Yuan Y

References (44)

Title : Construction of Virtual Compound Library and Screening of Acetylcholinesterase Inhibitor for the Medicinal Chemistry Laboratory - Yang_2024_J.Chem.Educ_101_1673
Author(s) : Yang J , Yuan Y , Wang N , Liu X , Gu J , Zeng R , Huang M , Zheng P , Wang Y , Huang C , Ouyang Q
Ref : Journal of Chemical Education , 101 :1673 , 2024
Abstract : The utilization of virtual compound libraries and virtual screening has become a routine method in drug discovery and has accelerated the research of pharmacy and translational medicine. With the development of computer-aided drug design (CADD), it is essential to incorporate virtual experiments into the education of medicinal chemistry. Herein, we describe a series of virtual experiments conducted by undergraduate students, including the construction of a virtual compound library, molecular docking, and the virtual screening of acetylcholinesterase inhibitors. Student feedback indicates that the virtual experiments are popular with students and effectively promote their interest in the drug discovery process.
ESTHER : Yang_2024_J.Chem.Educ_101_1673
PubMedSearch : Yang_2024_J.Chem.Educ_101_1673

Title : Infiltration of porcine pancreatic lipase into magnetic hierarchical mesoporous UiO-66-NH(2) metal-organic frameworks for efficient detoxification of patulin from apple juice - Yan_2024_Food.Chem_431_137172
Author(s) : Yan X , Chen K , Jia H , Zhao Q , Du G , Guo Q , Chen H , Yuan Y , Yue T
Ref : Food Chem , 431 :137172 , 2024
Abstract : Patulin (PAT) is a mycotoxin known to globally contaminate fruits. The economic losses and health hazards caused by PAT desires a safe and efficient strategy for detoxifying PAT. Here, a magnetic core-shell hierarchical mesoporous metal-organic framework (Fe(3)O(4)@HMUiO-66-NH(2)) was synthesized via a salt-assisted nanoemulsion guided assembly method. This mesoporous structure (centered at 4.25 nm) allowed porcine pancreatic lipase (PPL) to infiltrate into the MOF shell at an immobilized amount of 255 mg/g, providing protection for PPL and enabling rapid separation and recovery. Compared with free PPL, PPL/Fe(3)O(4)@HMUiO-66-NH(2) at 70 degreesC possessed 4.7 folds improved thermal stability in terms of half-life. The detoxification rates of immobilized enzyme for PAT in neutral water, acidic water, and apple juice were 99.6%, 60.9%, and 52.6%, respectively. Moreover, the so designed PPL/Fe(3)O(4)@HMUiO-66-NH(2) showed extraordinary storage stability, reusability, and biocompatibility. Crucially, the quality of apple juice did not change significantly after PPL/Fe(3)O(4)@HMUiO-66-NH(2) treatment, which facilitated its application in apple juice. The magnetic core-shell mesoporous structure along with the revealed mechanism of immobilized enzyme detoxification of PAT provide tremendous opportunity for designing a safe and efficient PAT detoxification method.
ESTHER : Yan_2024_Food.Chem_431_137172
PubMedSearch : Yan_2024_Food.Chem_431_137172
PubMedID: 37603997

Title : Integrated transcriptomics and metabolomics analyses reveal the aerobic biodegradation and molecular mechanisms of 2,3',4,4',5-pentachlorodiphenyl (PCB 118) in Methylorubrum sp. ZY-1 - Wu_2024_Chemosphere__141921
Author(s) : Wu Y , Zhu M , Ouyang X , Qi X , Guo Z , Yuan Y , Dang Z , Yin H
Ref : Chemosphere , :141921 , 2024
Abstract : 2,3',4,4',5-pentachlorodiphenyl (PCB 118), a highly representative PCB congener, has been frequently detected in various environments, garnering much attention across the scientific community. The degradation of highly chlorinated PCBs by aerobic microorganisms is challenging due to their hydrophobicity and persistence. Herein, the biodegradation and adaptation mechanisms of Methylorubrum sp. ZY-1 to PCB 118 were comprehensively investigated using an integrative approach that combined degradation performance, product identification, metabolomic and transcriptomic analyses. The results indicated that the highest degradation efficiency of 0.5 mg L(-1) PCB 118 reached 75.66% after seven days of inoculation when the bacteria dosage was 1.0 g L(-1) at pH 7.0. A total of eleven products were identified during the degradation process, including low chlorinated PCBs, hydroxylated PCBs, and ring-opening products, suggesting that strain ZY-1 degraded PCB 118 through dechlorination, hydroxylation, and ring-opening pathways. Metabolomic analysis demonstrated that the energy supply and redox metabolism of strain ZY-1 was disturbed with exposure to PCB 118. To counteract this environmental stress, strain ZY-1 adjusted both the fatty acid synthesis and purine metabolism. The analysis of transcriptomics disclosed that multiple intracellular and extracellular oxidoreductases (e.g., monooxygenase, alpha/beta hydrolase and cytochrome P450) participated in the degradation of PCB 118. Besides, active efflux of PCB 118 and its degradation intermediates mediated by multiple transporters (e.g., MFS transporter and ABC transporter ATP-binding protein) might enhance bacterial resistance against these substances. These discoveries provided the inaugural insights into the biotransformation of strain ZY-1 to PCB 118 stress, illustrating its potential in the remediation of contaminated environments.
ESTHER : Wu_2024_Chemosphere__141921
PubMedSearch : Wu_2024_Chemosphere__141921
PubMedID: 38588902
Gene_locus related to this paper: meted-c7c8u4 , meted-c7cge7 , meted-c7ci36

Title : Targeting ANGPTL3 by GalNAc-conjugated siRNA ANGsiR10 lowers blood lipids with long-lasting and potent efficacy in mice and monkeys - Wang_2023_Mol.Ther.Nucleic.Acids_31_68
Author(s) : Wang J , Zheng W , Zheng S , Yuan Y , Wen W , Cui W , Xue L , Sun X , Shang H , Zhang H , Xiao RP , Gao S , Zhang X
Ref : Mol Ther Nucleic Acids , 31 :68 , 2023
Abstract : Angiopoietin-like protein 3 (ANGPTL3) is an important regulator of lipoproteins by inhibiting both lipoprotein and endothelial lipases. It has been intensively investigated as a drug target for the treatment of dyslipidemia. In the present study, a modified small interfering RNA (siRNA) conjugated with GalNAc ANGsiR10 was characterized by insvivo and insvitro studies for its effect on ANGPTL3 silencing, the reduction of plasma triglycerides (TGs), and cholesterol levels in disease models. The results showed that ANGsiR10 displayed a significant and long-lasting efficacy in reducing blood TG and cholesterol levels in both mice and monkeys. Remarkably, the maximal reductions of plasma TG levels in the hApoC3-Tg mice, a model with high TG levels, and the spontaneous dyslipidemia model of rhesus monkey were 96.3% and 67.7%, respectively, after a single dose of ANGsiR10, with long-lasting effects up to 15sweeks. The cholesterol levels were also reduced in response to treatment, especially the non-HDL-c level, without altering the ApoA/ApoB ratio. This study showed that ANGsiR10 is effective in treating dyslipidemia and is worth further development.
ESTHER : Wang_2023_Mol.Ther.Nucleic.Acids_31_68
PubMedSearch : Wang_2023_Mol.Ther.Nucleic.Acids_31_68
PubMedID: 36618267

Title : Resensitizing Paclitaxel-Resistant Ovarian Cancer via Targeting Lipid Metabolism Key Enzymes CPT1A, SCD and FASN - Ma_2023_Int.J.Mol.Sci_24_
Author(s) : Ma Q , Liu Z , Wang T , Zhao P , Liu M , Wang Y , Zhao W , Yuan Y , Li S
Ref : Int J Mol Sci , 24 : , 2023
Abstract : Epithelial ovarian cancer (EOC) is a lethal gynecological cancer, of which paclitaxel resistance is the major factor limiting treatment outcomes, and identification of paclitaxel resistance-related genes is arduous. We obtained transcriptomic data from seven paclitaxel-resistant ovarian cancer cell lines and corresponding sensitive cell lines. Define genes significantly up-regulated in at least three resistant cell lines, meanwhile they did not down-regulate in the other resistant cell lines as candidate genes. Candidate genes were then ranked according to the frequencies of significant up-regulation in resistant cell lines, defining genes with the highest rankings as paclitaxel resistance-related genes (PRGs). Patients were grouped based on the median expression of PRGs. The lipid metabolism-related gene set and the oncological gene set were established and took intersections with genes co-upregulated with PRGs, obtaining 229 co-upregulated genes associated with lipid metabolism and tumorigenesis. The PPI network obtained 19 highly confidential synergistic targets (interaction score > 0.7) that directly associated with CPT1A. Finally, FASN and SCD were up-stream substrate provider and competitor of CPT1A, respectively. Western blot and qRT-PCR results confirmed the over-expression of CPT1A, SCD and FASN in the A2780/PTX cell line. The inhibition of CPT1A, SCD and FASN down-regulated cell viability and migration, pharmacological blockade of CPT1A and SCD increased apoptosis rate and paclitaxel sensitivity of A2780/PTX. In summary, our novel bioinformatic methods can overcome difficulties in drug resistance evaluation, providing promising therapeutical strategies for paclitaxel-resistant EOC via taregting lipid metabolism-related enzymes.
ESTHER : Ma_2023_Int.J.Mol.Sci_24_
PubMedSearch : Ma_2023_Int.J.Mol.Sci_24_
PubMedID: 38003694

Title : Construction of a QSAR Model Based on Flavonoids and Screening of Natural Pancreatic Lipase Inhibitors - Yuan_2023_Nutrients_15_
Author(s) : Yuan Y , Pan F , Zhu Z , Yang Z , Wang O , Li Q , Zhao L
Ref : Nutrients , 15 : , 2023
Abstract : Pancreatic lipase (PL) is a key hydrolase in lipid metabolism. Inhibition of PL activity can intervene in obesity, a global sub-health disease. The natural product is considered a good alternative to chemically synthesized drugs due to its advantages, such as low side effects. However, traditional experimental screening methods are labor-intensive and cost-consuming, and there is an urgent need to develop high-throughput screening methods for the discovery of anti-PL natural products. In this study, a high-throughput virtual screening process for anti-PL natural products is provided. Firstly, a predictable anti-PL natural product QSAR model (R(2)(train) = 0.9444, R(2)(test) = 0.8962) were developed using the artificial intelligence drug design software MolAIcal based on genetic algorithms and their conformational relationships. 1068 highly similar (FS > 0.8) natural products were rapidly enriched based on the structure-activity similarity principle, combined with the QSAR model and the ADMET model, for rapid prediction of a total of five potentially efficient anti-PL natural products (IC(50pre) < 2 microM). Subsequently, molecular docking, molecular dynamics simulation, and MMGBSA free energy calculation were performed to not only reveal the interaction of candidate novel natural products with the amino acid residues of PL but also to validate the stability of these novel natural compounds bound to PL. In conclusion, this study greatly simplifies the screening and discovery of anti-PL natural products and accelerates the development of novel anti-obesity functional foods.
ESTHER : Yuan_2023_Nutrients_15_
PubMedSearch : Yuan_2023_Nutrients_15_
PubMedID: 37571426

Title : Bioaccumulation and toxicity of terbuthylazine in earthworms (Eisenia fetida) - Li_2022_Environ.Toxicol.Pharmacol_97_104016
Author(s) : Li S , Yuan Y , Wang X , Cai L , Wang J , Zhao Y , Jiang L , Yang X
Ref : Environ Toxicol Pharmacol , 97 :104016 , 2022
Abstract : Terbuthylazine is an effective and widely used s-triazine herbicide. However, limited data exists on its toxicity and bioaccumulation in earthworms (Eisenia fetida). In this study, we investigated the bioaccumulation, antioxidant enzyme activity, detoxification enzyme activity, and DNA damage in earthworms when exposed to terbuthylazine. The results indicated that terbuthylazine in soil had low bioaccumulation in earthworms and the biota-soil accumulation factors of terbuthylazine declined with an increasing soil terbuthylazine concentration. In the enzyme activity assays, the superoxide dismutase (SOD), catalase (CAT), and glutathione-S-transferase (GST) activities showed upward trends when compared with the control. The carboxylesterase (CarE) activity increased on day 21. The 8-hydroxy-2-deoxyguanosine (8-OHdG) content, a DNA damage bioindicator, was higher than that of the control on day 21. Combined with the integrated biological response index version 2 analysis, these results can provide a comprehensive evaluation of the toxicological effects that terbuthylazine has on earthworms and soil ecosystems.
ESTHER : Li_2022_Environ.Toxicol.Pharmacol_97_104016
PubMedSearch : Li_2022_Environ.Toxicol.Pharmacol_97_104016
PubMedID: 36435387

Title : Antibacterial Efficacy and Mechanisms of Curcumin-Based Photodynamic Treatment against Staphylococcus aureus and Its Application in Juices - Yuan_2022_Molecules_27_
Author(s) : Yuan Y , Liu Q , Huang Y , Qi M , Yan H , Li W , Zhuang H
Ref : Molecules , 27 : , 2022
Abstract : Antimicrobial Photodynamic Treatment (aPDT) is a non-thermal sterilization technology, which can inactivate common foodborne pathogens. In the present study, photodynamic inactivation on Staphylococcus aureus (S. aureus) with different concentrations of curcumin and light dose was evaluated and the mechanisms were also investigated. The results showed that curcumin-based aPDT could inactivate S. aureus cells by 6.9 log CFU/mL in phosphate buffered saline (PBS). Moreover, the modified Gompertz model presented a good fit at the inactivation data of S. aureus. Photodynamic treatment caused cell membrane damage as revealed by analyzing scanning electron microscopy (SEM) images. Leakage of intracellular constituents further indicated that cell membrane permeability was changed. Flow cytometry with double staining demonstrated that cell membrane integrity and the activity of nonspecific esterase were destroyed. Compared with the control group, intracellular reactive oxygen species (ROS) levels caused by photodynamic treatment significantly increased. Furthermore, curcumin-based aPDT reduced S. aureus by 5 log CFU/mL in juices. The color of the juices was also tested using a Chromatic meter, and it was found that b* values were the most markedly influenced by photodynamic treatment. Overall, curcumin-based aPDT had strong antibacterial activity against S. aureus. This approach has the potential to remove foodborne pathogens from liquid food.
ESTHER : Yuan_2022_Molecules_27_
PubMedSearch : Yuan_2022_Molecules_27_
PubMedID: 36296729

Title : Valorization of Polyethylene Terephthalate to Muconic Acid by Engineering Pseudomonas Putida - Liu_2022_Int.J.Mol.Sci_23_10997
Author(s) : Liu P , Zheng Y , Yuan Y , Zhang T , Li Q , Liang Q , Su T , Qi Q
Ref : Int J Mol Sci , 23 : , 2022
Abstract : Plastic waste is rapidly accumulating in the environment and becoming a huge global challenge. Many studies have highlighted the role of microbial metabolic engineering for the valorization of polyethylene terephthalate (PET) waste. In this study, we proposed a new conceptual scheme for upcycling of PET. We constructed a multifunctional Pseudomonas putida KT2440 to simultaneously secrete PET hydrolase LCC, a leaf-branch compost cutinase, and synthesize muconic acid (MA) using the PET hydrolysate. The final product MA and extracellular LCC can be separated from the supernatant of the culture by ultrafiltration, and the latter was used for the next round of PET hydrolysis. A total of 0.50 g MA was produced from 1 g PET in each cycle of the whole biological processes, reaching 68% of the theoretical conversion. This new conceptual scheme for the valorization of PET waste should have advantages over existing PET upcycling schemes and provides new ideas for the utilization of other macromolecular resources that are difficult to decompose, such as lignin.
ESTHER : Liu_2022_Int.J.Mol.Sci_23_10997
PubMedSearch : Liu_2022_Int.J.Mol.Sci_23_10997
PubMedID: 36232310

Title : Construction of microbial consortia for microbial degradation of complex compounds - Cao_2022_Front.Bioeng.Biotechnol_10_1051233
Author(s) : Cao Z , Yan W , Ding M , Yuan Y
Ref : Front Bioeng Biotechnol , 10 :1051233 , 2022
Abstract : Increasingly complex synthetic environmental pollutants are prompting further research into bioremediation, which is one of the most economical and safest means of environmental restoration. From the current research, using microbial consortia to degrade complex compounds is more advantageous compared to using isolated bacteria, as the former is more adaptable and stable within the growth environment and can provide a suitable catalytic environment for each enzyme required by the biodegradation pathway. With the development of synthetic biology and gene-editing tools, artificial microbial consortia systems can be designed to be more efficient, stable, and robust, and they can be used to produce high-value-added products with their strong degradation ability. Furthermore, microbial consortia systems are shown to be promising in the degradation of complex compounds. In this review, the strategies for constructing stable and robust microbial consortia are discussed. The current advances in the degradation of complex compounds by microbial consortia are also classified and detailed, including plastics, petroleum, antibiotics, azo dyes, and some pollutants present in sewage. Thus, this paper aims to support some helps to those who focus on the degradation of complex compounds by microbial consortia.
ESTHER : Cao_2022_Front.Bioeng.Biotechnol_10_1051233
PubMedSearch : Cao_2022_Front.Bioeng.Biotechnol_10_1051233
PubMedID: 36561050

Title : Current Advances in the Biodegradation and Bioconversion of Polyethylene Terephthalate - Qi_2021_Microorganisms_10_
Author(s) : Qi X , Yan W , Cao Z , Ding M , Yuan Y
Ref : Microorganisms , 10 : , 2021
Abstract : Polyethylene terephthalate (PET) is a widely used plastic that is polymerized by terephthalic acid (TPA) and ethylene glycol (EG). In recent years, PET biodegradation and bioconversion have become important in solving environmental plastic pollution. More and more PET hydrolases have been discovered and modified, which mainly act on and degrade the ester bond of PET. The monomers, TPA and EG, can be further utilized by microorganisms, entering the tricarboxylic acid cycle (TCA cycle) or being converted into high value chemicals, and finally realizing the biodegradation and bioconversion of PET. Based on synthetic biology and metabolic engineering strategies, this review summarizes the current advances in the modified PET hydrolases, engineered microbial chassis in degrading PET, bioconversion pathways of PET monomers, and artificial microbial consortia in PET biodegradation and bioconversion. Artificial microbial consortium provides novel ideas for the biodegradation and bioconversion of PET or other complex polymers. It is helpful to realize the one-step bioconversion of PET into high value chemicals.
ESTHER : Qi_2021_Microorganisms_10_
PubMedSearch : Qi_2021_Microorganisms_10_
PubMedID: 35056486

Title : Evaluation of PET Degradation Using Artificial Microbial Consortia - Qi_2021_Front.Microbiol_12_778828
Author(s) : Qi X , Ma Y , Chang H , Li B , Ding M , Yuan Y
Ref : Front Microbiol , 12 :778828 , 2021
Abstract : Polyethylene terephthalate (PET) biodegradation is regarded as an environmentally friendly degradation method. In this study, an artificial microbial consortium composed of Rhodococcus jostii, Pseudomonas putida and two metabolically engineered Bacillus subtilis was constructed to degrade PET. First, a two-species microbial consortium was constructed with two engineered B. subtilis that could secrete PET hydrolase (PETase) and monohydroxyethyl terephthalate hydrolase (MHETase), respectively; it could degrade 13.6% (weight loss) of the PET film within 7 days. A three-species microbial consortium was further obtained by adding R. jostii to reduce the inhibition caused by terephthalic acid (TPA), a breakdown product of PET. The weight of PET film was reduced by 31.2% within 3 days, achieving about 17.6% improvement compared with the two-species microbial consortium. Finally, P. putida was introduced to reduce the inhibition caused by ethylene glycol (EG), another breakdown product of PET, obtaining a four-species microbial consortium. With the four-species consortium, the weight loss of PET film reached 23.2% under ambient temperature. This study constructed and evaluated the artificial microbial consortia in PET degradation, which demonstrated the great potential of artificial microbial consortia in the utilization of complex substrates, providing new insights for biodegradation of complex polymers.
ESTHER : Qi_2021_Front.Microbiol_12_778828
PubMedSearch : Qi_2021_Front.Microbiol_12_778828
PubMedID: 35003008

Title : Bio-Potency and Molecular Docking Studies of Isolated Compounds from Grewia optiva J.R. Drumm. ex Burret - Ul_2021_Molecules_26_
Author(s) : Ul Bari W , Ur Rehman N , Khan A , Ahsan Halim S , Yuan Y , Blaskovich MAT , Ziora ZM , Zahoor M , Naz S , Ullah R , Alotaibi A , Al-Harrasi A
Ref : Molecules , 26 : , 2021
Abstract : In the study, two novel compounds along with two new compounds were isolated from Grewia optiva. The novel compounds have never been reported in any plant source, whereas the new compounds are reported for the first time from the studied plant. The four compounds were characterized as: 5,5,7,7,11,13-hexamethyl-2-(5-methylhexyl)icosahydro-1H-cyclopenta[a]chrysen-9-ol (IX), docosanoic acid (X), methanetriol mano formate (XI) and 2,2'-(1,4-phenylene)bis(3-methylbutanoic acid (XII). The anticholinesterase, antidiabetic, and antioxidant potentials of these compounds were determined using standard protocols. All the isolated compounds exhibited a moderate-to-good degree of activity against acetylcholinesterases (AChE) and butyrylcholinesterase (BChE). However, compound XII was particularly effective with IC(50) of 55 microg/mL (against AChE) and 60 microg/mL (against BChE), and this inhibitory activity is supported by in silico docking studies. The same compound was also effective against DPPH (2,2-diphenyl-1-picrylhydrazyl) and ABTS (2,2'-azinobis-3-ethylbenzothiazoline-6-sulfonic acid) radicals with IC(50) values of 60 and 62 microg/mL, respectively. The compound also significantly inhibited the activities of alpha-amylase and alpha-glucosidase in vitro. The IC(50) values for inhibition of the two enzymes were recorded as 90 and 92 microg/mL, respectively. The in vitro potentials of compound XII to treat Alzheimer's disease (in terms of AchE and BChE inhibition), diabetes (in terms of alpha-amylase and alpha-glucosidase inhibition), and oxidative stress (in terms of free radical scavenging) suggest further in vivo investigations of the compound for assessing its efficacy, safety profile, and other parameters to proclaim the compound as a potential drug candidate.
ESTHER : Ul_2021_Molecules_26_
PubMedSearch : Ul_2021_Molecules_26_
PubMedID: 33916198

Title : Presence of L1014F Knockdown-Resistance Mutation in Anopheles gambiae s.s. From So Tom and Prncipe - Zhang_2021_Front.Cell.Infect.Microbiol_11_633905
Author(s) : Zhang H , Li M , Tan R , Deng C , Huang B , Wu Z , Zheng S , Guo W , Tuo F , Yuan Y , Bandeira CA , Rompao DH , Xu Q , Song J , Wang Q
Ref : Front Cell Infect Microbiol , 11 :633905 , 2021
Abstract : Malaria, one of the most serious parasitic diseases, kills thousands of people every year, especially in Africa. Sao Tome and Prncipe are known to have stable transmission of malaria. Indoor residual spraying (IRS) of insecticides and long-lasting insecticidal nets (LLIN) are considered as an effective malaria control interventions in these places. The resistance status of Anopheles gambiae s.s. from Agua Grande, Caue, and Lemba of Sao Tome and Prncipe to insecticides, such as dichlorodiphenyltrichloroethane (DDT) (4.0%), deltamethrin (0.05%), permethrin (0.75%), fenitrothion (1.0%), and malathion (5.0%), were tested according to the WHO standard protocol. DNA extraction, species identification, as well as kdr and ace-1(R) genotyping were done with the surviving and dead mosquitoes post testing. They showed resistance to cypermethrin with mortality rates ranging from 89.06% to 89.66%. Mosquitoes collected from Agua Grande, Caue, and Lemba displayed resistance to DDT and fenitrothion with mortality rates higher than 90%. No other species were detected in these study localities other than Anopheles gambiae s.s. The frequency of L1014F was high in the three investigated sites, which was detected for the first time in Sao Tome and Prncipe. No ace(-1R) mutation was detected in all investigated sites. The high frequency of L1014F showed that kdr L1014F mutation might be related to insecticide resistance to Anopheles gambiae s.s. populations from Sao Tome and Prncipe. Insecticide resistance status is alarming and, therefore, future malaria vector management should be seriously considered by the government of Sao Tome and Prncipe.
ESTHER : Zhang_2021_Front.Cell.Infect.Microbiol_11_633905
PubMedSearch : Zhang_2021_Front.Cell.Infect.Microbiol_11_633905
PubMedID: 34307185

Title : Congenital myasthenic syndrome in China: genetic and myopathological characterization - Zhao_2021_Ann.Clin.Transl.Neurol__
Author(s) : Zhao Y , Li Y , Bian Y , Yao S , Liu P , Yu M , Zhang W , Wang Z , Yuan Y
Ref : Ann Clin Transl Neurol , : , 2021
Abstract : OBJECTIVE: We aimed to summarize the clinical, genetic, and myopathological features of a cohort of Chinese patients with congenital myasthenic syndrome, and follow up on therapeutic outcomes. METHODS: The clinical spectrum, mutational frequency of genes, and pathological diagnostic clues of various subtypes of patients with congenital myasthenic syndrome were summarized. Therapeutic effects were followed up. RESULTS: Thirty-five patients from 29 families were recruited. Ten genes were identified: GFPT1 (27.6%), AGRN (17.2%), CHRNE (17.2%), COLQ (13.8%), GMPPB (6.9%), CHAT, CHRNA1, DOK7, COG7, and SLC25A1 (3.4% each, respectively). Sole limb-girdle weakness was found in patients with AGRN (1/8) and GFPT1 (7/8) mutations, whereas distal weakness was all observed in patients with AGRN (6/8) mutations. Tubular aggregates were only found in patients with GFPT1 mutations (5/6). The patients with GMPPB mutations (2/2) had decreased alpha-dystroglycan. Acetylcholinesterase inhibitor therapy resulted in no response or worsened symptoms in patients with COLQ mutations, a diverse response in patients with AGRN mutations, and a good response in patients with other subtypes. Albuterol therapy was effective or harmless in most subtypes. Therapy effects became attenuated with long-term use in patients with COLQ or AGRN mutations. INTERPRETATION: The genetic distribution of congenital myasthenic syndrome in China is distinct from that of other ethnic origins. The appearance of distal weakness, selective limb-girdle myasthenic syndrome, tubular aggregates, and decreased alpha-dystroglycan were indicative of the specific subtypes. Based on the follow-up findings, we suggest cautious evaluation of the long-term efficacy of therapeutic agents in congenital myasthenic syndrome.
ESTHER : Zhao_2021_Ann.Clin.Transl.Neurol__
PubMedSearch : Zhao_2021_Ann.Clin.Transl.Neurol__
PubMedID: 33756069

Title : Effect of Tannic Acid on Nutrition and Activities of Detoxification Enzymes and Acetylcholinesterase of the Fall Webworm (Lepidoptera: Arctiidae) - Yuan_2020_J.Insect.Sci_20_
Author(s) : Yuan Y , Li L , Zhao J , Chen M
Ref : J Insect Sci , 20 : , 2020
Abstract : Plant tannins, polyphenolic plant secondary metabolites are involved in important chemical defense processes in plants. In this study, tannic acid was used as the standard of plant tannins to determine the effects on nutritional indices and activities of glutathione S-transferases (GSTs), cytochrome P450 monooxygenase (CYP450), carboxylesterase (CarE), and acetylcholinesterase (AChE) in fourth-instar larvae of Hyphantria cunea (Drury) by feeding on an artificial diet containing tannic acid under different treatments. We found that tannic acid significantly affected the digestive capacity and food utilization rate of H. cunea larvae. A tannic acid concentration of less than 2.0% promoted feeding and the utilization of undesirable food by H. cunea larvae, while inhibitory effects were observed at high concentrations (>2.5%). Tannic acid had a significant effect on the activity of detoxification enzymes and AChE in H. cunea larvae in concentration-dependent and time-dependent manners (P < 0.05). These results provide new insights into the potential mechanisms underlying detoxification in H. cunea larvae against tannic acid in host plants.
ESTHER : Yuan_2020_J.Insect.Sci_20_
PubMedSearch : Yuan_2020_J.Insect.Sci_20_
PubMedID: 32061083

Title : Molecular Basis of Binding between Middle East Respiratory Syndrome Coronavirus and CD26 from Seven Bat Species - Yuan_2020_J.Virol_94_e01387
Author(s) : Yuan Y , Qi J , Peng R , Li C , Lu G , Yan J , Wang Q , Gao GF
Ref : J Virol , 94 :e01387 , 2020
Abstract : Continued reports of Middle East respiratory syndrome coronavirus (MERS-CoV) infecting humans have occurred since the identification of this virus in 2012. MERS-CoV is prone to cause endemic disease in the Middle East, with several dozen spillover infections to other continents. It is hypothesized that MERS-CoV originated from bat coronaviruses and that dromedary camels are its natural reservoir. Although gene segments identical to MERS-CoV were sequenced from certain species of bats and one species experimentally shed the virus, it is still unknown whether other bats can transmit the virus. Here, at the molecular level, we found that all purified bat CD26s (bCD26s) from a diverse range of species interact with the receptor binding domain (RBD) of MERS-CoV, with equilibrium dissociation constant values ranging from several to hundreds at the micromolar level. Moreover, all bCD26s expressed in this study mediated the entry of pseudotyped MERS-CoV to receptor-expressing cells, indicating the broad potential engagement of bCD26s as MERS-CoV receptors. Further structural analysis indicated that in the bat receptor, compared to the human receptor, substitutions of key residues and their adjacent amino acids leads to decreased binding affinity to the MERS-RBD. These results add more evidence to the existing belief that bats are the original source of MERS-CoV and suggest that bCD26s in many species can mediate the entry of the virus, which has significant implications for the surveillance and control of MERS-CoV infection.IMPORTANCE In this study, we found that bat CD26s (bCD26s) from different species exhibit large diversities, especially in the region responsible for binding to the receptor binding domain (RBD) of Middle East respiratory syndrome coronavirus (MERS-CoV). However, they maintain the interaction with MERS-RBD at varied affinities and support the entry of pseudotyped MERS-CoV. These bat receptors polymorphisms seem to confer evolutionary pressure for the adaptation of CD26-binding virus, such as the ancestor of MERS-CoV, and led to the generation of diversified CD26-engaging CoV strains. Thus, our data add more evidence to support that bats are the reservoir of MERS-CoV and similar viruses, as well as further emphasize the necessity to survey MERS-CoV and other CoVs among bats.
ESTHER : Yuan_2020_J.Virol_94_e01387
PubMedSearch : Yuan_2020_J.Virol_94_e01387
PubMedID: 31776269
Gene_locus related to this paper: myods-l5lq33

Title : Runx2 Regulates Mouse Tooth Root Development Via Activation of WNT Inhibitor NOTUM - Wen_2020_J.Bone.Miner.Res_35_2252
Author(s) : Wen Q , Jing J , Han X , Feng J , Yuan Y , Ma Y , Chen S , Ho TV , Chai Y
Ref : J Bone Miner Res , 35 :2252 , 2020
Abstract : Progenitor cells are crucial in controlling organ morphogenesis. Tooth development is a well-established model for investigating the molecular and cellular mechanisms that regulate organogenesis. Despite advances in our understanding of how tooth crown formation is regulated, we have limited understanding of tooth root development. Runt-related transcription factor 2 (RUNX2) is a well-known transcription factor in osteogenic differentiation and early tooth development. However, the function of RUNX2 during tooth root formation remains unknown. We revealed in this study that RUNX2 is expressed in a subpopulation of GLI1+ root progenitor cells, and that loss of Runx2 in these GLI1+ progenitor cells and their progeny results in root developmental defects. Our results provide in vivo evidence that Runx2 plays a crucial role in tooth root development and in regulating the differentiation of root progenitor cells. Furthermore, we identified that Gli1, Pcp4, NOTUM, and Sfrp2 are downstream targets of Runx2 by integrating bulk and single-cell RNA sequencing analyses. Specifically, ablation of Runx2 results in downregulation of WNT inhibitor NOTUM and upregulation of canonical WNT signaling in the odontoblastic site, which disturbs normal odontoblastic differentiation. Significantly, exogenous NOTUM partially rescues the impaired root development in Runx2 mutant molars. Collectively, our studies elucidate how Runx2 achieves functional specificity in regulating the development of diverse organs and yields new insights into the network that regulates tooth root development. 2020 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
ESTHER : Wen_2020_J.Bone.Miner.Res_35_2252
PubMedSearch : Wen_2020_J.Bone.Miner.Res_35_2252
PubMedID: 32569388

Title : The toxicity assessment of extract of Peganum harmala L. seeds in Caenorhabditis elegans - Miao_2020_BMC.Complement.Med.Ther_20_256
Author(s) : Miao X , Zhang X , Yuan Y , Zhang Y , Gao J , Kang N , Liu X , Wu J , Liu Y , Tan P
Ref : BMC Complement Med Ther , 20 :256 , 2020
Abstract : BACKGROUND: Peganum harmala L. is a medicinal herb extensively used in traditional Chinese medicine (TCM). So far, relevant reports on the toxicity of Peganum harmala L. seeds (PHS) are hardly available. Especially, we still know little about the in vivo mechanism for PHS toxicity. This study aims to evaluate the toxicity effects of PHS in Caenorhabditis elegans (C. elegans), investigate the possible mechanism of the toxicity effects of PHS, and provide reference for the pharmacological research of PHS. METHODS: In the present study, the C. elegans was exposed to 0.25, 0.50, 1.00 mg/mL of PHS in nematode growth medium (NGM) at 22 degC in the presence of food. Lethality, lifespan, growth, reproduction, and locomotion behavior assays were performed to evaluate the toxicity effects of PHS in C. elegans. We then determined the mechanism of the toxicity effect of PHS by quantitative real-time polymerase chain reaction (qRT-PCR), acetylcholinesterase (AChE) activity assay, and oxidative stress resistance assays. The main components of PHS were detected by high performance liquid chromatography (HPLC). RESULTS: Compared with the control group, the lethality of C. elegans was significantly increased when they were exposed to the ethanol extract of PHS at 0.25, 0.50 and 1.00 mg/mL (P < 0.01), and the mean lifespan was significantly decreased (P < 0.01). We also observed that PHS exposure could induce the toxicity on body length, brood size, and locomotion behavior. CONCLUSION: Our study shows that the ethanol extract of PHS exerts obvious toxic effects on C. elegans, which would provide new ideas and methods for the biological evaluation of the toxicity of Chinese medicinal materials.
ESTHER : Miao_2020_BMC.Complement.Med.Ther_20_256
PubMedSearch : Miao_2020_BMC.Complement.Med.Ther_20_256
PubMedID: 32807143

Title : Structure-based virtual screening leading to discovery of highly selective butyrylcholinesterase inhibitors with solanaceous alkaloid scaffolds - Zhou_2019_Chem.Biol.Interact_13ChEPon_308_372
Author(s) : Zhou S , Yuan Y , Zheng F , Zhan CG
Ref : Chemico-Biological Interactions , 308 :372 , 2019
Abstract : According to recent research advance, it is interesting to identify new, potent and selective inhibitors of human butyrylcholinesterase (BChE) for therapeutic treatment of both the Alzheimer's disease (AD) and heroin abuse. In this study, we carried out a structure-based virtual screening followed by in vitro activity assays, with the goal to identify new inhibitors that are selective for BChE over acetylcholinesterase (AChE). As a result, a set of new, selective inhibitors of human BChE were identified from natural products with solanaceous alkaloid scaffolds. The most active one of the natural products (compound 1) identified has an IC50 of 16.8nM against BChE. It has been demonstrated that the desirable selectivity of these inhibitors for BChE over AChE is mainly controlled by three key residues in the active site cavity, i.e. residues Q119, A277, and A328 in BChE versus the respective residues Y124, W286, and Y337 in AChE. Based on this structural insight, future rational design of new, potent and selective BChE inhibitors may focus on these key structural differences in the active site cavity.
ESTHER : Zhou_2019_Chem.Biol.Interact_13ChEPon_308_372
PubMedSearch : Zhou_2019_Chem.Biol.Interact_13ChEPon_308_372
PubMedID: 31152736

Title : Functional analysis of the GbDWARF14 gene associated with branching development in cotton - Wang_2019_PeerJ_7_e6901
Author(s) : Wang P , Zhang S , Qiao J , Sun Q , Shi Q , Cai C , Mo J , Chu Z , Yuan Y , Du X , Miao Y , Zhang X , Cai Y
Ref : PeerJ , 7 :e6901 , 2019
Abstract : Plant architecture, including branching pattern, is an important agronomic trait of cotton crops. In recent years, strigolactones (SLs) have been considered important plant hormones that regulate branch development. In some species such as Arabidopsis, DWARF14 is an unconventional receptor that plays an important role in the SL signaling pathway. However, studies on SL receptors in cotton are still lacking. Here, we cloned and analysed the structure of the GbD14 gene in Gossypium barbadense and found that it contains the domains necessary for a SL receptor. The GbD14 gene was expressed primarily in the roots, leaves and vascular bundles, and the GbD14 protein was determined via GFP to localize to the cytoplasm and nucleus. Gene expression analysis revealed that the GbD14 gene not only responded to SL signals but also was differentially expressed between cotton plants whose types of branching differed. In particular, GbD14 was expressed mainly in the axillary buds of normal-branching cotton, while it was expressed the most in the leaves of nulliplex-branch cotton. In cotton, the GbD14 gene can be induced by SL and other plant hormones, such as indoleacetic acid, abscisic acid, and jasmonic acid. Compared with wild-type Arabidopsis, GbD14-overexpressing Arabidopsis responded more rapidly to SL signals. Moreover, we also found that GbD14 can rescue the multi-branched phenotype of Arabidopsis Atd14 mutants. Our results indicate that the function of GbD14 is similar to that of AtD14, and GbD14 may be a receptor for SL in cotton and involved in regulating branch development. This research provides a theoretical basis for a profound understanding of the molecular mechanism of branch development and ideal plant architecture for cotton breeding improvements.
ESTHER : Wang_2019_PeerJ_7_e6901
PubMedSearch : Wang_2019_PeerJ_7_e6901
PubMedID: 31143538

Title : [Distribution characteristics and correlation analysis of antibody detection value in myasthenia gravis] - Liu_2019_Zhonghua.Yi.Xue.Za.Zhi_99_3221
Author(s) : Liu YL , Zheng YM , Luo JJ , Zhang W , Gao F , Yuan Y , Hao HJ
Ref : Zhonghua Yi Xue Za Zhi , 99 :3221 , 2019
Abstract : Objective: To determine the factors affecting distribution and magnitude of antibody detection value in myasthenia gravis (MG). Methods: A total of 406 MG patients diagnosed at Department of Neurology, Peking University First Hospital from May 2015 to November 2017 were included.All of them exhibited muscle fatigue with decreased response in repetitive nerve stimulation test. There were 200 males and 206 females whose ages ranged from 2 to 85 years old. According to clinical classification of MG recommended by Myasthenia Gravis Foundation of America (MGFA), patients assigned to class I to class V included 200,140, 46, 15 and 5 cases, respectively. There were 33 cases of thymic hyperplasia and 63 cases of thymoma confirmed by radiological or pathological findings. Quantile plots and quantile regression model were used to determine the effects of age, gender and MGFA classification, thymus disease on acetylcholine receptors (AChR)antibody, acetylcholinesterase (AChE) antibody, Titin antibody, ryanodine receptor (RyR) antibody and muscle-specific tyrosine kinase (MuSK) antibody detection values detected by enzyme-linked immunosorbent assay (ELISA). Results: MGFA classification had effects on distribution of AChR antibody level. There was a positive correlation between age and AChR antibody level(P<0.05). Negative correlation was found between age and AChE, Titin and RyR antibody level (P<0.05). No significant correlation was shown between any factors and MuSK antibody level(P>/=0.05). MGFA classification had a positive correlation with AChR antibody level (P<0.05) and no correlation with other antibody levels (P>0.05). Gender and thymus disease had no correlation with any tested antibody levels (P>0.05). Conclusion: MGFA classification has significant effects on distribution of AChR antibody level. Age and MGFA classification have positive correlation with AChR antibody level.
ESTHER : Liu_2019_Zhonghua.Yi.Xue.Za.Zhi_99_3221
PubMedSearch : Liu_2019_Zhonghua.Yi.Xue.Za.Zhi_99_3221
PubMedID: 31694116

Title : New amide alkaloids from Delphinium brunonianum - Zou_2019_Fitoterapia__104186
Author(s) : Zou YS , Dawa Z , Lin CZ , Zhang QY , Yao YF , Yuan Y , Zhu CC , Wang ZY
Ref : Fitoterapia , :104186 , 2019
Abstract : Five new amide alkaloids, named delamide A-E (1-5), along with five known ones, methyl-N-(3-carboxy-2-methylpropanoyl) anthranilate (6), benzoic acid, 2-[(1-oxodecyl) amino]-methylester (7), puberline (8), benzoic acid, 2-[(4-methoxy-2-methyl-1, 4-dioxobutyl) amino]-methylester (9) and benzoic acid, 2-[(4-methoxy-3-methyl-1, 4-dioxobutyl) amino]-methylester (10) were isolated from the extract of Delphinium brunonianum. Their structures were elucidated by extensive spectroscopic analyses (including 1D-, 2D-NMR, and HR-ESI-MS). 1-10 were also evaluated for their acetylcholinesterase (AChE) inhibiting activity by the Ellman's method. Delamide A (1) showed highly selective AChE inhibition activity. The kinetic analysis revealed that 1 was a mixed-type reversible inhibitor of AChE.
ESTHER : Zou_2019_Fitoterapia__104186
PubMedSearch : Zou_2019_Fitoterapia__104186
PubMedID: 31150769

Title : Online acetylcholinesterase inhibition evaluation by high-performance liquid chromatography-mass spectrometry hyphenated with an immobilized enzyme reactor - Yuan_2019_J.Chromatogr.A__460506
Author(s) : Yuan Y , Zhao M , Riffault-Valois L , Ennahar S , Bergaentzle M , Marchioni E
Ref : Journal of Chromatography A , :460506 , 2019
Abstract : A high-performance liquid chromatography-mass spectrometry technique hyphenated on-line with an immobilized enzyme reactor (IMER) was developed by the use of 3 known acetylcholinesterase (AChE) inhibitors (galanthamine, huperzine A and tacrine). This bioanalytical device allows qualitative comparison of the inhibitory strengths of AChE inhibitors. The AChE inhibitory strengths were evaluated and compared by the corresponding acetylcholine peak areas (mass signal) obtained after a chromatographic separation and the elution through the IMER. Only one injection of the analytes is needed to get this comparative analysis. This bioanalytical device was then applied to the extract of a natural plant, Lycoris radiata, which is known to contain AChE inhibitors such as galanthamine and lycoramine. Aside from the demonstration of the inhibitory activity of the two known AChE inhibitors, the AChE inhibitory activity of another compound (dihydro-latifaliumin C) was revealed. This is the first report describing the AChE inhibitory activity of this compound.
ESTHER : Yuan_2019_J.Chromatogr.A__460506
PubMedSearch : Yuan_2019_J.Chromatogr.A__460506
PubMedID: 31526637

Title : Lipolysis Triggers a Systemic Insulin Response Essential for Efficient Energy Replenishment of Activated Brown Adipose Tissue in Mice - Heine_2018_Cell.Metab_28_644
Author(s) : Heine M , Fischer AW , Schlein C , Jung C , Straub LG , Gottschling K , Mangels N , Yuan Y , Nilsson SK , Liebscher G , Chen O , Schreiber R , Zechner R , Scheja L , Heeren J
Ref : Cell Metab , 28 :644 , 2018
Abstract : The coordination of the organ-specific responses regulating systemic energy distribution to replenish lipid stores in acutely activated brown adipose tissue (BAT) remains elusive. Here, we show that short-term cold exposure or acute beta3-adrenergic receptor (beta3AR) stimulation results in secretion of the anabolic hormone insulin. This process is diminished in adipocyte-specific Atgl(-/-) mice, indicating that lipolysis in white adipose tissue (WAT) promotes insulin secretion. Inhibition of pancreatic beta cells abolished uptake of lipids delivered by triglyceride-rich lipoproteins into activated BAT. Both increased lipid uptake into BAT and whole-body energy expenditure in response to beta3AR stimulation were blunted in mice treated with the insulin receptor antagonist S961 or lacking the insulin receptor in brown adipocytes. In conclusion, we introduce the concept that acute cold and beta3AR stimulation trigger a systemic response involving WAT, beta cells, and BAT, which is essential for insulin-dependent fuel uptake and adaptive thermogenesis.
ESTHER : Heine_2018_Cell.Metab_28_644
PubMedSearch : Heine_2018_Cell.Metab_28_644
PubMedID: 30033199

Title : Enhanced Poly(ethylene terephthalate) Hydrolase Activity by Protein Engineering - Ma_2018_Engineering.(Beijing)_4_888
Author(s) : Ma Y , Yao M , Li B , Ding M , He B , Chen S , Zhou X , Yuan Y
Ref : Engineering (Beijing) , 4 :888 , 2018
Abstract : Poly(ethylene terephthalate) hydrolase (PETase) from Ideonella sakaiensis exhibits a strong ability to degrade poly(ethylene terephthalate) (PET) at room temperature, and is thus regarded as a potential tool to solve the issue of polyester plastic pollution. Therefore, we explored the interaction between PETase and the substrate (a dimer of the PET monomer ethylene terephthalate, 2PET), using a model of PETase and its substrate. In this study, we focused on six key residues around the substrate-binding groove in order to create novel high-efficiency PETase mutants through protein engineering. These PETase mutants were designed and tested. The enzymatic activities of the R61A, L88F, and I179F mutants, which were obtained with a rapid cell-free screening system, exhibited 1.4 fold, 2.1 fold, and 2.5 fold increases, respectively, in comparison with wild-type PETase. The I179F mutant showed the highest activity, with the degradation rate of a PET film reaching 22.5 mg per micromol/L PETase per day. Thus, this study has created enhanced artificial PETase enzymes through the rational protein engineering of key hydrophobic sites, and has further illustrated the potential of biodegradable plastics.
ESTHER : Ma_2018_Engineering.(Beijing)_4_888
PubMedSearch : Ma_2018_Engineering.(Beijing)_4_888
Gene_locus related to this paper: idesa-peth

Title : Molecular interaction studies of acetylcholinesterase with potential acetylcholinesterase inhibitors from the root of Rhodiola crenulata using molecular docking and isothermal titration calorimetry methods - Li_2017_Int.J.Biol.Macromol_104_527
Author(s) : Li FJ , Liu Y , Yuan Y , Yang B , Liu ZM , Huang LQ
Ref : Int J Biol Macromol , 104 :527 , 2017
Abstract : (-)-Epicatechin gallate ((-)-ECG), 1,2,3,4,6-O-pentagalloylglucose (PGG), rhodionin, herbacetin and rhodiosin isolated from the root of Rhodiola crenulata exhibited potent, dose-dependent inhibitory effects on acetylcholinesterase (AChE) with IC50 ranged from 57.50+/-5.83 to 2.43+/-0.34mug/mL. With the aim of explaining the differences in activity of these active ingredients and clarifying how they inhibit AChE, the AChE-inhibitor interactions were further explored using molecular docking and isothermal titration calorimetry (ITC) methods in the present study. Molecular docking studies revealed that all compounds except PGG showed binding energy values ranging from -10.30 to -8.00kcal/mol while the binding energy of galantamine, a known AChE inhibitor, was -9.53kcal/mol; they inhibited the AChE by binding into the ligand pocket with the similar binding pattern to that of galantamine by interacting with Glu199 of AChE. Inhibition constant of these active ingredients had a positive correlation with binding energy. The interaction between AChE and PGG was further evaluated with the ITC method and the results indicated that the PGG-AChE interaction was relevant to AChE concentration. The results revealed a possible mechanism for the AChE inhibition activity of these bioactive ingredients, which may provide some help in lead compounds optimization in the future.
ESTHER : Li_2017_Int.J.Biol.Macromol_104_527
PubMedSearch : Li_2017_Int.J.Biol.Macromol_104_527
PubMedID: 28625836

Title : Regulation of growth, antioxidant capacity, fatty acid profiles, hematological characteristics and expression of lipid related genes by different dietary n-3 highly unsaturated fatty acids in juvenile black seabream (Acanthopagrus schlegelii) - Jin_2017_Aquaculture_471_55
Author(s) : Jin M , Lu Y , Yuan Y , Li Y , Qiu H , Sun P , Ma H-N , Ding L-Y , Zhou Q-C
Ref : Aquaculture , 471 :55 , 2017
Abstract : An 8-week feeding trial was conducted to investigate the effects of dietary n-3 highly unsaturated fatty acid (n-3HUFA) on growth performance, antioxidant capacity, fatty acid profiles, hematological characteristics and expression of some lipid related genes of juvenile black seabream (Acanthopagrus schlegelii) (initial weight 3.770.00g). Five isonitrogenous and isolipidic experimental diets were formulated with graded levels of n-3 HUFA (0.23, 0.87, 1.29, 1.75 and 2.53% of dry weight, DHA/EPA ratio approximately at 1.0). The results revealed that fish fed the diet containing 1.75% n-3 HUFA had higher weight gain (WG) and specific growth rate (SGR) than those fed the control diet. Fish fed diets containing 1.29% and 1.75% n-3 HUFA had higher feed efficiency (FE) than those fed the other diets. Hepatic and muscular fatty acid profiles reflected that of diets. The content of malondialdehyde (MDA) increased both in the serum and liver of fish fed high n-3 HUFA level diets, and the highest hepatic activity of glutathione peroxidase (GSH-PX) was recorded in fish fed the diet containing 1.29% n-3 HUFA. The expression of acc, g6pd, fas, srebp-1, lpl, atgl, hsl, elovl5 and fads2 was down-regulated in fish fed the diets with high n-3 HUFA levels. However, the expression levels of 6pgd and ppar significantly increased when the dietary contents of n-3 HUFA increased from 0.23% to 1.29% and then decreased when dietary n-3 HUFA levels increased from 1.75% to 2.53%. The highest expression of cpt1a was found in fish fed the diet containing 1.75% n-3 HUFA. The content of cholesterol (CHOL) in serum increased along with n-3 HUFA level. Over all, this study indicated that fish fed moderate dietary n-3 HUFA (1.341.80% n-3 HUFA) could enhance growth, feed utilization and antioxidant capacity. Different dietary levels of n-3 HUFA could strongly affect expression levels of some lipid metabolism relevant genes of the juvenile black seabream. This may contribute to our understanding of the mechanisms related to lipid metabolism (anabolism and catabolism) effects of different dietary levels of n-3 HUFA.
ESTHER : Jin_2017_Aquaculture_471_55
PubMedSearch : Jin_2017_Aquaculture_471_55
Gene_locus related to this paper: acasc-a0a1s5r938

Title : High-throughput proteomics integrated with gene microarray for discovery of colorectal cancer potential biomarkers - Yu_2016_Oncotarget_7_75279
Author(s) : Yu J , Li X , Zhong C , Li D , Zhai X , Hu W , Guo C , Yuan Y , Zheng S
Ref : Oncotarget , 7 :75279 , 2016
Abstract : Proteins, as executives of genes' instructions, are responsible for cellular phenotypes. Integratingproteomics with gene microarray, we conducted this study to identify potential protein biomarkers of colorectal cancer (CRC). Isobaric tags with related and absolute quantitation (iTRAQ) labeling mass spectrometry (MS) was applied to screen and identify differentially expressed proteins between paired CRC and adjacent normal mucosa. Meanwhile, Affymetrix U133plus2.0 microarrays were used to perform gene microarray analysis. Verification experiments included immunohistochemistry (IHC), western blot and enzyme-linked immunosorbent assay (ELISA) of selected proteins. Overall, 5469 differentially expressed proteins were detected with iTRAQ-MS from 24 matched CRC and adjacent normal tissues. And gene microarray identified 39859 differential genes from 52 patients. Of these, 3083 differential proteins had corresponding differentially expressed genes, with 245 proteins and their genes showed >1.5-fold change in expression level. Gene ontology enrichment analysis revealed that up-regulated proteins were more involved in cell adhesion and motion than down-regulated proteins. In addition, up-regulated proteins were more likely to be located in nucleus and vesicles. Further verification experiments with IHC confirmed differential expression levels of 5 proteins (S100 calcium-binding protein A9, annexin A3, nicotinamide phosphoribosyltransferase, carboxylesterase 2 and calcium activated chloride channel A1) between CRC and normal tissues. Besides, western blot showed a stepwise increase of annexin A3 abundance in normal colorectal mucosa, adenoma and CRC tissues. ELISAresults revealed significantly higher serum levels of S100 calcium-binding protein A9 and annexin A3 in CRC patients than healthy controls, validating diagnostic value of these proteins. Cell experiments showed that inhibition of annexin A3 could suppress CRC cell proliferation and aggressiveness. S100 calcium-binding protein A9, annexin A3, nicotinamide phosphoribosyltransferase, carboxylesterase 2 and calcium activated chloride channel A1 were probably potential biomarkers of colorectal cancer. Annexin A3 was a potentially valuable therapeutic target of CRC.
ESTHER : Yu_2016_Oncotarget_7_75279
PubMedSearch : Yu_2016_Oncotarget_7_75279
PubMedID: 27661117

Title : Unexpected Reaction Pathway for butyrylcholinesterase-catalyzed inactivation of hunger hormone ghrelin - Yao_2016_Sci.Rep_6_22322
Author(s) : Yao J , Yuan Y , Zheng F , Zhan CG
Ref : Sci Rep , 6 :22322 , 2016
Abstract : Extensive computational modeling and simulations have been carried out, in the present study, to uncover the fundamental reaction pathway for butyrylcholinesterase (BChE)-catalyzed hydrolysis of ghrelin, demonstrating that the acylation process of BChE-catalyzed hydrolysis of ghrelin follows an unprecedented single-step reaction pathway and the single-step acylation process is rate-determining. The free energy barrier (18.8 kcal/mol) calculated for the rate-determining step is reasonably close to the experimentally-derived free energy barrier (~19.4 kcal/mol), suggesting that the obtained mechanistic insights are reasonable. The single-step reaction pathway for the acylation is remarkably different from the well-known two-step acylation reaction pathway for numerous ester hydrolysis reactions catalyzed by a serine esterase. This is the first time demonstrating that a single-step reaction pathway is possible for an ester hydrolysis reaction catalyzed by a serine esterase and, therefore, one no longer can simply assume that the acylation process must follow the well-known two-step reaction pathway.
ESTHER : Yao_2016_Sci.Rep_6_22322
PubMedSearch : Yao_2016_Sci.Rep_6_22322
PubMedID: 26922910

Title : Putative Receptor Binding Domain of Bat-Derived Coronavirus HKU9 Spike Protein: Evolution of Betacoronavirus Receptor Binding Motifs - Huang_2016_Biochemistry_55_5977
Author(s) : Huang C , Qi J , Lu G , Wang Q , Yuan Y , Wu Y , Zhang Y , Yan J , Gao GF
Ref : Biochemistry , 55 :5977 , 2016
Abstract : The suggested bat origin for Middle East respiratory syndrome coronavirus (MERS-CoV) has revitalized the studies of other bat-derived coronaviruses with respect to interspecies transmission potential. Bat coronavirus (BatCoV) HKU9 is an important betacoronavirus (betaCoV) that is phylogenetically affiliated with the same genus as MERS-CoV. The bat surveillance data indicated that BatCoV HKU9 has been widely spreading and circulating in bats. This highlights the necessity of characterizing the virus for its potential to cross species barriers. The receptor binding domain (RBD) of the coronavirus spike (S) protein recognizes host receptors to mediate virus entry and is therefore a key factor determining the viral tropism and transmission capacity. In this study, the putative S RBD of BatCoV HKU9 (HKU9-RBD), which is homologous to other betaCoV RBDs that have been structurally and functionally defined, was characterized via a series of biophysical and crystallographic methods. By using surface plasmon resonance, we demonstrated that HKU9-RBD binds to neither SARS-CoV receptor ACE2 nor MERS-CoV receptor CD26. We further determined the atomic structure of HKU9-RBD, which as expected is composed of a core and an external subdomain. The core subdomain fold resembles those of other betaCoV RBDs, whereas the external subdomain is structurally unique with a single helix, explaining the inability of HKU9-RBD to react with either ACE2 or CD26. Via comparison of the available RBD structures, we further proposed a homologous intersubdomain binding mode in betaCoV RBDs that anchors the external subdomain to the core subdomain. The revealed RBD features would shed light on the evolution route of betaCoV.
ESTHER : Huang_2016_Biochemistry_55_5977
PubMedSearch : Huang_2016_Biochemistry_55_5977
PubMedID: 27696819

Title : Perilipin 5 improves hepatic lipotoxicity by inhibiting lipolysis - Wang_2015_Hepatology_61_870
Author(s) : Wang C , Zhao Y , Gao X , Li L , Yuan Y , Liu F , Zhang L , Wu J , Hu P , Zhang X , Gu Y , Xu Y , Wang Z , Li Z , Zhang H , Ye J
Ref : Hepatology , 61 :870 , 2015
Abstract : Abnormal metabolism of nonesterified fatty acids (NEFAs) and their derivatives has been reported to be the main cause of intracellular lipotoxic injury. Normally, NEFAs are stored in lipid droplets (LDs) in the form of triglyceride (TG), which could reduce the lipotoxicity of cytosolic NEFAs. Previous studies have implicated that Perilipin 5 (Plin5), an LD-binding protein, regulates the storage and hydrolysis of TG in LD. However, its roles and underlying mechanisms in the liver remain unknown. Here we found that Plin5 expression was increased in steatotic livers. Using Plin5 knockout mice, we found that Plin5 deficiency resulted in reduced hepatic lipid content and smaller-sized LDs, which was due to the elevated lipolysis rate and fatty acid utilization. Plin5-deficient hepatocytes showed increased mitochondria proliferation, which could be explained by the increased expression and activity of PPARalpha stimulated by the increased NEFA levels. Meanwhile, Plin5-deficient livers also exhibited enhanced mitochondrial oxidative capacity. We also found that Plin5 deficiency induces lipotoxic injury in hepatocytes, attributed to lipid peroxidation. Mechanistically, we found that Plin5 blocks adipose triglyceride lipase (ATGL)-mediated lipolysis by competitively binding to comparative gene identification-58 (CGI-58) and disrupting the interaction between CGI-58 and ATGL. CONCLUSION: Plin5 is an important protective factor against hepatic lipotoxicity induced by NEFAs generated from lipolysis. This provides an important new insight into the regulation of hepatic lipid storage and relation between lipid storage and lipotoxicity.
ESTHER : Wang_2015_Hepatology_61_870
PubMedSearch : Wang_2015_Hepatology_61_870
PubMedID: 25179419

Title : Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution - Li_2015_Nat.Biotechnol_33_524
Author(s) : Li F , Fan G , Lu C , Xiao G , Zou C , Kohel RJ , Ma Z , Shang H , Ma X , Wu J , Liang X , Huang G , Percy RG , Liu K , Yang W , Chen W , Du X , Shi C , Yuan Y , Ye W , Liu X , Zhang X , Liu W , Wei H , Wei S , Zhu S , Zhang H , Sun F , Wang X , Liang J , Wang J , He Q , Huang L , Cui J , Song G , Wang K , Xu X , Yu JZ , Zhu Y , Yu S
Ref : Nat Biotechnol , 33 :524 , 2015
Abstract : Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6% approximately 96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.
ESTHER : Li_2015_Nat.Biotechnol_33_524
PubMedSearch : Li_2015_Nat.Biotechnol_33_524
PubMedID: 25893780
Gene_locus related to this paper: gosra-a0a0d2rxs2 , gosra-a0a0d2tng2 , gosra-a0a0d2twz7 , goshi-a0a1u8hr03 , gosra-a0a0d2vdc5 , goshi-a0a1u8ljh5 , gosra-a0a0d2vj24 , goshi-a0a1u8pxd3 , gosra-a0a0d2sr31 , goshi-a0a1u8knd1 , goshi-a0a1u8nhw9 , goshi-a0a1u8mt09 , goshi-a0a1u8kis4 , goshi-a0a1u8ibk3 , goshi-a0a1u8ieg2 , goshi-a0a1u8iki6 , goshi-a0a1u8jvp4 , goshi-a0a1u8jw35 , gosra-a0a0d2pzd7 , goshi-a0a1u8ied7

Title : The Toxicity and Detoxifying Mechanism of Cycloxaprid and Buprofezin in Controlling Sogatella furcifera (Homoptera: Delphacidae) - Chang_2015_J.Insect.Sci_15_
Author(s) : Chang X , Yuan Y , Zhang T , Wang D , Du X , Wu X , Chen H , Chen Y , Jiao Y , Teng H
Ref : J Insect Sci , 15 : , 2015
Abstract : The effects of cycloxaprid (a modified neonicotinoid insecticide) and buprofezin (a thiadiazine insecticide) on mortality of the white-backed planthopper (WBPH), Sogatella furcifera, were determined in laboratory assays. Cycloxaprid killed WBPH nymphs and adults but buprofezin killed only nymphs, and cycloxaprid acted faster than buprofezin. One day after infestation, mortality of third-instar nymphs was >65% with cycloxaprid at 125 mg liter(-1) but was <38% with buprofezin at 148 mg liter(-1). By the 4th day after infestation, however, control of nymphs by the two insecticides was similar, and cycloxaprid at 125 mg liter(-1) caused >/=80% mortality of adults but buprofezin at 148 mg liter(-1) (the highest rate tested) caused almost no adult mortality. LC50 values for cycloxaprid were lowest with nymphs, intermediate with adult males, and highest with adult females. Although buprofezin was slower acting than cycloxaprid, its LC50 for nymphs 5 d after infestation was 3.79-fold lower than that of cycloxaprid. Mean carboxylesterase (CarE) specific activity of nymphal WBPH treated with cycloxaprid and buprofezin was higher than that of control, but there was no significant difference between cycloxaprid and control (no insecticide), and it was significantly higher for buprofezin than those of cycloxaprid and control. For glutathione S-transferase and mixed function oxygenase, the specific activity of nymphal WBPH treated with buprofezin was significantly higher than those of cycloxaprid and control, too.
ESTHER : Chang_2015_J.Insect.Sci_15_
PubMedSearch : Chang_2015_J.Insect.Sci_15_
PubMedID: 26175461

Title : Bat origins of MERS-CoV supported by bat coronavirus HKU4 usage of human receptor CD26 - Wang_2014_Cell.Host.Microbe_16_328
Author(s) : Wang Q , Qi J , Yuan Y , Xuan Y , Han P , Wan Y , Ji W , Li Y , Wu Y , Wang J , Iwamoto A , Woo PC , Yuen KY , Yan J , Lu G , Gao GF
Ref : Cell Host Microbe , 16 :328 , 2014
Abstract : The recently reported Middle East respiratory syndrome coronavirus (MERS-CoV) is phylogenetically closely related to the bat coronaviruses (BatCoVs) HKU4 and HKU5. However, the evolutionary pathway of MERS-CoV is still unclear. A receptor binding domain (RBD) in the MERS-CoV envelope-embedded spike protein specifically engages human CD26 (hCD26) to initiate viral entry. The high sequence identity in the viral spike protein prompted us to investigate if HKU4 and HKU5 can recognize hCD26 for cell entry. We found that HKU4-RBD, but not HKU5-RBD, binds to hCD26, and pseudotyped viruses embedding HKU4 spike can infect cells via hCD26 recognition. The structure of the HKU4-RBD/hCD26 complex revealed a hCD26-binding mode similar overall to that observed for MERS-RBD. HKU4-RBD, however, is less adapted to hCD26 than MERS-RBD, explaining its lower affinity for receptor binding. Our findings support a bat origin for MERS-CoV and indicate the need for surveillance of HKU4-related viruses in bats.
ESTHER : Wang_2014_Cell.Host.Microbe_16_328
PubMedSearch : Wang_2014_Cell.Host.Microbe_16_328
PubMedID: 25211075
Gene_locus related to this paper: human-DPP4

Title : Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing - Hellsten_2013_Proc.Natl.Acad.Sci.U.S.A_110_19478
Author(s) : Hellsten U , Wright KM , Jenkins J , Shu S , Yuan Y , Wessler SR , Schmutz J , Willis JH , Rokhsar DS
Ref : Proc Natl Acad Sci U S A , 110 :19478 , 2013
Abstract : Meiotic recombination rates can vary widely across genomes, with hotspots of intense activity interspersed among cold regions. In yeast, hotspots tend to occur in promoter regions of genes, whereas in humans and mice, hotspots are largely defined by binding sites of the positive-regulatory domain zinc finger protein 9. To investigate the detailed recombination pattern in a flowering plant, we use shotgun resequencing of a wild population of the monkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries of historic crossovers or gene conversion tracts. Their distribution defines some 13,000 hotspots of varying strengths, interspersed with cold regions of undetectably low recombination. Average recombination rates peak near starts of genes and fall off sharply, exhibiting polarity. Within genes, recombination tracts are more likely to terminate in exons than in introns. The general pattern is similar to that observed in yeast, as well as in positive-regulatory domain zinc finger protein 9-knockout mice, suggesting that recombination initiation described here in Mimulus may reflect ancient and conserved eukaryotic mechanisms.
ESTHER : Hellsten_2013_Proc.Natl.Acad.Sci.U.S.A_110_19478
PubMedSearch : Hellsten_2013_Proc.Natl.Acad.Sci.U.S.A_110_19478
PubMedID: 24225854
Gene_locus related to this paper: erygu-a0a022qsc9 , erygu-a0a022qjb4 , erygu-a0a022px28 , erygu-a0a022rcn8 , erygu-a0a022r7z4 , erygu-a0a022rcp2 , erygu-a0a022r9s7 , erygu-a0a022put8 , erygu-a0a022r922 , erygu-a0a022qmg0 , erygu-a0a022rf01 , erygu-a0a022qnf5 , erygu-a0a022qs63 , erygu-a0a022rvn4 , erygu-a0a022rnw2 , erygu-a0a022s0h3 , erygu-a0a022qr26 , erygu-a0a022qi72 , erygu-a0a022qi30 , erygu-a0a022q165 , erygu-a0a022r728 , erygu-a0a022r7n8 , erygu-a0a022rm64 , erygu-a0a022s4c6 , erygu-a0a022rbl0 , erygu-a0a022rwi3 , erygu-a0a022rzg9

Title : Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 - Lu_2013_Nature_500_227
Author(s) : Lu G , Hu Y , Wang Q , Qi J , Gao F , Li Y , Zhang Y , Zhang W , Yuan Y , Bao J , Zhang B , Shi Y , Yan J , Gao GF
Ref : Nature , 500 :227 , 2013
Abstract : The newly emergent Middle East respiratory syndrome coronavirus (MERS-CoV) can cause severe pulmonary disease in humans, representing the second example of a highly pathogenic coronavirus, the first being SARS-CoV. CD26 (also known as dipeptidyl peptidase 4, DPP4) was recently identified as the cellular receptor for MERS-CoV. The engagement of the MERS-CoV spike protein with CD26 mediates viral attachment to host cells and virus-cell fusion, thereby initiating infection. Here we delineate the molecular basis of this specific interaction by presenting the first crystal structures of both the free receptor binding domain (RBD) of the MERS-CoV spike protein and its complex with CD26. Furthermore, binding between the RBD and CD26 is measured using real-time surface plasmon resonance with a dissociation constant of 16.7 nM. The viral RBD is composed of a core subdomain homologous to that of the SARS-CoV spike protein, and a unique strand-dominated external receptor binding motif that recognizes blades IV and V of the CD26 beta-propeller. The atomic details at the interface between the two binding entities reveal a surprising protein-protein contact mediated mainly by hydrophilic residues. Sequence alignment indicates, among betacoronaviruses, a possible structural conservation for the region homologous to the MERS-CoV RBD core, but a high variation in the external receptor binding motif region for virus-specific pathogenesis such as receptor recognition.
ESTHER : Lu_2013_Nature_500_227
PubMedSearch : Lu_2013_Nature_500_227
PubMedID: 23831647
Gene_locus related to this paper: human-DPP4

Title : DWARF 53 acts as a repressor of strigolactone signalling in rice - Jiang_2013_Nature_504_401
Author(s) : Jiang L , Liu X , Xiong G , Liu H , Chen F , Wang L , Meng X , Liu G , Yu H , Yuan Y , Yi W , Zhao L , Ma H , He Y , Wu Z , Melcher K , Qian Q , Xu HE , Wang Y , Li J
Ref : Nature , 504 :401 , 2013
Abstract : Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching. SL signalling requires the hormone-dependent interaction of DWARF 14 (D14), a probable candidate SL receptor, with DWARF 3 (D3), an F-box component of the Skp-Cullin-F-box (SCF) E3 ubiquitin ligase complex. Here we report the characterization of a dominant SL-insensitive rice (Oryza sativa) mutant dwarf 53 (d53) and the cloning of D53, which encodes a substrate of the SCF(D3) ubiquitination complex and functions as a repressor of SL signalling. Treatments with GR24, a synthetic SL analogue, cause D53 degradation via the proteasome in a manner that requires D14 and the SCF(D3) ubiquitin ligase, whereas the dominant form of D53 is resistant to SL-mediated degradation. Moreover, D53 can interact with transcriptional co-repressors known as TOPLESS-RELATED PROTEINS. Our results suggest a model of SL signalling that involves SL-dependent degradation of the D53 repressor mediated by the D14-D3 complex.
ESTHER : Jiang_2013_Nature_504_401
PubMedSearch : Jiang_2013_Nature_504_401
PubMedID: 24336200

Title : Enhanced performance of lipase-catalyzed kinetic resolution of secondary alcohols in monoether-functionalized ionic liquids - Zhou_2011_Bioresour.Technol_102_5562
Author(s) : Zhou H , Chen J , Ye L , Lin H , Yuan Y
Ref : Bioresour Technol , 102 :5562 , 2011
Abstract : Several cationic monoether-functionalized ionic liquids (MEF-ILs) with different substituents were synthesized and used as media for kinetic resolution of secondary alcohols catalyzed by several lipases. The results indicate that Novozym 435 (an immobilized Candida antarctica Lipase B) had higher efficiency compared to other lipases in deracemization. The alkyl substituents at the 2- and 3-positions in the imidazolium ring of MEF-ILs were found to contribute to the increased enantioselectivity and enhancement of the reaction rate, respectively, while the higher stereo-hindrance of ether bonds decreased the activity. An enantioselectivity higher than 99% with 50% conversion of rac-1-phenylethanol was achieved using the catalyst system comprised of Novozym 435 and the MEF-IL 1-(3-ethoxypropyl)-2,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide. The catalytic system could be separated and reused without considerable activity loss. MEF-ILs can be a new class of enzyme-benign media suitable for lipase-catalyzed kinetic resolution of secondary alcohols.
ESTHER : Zhou_2011_Bioresour.Technol_102_5562
PubMedSearch : Zhou_2011_Bioresour.Technol_102_5562
PubMedID: 21388804

Title : The neutral hydrolysis of simple carboxylic esters in water and the rate enhancements produced by acetylcholinesterase and other carboxylic acid esterases - Wolfenden_2011_J.Am.Chem.Soc_133_13821
Author(s) : Wolfenden R , Yuan Y
Ref : Journal of the American Chemical Society , 133 :13821 , 2011
Abstract : Experiments at elevated temperatures permit the determination of rate constant and thermodynamic activation parameters for the neutral hydrolysis of the neurotransmitter acetylcholine in water. At 25 degrees C, the extrapolated rate constant for the uncatalyzed (or neutral) hydrolysis of acetylcholine is 3.9 x 10(-7) s(-1) at 25 degrees C (DeltaH(double dagger) = 20.0 kcal/mol; TDeltaS(double dagger) = -6.1 kcal/mol). Acetylcholine is more susceptible to neutral and base-catalyzed hydrolysis than ethyl acetate but less susceptible to acid-catalyzed hydrolysis. For acetylcholinesterase from the electric eel, the catalytic proficiency [(k(cat)/K(m))/k(neutral)] is 2 x 10(16) M(-1), comparable in magnitude with the catalytic proficiencies of aminohydrolases that act on peptides and nucleosides.
ESTHER : Wolfenden_2011_J.Am.Chem.Soc_133_13821
PubMedSearch : Wolfenden_2011_J.Am.Chem.Soc_133_13821
PubMedID: 21793525

Title : The DNA sequence, annotation and analysis of human chromosome 3 - Muzny_2006_Nature_440_1194
Author(s) : Muzny DM , Scherer SE , Kaul R , Wang J , Yu J , Sudbrak R , Buhay CJ , Chen R , Cree A , Ding Y , Dugan-Rocha S , Gill R , Gunaratne P , Harris RA , Hawes AC , Hernandez J , Hodgson AV , Hume J , Jackson A , Khan ZM , Kovar-Smith C , Lewis LR , Lozado RJ , Metzker ML , Milosavljevic A , Miner GR , Morgan MB , Nazareth LV , Scott G , Sodergren E , Song XZ , Steffen D , Wei S , Wheeler DA , Wright MW , Worley KC , Yuan Y , Zhang Z , Adams CQ , Ansari-Lari MA , Ayele M , Brown MJ , Chen G , Chen Z , Clendenning J , Clerc-Blankenburg KP , Davis C , Delgado O , Dinh HH , Dong W , Draper H , Ernst S , Fu G , Gonzalez-Garay ML , Garcia DK , Gillett W , Gu J , Hao B , Haugen E , Havlak P , He X , Hennig S , Hu S , Huang W , Jackson LR , Jacob LS , Kelly SH , Kube M , Levy R , Li Z , Liu B , Liu J , Liu W , Lu J , Maheshwari M , Nguyen BV , Okwuonu GO , Palmeiri A , Pasternak S , Perez LM , Phelps KA , Plopper FJ , Qiang B , Raymond C , Rodriguez R , Saenphimmachak C , Santibanez J , Shen H , Shen Y , Subramanian S , Tabor PE , Verduzco D , Waldron L , Wang Q , Williams GA , Wong GK , Yao Z , Zhang J , Zhang X , Zhao G , Zhou J , Zhou Y , Nelson D , Lehrach H , Reinhardt R , Naylor SL , Yang H , Olson M , Weinstock G , Gibbs RA
Ref : Nature , 440 :1194 , 2006
Abstract : After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.
ESTHER : Muzny_2006_Nature_440_1194
PubMedSearch : Muzny_2006_Nature_440_1194
PubMedID: 16641997
Gene_locus related to this paper: human-AADAC , human-AADACL2 , human-ABHD5 , human-ABHD6 , human-ABHD10 , human-ABHD14A , human-APEH , human-BCHE , human-CIB , human-LIPH , human-MGLL , human-NLGN1 , human-PLA1A

Title : [Two novel mutations in palmitoyl-protein thioesterase gene in two Chinese babies with infantile neuronal ceroid lipofuscinosis] - Bi_2006_Zhonghua.Er.Ke.Za.Zhi_44_496
Author(s) : Bi HY , Yao S , Bu DF , Wang ZX , Zhang Y , Qin J , Yang YL , Yuan Y
Ref : Zhonghua Er Ke Za Zhi , 44 :496 , 2006
Abstract : OBJECTIVE: To search for possible novel mutations in palmitoyl-protein thioesterase 1 (PPT1) gene in two Chinese babies with infantile neuronal ceroid lipofuscinosis (INCL).
METHODS: Two probands with INCL, confirmed clinically and pathologically, were used for mutation search in PPT1 gene. Onset of the disease occurred before the age of 1 year and they mainly showed progressive mental and motor retardation. The 9 coding exons and their flanking intron sequences of palmitoyl-protein thioesterase 1 (PPT1) gene were amplified by using PCR and sequenced. The parents of proband 1 were also examined.
RESULTS: One splicing mutation and two missense mutations were identified in the two probands: the proband 1 carrying a compound heterozygous mutation of a IVS1 + 1G-->A mutation in intron 1 and a c550G-->A mutation in exon 6 leading to the amino acid substitution of E184K. Additionally, the parents of the proband 1 also harbored one of the mutations of the patient, respectively. The proband 2 carrying a homozygous mutation of c272A-->C in exon 3, which resulted in the amino acid substitutions of Q91P.
CONCLUSIONS: The IVS1 + 1G-->A mutation and Q91P mutation are novel mutations, which lead to INCL. The genetic abnormalities of PPT1 in Chinese patients may not be completely the same as those in the patients of other regions of the world.
ESTHER : Bi_2006_Zhonghua.Er.Ke.Za.Zhi_44_496
PubMedSearch : Bi_2006_Zhonghua.Er.Ke.Za.Zhi_44_496
PubMedID: 17044973
Gene_locus related to this paper: human-PPT1

Title : The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC) - Gerhard_2004_Genome.Res_14_2121
Author(s) : Gerhard DS , Wagner L , Feingold EA , Shenmen CM , Grouse LH , Schuler G , Klein SL , Old S , Rasooly R , Good P , Guyer M , Peck AM , Derge JG , Lipman D , Collins FS , Jang W , Sherry S , Feolo M , Misquitta L , Lee E , Rotmistrovsky K , Greenhut SF , Schaefer CF , Buetow K , Bonner TI , Haussler D , Kent J , Kiekhaus M , Furey T , Brent M , Prange C , Schreiber K , Shapiro N , Bhat NK , Hopkins RF , Hsie F , Driscoll T , Soares MB , Casavant TL , Scheetz TE , Brown-stein MJ , Usdin TB , Toshiyuki S , Carninci P , Piao Y , Dudekula DB , Ko MS , Kawakami K , Suzuki Y , Sugano S , Gruber CE , Smith MR , Simmons B , Moore T , Waterman R , Johnson SL , Ruan Y , Wei CL , Mathavan S , Gunaratne PH , Wu J , Garcia AM , Hulyk SW , Fuh E , Yuan Y , Sneed A , Kowis C , Hodgson A , Muzny DM , McPherson J , Gibbs RA , Fahey J , Helton E , Ketteman M , Madan A , Rodrigues S , Sanchez A , Whiting M , Madari A , Young AC , Wetherby KD , Granite SJ , Kwong PN , Brinkley CP , Pearson RL , Bouffard GG , Blakesly RW , Green ED , Dickson MC , Rodriguez AC , Grimwood J , Schmutz J , Myers RM , Butterfield YS , Griffith M , Griffith OL , Krzywinski MI , Liao N , Morin R , Palmquist D , Petrescu AS , Skalska U , Smailus DE , Stott JM , Schnerch A , Schein JE , Jones SJ , Holt RA , Baross A , Marra MA , Clifton S , Makowski KA , Bosak S , Malek J
Ref : Genome Res , 14 :2121 , 2004
Abstract : The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.
ESTHER : Gerhard_2004_Genome.Res_14_2121
PubMedSearch : Gerhard_2004_Genome.Res_14_2121
PubMedID: 15489334
Gene_locus related to this paper: human-AFMID , human-CES4A , human-CES5A , human-NOTUM , human-SERAC1 , human-SERHL2 , human-TMEM53 , mouse-acot1 , mouse-adcl4 , mouse-Ces2f , mouse-Ces4a , mouse-notum , mouse-q6wqj1 , mouse-Q9DAI6 , mouse-rbbp9 , mouse-SERHL , mouse-srac1 , mouse-tmm53 , rat-abhd6 , rat-abhda , rat-abhea , rat-abheb , rat-Ldah , rat-cd029 , rat-estd , rat-Kansl3 , rat-nceh1 , ratno-acph , ratno-CMBL , mouse-b2rwd2 , rat-b5den3 , rat-ab17c

Title : Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen - Stover_2000_Nature_406_959
Author(s) : Stover CK , Pham XQ , Erwin AL , Mizoguchi SD , Warrener P , Hickey MJ , Brinkman FS , Hufnagle WO , Kowalik DJ , Lagrou M , Garber RL , Goltry L , Tolentino E , Westbrock-Wadman S , Yuan Y , Brody LL , Coulter SN , Folger KR , Kas A , Larbig K , Lim R , Smith K , Spencer D , Wong GK , Wu Z , Paulsen IT , Reizer J , Saier MH , Hancock RE , Lory S , Olson MV
Ref : Nature , 406 :959 , 2000
Abstract : Pseudomonas aeruginosa is a ubiquitous environmental bacterium that is one of the top three causes of opportunistic human infections. A major factor in its prominence as a pathogen is its intrinsic resistance to antibiotics and disinfectants. Here we report the complete sequence of P. aeruginosa strain PAO1. At 6.3 million base pairs, this is the largest bacterial genome sequenced, and the sequence provides insights into the basis of the versatility and intrinsic drug resistance of P. aeruginosa. Consistent with its larger genome size and environmental adaptability, P. aeruginosa contains the highest proportion of regulatory genes observed for a bacterial genome and a large number of genes involved in the catabolism, transport and efflux of organic compounds as well as four potential chemotaxis systems. We propose that the size and complexity of the P. aeruginosa genome reflect an evolutionary adaptation permitting it to thrive in diverse environments and resist the effects of a variety of antimicrobial substances.
ESTHER : Stover_2000_Nature_406_959
PubMedSearch : Stover_2000_Nature_406_959
PubMedID: 10984043
Gene_locus related to this paper: pseae-clipa , pseae-CPO , pseae-metx , pseae-PA0201 , pseae-PA0231 , pseae-PA0308 , pseae-PA0368 , pseae-PA0480 , pseae-PA0502 , pseae-PA0543 , pseae-PA0599 , pseae-PA0829 , pseae-PA1166 , pseae-PA1211 , pseae-PA1239 , pseae-PA1291 , pseae-PA1304 , pseae-PA1510 , pseae-PA1558 , pseae-PA1597 , pseae-PA1621 , pseae-PA1622 , pseae-PA1680 , pseae-PA1771 , pseae-PA1888 , pseae-PA1907 , pseae-PA1990 , pseae-PA2086 , pseae-PA2098 , pseae-PA2168 , pseae-PA2302 , pseae-PA2411 , pseae-PA2425 , pseae-PA2451 , pseae-PA2540 , pseae-PA2682 , pseae-PA2689 , pseae-PA2745 , pseae-PA2764 , pseae-PA2927 , pseae-PA2934 , pseae-PA2949 , pseae-PA3053 , pseae-PA3132 , pseae-PA3226 , pseae-PA3301 , pseae-PA3324 , pseae-PA3327 , pseae-PA3429 , pseae-PA3509 , pseae-PA3586 , pseae-PA3628 , pseae-PA3695 , pseae-PA3734 , pseae-PA3829 , pseae-PA3859 , pseae-PA3994 , pseae-PA4008 , pseae-PA4152 , pseae-PA4440 , pseae-PA4968 , pseae-PA5080 , pseae-PA5384 , pseae-PA5513 , pseae-PCHC , pseae-PCHF , pseae-PHAC1 , pseae-PHAC2 , pseae-phaD , pseae-phag , pseae-PVDD , pseae-q9i4b9 , pseae-q9i538 , pseae-rhla , pseae-Y2218 , pseae-q9hyv3 , pseae-q9i252 , pseae-q9i6m9