [TNF-α] gene), an NF-κB pathway gene (the IκB-α gene), the caspase-2 gene, and several other genes. VTRS1 induced significantly higher levels of transcription of 40 proinflammatory genes than S1330. A Mann-Whitney U test confirmed the proinflammatory response in VTRS1-infected macrophages. Increased production of TNF-α and interleukin 1β (IL-1β) were also detected in the supernatants in VTRS1-infected macrophage cell culture. Hyperphosphorylation of IκB-α was observed in macrophages infected with VTRS1 but not S1330. The important roles of TNF-α and IκB-α in VTRS1-induced macrophage cell death were further confirmed by individual inhibition studies. VTRS1-induced macrophage cell death was significantly inhibited by a caspase-2 inhibitor but not a caspase-1 inhibitor. The role of caspase-2 in regulating the programmed cell death of VTRS1-infected macrophages was confirmed in another study using caspase-2-knockout mice. In summary, VTRS1 induces a proinflammatory, caspase-2- and NF-κB-mediated macrophage cell death. This unique cell death differs from apoptosis, which is not proinflammatory. It is also different from classical pyroptosis, which is caspase-1 mediated.
- Published
- 2011
40. Peptidoglycan Recognition Proteins Protect Mice from Experimental Colitis by Promoting Normal Gut Flora and Preventing Induction of Interferon-γ
- Author
-
Roman Dziarski, Xinna Li, Xuefang Jing, Shiyong Wang, Dipika Gupta, Sukumar Saha, and Shin Yong Park
- Subjects
Cancer Research ,MICROBIO ,Colon ,Biology ,Gut flora ,Microbiology ,Article ,Interferon-gamma ,Mice ,chemistry.chemical_compound ,Intestinal mucosa ,Virology ,Immunology and Microbiology(all) ,medicine ,Animals ,Genetic Predisposition to Disease ,Interferon gamma ,Intestinal Mucosa ,Colitis ,MOLIMMUNO ,Molecular Biology ,Mice, Knockout ,Mice, Inbred BALB C ,Lamina propria ,Dextran Sulfate ,Pattern recognition receptor ,medicine.disease ,biology.organism_classification ,Intestinal epithelium ,digestive system diseases ,Killer Cells, Natural ,Disease Models, Animal ,medicine.anatomical_structure ,chemistry ,CELLIMMUNO ,Immunology ,Female ,Parasitology ,Peptidoglycan ,Carrier Proteins ,medicine.drug - Abstract
There are multiple mechanisms that protect the intestine from an excessive inflammatory response to intestinal microorganisms. We report here that all four mammalian peptidoglycan recognition proteins (PGRPs or Pglyrps) protect the host from colitis induced by dextran sulfate sodium (DSS). Pglyrp1(-/-), Pglyrp2(-/-), Pglyrp3(-/-), and Pglyrp4(-/-) mice are all more sensitive than wild-type mice to DSS-induced colitis due to a more inflammatory gut microflora, higher production of interferon-gamma, higher expression of interferon-inducible genes, and an increased number of NK cells in the colon upon initial exposure to DSS, which leads to severe hyperplasia of the lamina propria, loss of epithelial cells, and ulceration in the colon. Thus, during experimental colitis, PGRPs protect the colon of wild-type mice from an early inflammatory response and the loss of the barrier function of intestinal epithelium by promoting normal bacterial flora and by preventing damaging production of interferon-gamma by NK cells in response to injury.
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- 2010
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41. Human Peptidoglycan Recognition Proteins Require Zinc to Kill Both Gram-Positive and Gram-Negative Bacteria and Are Synergistic with Antibacterial Peptides
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Xiaofeng Lu, Shiyong Wang, Xinna Li, Minhui Wang, Li Hui Liu, Roman Dziarski, and Dipika Gupta
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Glycosylation ,Gram-negative bacteria ,Immunology ,Colony Count, Microbial ,Dose-Response Relationship, Immunologic ,Microbiology ,chemistry.chemical_compound ,Gram-Negative Bacteria ,Humans ,Immunology and Allergy ,Innate immune system ,biology ,Effector ,Pattern recognition receptor ,biology.organism_classification ,Immunity, Innate ,Anti-Bacterial Agents ,Zinc ,chemistry ,Biochemistry ,Peptidoglycan recognition protein 1 ,Calcium ,Peptidoglycan ,Carrier Proteins ,Peptides ,Bacteria - Abstract
Mammals have four peptidoglycan recognition proteins (PGRPs or PGLYRPs), which are secreted innate immunity pattern recognition molecules with effector functions. In this study, we demonstrate that human PGLYRP-1, PGLYRP-3, PGLYRP-4, and PGLYRP-3:4 have Zn2+-dependent bactericidal activity against both Gram-positive and Gram-negative bacteria at physiologic Zn2+ concentrations found in serum, sweat, saliva, and other body fluids. The requirement for Zn2+ can only be partially replaced by Ca2+ for killing of Gram-positive bacteria but not for killing of Gram-negative bacteria. The bactericidal activity of PGLYRPs is salt insensitive and requires N-glycosylation of PGLYRPs. The LD99 of PGLYRPs for Gram-positive and Gram-negative bacteria is 0.3–1.7 μM, and killing of bacteria by PGLYRPs, in contrast to killing by antibacterial peptides, does not involve permeabilization of cytoplasmic membrane. PGLYRPs and antibacterial peptides (phospholipase A2, α- and β-defensins, and bactericidal permeability-increasing protein), at subbactericidal concentrations, synergistically kill Gram-positive and Gram-negative bacteria. These results demonstrate that PGLYRPs are a novel class of recognition and effector molecules with broad Zn2+-dependent bactericidal activity against both Gram-positive and Gram-negative bacteria that are synergistic with antibacterial peptides.
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- 2007
42. [Detection of Middle East Respiratory Syndrome Coronavirus by Reverse-transcription Loop-Mediated Isothermal Amplification]
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Guan, Li, Kai, Nie, Dan, Zhang, Xinna, Li, Yanqun, Wang, Wenjie, Tan, and Xuejun, Ma
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Middle East Respiratory Syndrome Coronavirus ,Humans ,Reverse Transcription ,Coronavirus Infections ,Nucleic Acid Amplification Techniques ,DNA Primers - Abstract
A simple, rapid and sensitive colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) was developed for rapid detection of Middle East respiratory syndrome coronavirus (MERS-CoV). The method employed six primers that recognized sequences of a nucleocapsid gene for amplification of nucleic acids under isothermal conditions at 63 degrees C for 60 min. Products were detected through a LA-320c Loopamp Turbidimeter (real-time RT-LAMP) or visual inspection of color change by pre-addition of Hydroxynaphthol Blue dye (visual RT-LAMP). Specificity of RT-LAMP was validated by detection of several human coronaviruses and common respiratory viruses. MERS-CoV real-time RT-LAMP had a linear correlation (R2) of 0.995 at 10(3)-10(6) copies. The limit of detection of real-time RT-LAMP, visual RT-LAMP and quantitative real-time PCR was 500, 1000 and 100 copies/reaction, respectively. The established RT-LAMP assay was demonstrated to be a rapid screening tool for MERS-CoV infection, and could be suitable in resource-limited clinical sites and for field studies.
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- 2015
43. Erratum for Kang et al., Flexibility and Symmetry of Prokaryotic Genome Rearrangement Reveal Lineage-Associated Core-Gene-Defined Genome Organizational Frameworks
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Yue Wang, Aftab Ahmed Khan, Chaohao Gu, Zhang Zhang, Lina Yuan, Jingfa Xiao, Yanmin Zhu, Jun Yu, Fei Chen, Xinna Li, Minping Qian, Da-Quan Jiang, Qibin Luo, and Yu Kang
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Genetics ,Gene Rearrangement ,Lineage (genetic) ,Genes, Essential ,Bacteria ,Computational Biology ,Biology ,Genome rearrangement ,Genome ,Microbiology ,Archaea ,Synteny ,QR1-502 ,Genomic Instability ,Evolutionary biology ,Genome, Archaeal ,Virology ,Genomic Structural Variation ,Symmetry (geometry) ,Erratum ,Core gene ,Genome, Bacterial - Abstract
The prokaryotic pangenome partitions genes into core and dispensable genes. The order of core genes, albeit assumed to be stable under selection in general, is frequently interrupted by horizontal gene transfer and rearrangement, but how a core-gene-defined genome maintains its stability or flexibility remains to be investigated. Based on data from 30 species, including 425 genomes from six phyla, we grouped core genes into syntenic blocks in the context of a pangenome according to their stability across multiple isolates. A subset of the core genes, often species specific and lineage associated, formed a core-gene-defined genome organizational framework (cGOF). Such cGOFs are either single segmental (one-third of the species analyzed) or multisegmental (the rest). Multisegment cGOFs were further classified into symmetric or asymmetric according to segment orientations toward the origin-terminus axis. The cGOFs in Gram-positive species are exclusively symmetric and often reversible in orientation, as opposed to those of the Gram-negative bacteria, which are all asymmetric and irreversible. Meanwhile, all species showing strong strand-biased gene distribution contain symmetric cGOFs and often specific DnaE (α subunit of DNA polymerase III) isoforms. Furthermore, functional evaluations revealed that cGOF genes are hub associated with regard to cellular activities, and the stability of cGOF provides efficient indexes for scaffold orientation as demonstrated by assembling virtual and empirical genome drafts. cGOFs show species specificity, and the symmetry of multisegmental cGOFs is conserved among taxa and constrained by DNA polymerase-centric strand-biased gene distribution. The definition of species-specific cGOFs provides powerful guidance for genome assembly and other structure-based analysis.Prokaryotic genomes are frequently interrupted by horizontal gene transfer (HGT) and rearrangement. To know whether there is a set of genes not only conserved in position among isolates but also functionally essential for a given species and to further evaluate the stability or flexibility of such genome structures across lineages are of importance. Based on a large number of multi-isolate pangenomic data, our analysis reveals that a subset of core genes is organized into a core-gene-defined genome organizational framework, or cGOF. Furthermore, the lineage-associated cGOFs among Gram-positive and Gram-negative bacteria behave differently: the former, composed of 2 to 4 segments, have their fragments symmetrically rearranged around the origin-terminus axis, whereas the latter show more complex segmentation and are partitioned asymmetrically into chromosomal structures. The definition of cGOFs provides new insights into prokaryotic genome organization and efficient guidance for genome assembly and analysis.
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- 2015
44. Peptidoglycan Recognition Proteins Are a New Class of Human Bactericidal Proteins
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Minhui Wang, Roman Dziarski, Jin Qi, Xinna Li, Haitao Wang, Xiaofeng Lu, and Dipika Gupta
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Antimicrobial peptides ,Microbial Sensitivity Tests ,Biology ,Biochemistry ,Microbiology ,Cell wall ,Mice ,chemistry.chemical_compound ,Anti-Infective Agents ,In vivo ,Animals ,Humans ,Tissue Distribution ,Molecular Biology ,Pattern recognition receptor ,Bacterial Infections ,Cell Biology ,biology.organism_classification ,chemistry ,Peptidoglycan recognition protein 1 ,Cytokines ,Peptidoglycan ,Carrier Proteins ,Bacteria ,Function (biology) ,Antimicrobial Cationic Peptides - Abstract
Skin and mucous membranes come in contact with external environment and protect tissues from infections by producing antimicrobial peptides. We report that human peptidoglycan recognition proteins 3 and 4 (PGLYRP3 and PGLYRP4) are secreted as 89-115-kDa disulfide-linked homo- and heterodimers and are bactericidal against several pathogenic and nonpathogenic transient, but not normal flora, Gram-positive bacteria. PGLYRP3 and PGLYRP4 are also bacteriostatic toward all other tested bacteria, which include Gram-negative bacteria and normal flora Gram-positive bacteria. PGLYRP3 and PGLYRP4 are also active in vivo and protect mice against experimental lung infection. In contrast to antimicrobial peptides, PGLYRPs kill bacteria by interacting with their cell wall peptidoglycan, rather than permeabilizing their membranes. PGLYRP3 and PGLYRP4 are expressed in the skin, eyes, salivary glands, throat, tongue, esophagus, stomach, and intestine. Thus, we have identified the function of mammalian PGLYRP3 and PGLYRP4, and show that they are a new class of bactericidal and bacteriostatic proteins that have different structures, mechanism of actions, and expression patterns than antimicrobial peptides.
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- 2006
45. Regulation of mTOR activity in Snell dwarf and GH receptor gene-disrupted mice
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Richard A. Miller, Darlene E. Berryman, Graham Dominick, Edward O. List, Gonzalo G. Garcia, Xinna Li, and John J. Kopchick
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Male ,medicine.medical_specialty ,Growth Hormone-Somatostatin-GRH ,Transgene ,Dwarfism ,Mice, Transgenic ,mTORC1 ,Growth hormone receptor ,Mechanistic Target of Rapamycin Complex 2 ,Biology ,Mechanistic Target of Rapamycin Complex 1 ,mTORC2 ,Endocrinology ,Internal medicine ,medicine ,Animals ,Receptor ,Dwarfism, Pituitary ,PI3K/AKT/mTOR pathway ,Mice, Inbred C3H ,TOR Serine-Threonine Kinases ,Fasting ,Receptors, Somatotropin ,medicine.disease ,Mice, Inbred C57BL ,Liver ,Multiprotein Complexes ,Female ,hormones, hormone substitutes, and hormone antagonists ,Hormone - Abstract
The involvement of mammalian target of rapamycin (mTOR) in lifespan control in invertebrates, calorie-restricted rodents, and extension of mouse lifespan by rapamycin have prompted speculation that diminished mTOR function may contribute to mammalian longevity in several settings. We show here that mTOR complex-1 (mTORC1) activity is indeed lower in liver, muscle, heart, and kidney tissue of Snell dwarf and global GH receptor (GHR) gene-disrupted mice (GHR−/−), consistent with previous studies. Surprisingly, activity of mTORC2 is higher in fasted Snell and GHR−/− than in littermate controls in all 4 tissues tested. Resupply of food enhanced mTORC1 activity in both controls and long-lived mutant mice but diminished mTORC2 activity only in the long-lived mice. Mice in which GHR has been disrupted only in the liver do not show extended lifespan and also fail to show the decline in mTORC1 and increase in mTORC2 seen in mice with global loss of GHR. The data suggest that the antiaging effects in the Snell dwarf and GHR−/− mice are accompanied by both a decline in mTORC1 in multiple organs and an increase in fasting levels of mTORC2. Neither the lifespan nor mTOR effects appear to be mediated by direct GH effects on liver or by the decline in plasma IGF-I, a shared trait in both global and liver-specific GHR−/− mice. Our data suggest that a more complex pattern of hormonal effects and intertissue interactions may be responsible for regulating both lifespan and mTORC2 function in these mouse models of delayed aging.
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- 2014
46. Human Peptidoglycan Recognition Protein-L Is an N-Acetylmuramoyl-L-alanine Amidase
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Xinna Li, Koichi Fukase, Shoichi Kusumoto, Zheng-Ming Wang, Seiichi Inamura, Dipika Gupta, Minhui Wang, Roman Dziarski, Mu Wang, and Ross Cocklin
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Molecular Sequence Data ,Biology ,Biochemistry ,Amidase ,Microbiology ,chemistry.chemical_compound ,Amidase activity ,Animals ,Humans ,Amino Acid Sequence ,N-acetylmuramoyl-L-alanine amidase ,Molecular Biology ,Peptide sequence ,DNA Primers ,chemistry.chemical_classification ,Base Sequence ,Sequence Homology, Amino Acid ,N-Acetylmuramoyl-L-alanine Amidase ,Cell Biology ,Amino acid ,Zinc ,Enzyme ,Carbohydrate Sequence ,chemistry ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,COS Cells ,Peptidoglycan recognition protein 1 ,Peptidoglycan ,Carrier Proteins - Abstract
Peptidoglycan recognition proteins (PGRPs) are pattern recognition molecules coded by up to 13 genes in insects and 4 genes in mammals. In insects PGRPs activate antimicrobial pathways in the hemolymph and cells, or are peptidoglycan (PGN)-lytic amidases. In mammals one PGRP is an antibacterial neutrophil protein. We report that human PGRP-L is a Zn2+-dependent N-acetylmuramoyl-l-alanine amidase (EC 3.5.1.28), an enzyme that hydrolyzes the amide bond between MurNAc and l-Ala of bacterial PGN. The minimum PGN fragment hydrolyzed by PGRP-L is MurNAc-tripeptide. PGRP-L has no direct bacteriolytic activity. The other members of the human PGRP family, PGRP-Ialpha, PGRP-Ibeta, and PGRP-S, do not have the amidase activity. The C-terminal region of PGRP-L, homologous to bacteriophage and bacterial amidases, is required and sufficient for the amidase activity of PGRP-L, although its activity (in the N-terminal delta1-343 deletion mutant) is reduced. The Zn2+ binding amino acids (conserved in PGRP-L and T7 amidase) and Cys-419 (not conserved in T7 amidase) are required for the amidase activity of PGRP-L, whereas three other amino acids, needed for the activity of T7 amidase, are not required for the activity of PGRP-L. These amino acids, although required, are not sufficient for the amidase activity, because changing them to the "active" configuration does not convert PGRP-S into an active amidase. In conclusion, human PGRP-L is an N-acetylmuramoyl-l-alanine amidase and this function is conserved in prokaryotes, insects, and mammals.
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- 2003
47. DNAVaxDB: the first web-based DNA vaccine database and its data analysis
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Xinna Li, Zuoshuang Xiang, Yongqun He, Mukti Patel, and Rebecca Racz
- Subjects
DNA vaccine ,DNAVaxDB ,Biology ,computer.software_genre ,Biochemistry ,Cancer Vaccines ,DNA vaccination ,Plasmid ,Antigen ,Structural Biology ,Neoplasms ,plasmid ,Vaccines, DNA ,Humans ,protective antigen ,Molecular Biology ,database ,Antigens, Bacterial ,Internet ,Database ,Bacteria ,Applied Mathematics ,Viral Vaccine ,Research ,Proteins ,Viral Vaccines ,Bacterial Infections ,bioinformatics ,Virology ,3. Good health ,Computer Science Applications ,Vaccination ,Bacterial vaccine ,Bacterial adhesin ,Virus Diseases ,Bacterial Vaccines ,Viruses ,DNA microarray ,Databases, Nucleic Acid ,computer ,Software - Abstract
Since the first DNA vaccine studies were done in the 1990s, thousands more studies have followed. Here we report the development and analysis of DNAVaxDB (http://www.violinet.org/dnavaxdb), the first publically available web-based DNA vaccine database that curates, stores, and analyzes experimentally verified DNA vaccines, DNA vaccine plasmid vectors, and protective antigens used in DNA vaccines. All data in DNAVaxDB are annotated from reliable resources, particularly peer-reviewed articles. Among over 140 DNA vaccine plasmids, some plasmids were more frequently used in one type of pathogen than others; for example, pCMVi-UB for G- bacterial DNA vaccines, and pCAGGS for viral DNA vaccines. Presently, over 400 DNA vaccines containing over 370 protective antigens from over 90 infectious and non-infectious diseases have been curated in DNAVaxDB. While extracellular and bacterial cell surface proteins and adhesin proteins were frequently used for DNA vaccine development, the majority of protective antigens used in Chlamydophila DNA vaccines are localized to the inner portion of the cell. The DNA vaccine priming, other vaccine boosting vaccination regimen has been widely used to induce protection against infection of different pathogens such as HIV. Parasitic and cancer DNA vaccines were also systematically analyzed. User-friendly web query and visualization interfaces are available in DNAVaxDB for interactive data search. To support data exchange, the information of DNA vaccines, plasmids, and protective antigens is stored in the Vaccine Ontology (VO). DNAVaxDB is targeted to become a timely and vital source of DNA vaccines and related data and facilitate advanced DNA vaccine research and development.
- Published
- 2014
48. Rapamycin-mediated lifespan increase in mice is dose and sex dependent and metabolically distinct from dietary restriction
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Xinna Li, Kevin Flurkey, Elizabeth Fernandez, David E. Harrison, Zelton D Sharp, Richard A. Miller, Scott D. Pletcher, Randy Strong, Martin A. Javors, James F. Nelson, Clinton M. Astle, Nancy L. Nadon, Adam B. Salmon, Melissa Han, Sabrina Van Roekel, and Lynn Winkleman
- Subjects
Male ,medicine.medical_specialty ,insulin ,medicine.medical_treatment ,Longevity ,Biology ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Sex Factors ,Internal medicine ,medicine ,Endocrine system ,Animals ,glucose ,PI3K/AKT/mTOR pathway ,mouse ,030304 developmental biology ,Sirolimus ,0303 health sciences ,Dose-Response Relationship, Drug ,rapamycin ,Insulin ,TOR Serine-Threonine Kinases ,aging ,Age Factors ,Cell Biology ,Original Articles ,xenobiotic metabolism ,Sexual dimorphism ,Dose–response relationship ,Endocrinology ,IGF-1 ,mTOR ,Female ,caloric restriction ,030217 neurology & neurosurgery ,Drug metabolism ,medicine.drug - Abstract
Rapamycin, an inhibitor of mTOR kinase, increased median lifespan of genetically heterogeneous mice by 23% (males) to 26% (females) when tested at a dose threefold higher than that used in our previous studies; maximal longevity was also increased in both sexes. Rapamycin increased lifespan more in females than in males at each dose evaluated, perhaps reflecting sexual dimorphism in blood levels of this drug. Some of the endocrine and metabolic changes seen in diet-restricted mice are not seen in mice exposed to rapamycin, and the pattern of expression of hepatic genes involved in xenobiotic metabolism is also quite distinct in rapamycin-treated and diet-restricted mice, suggesting that these two interventions for extending mouse lifespan differ in many respects.
- Published
- 2013
49. Effect of Zishenshengxue capsule on myelosuppression in mice induced by cyclophosphamide
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Xinna Li, Ying Zhao, and Wei Li
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Male ,Cyclophosphamide ,Myelosuppression ,Bone Marrow Cells ,Capsules ,Pharmacology ,Leukocyte Count ,Mice ,Bone Marrow ,medicine ,Leukocytes ,Animals ,Humans ,Progenitor cell ,Cell proliferation ,Medicine(all) ,Cell growth ,business.industry ,Cell Cycle ,Capsule ,Anemia, Aplastic ,General Medicine ,Cell cycle ,Peripheral ,Haematopoiesis ,medicine.anatomical_structure ,Zishenshengxue capsule ,Immunology ,Bone marrow ,business ,medicine.drug ,Drugs, Chinese Herbal - Abstract
ObjectiveTo explore the inhibitory effect of Zishenshengxue capsule (ZSC) on myelosuppression in mice induced by cyclophosphamide.MethodsKunming mice were randomly assigned into a control group, myelosuppression group, or groups for mice with myelosuppression receiving high dose ZSC, middle dose ZSC, low dose ZSC or Yixuesheng. Myelosuppression was induced by peritoneal injection of cyclophosphamide. ZSC and cyclophosphamide were administered simultaneously. The numbers of peripheral blood cells and bone marrow karyocytes were counted. Cell proliferation activity and colony formation of granulocyte-monocyte series hemopoietic progenitor cells (C-GMs) and cell cycle were detected.ResultsThe numbers of white blood cells in the middle and high dose ZSC groups were significantly increased at the 12th and 13th day (P
- Published
- 2013
50. De-etiolation of wheat seedling leaves: cross talk between heme oxygenase/carbon monoxide and nitric oxide
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Langlai Xu, Xinna Li, Wenbiao Shen, and Yahui Liu
- Subjects
lcsh:Medicine ,Nitric Oxide ,Nitric oxide ,chemistry.chemical_compound ,medicine ,lcsh:Science ,Heme ,Triticum ,Carbon Monoxide ,Multidisciplinary ,biology ,Zinc protoporphyrin ,lcsh:R ,Nitric oxide synthase ,Heme oxygenase ,Plant Leaves ,Biochemistry ,chemistry ,Seedlings ,Chlorophyll ,Etiolation ,Heme Oxygenase (Decyclizing) ,biology.protein ,lcsh:Q ,Sodium nitroprusside ,medicine.drug ,Research Article - Abstract
Greening of etiolated plants is predominantly stimulated by light but the complete molecular mechanism is still unknown. Multiple studies currently focus on the important physiological effects of heme oxygenase (HO)/carbon monoxide (CO) in plants. In this report, firstly, the role of HO/CO in light-induced de-etiolation process was investigated. We discovered that light could significantly increase HO activities, HO-1 gene expression, CO release, and chlorophyll accumulation, all of which were sensitive to zinc protoporphyrin (ZnPPIX), the potent inhibitor of HO-1, respectively. Both HO-1 inducer hematin (H) and CO aqueous solution were able to relieve etiolation in wheat seedling leaves under completely darkness by up-regulating endogenous HO/CO system, so as nitric oxide (NO) donor sodium nitroprusside (SNP) did. Similarly, endogenous NO production was also boost in response to light, SNP, hematin and CO aqueous solution in wheat seedling leaves. Additionally, the restoration of chlorophyll contents was blocked, when the inhibitor of mammalian nitric oxide synthase N(G)-nitro-L-arginine methylester hydrochloride (L-NAME) or the specific scavenger of NO 2-(4-carboxyphenyl)-4, 4, 5, 5-tetramethylimidazoline-1-oxyl-3-oxide potassium salt (cPTIO) was added, respectively. Furthermore, the inducible effects of light were different from those of SNP, hematin, and CO on Pfr accumulation and PHYA transcripts. However, all of sodium nitroprusside (SNP), hematin, and CO could accelerate NO emission, which suggested that HO/CO in wheat seedlings de-etiolation under dark-light transition may have a cross talk with NO.
- Published
- 2013
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