Yang S

References (78)

Title : Role of soluble epoxide hydrolase in pain and depression comorbidity - Bu_2024_Neurobiol.Dis_193_106443
Author(s) : Bu Y , Yang S , Wang D , Hu S , Zhang Q , Wu Z , Yang C
Ref : Neurobiol Dis , 193 :106443 , 2024
Abstract : The coexistence of chronic pain and depression in clinical practice places a substantial social burden and profoundly impacts in patients. Although a clear correlation exists, the underlying mechanism of comorbidity between chronic pain and depression remains elusive. Research conducted in recent decades has uncovered that soluble epoxide hydrolase, a pivotal enzyme in the metabolism of polyunsaturated fatty acids, plays a crucial role in inflammation. Interestingly, this enzyme is intricately linked to the development of both pain and depression. With this understanding, this review aims to summarize the roles of soluble epoxide hydrolase in pain, depression, and their comorbidity. Simultaneously, we will also explore the underlying mechanisms, providing guidance for future research and drug development.
ESTHER : Bu_2024_Neurobiol.Dis_193_106443
PubMedSearch : Bu_2024_Neurobiol.Dis_193_106443
PubMedID: 38395315

Title : Design, synthesis, and activity evaluation of novel multitargeted l-tryptophan derivatives with powerful antioxidant activity against Alzheimer's disease - Zeng_2024_Arch.Pharm.(Weinheim)__e2300603
Author(s) : Zeng X , Cheng S , Li H , Yu H , Cui Y , Fang Y , Yang S , Feng Y
Ref : Arch Pharm (Weinheim) , :e2300603 , 2024
Abstract : Alzheimer's disease (AD) is a multifactorial neurological disease, and the multitarget directed ligand (MTDL) strategy may be an effective approach to delay its progression. Based on this strategy, 27 derivatives of l-tryptophan, 3a-1-3d-1, were designed, synthesized, and evaluated for their biological activity. Among them, IC(50) (inhibitor concentration resulting in 50% inhibitory activity) values of compounds 3a-18 and 3b-1 were 0.58 and 0.44 microM for human serum butyrylcholinesterase (hBuChE), respectively, and both of them exhibited more than 30-fold selectivity for human serum acetylcholinesterase. Enzyme kinetics studies showed that these two compounds were mixed inhibitors of hBuChE. In addition, these two derivatives possessed extraordinary antioxidant activity in OH radical scavenging and oxygen radical absorption capacity fluorescein assays. Meanwhile, these compounds could also prevent beta-amyloid (Abeta) self-aggregation and possessed low toxicity on PC12 and AML12 cells. Molecular modeling studies revealed that these two compounds could interact with the choline binding site, acetyl binding site, and peripheral anionic site to exert submicromolar BuChE inhibitory activity. In the vitro blood-brain barrier permeation assay, compounds 3a-18 and 3b-1 showed enough blood-brain barrier permeability. In drug-likeness prediction, compounds 3a-18 and 3b-1 showed good gastrointestinal absorption and a low risk of human ether-a-go-go-related gene toxicity. Therefore, compounds 3a-18 and 3b-1 are potential multitarget anti-AD lead compounds, which could work as powerful antioxidants with submicromolar selective inhibitory activity for hBuChE as well as prevent Abeta self-aggregation.
ESTHER : Zeng_2024_Arch.Pharm.(Weinheim)__e2300603
PubMedSearch : Zeng_2024_Arch.Pharm.(Weinheim)__e2300603
PubMedID: 38290060

Title : Determination of carboxylesterase by fluorescence probe to guide detection of carbamate pesticide - Feng_2023_Luminescence__
Author(s) : Feng J , Gong Y , Yang S , Qiu G , Tian H , Sun B
Ref : Luminescence , : , 2023
Abstract : A carboxylesterase fluorescent probe (Probe 1) was developed for determination of carboxylesterase to guide detection of carbamate pesticide. The probe uses benzothiazole as fluorescence group and phenyldimethyl carbamate as recognition group. The solution of the fluorescent probe gradually changes from light blue to dark blue as the concentration of carbamate pesticides increases. The concentration of carbamate pesticides can be quickly calculated according to the colour of the probe solution through Get Color software on a smartphone. It showed that Probe 1 can be used as a rapid detection tool to achieve rapid detection of carbamate pesticides in juice samples without professional personnel and equipment. Furthermore, the probe has been successfully used to detect carbamate pesticides in fruit juice and vegetable juice.
ESTHER : Feng_2023_Luminescence__
PubMedSearch : Feng_2023_Luminescence__
PubMedID: 37947027

Title : Mentha spp. Essential Oils: A Potential Toxic Fumigant with Inhibition of Acetylcholinesterase Activity on Reticulitermes dabieshanensis - Wu_2023_Plants.(Basel)_12_
Author(s) : Wu Z , Jin C , Chen Y , Yang S , Yang X , Zhang D , Xie Y
Ref : Plants (Basel) , 12 : , 2023
Abstract : In this study, we analyzed the components of Mentha spp. essential oils (EOs) and evaluated their major constituents and binary combinations against Reticulitermes dabieshanensis. We also determined the activities of esterases (ESTs), glutathione S-transferases (GSTs), and acetylcholinesterase activity (AChE) in treated insects. According to our findings, the most effective oils were those obtained from M. citrata (with the major constituent linalool constituting 45.1%), M. piperita (menthol, 49.1%), and M. spicata (carvone, 69.0%), with LC(50) values of 0.176, 0.366, and 0.146 microL/L, respectively. The LC(50) values were recorded for linalool (0.303 microL/L), followed by menthol (0.272 microL/L), and carvone (0.147 microL/L). The insecticidal potency increased with binary mixtures of major active constituents, with carvone strongly synergizing the toxicity of linalool and menthol against R. dabieshanensis. Compared to the control, except for M. citrata treated with no difference in alpha-NA or GST activity, the activities of ESTs and GST in other treatment groups were significantly increased. Additionally, our results found that Mentha spp. EOs and their major constituents inhibited the activity of AChE in vivo and in vitro. Finally, we performed a structure-based virtual screening of linalool, menthol, and carvone to identify that linalool had the greatest potential to bind to the active site of AChE. The present study suggests that Mentha spp. EOs could provide an additional approach for the management of termites over synthetic insecticides.
ESTHER : Wu_2023_Plants.(Basel)_12_
PubMedSearch : Wu_2023_Plants.(Basel)_12_
PubMedID: 38068668

Title : Loss-of-Function Homozygous Variant in LPL Causes Type I Hyperlipoproteinemia and Renal Lipidosis - Wu_2023_Kidney.Int.Rep_8_2428
Author(s) : Wu H , Xu H , Lei S , Yang Z , Yang S , Du J , Zhou Y , Liu Y , Yang Y , Hu Z
Ref : Kidney Int Rep , 8 :2428 , 2023
Abstract : INTRODUCTION: Lipoprotein lipase (LPL) is an important enzyme in lipid metabolism, individuals with LPL gene variants could present type I hyperlipoproteinemia, lipemia retinalis, hepatosplenomegaly, and pancreatitis. To date, there are no reports of renal lipidosis induced by type I hyperlipoproteinemia due to LPL mutation. METHODS: Renal biopsy was conducted to confirm the etiological factor of nephrotic syndrome in a 44-year-old Chinese man. Lipoprotein electrophoresis, apoE genotype detection, and whole-exome sequencing were performed to confirm the dyslipidemia type and genetic factor. Analysis of the 3-dimensional protein structure and in vitro functional study were conducted to verify variant pathogenicity. RESULTS: Renal biopsy revealed numerous CD68 positive foam cells infiltrated in the glomeruli; immunoglobulin and complement staining were negative; and electron microscopy revealed numerous lipid droplets and cholesterol clefts in the cytoplasm of foam cells. Lipoprotein electrophoresis revealed that the patient fulfilled the diagnostic criteria of type I hyperlipoproteinemia. The apoE genotype of the patient was the sigma3/sigma3 genotype. Whole-exome sequencing revealed an LPL (c.292G > A, p.A98T) homozygous variant with alpha-helix instability and reduced post-heparin LPL activity but normal lipid uptake capability compared to the wild-type variant. CONCLUSION: LPL (c.292G > A, p.A98T) is a pathogenic variant that causes renal lipidosis associated with type I hyperlipoproteinemia. This study provides adequate evidence of the causal relationship between dyslipidemia and renal lesions. However, further research is needed to better understand the pathogenetic mechanism of LPL variant-related renal lesions.
ESTHER : Wu_2023_Kidney.Int.Rep_8_2428
PubMedSearch : Wu_2023_Kidney.Int.Rep_8_2428
PubMedID: 38025240
Gene_locus related to this paper: human-LPL

Title : Carboxy-Functionalized Covalent Organic Framework as a Carrier for Lipase Immobilization and Its Application in Inhibitors Screening - Liu_2023_Appl.Biochem.Biotechnol__
Author(s) : Liu X , Wu J , Yang S , Li L , Ji Y
Ref : Appl Biochem Biotechnol , : , 2023
Abstract : Covalent organic frameworks (COFs) with large specific surface areas, high porosity, good stability, and designable structure are promising carriers for immobilized enzymes. It is important to explore lipase inhibitors from natural foods as lipase inhibitors are closely related to the treatment of obesity. In this work, a carboxyl functionalized covalent organic framework (TpBD-3COOH) was prepared by solvothermal method for covalent immobilization of porcine pancreatic lipase (PPL) and obtained the enzyme-decorated COF (PPL@COF). The immobilized lipase showed wider pH and temperature tolerance with the same optimal pH and temperature of 7.5 and 50 degC compared to free lipase. After 6 successive reuses, the PPL@COF maintained 53.0% of its original activity. Immobilized lipase also displayed enhanced storage stability (55.4% after 14 days at 4 degC). When p-nitrophenyl acetate was applied as the substrate, the calculated Michaelis constant was 3.57 mM and the half maximal inhibitory concentration of orlistat was 3.20 microM. Finally, the PPL@COF was used for enzyme inhibitors screening from natural foods combined with UV spectrophotometry, and Hawthorn was screened for excellent lipase inhibitory activity.
ESTHER : Liu_2023_Appl.Biochem.Biotechnol__
PubMedSearch : Liu_2023_Appl.Biochem.Biotechnol__
PubMedID: 37819460

Title : A colorimetric fluorescent probe for the detection of carboxylesterase and carbamate pesticides - Feng_2023_Anal.Sci__
Author(s) : Feng J , Gong Y , Yang S , Tian H , Sun B
Ref : Anal Sci , : , 2023
Abstract : A colorimetric fluorescent probe (BTCNA) was developed for the determination of carboxylesterase and carbamate pesticides. The probe used naphthalene-benzothiazole as the fluorescent group and naphthyl acetate as the recognition group. The recognition mechanism of BTCNA for carboxylesterase was based on the enzymatic hydrolysis of naphthyl acetate by carboxylesterase (CES). The test paper of the BTCNA gradually changed from light blue to bright yellow with the increase of CES activity. The probe solution gradually changed from light blue to earth-yellow as the carbaryl concentration increased. There was a linear functional relationship between the R*G (red, green) value of the photo and the CES activity. And a linear functional relationship between the carbaryl concentration and the R*G value of the photo was found. Additionally, BTCNA was successfully used to detect the concentration of carbaryl in actual samples. BTCNA is a rapid detection tool for CES activity and carbamate pesticides using a smartphone.
ESTHER : Feng_2023_Anal.Sci__
PubMedSearch : Feng_2023_Anal.Sci__
PubMedID: 37548851

Title : Plants of the genus Mahonia as a Potential Traditional Chinese Medicine for the Prevention and Treatment of Alzheimer's Disease - Yang_2023_Curr.Top.Med.Chem__
Author(s) : Yang S , Shao H , Chen X , Liu Q , Huang S , Huang Y
Ref : Curr Top Med Chem , : , 2023
Abstract : Alzheimer's disease (AD), a prevalent multiple neurodegenerative disease, has gained attention, particularly in the aging population. However, presently available therapies merely focus on alleviating the symptoms of AD and fail to slow disease progression significantly. Traditional Chinese medicine (TCM) has been used to ameliorate symptoms or interfere with the pathogenesis of aging-associated diseases for many years based on disease-modifying in multiple pathological roles with multi-targets, multi-systems and multi-aspects. Mahonia species as a TCM present potential for anti-inflammatory activity, antioxidant activity, anti-acetylcholinesterase activity, and anti-amyloid-beta activity that was briefly discussed in this review. They are regarded as promising drug candidates for AD therapy. The findings in this review support the use of Mahonia species as an alternative therapy source for treating AD.
ESTHER : Yang_2023_Curr.Top.Med.Chem__
PubMedSearch : Yang_2023_Curr.Top.Med.Chem__
PubMedID: 37005525

Title : Identifying Sex-Specific Serum Patterns of Alzheimer's Mice through Deep TMT Profiling and a Concentration-Dependent Concatenation Strategy - Dey_2023_J.Proteome.Res__
Author(s) : Dey KK , Yarbro JM , Liu D , Han X , Wang Z , Jiao Y , Wu Z , Yang S , Lee D , Dasgupta A , Yuan ZF , Wang X , Zhu L , Peng J
Ref : J Proteome Res , : , 2023
Abstract : Alzheimer's disease (AD) is the most prevalent form of dementia, disproportionately affecting women in disease prevalence and progression. Comprehensive analysis of the serum proteome in a common AD mouse model offers potential in identifying possible AD pathology- and gender-associated biomarkers. Here, we introduce a multiplexed, nondepleted mouse serum proteome profiling via tandem mass-tag (TMTpro) labeling. The labeled sample was separated into 475 fractions using basic reversed-phase liquid chromatography (RPLC), which were categorized into low-, medium-, and high-concentration fractions for concatenation. This concentration-dependent concatenation strategy resulted in 128 fractions for acidic RPLC-tandem mass spectrometry (MS/MS) analysis, collecting -5 million MS/MS scans and identifying 3972 unique proteins (3413 genes) that cover a dynamic range spanning at least 6 orders of magnitude. The differential expression analysis between wild type and the commonly used AD model (5xFAD) mice exhibited minimal significant protein alterations. However, we detected 60 statistically significant (FDR < 0.05), sex-specific proteins, including complement components, serpins, carboxylesterases, major urinary proteins, cysteine-rich secretory protein 1, pregnancy-associated murine protein 1, prolactin, amyloid P component, epidermal growth factor receptor, fibrinogen-like protein 1, and hepcidin. The results suggest that our platform possesses the sensitivity and reproducibility required to detect sex-specific differentially expressed proteins in mouse serum samples.
ESTHER : Dey_2023_J.Proteome.Res__
PubMedSearch : Dey_2023_J.Proteome.Res__
PubMedID: 37910662

Title : Structure-based molecular docking and molecular dynamics simulations study for the identification of dipeptidyl peptidase 4 inhibitors in type 2 diabetes - Chen_2023_J.Biomol.Struct.Dyn__1
Author(s) : Chen X , Xue B , Wahab S , Sultan A , Khalid M , Yang S
Ref : J Biomol Struct Dyn , :1 , 2023
Abstract : Inhibition of dipeptidyl peptidase-4 (DPP4) activity has emerged as a promising therapeutic approach for the treatment of type 2 diabetes mellitus (T2DM). Bioinformatics-driven approaches have emerged as crucial tools in drug discovery. Molecular docking and molecular dynamics (MD) simulations are effective tools in drug discovery, as they reduce the time and cost associated with experimental screening. In this study, we employed structure-assisted in-silico methods, including molecular docking and MD simulations, to identify SRT2183, a small molecule that may potentially inhibit the activity of DPP4 enzyme. The interaction between the small molecule "SRT2183" and DPP4 exhibited a binding affinity of -9.9 Kcal/Mol, leading to the formation of hydrogen bonds with the amino acid residues MET348, SER376, and THR351 of DPP4. The MD simulations over a period of 100 ns indicated stable protein-ligand interactions, with no significant conformational rearrangements observed within the simulated timeframe. In conclusion, our results suggest that the small molecule SRT2183 may have the potential to inhibit the DPP4 enzyme and pave the way for the therapeutics of T2DM.Communicated by Ramaswamy H. Sarma.
ESTHER : Chen_2023_J.Biomol.Struct.Dyn__1
PubMedSearch : Chen_2023_J.Biomol.Struct.Dyn__1
PubMedID: 38100564

Title : Construction and Manipulation of Serial Gradient Dilution Array on a Microfluidic Slipchip for Screening and Characterizing Inhibitors against Human Pancreatic Lipase - Yang_2023_Biosensors.(Basel)_13_
Author(s) : Yang J , Deng Y , Zhang M , Feng S , Peng S , Yang S , Liu P , Cai G , Ge G
Ref : Biosensors (Basel) , 13 : , 2023
Abstract : Obesity is one of the foremost public health concerns. Human pancreatic lipase (hPL), a crucial digestive enzyme responsible for the digestion of dietary lipids in humans, has been validated as an important therapeutic target for preventing and treating obesity. The serial dilution technique is commonly used to generate solutions with different concentrations and can be easily modified for drug screening. Conventional serial gradient dilution is often performed with tedious multiple manual pipetting steps, where it is difficult to precisely control fluidic volumes at low microliter levels. Herein, we presented a microfluidic SlipChip that enabled formation and manipulation of serial dilution array in an instrument-free manner. With simple slipping steps, the compound solution could be diluted to seven gradients with the dilution ratio of 1:1 and co-incubated with the enzyme (hPL)-substrate system for screening the anti-hPL potentials. To ensure complete mixing of solution and diluent during continuous dilution, we established a numerical simulation model and conducted an ink mixing experiment to determine the mixing time. Furthermore, we also demonstrated the serial dilution ability of the proposed SlipChip using standard fluorescent dye. As a proof of concept, we tested this microfluidic SlipChip using one marketed anti-obesity drug (Orlistat) and two natural products (1,2,3,4,6-penta-O-galloyl-beta-D-glucopyranose (PGG) and sciadopitysin) with anti-hPL potentials. The IC(50) values of these agents were calculated as 11.69 nM, 8.22 nM and 0.80 microM, for Orlistat, PGG and sciadopitysin, respectively, which were consistent with the results obtained by conventional biochemical assay.
ESTHER : Yang_2023_Biosensors.(Basel)_13_
PubMedSearch : Yang_2023_Biosensors.(Basel)_13_
PubMedID: 36832040

Title : TPPU Downregulates Oxidative Stress Damage and Induces BDNF Expression in PC-12 Cells - Wu_2022_Comput.Math.Methods.Med_2022_7083022
Author(s) : Wu Q , Lin M , Wu P , Zhao C , Yang S , Yu H , Xian W , Song J
Ref : Comput Math Methods Med , 2022 :7083022 , 2022
Abstract : OBJECTIVE: Ischemia-reperfusion is an ongoing clinical challenge that can lead to a series of pathological changes including oxidative stress. The inhibition of soluble epoxide hydrolase inhibitor (sEH) by 1-(1-propanoylpiperidin-4-yl)-3-[4-(trifluoromethoxy)phenyl]urea (TPPU) results in an anti-inflammatory, cardioprotective, and blood vessel growth-promoting effects. Therefore, this study focused on the protective effect of TPPU on a rat pheochromocytoma (PC-12) cell oxidative stress model induced by H(2)O(2). METHODS: CCK-8 and Hoechst 33342 were used to evaluate cell apoptosis and western blot to detect the apoptotic proteins and brain-derived neurotrophic factor (BDNF) expression. RESULT: The incubation with 100 microM, 50 microM, and 25 microM TPPU significantly increased PC-12 cell viability. Epoxyeicosatrienoic acid (EET) pretreatment also protected PC-12 cells from oxidative stress. In addition, TPPU reduced caspase-3 and Bax expression and induced Bcl-2 expression, and EETs exerted the same effect on caspase-3 expression as TPPU. A positive relationship was found between TPPU or EET incubation and BDNF expression. CONCLUSION: These results revealed that TPPU reduced PC-12 cell oxidative stress injury induced by H(2)O(2) and promoted BDNF expression.
ESTHER : Wu_2022_Comput.Math.Methods.Med_2022_7083022
PubMedSearch : Wu_2022_Comput.Math.Methods.Med_2022_7083022
PubMedID: 35872930

Title : Dioscin alleviates Alzheimer's disease through regulating RAGE\/NOX4 mediated oxidative stress and inflammation - Guan_2022_Biomed.Pharmacother_152_113248
Author(s) : Guan L , Mao Z , Yang S , Wu G , Chen Y , Yin L , Qi Y , Han L , Xu L
Ref : Biomed Pharmacother , 152 :113248 , 2022
Abstract : Alzheimer's disease (AD) is a neurodegenerative disease with amyloid beta (Abeta) deposition and intracellular neurofibrillary tangles (NFTs) as its characteristic pathological changes. Ameliorating oxidative stress and inflammation has become a new trend in the prevention and treatment of AD. Dioscin, a natural steroidal saponin which exists in Dioscoreae nipponicae rhizomes, displays various pharmacological activities, but its role in Alzheimer's disease (AD) is still unknown. In the present work, effect of dioscin on AD was evaluated in injured SH-SY5Y cells induced by H(2)O(2) and C57BL/6 mice with AD challenged with AlCl combined with D-galactose. Results showed that dioscin obviously increased cell viability and decreased reactive oxygen species (ROS) level in injured SH-SY5Y cells. In vivo, dioscin obviously improved the spatial learning and memory abilities as well as gait and interlimb coordination disorders of mice with AD. Moreover, dioscin distinctly restored the levels of malondialdehyde (MDA), superoxide dismutase (SOD), amyloid beta 42 (Abeta(42)), acetylcholine (ACh) and acetylcholinesterase (AChE) of mice, and reversed the histopathological changes of brain tissue. Mechanism studies revealed that dioscin markedly down-regulated the expression levels of RAGE and NOX4. Subsequently, dioscin markedly up-regulated the expression levels of Nrf2 and HO-1 related to oxidative stress, and down-regulated the levels of p-NF-kappaB(p-p65)/NF-kappaB(p65), AP-1 and inflammatory factors involved in inflammatory pathway. RAGE siRNAs transfection further clarified that the pharmacological activity of dioscin in AD was achieved by regulating RAGE/NOX4 pathway. In conclusion, dioscin showed excellent anti-AD effect by adjusting RAGE/NOX4-mediated oxidative stress and inflammation, which provided the basis for the further research and development against AD.
ESTHER : Guan_2022_Biomed.Pharmacother_152_113248
PubMedSearch : Guan_2022_Biomed.Pharmacother_152_113248
PubMedID: 35691153

Title : Recent Advances on the Role of ATGL in Cancer - Zhang_2022_Front.Oncol_12_944025
Author(s) : Zhang R , Meng J , Yang S , Liu W , Shi L , Zeng J , Chang J , Liang B , Liu N , Xing D
Ref : Front Oncol , 12 :944025 , 2022
Abstract : The hypoxic state of the tumor microenvironment leads to reprogramming lipid metabolism in tumor cells. Adipose triglyceride lipase, also known as patatin-like phospholipase= domain-containing protein 2 and Adipose triglyceride lipase (ATGL), as an essential lipid metabolism-regulating enzyme in cells, is regulated accordingly under hypoxia induction. However, studies revealed that ATGL exhibits both tumor-promoting and tumor-suppressing effects, which depend on the cancer cell type and the site of tumorigenesis. For example, elevated ATGL expression in breast cancer is accompanied by enhanced fatty acid oxidation (FAO), enhancing cancer cells' metastatic ability. In prostate cancer, on the other hand, tumor activity tends to be negatively correlated with ATGL expression. This review outlined the regulation of ATGL-mediated lipid metabolism pathways in tumor cells, emphasizing the Hypoxia-inducible factors 1 (HIF-1)/Hypoxia-inducible lipid droplet-associated (HIG-2)/ATGL axis, peroxisome proliferator-activated receptor (PPAR)/G0/G1 switch gene 2 (G0S2)/ATGL axis, and fat-specific protein 27 (FSP-27)/Early growth response protein 1 (EGR-1)/ATGL axis. In the light of recent research on different cancer types, the role of ATGL on tumorigenesis, tumor proliferation, and tumor metastasis was systemically reviewed.
ESTHER : Zhang_2022_Front.Oncol_12_944025
PubMedSearch : Zhang_2022_Front.Oncol_12_944025
PubMedID: 35912266

Title : Jasmonic Acid-Treated Cotton Plant Leaves Impair Larvae Growth Performance, Activities of Detoxification Enzymes, and Insect Humoral Immunity of Cotton Bollworm - Yang_2022_Neotrop.Entomol__
Author(s) : Yang S , Cao Q , Peng K , Xie J
Ref : Neotrop Entomol , : , 2022
Abstract : Enhancement of plant defense by exogenous elicitors is a promising tool for integrated pest management strategy. In the present study, cotton plants were treated with different concentrations (0, 0.01, 0.1, and 1.0 mM) of the natural plant defense elicitor, jasmonic acid (JA), and defense-related indicators in the plants were then determined. The cotton bollworm larvae were fed with JA-treated cotton leaves and larvae performances were discussed in terms of larvae relative growth rate (RGR), larval duration, pupal mass, humoral immunity, and activities of a target enzyme, three detoxification enzymes and two metabolic enzymes. Research results showed that JA treatment increased the contents of gossypol and H(2)O(2), and decreased that of the total soluble carbohydrates, and 0.1 mM JA was more powerful in the induction of defense-related parameters. As a consequence, cotton bollworm larvae reared on JA-treated cotton leaves showed slower RGR, prolonged larvae duration, and decreased pupal mass. In addition, when larvae were fed with JA-treated cotton leaves, activities of phenoloxidae (an indicator of humoral immunity) and acetylcholinesterase (AchE, a target enzyme), alkaline phosphatases (ALP), acidic phosphatase (ACP), and three detoxification enzymes, carboxylesterase (CarE), glutathione S-transferase (GST), and cytochrome P450 (P450), were all reduced compared to the control. Taken together, the results suggest that JA can be an alternative agent for pest management by delaying insect growth and inhibiting immune defense and detoxification capacity of the cotton bollworm, which may reduce the use of synthetic pesticides.
ESTHER : Yang_2022_Neotrop.Entomol__
PubMedSearch : Yang_2022_Neotrop.Entomol__
PubMedID: 35680779

Title : Molecular understanding of acetylcholinesterase adsorption on functionalized carbon nanotubes for enzymatic biosensors - Yang_2022_Phys.Chem.Chem.Phys__
Author(s) : Yang S , Zhao D , Xu Z , Yu H , Zhou J
Ref : Phys Chem Chem Phys , : , 2022
Abstract : The immobilization of acetylcholinesterase on different nanomaterials has been widely used in the field of amperometric organophosphorus pesticide (OP) biosensors. However, the molecular adsorption mechanism of acetylcholinesterase on a nanomaterial's surface is still unclear. In this work, multiscale simulations were utilized to study the adsorption behavior of acetylcholinesterase from Torpedo californica (TcAChE) on amino-functionalized carbon nanotube (CNT) (NH(2)-CNT), carboxyl-functionalized CNT (COOH-CNT) and pristine CNT surfaces. The simulation results show that the active center and enzyme substrate tunnel of TcAChE are both close to and oriented toward the surface when adsorbed on the positively charged NH(2)-CNT, which is beneficial to the direct electron transfer (DET) and accessibility of the substrate molecule. Meanwhile, the NH(2)-CNT can also reduce the tunnel cost of the enzyme substrate of TcAChE, thereby further accelerating the transfer rate of the substrate from the surface or solution to the active center. However, for the cases of TcAChE adsorbed on COOH-CNT and pristine CNT, the active center and substrate tunnel are far away from the surface and face toward the solution, which is disadvantageous for the DET and transportation of enzyme substrate. These results indicate that NH(2)-CNT is more suitable for the immobilization of TcAChE. This work provides a better molecular understanding of the adsorption mechanism of TcAChE on functionalized CNT, and also provides theoretical guidance for the ordered immobilization of TcAChE and the design, development and improvement of TcAChE-OPs biosensors based on functionalized carbon nanomaterials.
ESTHER : Yang_2022_Phys.Chem.Chem.Phys__
PubMedSearch : Yang_2022_Phys.Chem.Chem.Phys__
PubMedID: 35060980

Title : Toxic effects of glyphosate on the intestine, liver, brain of carp and on epithelioma papulosum cyprinid cells: Evidence from in vivo and in vitro research - Cao_2022_Chemosphere__134691
Author(s) : Cao X , Rao C , Cui H , Sun D , Li L , Guo S , Zhou J , Yuan R , Yang S , Chen J
Ref : Chemosphere , :134691 , 2022
Abstract : Glyphosate (GLY) is the most widely used organophosphorus herbicide in agriculture. The present study aimed to analyze the comprehensive toxicological effects of GLY on juvenile common carp and an epithelioma papulosum cyprinid (EPC) cell line. In the in vivo experiments, exposure to GLY (5 and 15 mg/L) for 30 days induced liver inflammation and oxidative damage in common carp and changed the physical barrier of the intestine. Histopathological analysis of the intestine, liver, brain, and changes in oxidative stress biomarkers provided evidence of damage and immune system responses to GLY. Moreover, an inhibitory effect of 15 mg/L GLY on acetylcholinesterase (AChE) activity was found in the brain, which may be an important reason for the significant decrease in both swimming distance and average acceleration of common carp. Cell experiments showed that 0.65 and 3.25 mg/L GLY inhibited the viability of EPCs. Furthermore, oxidative DNA damage, mitochondrial dysfunction, and reactive oxygen species (ROS) production were observed in EPC cells following GLY exposure. Taken together, this study not only highlights the negative effects of GLY on common carp but also enriches the knowledge of the cytotoxicity mechanism to further clarify the comprehensive toxicity of GLY in common carp.
ESTHER : Cao_2022_Chemosphere__134691
PubMedSearch : Cao_2022_Chemosphere__134691
PubMedID: 35489457

Title : Correlating two-dimensional shear wave elastography of acute pancreatitis with Spec cPL in dogs - Cho_2022_J.Vet.Sci_23_e79
Author(s) : Cho H , Yang S , Suh G , Choi J
Ref : J Vet Sci , 23 :e79 , 2022
Abstract : BACKGROUND: Pancreatitis is a common disease in which 37% of dogs had evidence of acute or chronic pancreatitis at necropsy. Although biopsy is still the gold standard to diagnose acute pancreatitis, clinical data including ultrasonographic findings and measurement of canine serum pancreatic lipase immunoreactivity (cPLI) are used in routine. However, it may be insufficient in the diagnostic approach to acute pancreatitis. OBJECTIVES: To evaluate the clinical diagnostic feasibility of two-dimensional shear wave elastography (2D SWE) on canine acute pancreatitis for enhanced diagnostic confidence. METHODS: 2D SWE was used to assess pancreatic stiffness and determine the correlation between pancreatic shear wave velocity (SWV) and Spec cPL concentration in 31 dogs with healthy pancreas and 10 dogs with acute pancreatitis. RESULTS: The pancreatic SWV was significantly higher in the acute pancreatitis group (2.67 +/- 0.20 m/s) than in the healthy pancreas group (2.30 +/- 0.26 m/s; p < 0.05). The moderate positive correlation was found between the pancreatic SWV and Spec cPL concentration (95% confidence interval, 0.214-0.693; r = 0.489; p < 0.05). CONCLUSIONS: These results indicated that 2D SWE was feasible for assessing pancreatic stiffness in acute pancreatitis, and that pancreatic SWV using 2D SWE correlated with Spec cPL concentration. SWE could provide a quantitative measure of pancreatic stiffness, which can increase the accuracy of diagnosing acute pancreatitis in dogs. The 2D SWE can be used as a complementary imaging modality for diagnosing acute pancreatitis in dogs.
ESTHER : Cho_2022_J.Vet.Sci_23_e79
PubMedSearch : Cho_2022_J.Vet.Sci_23_e79
PubMedID: 36174983

Title : Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1 - Zhang_2022_J.Hazard.Mater_437_129406
Author(s) : Zhang K , Hu J , Yang S , Xu W , Wang Z , Zhuang P , Grossart HP , Luo Z
Ref : J Hazard Mater , 437 :129406 , 2022
Abstract : Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80% of Impranil PU after 3 days of incubation at 28 degC by breaking the carbonyl groups (1732 cm(-1)) and C-N-H bonds (1532 cm(-1) and 1247 cm(-1)) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation" was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.
ESTHER : Zhang_2022_J.Hazard.Mater_437_129406
PubMedSearch : Zhang_2022_J.Hazard.Mater_437_129406
PubMedID: 35753302

Title : Combined effects of polyethylene and organic contaminant on zebrafish (Danio rerio): Accumulation of 9-Nitroanthracene, biomarkers and intestinal microbiota - Zhang_2021_Environ.Pollut_277_116767
Author(s) : Zhang J , Meng H , Kong X , Cheng X , Ma T , He H , Du W , Yang S , Li S , Zhang L
Ref : Environ Pollut , 277 :116767 , 2021
Abstract : Microplastics, as emerging pollutant, are predicted to act as carriers for organic pollutants, but the carrier role and bio-toxic effects with other pollutants in environments are poorly acknowledged. In this study, both the single and combined effects of polyethylene (PE, 10 and 40 mg/L) with the particle size of 100-150 microm and 9-Nitroanthracene (9-NAnt, 5 and 500 microg/L) on zebrafish (Danio rerio) had been investigated. The results illustrated that PE could be as 9-NAnt carrier to enter into zebrafish body, but significantly reduced the bioaccumulation of 9-NAnt, due to the occurrence of adsorption interactions between the simultaneous presence of both PE and 9-NAnt. After 4 days, the enzymes activity of cytochrome P4501A, acetylcholinesterase (AChE), superoxide dismutase (SOD), catalase (CAT), lactate dehydrogenase (LDH), and the abundance of malondialdehyde (MDA), lipid peroxide (LPO) responded strongly to low-dose PE exposure (10 mg/L). After 7 days exposure to PE-9-NAnt (40 mg/L), the P4501A activity increased significantly, but the activities of AChE and LDH were inhibited clearly, causing certain neurotoxicity and disorders of energy metabolism to zebrafish. The analysis of integrated biomarker response index (IBR) suggested that PE had greater bio-toxicity to zebrafish in all exposure groups after short-term exposure, but the PE-9-NAnt complex showed greater bio-toxicity after 7 days, which indicated that complex exposure of PE-9-NAnt had a delayed effect on the bio-toxicity of zebrafish. Furthermore, analysis of the intestinal microbiota exhibited that under the conditions of the exposure group with 9-NAnt, the relative abundance of the five dominant bacterial phyla (Proteobacteria, Firmicutes, Fusobacteriota, Bacteroidota and Verrucomicrobiota) changed greatly. Overall, this study confirmed that PE could carry 9-NAnt into fish causing bioaccumulation, but in the case of coexisting exposures, PE reduced 9-NAnt bioaccumulation, suggesting that microplastics with other emerging pollutants in chronic toxicity are probably next objects in future works.
ESTHER : Zhang_2021_Environ.Pollut_277_116767
PubMedSearch : Zhang_2021_Environ.Pollut_277_116767
PubMedID: 33640823

Title : Rational Design for Broadened Substrate Specificity and Enhanced Activity of a Novel Acetyl Xylan Esterase from Bacteroides thetaiotaomicron - Wang_2021_J.Agric.Food.Chem_69_6665
Author(s) : Wang L , Han X , Wang Y , Wei X , Liu S , Shao S , Yang S , Sun L , Xin F
Ref : Journal of Agricultural and Food Chemistry , 69 :6665 , 2021
Abstract : Gut bacteria-derived enzymes play important roles in the metabolism of dietary fiber through enabling the hydrolysis of polysaccharides. In this study, we identified and characterized a 29 kDa novel acetyl xylan esterase, BTAxe1, from Bacteroides thetaiotaomicron VPI5482. Then, we solved the structure of BTAxe1 and performed the rational design. Mutants N65S and N65A increased the activities toward short-chain (pNPA, pNPB) to near four-fold, and gained the activities toward longer-chain substrate (pNPO). Molecular docking analysis showed that the mutant N65S had a larger substrate binding pocket than the wild type. Hydrolysis studies using natural substrates showed that either N65S or N65A showed higher activity of that of wild-type, yielding 131.31 and 136.09 mM of acetic acid from xylan. This is the first study on the rational design of gut bacteria-derived Axes with broadened substrate specificity and enhanced activity, which can be referenced by other acetyl esterases or gut-derived enzymes.
ESTHER : Wang_2021_J.Agric.Food.Chem_69_6665
PubMedSearch : Wang_2021_J.Agric.Food.Chem_69_6665
PubMedID: 34074097
Gene_locus related to this paper: bacth-BT1008

Title : Long-term exposure to polyethylene microplastics and glyphosate interferes with the behavior, intestinal microbial homeostasis, and metabolites of the common carp (Cyprinus carpio L.) - Chen_2021_Sci.Total.Environ__152681
Author(s) : Chen J , Rao C , Yuan R , Sun D , Guo S , Li L , Yang S , Qian D , Lu R , Cao X
Ref : Sci Total Environ , :152681 , 2021
Abstract : Polyethylene microplastics (PE-MPs) and glyphosate (GLY) occur widely and have toxic characteristics, resulting in increased research interest. In this study, common carp were used to assess the individual and combined toxicity of PE-MPs (0, 1.5, or 4.5 mg/L) and GLY (0, 5, or 15 mg/L) on the brain-gut axis. After 60 days of exposure, the developmental toxicity, blood-brain barrier (BBB), locomotor behavior, intestinal barrier (physical barrier, chemical barrier, microbial barrier), and intestinal content metabolism of common carp were evaluated. Results showed that 15 mg/L of GLY exposure significantly reduced the mRNA expression of tight-junction genes (occludin, claudin-2, and ZO-1) in the brain, and acetylcholinesterase (AChE) activity was clearly inhibited by high concentrations of GLY. However, different concentrations of PE-MPs had no significant effect on the activity of AChE. Furthermore, the free-swimming behavior of common carp was distinctly inhibited by treatment with a combination of 15 mg/L GLY and 4.5 mg/L PE-MPs. Histological studies indicated that PE-MPs alone and in combination with GLY could disrupt the physical and chemical intestinal barriers of common carp. Additionally, the abundance and diversity of gut microbiota in common carp were significantly changed when exposed to a combination of PE-MPs and GLY. Metabolomics further revealed that PE-MPs combined with GLY triggered metabolic changes and that differential metabolites were related to amino acid and lipid metabolism. These findings illustrate that exposure to PE-MPs or GLY alone is toxic to fish and results in physiological changes to the brain-gut axis. This work offers a robust analysis to understand the mechanisms underlying GLY and MP-induced aquatic toxicity.
ESTHER : Chen_2021_Sci.Total.Environ__152681
PubMedSearch : Chen_2021_Sci.Total.Environ__152681
PubMedID: 34973326

Title : Study on Hepatotoxicity of Rhubarb Based on Metabolomics and Network Pharmacology - Li_2021_Drug.Des.Devel.Ther_15_1883
Author(s) : Li S , Wang Y , Li C , Yang N , Yu H , Zhou W , Chen S , Yang S , Li Y
Ref : Drug Des Devel Ther , 15 :1883 , 2021
Abstract : BACKGROUND: Rhubarb, as a traditional Chinese medicine, is the preferred drug for the treatment of stagnation and constipation in clinical practice. It has been reported that rhubarb possesses hepatotoxicity, but its mechanism in vivo is still unclear. METHODS: In this study, the chemical components in rhubarb were identified based on UPLC-Q-TOF/MS combined with data postprocessing technology. The metabolic biomarkers obtained through metabolomics technology were related to rhubarb-induced hepatotoxicity. Furthermore, the potential targets of rhubarb-induced hepatotoxicity were obtained by network pharmacology involving the above components and metabolites. Meanwhile, GO gene enrichment analysis and KEGG pathway analysis were performed on the common targets. RESULTS: Twenty-eight components in rhubarb were identified based on UPLC-Q-TOF/MS, and 242 targets related to rhubarb ingredients were predicted. Nine metabolic biomarkers obtained through metabolomics technology were closely related to rhubarb-induced hepatotoxicity, and 282 targets of metabolites were predicted. Among them, the levels of 4 metabolites, namely dynorphin B (10-13), cervonoyl ethanolamide, lysoPE (18:2), and 3-hydroxyphenyl 2-hydroxybenzoate, significantly increased, while the levels of 5 metabolites, namely dopamine, biopterin, choline, coenzyme Q9 and P1, P4-bis (5'-uridyl) tetraphosphate significantly decreased. In addition, 166 potential targets of rhubarb-induced hepatotoxicity were obtained by network pharmacology. The KEGG pathway analysis was performed on the common targets to obtain 46 associated signaling pathways. CONCLUSION: These data suggested that rhubarb may cause liver toxicity due to its action on dopamine D1 receptor (DRD1), dopamine D2 receptor (DRD2), phosphodiesterase 4B (PDE4B), vanilloid receptor (TRPV1); transient receptor potential cation channel subfamily M member 8 (TRPM8), prostanoid EP2 receptor (PTGER2), acetylcholinesterase (ACHE), muscarinic acetylcholine receptor M3 (CHRM3) through the cAMP signaling pathway, cholinergic synapses, and inflammatory mediators to regulate TRP channels. Metabolomics technology and network pharmacology were integrated to explore rhubarb hepatotoxicity to promote the reasonable clinical application of rhubarb.
ESTHER : Li_2021_Drug.Des.Devel.Ther_15_1883
PubMedSearch : Li_2021_Drug.Des.Devel.Ther_15_1883
PubMedID: 33976539

Title : Dammarane Sapogenins Improving Simulated Weightlessness-Induced Depressive-Like Behaviors and Cognitive Dysfunction in Rats - Wang_2021_Front.Psychiatry_12_638328
Author(s) : Wang Q , Dong L , Wang M , Chen S , Li S , Chen Y , He W , Zhang H , Zhang Y , Pires Dias AC , Yang S , Liu X
Ref : Front Psychiatry , 12 :638328 , 2021
Abstract : Background: Our studies demonstrated that the space environment has an impact on the brain function of astronauts. Numerous ground-based microgravity and social isolation showed that the space environment can induce brain function damages in humans and animals. Dammarane sapogenins (DS), an active fraction from oriental ginseng, possesses neuropsychic protective effects and has been shown to improve depression and memory. This study aimed to explore the effects and mechanisms of DS in attenuating depressive-like behaviors and cognitive deficiency induced by simulated weightlessness and isolation [hindlimb suspension and isolation (HLSI)] in rats. Methods: Male rats were orally administered with two different doses of DS (37.5, 75 mg/kg) for 14 days, and huperzine-A (1 mg/kg) served as positive control. Rats were subjected to HLSI for 14 days except the control group during drug administration. The depressive-like behaviors were then evaluated by the open-field test, the novel object recognition test, and the forced swimming test. The spatial memory and working memory were evaluated by the Morris water maze (MWM) test, and the related mechanism was further explored by analyzing the activity of choline acetyltransferase (ChAT), acetylcholinesterase (AChE), and superoxide dismutase (SOD) in the hippocampus of rats. Results: The results showed that DS treatment significantly reversed the HLSI-induced depressive-like behaviors in the open-field test, the novel object recognition test, and the forced swimming test and improved the HLSI-induced cognitive impairment in the MWM test. Furthermore, after DS treatment, the ChAT and SOD activities of HLSI rats were increased while AChE activity was significantly suppressed. Conclusions: These findings clearly demonstrated that DS might exert a significant neuropsychic protective effect induced by spaceflight environment, driven in part by the modulation of cholinergic system and anti-oxidation in the hippocampus.
ESTHER : Wang_2021_Front.Psychiatry_12_638328
PubMedSearch : Wang_2021_Front.Psychiatry_12_638328
PubMedID: 33841208

Title : Simulated revelation of the adsorption behaviours of acetylcholinesterase on charged self-assembled monolayers - Yang_2020_Nanoscale__
Author(s) : Yang S , Liu J , Zheng H , Zhong J , Zhou J
Ref : Nanoscale , : , 2020
Abstract : An acetylcholinesterase (AChE)-based electrochemical biosensor, as a promising alternative to detect organophosphates (OPs) and carbamate pesticides, has gained considerable attention in recent years, due to the advantages of simplicity, rapidity, reliability and low cost. The bio-activity of AChE immobilized on the surface and the direct electron transfer (DET) rate between an enzyme and an electrode directly determined the analytical performances of the AChE-based biosensor, and experimental studies have shown that the charged surfaces have a strong impact on the detectability of the AChE-based biosensor. Therefore, it is very important to reveal the behaviour of AChE in bulk solution and on charged surfaces at the molecular level. In this work, the adsorption orientation and conformation of AChE from Torpedo californica (TcAChE) on oppositely charged self-assembled monolayers (SAMs), COOH-SAM and NH2-SAM with different surface charge densities, were investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics simulations (AAMD). Simulation results show that TcAChE could spontaneously and stably adsorb on two oppositely charged surfaces by the synergy of an electric dipole and charged residue patch, and opposite orientations were observed. The active-site gorge of TcAChE is oriented toward the surface with the "end-on" orientation and the active sites are close to the surface when it is adsorbed on the positively charged surface and the tunnel cost for the substrate is lower than that on the negatively charged surface and in bulk solution, while for TcAChE adsorbed on the negatively charged surface, the active site of TcAChE is far away from the surface and the active-site gorge is oriented toward the solution with a "back-on" orientation. It suggests that the positively charged surface could provide a better microenvironment for the efficient bio-catalytic reaction and quick DET between TcAChE and the electrode surface. Moreover, the RMSD, RMSF, dipole moment, gyration radius, eccentricity and superimposed structures show that only a slight conformational change occurred on the relatively flexible structure of TcAChE during simulations, and the native conformation is well preserved after adsorption. This work helps us better comprehend the adsorption mechanism of TcAChE on charged surfaces and might provide some guidelines for the development of new TcAChE-based amperometric biosensors for the detection of organophosphorus pesticides.
ESTHER : Yang_2020_Nanoscale__
PubMedSearch : Yang_2020_Nanoscale__
PubMedID: 32022070

Title : The impact of sialylation linkage-type on the pharmacokinetics of recombinant butyrylcholinesterases - Chung_2020_Biotechnol.Bioeng_117_157
Author(s) : Chung CY , Wang Q , Yang S , Chough S , Seo Y , Cipollo JF , Balthasar JP , Betenbaugh MJ
Ref : Biotechnol Bioeng , 117 :157 , 2020
Abstract : Chinese hamster ovary (CHO) cells typically produce glycoproteins with N-glycans terminating in alpha-2,3 sialylation. Human cells produce glycoproteins that include alpha-2,3 and alpha-2,6 sialic acids. To examine the impact of altering protein sialylation on pharmacokinetic properties, recombinant human butyrylcholinesterase (BChE) was produced in CHO cells by knocking out the alpha-2,3 sialyltransferase genes followed by overexpression of the alpha-2,6 sialyltransferase (26BChE) enzyme. The N-glycan composition of 26BChE was compared to BChE with alpha-2,3 sialylation (23BChE) derived from wild-type CHO cells. Both 23BChE and 26BChE exhibited comparable antennarity distributions with bi-antennary di-sialylated glycans representing the most abundant glycoform. CD-1 mice were intravenously injected with the 23BChE or 26BChE, and residual BChE activities from blood collected at various time points for pharmacokinetic analyses. Although 23BChE contained a slightly lower initial sialylation level compared to 26BChE, the molecule exhibited higher residual activity between 5 and 24 hr postinjection. Pharmacokinetic analyses indicated that 23BChE exhibited an increase in area under the curve and a lower volume of distribution at steady state than that of 26BChE. These findings suggest that the type of sialylation linkage may play a significant role in the pharmacokinetic behavior of a biotherapeutic when tested in in vivo animal models.
ESTHER : Chung_2020_Biotechnol.Bioeng_117_157
PubMedSearch : Chung_2020_Biotechnol.Bioeng_117_157
PubMedID: 31544955

Title : Characterization of a novel carboxylesterase from Bacillus velezensis SYBC H47 and its application in degradation of phthalate esters - Huang_2020_J.Biosci.Bioeng_129_588
Author(s) : Huang L , Meng D , Tian Q , Yang S , Deng H , Guan Z , Cai Y , Liao X
Ref : J Biosci Bioeng , 129 :588 , 2020
Abstract : Recently, residual plasticizer phthalate esters (PAEs) in the different environments pose a serious health threat to humans and mammals. Biodegradation has been considered a promising and eco-friendly way to eliminate PAEs. In this study, a gene (baces04) encoding the novel PAEs hydrolase, carboxylesterase (BaCEs04), was screened from the genome of Bacillus velezensis SYBC H47 via bioinformatics analysis. Then, baces04 was cloned and expressed in Escherichia coli BL21 (DE3). BaCEs04 belonged to the esterase family VI. It contained a conserved domain (Gly159-His160-Ser161-Leu162-Gly163) and a typical serine hydrolase catalytic site (Ser161-Asp204-His261). The characterization of BaCEs04 showed that the activity was optimal at 60 degrees C and pH 7.5. This enzyme also displayed high resistance to metal ions, organic solvents, and detergents. After treatment with BaCEs04 for 5 h, the degradation ratio of four different 1 mM PAEs, including dimethyl phthalate, diethyl phthalate, dipropyl phthalate, and dibutyl phthalate, was 32.4%, 50.5%, 77.9%, and 86.8%, respectively. The degradation products of four PAEs were identified as their corresponding monoalkyl phthalates. This is the first report that family VI esterase displaying PAE-hydrolysis activity. This study also proved that BaCEs04 could be used as an ideal candidate for the application in bioremediation and industry.
ESTHER : Huang_2020_J.Biosci.Bioeng_129_588
PubMedSearch : Huang_2020_J.Biosci.Bioeng_129_588
PubMedID: 31761671
Gene_locus related to this paper: baca2-a7z8b1

Title : Inducing secondary metabolite production from Daldinia eschscholzii JC-15 by red ginseng medium - Wang_2019_Nat.Prod.Res__1
Author(s) : Wang BY , Yang YB , Yang XQ , Zhu CH , Yang S , Xu TT , Wang XY , Tan NH , Zhou H , Ding ZT
Ref : Nat Prod Res , :1 , 2019
Abstract : Red ginseng (RG) is one of the most popular herbal medicines and used as a dietary supplement in recent years. The bioactive ingredient in RG can induce the production of novel microbial metabolite from fermented RG. Using the one strain-many compounds strategy, the reinvestigation of the metabolites from Daldinia eschscholzii JC-15 cultured in red ginseng medium led to the isolation of an unprecedented benzopyran-naphthalene hybrid, daldinsin (1) and a new lactone (2). In this research, a new lactone, 8-hydroxylhelicascolide A (2) instead of helicascolide A was produced by the D. eschscholzii JC-15 induced by the red ginseng medium. Compound 1 showed anti-acetylcholinesterase activity with the inhibition ratio of 38.8% at 50 muM. Compound 2 indicated antimicrobial activities against Fusarium Solani, F. oxysporum, and Escherichia coli with MICs at 128 mug/mL. RG is therefore a promising activator in production of novel microbial metabolite.
ESTHER : Wang_2019_Nat.Prod.Res__1
PubMedSearch : Wang_2019_Nat.Prod.Res__1
PubMedID: 31111733

Title : Biochemical characterization of a novel lipase from Malbranchea cinnamomea suitable for production of lipolyzed milkfat flavor and biodegradation of phthalate esters - Duan_2019_Food.Chem_297_124925
Author(s) : Duan X , Xiang M , Wang L , Yan Q , Yang S , Jiang Z
Ref : Food Chem , 297 :124925 , 2019
Abstract : A novel lipase gene (McLipB) was cloned from a thermophilic fungus Malbranchea cinnamomea and expressed in Pichia pastoris. The deduced amino acid sequence of the lipase (McLipB) shared the highest identity of 46% with the Candida rugosa lipase LIP4. The extracellular lipase activity of 4304 U/mL with protein concentration of 7.7 mg/mL was achieved in a 5-L fermentor. The optimal pH and temperature of McLipB were 7.5 and 40 degreesC, respectively. The lipase showed high specificity towards triglycerides with short and medium chain fatty acids, and had non-position specificity. McLipB hydrolyzed butter to produce mainly butyric acid, hexanoic acid and a small amount of octanoic acid and decanoic acid. Furthermore, it degraded more than 90% dipropyl phthalate, dibutyl phthalate and dihexyl phthalate to their corresponding monoalkyl phthalates. The properties of McLipB indicate that it has great application potential for production of lipolyzed milkfat flavor and biodegradation of phthalate esters.
ESTHER : Duan_2019_Food.Chem_297_124925
PubMedSearch : Duan_2019_Food.Chem_297_124925
PubMedID: 31253266
Gene_locus related to this paper: malci-McLipB

Title : Pyridostigmine alleviates cardiac dysfunction via improving mitochondrial cristae shape in a mouse model of metabolic syndrome - Xue_2019_Free.Radic.Biol.Med_134_119
Author(s) : Xue RQ , Yu XJ , Zhao M , Xu M , Wu Q , Cui YL , Yang S , Li DL , Zang WJ
Ref : Free Radic Biol Med , 134 :119 , 2019
Abstract : Insulin resistance and autonomic imbalance are important pathological processes in metabolic syndrome-induced cardiac remodeling. Recent studies determined that disruption of mitochondrial cristae shape is associated with myocardial ischemia; however, the change in cristae shape in metabolic syndrome-induced cardiac remodeling remains unclear. This study determined the effect of pyridostigmine (PYR), which reversibly inhibits cholinesterase to improve autonomic imbalance, on high-fat diet (HFD)-induced cardiac insulin resistance and explored the potential effect on the shape of mitochondrial cristae. Feeding of a HFD for 22 weeks led to an irregular and even lysed cristae structure in cardiac mitochondria, which contributed to decreased mitochondrial content and ATP production and increased oxygen species production, ultimately impairing insulin signaling and lipid metabolism. Interestingly, PYR enhanced vagal activity by increasing acetylcholine production and exerted mito-protective effects by activating the LKB1/AMPK/ACC signal pathway. Specifically, PYR upregulated OPA1 and Mfn1/2 expression, promoted the formation of the mitofilin/CHCHD3/Sam50 complex, and decreased p-Drp1 and Fis1 expression, resulting in tight and parallel cristae and increasing cardiac mitochondrial complex subunit expression and ATP generation as well as decreasing release of cytochrome C from mitochondria and oxidative damage. Furthermore, PYR improved glucose and insulin tolerance and insulin-stimulated Akt phosphorylation, decreased lipid toxicity, and ultimately ameliorated HFD-induced cardiac remodeling and dysfunction. In conclusion, PYR prevented cardiac and insulin insensitivity and remodeling by stimulating vagal activity to regulate mitochondrial cristae shape and function in HFD-induced metabolic syndrome in mice. These results provide novel insights for the development of a therapeutic strategy for obesity-induced cardiac dysfunction that targets mitochondrial cristae.
ESTHER : Xue_2019_Free.Radic.Biol.Med_134_119
PubMedSearch : Xue_2019_Free.Radic.Biol.Med_134_119
PubMedID: 30633969

Title : Carboxylesterase-Cleavable Biotinylated Nanoparticle for Tumor-Dual Targeted Imaging - Chen_2019_Theranostics_9_7359
Author(s) : Chen P , Kuang W , Zheng Z , Yang S , Liu Y , Su L , Zhao K , Liang G
Ref : Theranostics , 9 :7359 , 2019
Abstract : Near-infrared (NIR) nanoprobes with fluorescence "Turn-On" property are advantageous in cancer diagnosis but, to the best of our knowledge, "smart" nanoprobe that simultaneously targets both biotin receptor and carboxylesterase (CES) for HepG2 tumor-dual targeted imaging has not been reported. Methods: Using CBT-Cys click condensation reaction, we rationally designed a "smart" NIR fluorescence probe H2N-Cys(StBu)-Lys(Biotin)-Ser(Cy5.5)-CBT (NIR-CBT) and used it to facilely prepare the fluorescence-quenched nanoparticle NIR-CBT-NP. Results: In vitro results indicated that, after NIR-CBT-NP was incubated with CES for 6 h, its fluorescence was turned "On" by 69 folds. Cell experiments verified that NIR-CBT-NP was uptaken by HepG2 cells via biotin receptor-assisted endocytosis and its fluorescence was turned "On" by intracellular CES hydrolysis. Moreover, NIR-CBT-NP was successfully applied to image both biotin receptor- and CES-overexpressing HepG2 tumors. Conclusion: Fluorescence-quenched nanoparticle NIR-CBT-NP was facilely prepared to actively target biotin receptor-overexpressing HepG2 cancer cells and turn the fluorescence "On" by intracellular CES hydrolysis for tumor-dual targeted imaging. We anticipate that our fluorescence "Turn-On" nanoparticle could be applied for liver cancer diagnosis in clinic in the near future.
ESTHER : Chen_2019_Theranostics_9_7359
PubMedSearch : Chen_2019_Theranostics_9_7359
PubMedID: 31695773

Title : Designing of a Cofactor Self-Sufficient Whole-Cell Biocatalyst System for Production of 1,2-Amino Alcohols from Epoxides - Liu_2019_ACS.Synth.Biol_8_734
Author(s) : Liu S , Zhang X , Liu F , Xu M , Yang T , Long M , Zhou J , Osire T , Yang S , Rao Z
Ref : ACS Synth Biol , 8 :734 , 2019
Abstract : Optically pure 1,2-amino alcohols are highly valuable products as intermediates for chiral pharmaceutical products. Here we designed an environmentally friendly non-natural biocatalytic cascade for efficient synthesis of 1,2-amino alcohols from cheaper epoxides. A redesignated omega-transaminase PAKomega-TA was tested and showed good bioactivity at a lower pH than other reported transaminases. The cascade was efficiently constructed as a single one-pot E. coli recombinant, by coupling SpEH (epoxide hydrolase), MnADH (alcohol dehydrogenase), and PAKomega-TA. Furthermore, RBS regulation strategy was used to overcome the rate limiting step by increasing expression of MnADH. For cofactor regeneration and amino donor source, an interesting point was involved as that a cofactor self-sufficient system was designed by expression of GluDH. It established a "bridge" between the cofactor and the cosubstrate, such that the cofactor self-sufficient system could release cofactor (NADP(+)) and cosubstrate (l-Glutamine) regenerated simultaneously. The recombinant E. coli BL21 (SGMP) with cofactor self-sufficient whole-cell cascade biocatalysis showed high ee value (>99%) and high yield, with 99.6% conversion of epoxide ( S)-1a to 1,2-amino alcohol ( S)-1d in 10 h. It further converted ( S)-2a-5a to ( S)-2d-5d with varying conversion rates ranging between 65-96.4%. This study first provides one-step synthesis of optically pure 1,2-amino alcohols from ( S)-epoxides employing a synthetic redox-self-sufficient cascade.
ESTHER : Liu_2019_ACS.Synth.Biol_8_734
PubMedSearch : Liu_2019_ACS.Synth.Biol_8_734
PubMedID: 30840437

Title : Protective role of phenylethanoid glycosides, Torenoside B and Savatiside A, in Alzheimer's disease - Ji_2019_Exp.Ther.Med_17_3755
Author(s) : Ji S , Li S , Zhao X , Kang N , Cao K , Zhu Y , Peng P , Fan J , Xu Q , Yang S , Liu Y
Ref : Exp Ther Med , 17 :3755 , 2019
Abstract : The current study assessed the efficacy of two phenylethanoid glycosides (PhGs), Torenoside B (TB) and Savatiside A (SA), in the treatment of Alzheimer's disease (AD). The effects of TB and SA compounds were first assessed following amyloid beta (Abeta)25-35 induction in SH-SY5Y cells at a range of concentrations. Their effects on cell viability and reactive oxygen species (ROS) were determined by performing MTT and dichlorofluorescin diacetate assays, respectively. The concentration of intracellular Ca(2+) was determined using Fluo-3AM to stain SH-SY5Y cells. SA and TB treatments were also assessed in Abeta25-35-induced mice. Y-maze and Morris water maze methods were utilized to assess murine learning and memory capability. The pathological changes of murine hippocampi was determined using H&E and Nissl staining. In addition, biochemical parameters associated with intracellular reactive oxygen pathways including Maleic dialdehyde (MDA), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), acetylcholinesterase (AChE) and Calnexin were also assessed. TB and SA treatment in Abeta25-35-induced SH-SY5Y cells resulted in the restoration of cell morphology, an increase of SOD and GSH-Px activity, a decrease in ROS, Ca(2+) and MDA content, and a decrease in Calnexin expression. Furthermore, SA or TB treatment administered to Abeta25-35-induced mice improved their spatial/non-spatial learning and memory capabilities. The efficacy of treatment was also supported by a marked change in the morphological structure of pyramidal neurons in the CA1 areas of murine hippocampi, as well as an increase of SOD and GSH-Px activity. Treatment also resulted in a decrease in MDA content, AchE activity and Calnexin expression in murine hippocampal tissue. As potential AD treatment drugs, SA and TB compounds have been demonstrated to alleviate the oxidative stress induced by Abeta25-35 via the regulation of intracellular calcium homeostasis and Calnexin, preventing AD development.
ESTHER : Ji_2019_Exp.Ther.Med_17_3755
PubMedSearch : Ji_2019_Exp.Ther.Med_17_3755
PubMedID: 30988761

Title : LIPG SNPs, their haplotypes and gene-environment interactions on serum lipid levels - Yang_2019_Lipids.Health.Dis_18_10
Author(s) : Yang S , Yin RX , Miao L , Zhou YG , Wu J , Zhang QH
Ref : Lipids Health Dis , 18 :10 , 2019
Abstract : BACKGROUND: Maonan nationality is a relatively conservative and isolated minority in the Southwest of China. Little is known about the association of endothelial lipase gene (LIPG) single nucleotide polymorphisms (SNPs) and serum lipid levels in the Chinese populations. METHODS: A total of 1280 subjects of Maonan nationality and 1218 participants of Han nationality were randomly selected from our previous stratified randomized samples. Genotypes of the four LIPG SNPs were determined by polymerase chain reaction-restriction fragment length polymorphism, and then confirmed by direct sequencing. RESULTS: Several SNPs were associated with high-density lipoprotein cholesterol (rs3813082, rs2000813 and rs2097055) in the both ethnic groups; total cholesterol and apolipoprotein (Apo) A1 (rs2000813) in Han nationality; and low-density lipoprotein cholesterol, ApoB, triglyceride (rs2097055) and ApoA1 (rs3819166) in Maonan minority (P < 0.0125 for all after Bonferroni correction). The commonest haplotype was rs3813082T-rs2000813C-rs2097055T-rs3819166A (Han, 44.2% and Maonan, 48.7%). The frequencies of the T-C-T-A, T-C-T-G, T-T-C-G and G-T-C-G haplotypes were different between the Maonan and Han populations (P < 0.05-0.001). The associations between haplotypes and dyslipidemia were also different in the Han and/or Maonan populations (P < 0.05-0.001). CONCLUSIONS: The differences in serum lipid profiles between the two ethnic groups might partly be attributed to these LIPG SNPs, their haplotypes and gene-environmental interactions. TRIAL REGISTRATION: Retrospectively registered.
ESTHER : Yang_2019_Lipids.Health.Dis_18_10
PubMedSearch : Yang_2019_Lipids.Health.Dis_18_10
PubMedID: 30621702
Gene_locus related to this paper: human-LIPG

Title : Association between the LIPG polymorphisms and serum lipid levels in the Maonan and Han populations - Yang_2019_J.Gene.Med__e3071
Author(s) : Yang S , Yin RX , Miao L , Zhang QH , Zhou YG , Wu J
Ref : J Gene Med , :e3071 , 2019
Abstract : BACKGROUD: Maonan nationality is a relatively isolated minority in China. Little is known about the endothelial lipase gene (LIPG) single nucleotide polymorphisms (SNPs) and serum lipid levels in the Chinese populations. The present study was undertaken to detect the association of several LIPG SNPs and environmental factors with serum lipid levels in the Chinese Maonan and Han populations. METHODS: A total of 773 subjects of Maonan nationality and 710 participants of Han nationality were randomly selected from our previous stratified randomized samples. Genotypes of the LIPG rs2156552, rs4939883 and rs7241918 SNPs were determined by polymerase chain reaction-restriction fragment length polymorphism, and then confirmed by direct sequencing. RESULTS: The allelic (rs2156552, rs4939883 and rs7241918) and genotypic (rs2156552 and rs4939883) frequencies were different between the two ethnic groups (P < 0.05-0.01). The minor allele carriers had lower ApoA1/ApoB ratio (rs2156552 and rs7241918), high-density lipoprotein cholesterol (HDL-C) and apolipoprotein (Apo) A1 (rs2156552) levels and higher ApoB levels (rs4939883) in Han nationality; and lower HDL-C (rs2156552, rs4939883 and rs7241918) levels in Maonan minority than the minor allele non-carriers (P < 0.0167 after the Bonferroni correction). Subgroup analyses according to sex showed that the minor allele carriers had lower ApoA1/ApoB ratio (rs2156552 and rs7241918) and higher ApoB levels (rs7241918) in Han males; and lower ApoA1 and HDL-C levels in Maonan famales than the minor allele non-carriers (P < 0.0167-0.001). CONCLUSIONS: The present study demonstrates the association between the LIPG polymorphsims and serum lipid levels in the two ethnic groups. These associations might have an ethnic-and or/sex-specificity.
ESTHER : Yang_2019_J.Gene.Med__e3071
PubMedSearch : Yang_2019_J.Gene.Med__e3071
PubMedID: 30657227

Title : High-level expression of codon-optimized Thielavia terrestris cutinase suitable for ester biosynthesis and biodegradation - Duan_2019_Int.J.Biol.Macromol_135_768
Author(s) : Duan X , Jiang Z , Liu Y , Yan Q , Xiang M , Yang S
Ref : Int J Biol Macromol , 135 :768 , 2019
Abstract : A codon-optimized cutinase gene (TtCutopt) from Thielavia terrestris was over-expressed in Pichia pastoris. An extracellular activity reached 10,200U/mL using high cell density fermentation. The optimal pH and temperature of TtCutopt were 7.0 and 50 degrees C, respectively. It displayed high stability over a wide range of pH from 3.0 to 11.0 and up to 85 degrees C. Among tested p-nitrophenyl esters and triglycerides, TtCutopt showed the highest activity towards p-nitrophenyl butyrate and tributyrin, with specificity activity of 2322.4U/mg and 1152.5U/mg, respectively. It was extremely stable in organic solvents and surfactants. TtCutopt efficiently catalyzed the synthesis of butyl butyrate, hexyl butyrate, butyl hexanoate and hexyl hexanoate with esterification efficiency of >95%. Furthermore, it catalyzed the degradation of >90% of dimethyl phthalate, diethyl phthalate, dipropyl phthalate and dibutyl phthalate to release their corresponding monoalkyl phthalates within 24h. Thus, high yield, high stability, and esterification efficiency of TtCutopt make it an attractive candidate for ester biosynthesis and biodegradation.
ESTHER : Duan_2019_Int.J.Biol.Macromol_135_768
PubMedSearch : Duan_2019_Int.J.Biol.Macromol_135_768
PubMedID: 31129216
Gene_locus related to this paper: thite-g2rae6

Title : Expression of soluble epoxide hydrolase in renal tubular epithelial cells regulates macrophage infiltration and polarization in IgA nephropathy - Wang_2018_Am.J.Physiol.Renal.Physiol_315_F915
Author(s) : Wang Q , Liang Y , Qiao Y , Zhao X , Yang Y , Yang S , Li B , Zhao Q , Dong L , Quan S , Tian R , Liu Z
Ref : American Journal of Physiology Renal Physiol , 315 :F915 , 2018
Abstract : Tubulointerstitial inflammatory cell infiltration and activation contribute to kidney inflammation and fibrosis. Epoxyeicosatrienoic acids (EETs), which are rapidly metabolized to dihydroxyeicosatrienoic acids by the soluble epoxide hydrolase (sEH), have multiple biological functions, including vasodilation, anti-inflammatory action, and others. Inhibition of sEH has been demonstrated to attenuate inflammation in many renal disease models. However, the relationship between sEH expression and macrophage polarization in the kidney remains unknown. In this study, we investigated the relationships between the level of sEH and clinical and pathological parameters in IgA nephropathy. The level of sEH expression positively correlated with proteinuria and infiltration of macrophages. sEH-positive tubules were found to be surrounded by macrophages. Furthermore, we found that incubation of immortalized human proximal tubular HK-2 cells with total urinary protein and overexpression of sEH promoted inflammatory factor production, which was associated with M1 polarization. We also exposed RAW264.7 mouse leukemic monocytes/macrophages to different HK-2 cell culture media conditioned by incubation with various substances affecting sEH amount or activity. We found that the upregulation of sEH promoted M1 polarization. However, pharmacological inhibition of sEH and supplementation with EETs reversed the conditioning effects of urinary proteins by inhibiting M1 polarization through the NF-kappaB pathway and stimulating M2 polarization through the phosphatidylinositol 3-kinase pathway. These data suggest that inhibition of sEH could be a new strategy to prevent the progression of inflammation and to attenuate renal tubulointerstitial fibrosis.
ESTHER : Wang_2018_Am.J.Physiol.Renal.Physiol_315_F915
PubMedSearch : Wang_2018_Am.J.Physiol.Renal.Physiol_315_F915
PubMedID: 29717935

Title : High expression of NDRG3 associates with unfavorable overall survival in non-small cell lung cancer - Luo_2018_Cancer.Biomark_21_461
Author(s) : Luo X , Hou N , Chen X , Xu Z , Xu J , Wang L , Yang S , Liu S , Xu L , Chen Y , Xiong L , Wang J , Fan W
Ref : Cancer Biomark , 21 :461 , 2018
Abstract : BACKGROUND AND OBJECTIVE: N-myc downstream-regulated gene 3 (NDRG3) is one of the important members of the NDRG family which crucially take part in cell proliferation, differentiation and other biological processes. METHODS: In this present study, western-blotting analysis was performed to evaluate NDRG3 expression in NSCLC cell lines. One-step quantitative reverse transcription-polymerase chain reaction (qPCR) with 16 fresh-frozen NSCLC samples and immunohistochemistry (IHC) analysis in 100 NSCLC cases were conducted to explore the relationship between NDRG3 expression and the clinicopathological characteristics of NSCLC. RESULTS: NDRG3 expression levels were statistically higher in NSCLC cell lines and tissue samples, compared with that of in non-cancerous cell line and tissue samples (p< 0.05). The IHC data demonstrated that the NDRG3 expression was significantly correlated with pathological grade (p= 0.038), N (p= 0.020) and TNM stage (p= 0.002). Survival analysis and Kaplan-Meier curve indicated that NDRG3 expression (p= 0.002) and T (p= 0.047) were independently associated with the unfavorable overall survival of patients with NSCLC. CONCLUSIONS: The data implied that NDRG3 expression may be identified as a new predictor in NSCLC prognosis.
ESTHER : Luo_2018_Cancer.Biomark_21_461
PubMedSearch : Luo_2018_Cancer.Biomark_21_461
PubMedID: 29171988

Title : Deglucosylation of zearalenone-14-glucoside in animals and human liver leads to underestimation of exposure to zearalenone in humans - Yang_2018_Arch.Toxicol_92_2779
Author(s) : Yang S , Zhang H , Zhang J , Li Y , Jin Y , Zhang S , De Saeger S , Zhou J , Sun F , De Boevre M
Ref : Archives of Toxicology , 92 :2779 , 2018
Abstract : Zearalenone-14-glucoside (ZEN-14G), the modified mycotoxin of zearalenone (ZEN), has attracted considerable attention due to its high potential to be hydrolyzed into ZEN, which would exert toxicity. It has been confirmed that the microflora could metabolize ZEN-14G to ZEN. However, the metabolic profile of ZEN-14G and whether it could be deglucosidated in the liver are unknown. To thoroughly investigate the metabolism of ZEN-14G, in vitro metabolism including phase I and phase II metabolism was studied using liquid chromatography coupled to high-resolution mass spectrometry. Additionally, in vivo metabolism of ZEN-14G was conducted in model animals, rats, by oral administration. As a result, 29 phase I metabolites and 6 phase II metabolites were identified and significant inter-species metabolic differences were observed as well. What is more, ZEN-14G could be considerably deglucosidated into its free form of ZEN after the incubation with animals and human liver microsomes in the absence of NADPH, which was mainly metabolized by human carboxylesterase CES-I and II. Furthermore, results showed that the major metabolic pathways of ZEN-14G were deglucosylation, hydroxylation, hydrogenation and glucuronidation. Although interspecies differences in the biotransformation of ZEN-14G were observed, ZEN, alpha-ZEL-14G, beta-ZEL-14G, alpha-ZEL, ZEN-14G-16GlcA and ZEN-14GlcA were the major metabolites of ZEN-14G. Additionally, a larger yield of 6-OH-ZEN-14G and 8-OH-ZEN-14G was also observed in human liver microsomes. The obtained data would be of great importance for the safety assessment of modified mycotoxin, ZEN-14G, and provide another perspective for risk assessment of mycotoxin.
ESTHER : Yang_2018_Arch.Toxicol_92_2779
PubMedSearch : Yang_2018_Arch.Toxicol_92_2779
PubMedID: 30019167

Title : Quantitative investigation of the mechanisms of microplastics and nanoplastics toward zebrafish larvae locomotor activity - Chen_2017_Sci.Total.Environ_584-585_1022
Author(s) : Chen Q , Gundlach M , Yang S , Jiang J , Velki M , Yin D , Hollert H
Ref : Sci Total Environ , 584-585 :1022 , 2017
Abstract : This study investigated the direct and indirect toxic effects of microplastics and nanoplastics toward zebrafish (Danio rerio) larvae locomotor activity. Results showed that microplastics alone exhibited no significant effects except for the upregulated zfrho visual gene expression; whereas nanoplastics inhibited the larval locomotion by 22% during the last darkness period, and significantly reduced larvae body length by 6%, inhibited the acetylcholinesterase activity by 40%, and upregulated gfap, alpha1-tubulin, zfrho and zfblue gene expression significantly. When co-exposed with 2mug/L 17 alpha-ethynylestradiol (EE2), microplastics led to alleviation on EE2's inhibition effect on locomotion, which was probably due to the decreased freely dissolved EE2 concentration. However, though nanoplastics showed stronger adsorption ability for EE2, the hypoactivity phenomenon still existed in the nanoplastics co-exposure group. Moreover, when co-exposed with a higher concentration of EE2 (20mug/L), both plastics showed an enhanced effect on the hypoactivity. Principal component analysis was performed to reduce data dimensions and four principal components were reconstituted in terms of oxidative stress, body length, nervous and visual system related genes explaining 84% of total variance. Furthermore, oxidative damage and body length reduction were evaluated to be main reasons for the hypoactivity. Therefore, nanoplastics alone suppressed zebrafish larvae locomotor activity and both plastic particles can change the larvae swimming behavior when co-exposed with EE2. This study provides new insights into plastic particles' effects on zebrafish larvae, improving the understanding of their environmental risks to the aquatic environment.
ESTHER : Chen_2017_Sci.Total.Environ_584-585_1022
PubMedSearch : Chen_2017_Sci.Total.Environ_584-585_1022
PubMedID: 28185727

Title : Two new compounds from the fruiting bodies of Ganoderma philippii - Yang_2017_J.Asian.Nat.Prod.Res__1
Author(s) : Yang S , Ma QY , Kong FD , Xie QY , Huang SZ , Zhou LM , Dai HF , Yu ZF , Zhao YX
Ref : J Asian Nat Prod Res , :1 , 2017
Abstract : Two new compounds, philippin (1) and 3beta,9alpha,14alpha-trihydroxy-(22E,24R)-ergost-22-en-7-one (2), were isolated from the fruiting bodies of Ganoderma philippii. Their structures were elucidated on the basis of the spectroscopic technologies, including 1D and 2D NMR as well as MS. The bioassay of inhibitory activity against acetylcholinesterase (AChE) showed compound 1 exhibited weak inhibitory activity against AChE.
ESTHER : Yang_2017_J.Asian.Nat.Prod.Res__1
PubMedSearch : Yang_2017_J.Asian.Nat.Prod.Res__1
PubMedID: 28508676

Title : Enhanced uptake of BPA in the presence of nanoplastics can lead to neurotoxic effects in adult zebrafish - Chen_2017_Sci.Total.Environ_609_1312
Author(s) : Chen Q , Yin D , Jia Y , Schiwy S , Legradi J , Yang S , Hollert H
Ref : Sci Total Environ , 609 :1312 , 2017
Abstract : Plastic particles have been proven to be abundant in the aquatic environment, raising concerns about their potential toxic effects. In the present study, we determined the bioaccumulation potential of bisphenol A (BPA) in adult zebrafish (Danio rerio) in the absence and presence of nano-sized plastic particles (nanoplastics, NPPs). Results show that BPA can accumulate in the viscera, gill, head and muscle of zebrafish with 85, 43, 20, and 3mug/g ww after 1d exposure. NPPs were also found to accumulate in different tissues of the fish. Relative equilibrium was reached after 1d exposure in different tissues with 39 to 636mg/kg ww. Co-exposure of NPPs and BPA led to a 2.2 and 2.6-fold significant increment of BPA uptake in the head and viscera, if compared with BPA alone treatment after 3d exposure. As such, we further investigated several neurotoxic biomarker alterations in the fish head. It was found that either BPA or NPPs can cause myelin basic protein (MBP)/gene up-regulation in the central nervous system (CNS); meanwhile, both contaminants exhibited significant inhibition of acetylcholinesterase (AChE) activity, which is a well-known representative biomarker for neurotoxicity. Moreover, for the co-exposure treatment, biomarkers of myeline and tubulin protein/gene expressions, dopamine content, and the mRNA expression of mesencephalic astrocyte derived neurotrophic factor (MANF) were all significantly up-regulated, suggesting that an enhanced neurotoxic effects in both CNS and dopaminergic system occurred. However, AChE activity was no more inhibited in the co-exposure treatment, which implies that solely AChE measurement may not be sufficient to identify neurotoxic effects in the cholinergic system. Overall, the present study demonstrates that the presence of NPPs can increase BPA bioavailability and cause neurotoxicity in adult zebrafish.
ESTHER : Chen_2017_Sci.Total.Environ_609_1312
PubMedSearch : Chen_2017_Sci.Total.Environ_609_1312
PubMedID: 28793400

Title : High-level expression and characterization of a novel cutinase from Malbranchea cinnamomea suitable for butyl butyrate production - Duan_2017_Biotechnol.Biofuels_10_223
Author(s) : Duan X , Liu Y , You X , Jiang Z , Yang S
Ref : Biotechnol Biofuels , 10 :223 , 2017
Abstract : BACKGROUND: Butyl butyrate has been considered as a promising fuel source because it is a kind of natural ester which can be converted from renewable and sustainable lignocellulosic biomass. Compared with the conventional chemical methods for butyl butyrate production, the enzymatic approach has been demonstrated to be more attractive, mainly owing to the mild reaction conditions, high specificity, low energy consumption, and environmental friendliness. Cutinases play an important role in the butyl butyrate production process. However, the production level of cutinases is still relatively low. Thus, to identify novel cutinases suitable for butyl butyrate synthesis and enhance their yields is of great value in biofuel industry.
RESULTS: A novel cutinase gene (McCut) was cloned from a thermophilic fungus Malbranchea cinnamomea and expressed in Pichia pastoris. The highest cutinase activity of 12, 536 U/mL was achieved in 5-L fermentor, which is by far the highest production for a cutinase. McCut was optimally active at pH 8.0 and 45 degrees C. It exhibited excellent stability within the pH range of 3.0-10.5 and up to 75 degrees C. The cutinase displayed broad substrate specificity with the highest activity towards p-nitrophenyl butyrate and tributyrin. It was capable of hydrolyzing cutin, polycaprolactone, and poly(butylene succinate). Moreover, McCut efficiently synthesized butyl butyrate with a maximum esterification efficiency of 96.9% at 4 h. The overall structure of McCut was resolved as a typical alpha/beta-hydrolase fold. The structural differences between McCut and Aspergillus oryzae cutinase in groove and loop provide valuable information for redesign of McCut. These excellent features make it useful in biosynthesis and biodegradation fields.
CONCLUSIONS: A novel cutinase from M. cinnamomea was identified and characterized for the first time. High-level expression by P. pastoris is by far the highest for a cutinase. The enzyme exhibited excellent stability and high esterification efficiency for butyl butyrate production, which may make it a good candidate in biofuel and chemical industries.
ESTHER : Duan_2017_Biotechnol.Biofuels_10_223
PubMedSearch : Duan_2017_Biotechnol.Biofuels_10_223
PubMedID: 28932264
Gene_locus related to this paper: malci-a0a1s6yjf3

Title : Evaluation of Novel Dual Acetyl- and Butyrylcholinesterase Inhibitors as Potential Anti-Alzheimer's Disease Agents Using Pharmacophore, 3D-QSAR, and Molecular Docking Approaches - Pang_2017_Molecules_22_
Author(s) : Pang X , Fu H , Yang S , Wang L , Liu AL , Wu S , Du GH
Ref : Molecules , 22 : , 2017
Abstract : DL0410, containing biphenyl and piperidine skeletons, was identified as an acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibitor through high-throughput screening assays, and further studies affirmed its efficacy and safety for Alzheimer's disease treatment. In our study, a series of novel DL0410 derivatives were evaluated for inhibitory activities towards AChE and BuChE. Among these derivatives, compounds 6-1 and 7-6 showed stronger AChE and BuChE inhibitory activities than DL0410. Then, pharmacophore modeling and three-dimensional quantitative structure activity relationship (3D-QSAR) models were performed. The R(2) of AChE and BuChE 3D-QSAR models for training set were found to be 0.925 and 0.883, while that of the test set were 0.850 and 0.881, respectively. Next, molecular docking methods were utilized to explore the putative binding modes. Compounds 6-1 and 7-6 could interact with the amino acid residues in the catalytic anionic site (CAS) and peripheral anionic site (PAS) of AChE/BuChE, which was similar with DL0410. Kinetics studies also suggested that the three compounds were all mixed-types of inhibitors. In addition, compound 6-1 showed better absorption and blood brain barrier permeability. These studies provide better insight into the inhibitory behaviors of DL0410 derivatives, which is beneficial for rational design of AChE and BuChE inhibitors in the future.
ESTHER : Pang_2017_Molecules_22_
PubMedSearch : Pang_2017_Molecules_22_
PubMedID: 28933746

Title : Drug Therapy for Behavioral and Psychological Symptoms of Dementia - Wang_2016_Curr.Neuropharmacol_14_307
Author(s) : Wang F , Feng TY , Yang S , Preter M , Zhou JN , Wang XP
Ref : Curr Neuropharmacol , 14 :307 , 2016
Abstract : Dementia, which can be induced by diverse factors, is a clinical syndrome characterized by the decline of cognitive function. Behavioral and psychological symptoms of dementia (BPSD) include depression, agitation, and aggression. Dementia causes a heavy burden on patients and their caregivers. Patients with BPSD should be assessed comprehensively by practitioners and offered appropriate non-pharmacologic and pharmacologic therapy. Nonpharmacologic therapy has been recommended as the basal treatment for BPSD; however, pharmacologic therapy is required under many situations. Medications, including antipsychotic agents, antidepressants, sedative and hypnotic agents, mood stabilizers, cholinesterase inhibitors, and amantadine, are extensively used in clinical practice. We have reviewed the progression of pharmacologic therapy for BPSD.
ESTHER : Wang_2016_Curr.Neuropharmacol_14_307
PubMedSearch : Wang_2016_Curr.Neuropharmacol_14_307
PubMedID: 26644152

Title : Design, synthesis and biological evaluation of coumarin derivatives as novel acetylcholinesterase inhibitors that attenuate H2O2-induced apoptosis in SH-SY5Y cells - Yao_2016_Bioorg.Chem_68_112
Author(s) : Yao D , Wang J , Wang G , Jiang Y , Shang L , Zhao Y , Huang J , Yang S , Yu Y
Ref : Bioorg Chem , 68 :112 , 2016
Abstract : A novel series of coumarin derivatives were designed, synthesized and investigated for inhibition of cholinesterase, including acetyl cholinesterase (AChE) and butyrylcholinesterase (BuChE). This biological study showed that these compounds containing piperazine ring had significant inhibition activities on AChE rather than BuChE. Further study suggested that 9x, as one of this kind of structure derivative, showed the strongest inhibition activity on AChE with an IC50 value of 34nM. Moreover, molecular docking, flow cytometry (FCM), and western blot assay suggested that 9x could induce cytoprotective autophagy to attenuate H2O2-induced cell death in human neuroblastoma SH-SY5Y cells. These findings highlight a new approach for the development of a novel potential neuroprotective compound targeting AChE with autophagy-inducing activity in future Alzheimer's disease (AD) therapy.
ESTHER : Yao_2016_Bioorg.Chem_68_112
PubMedSearch : Yao_2016_Bioorg.Chem_68_112
PubMedID: 27479541

Title : High-level expression and biochemical characterization of a novel cold-active lipase from Rhizomucor endophyticus - Duan_2016_Biotechnol.Lett_38_2127
Author(s) : Duan X , Zheng M , Liu Y , Jiang Z , Yang S
Ref : Biotechnol Lett , 38 :2127 , 2016
Abstract : OBJECTIVES: To identify novel cold-active lipases from fungal sources and improve their production by heterologous expression in Pichia pastoris.
RESULTS: A novel cold-active lipase gene (ReLipB) from Rhizomucor endophyticus was cloned. ReLipB was expressed at a high level in Pichia pastoris using high cell-density fermentation in a 5-l fermentor with the highest lipase activity of 1395 U/ml. The recombinant lipase (RelipB) was purified and biochemically characterized. ReLipB was most active at pH 7.5 and 25 degrees C. It was stable from pH 4.5-9.0. It exhibited broad substrate specificity towards p-nitrophenyl (pNP) esters (C2-C16) and triacylglycerols (C2-C12), showing the highest specific activities towards pNP laurate (231 U/mg) and tricaprylin (1840 U/mg), respectively. In addition, the enzyme displayed excellent stability with high concentrations of organic solvents including cyclohexane, n-hexane, n-heptane, isooctane and petroleum ester and surfactants.
CONCLUSIONS: A novel cold-active lipase from Rhizomucor endophyticus was identified, expressed at a high level and biochemically characterized. The high yield and unique enzymatic properties make this lipase of some potential for industrial applications.
ESTHER : Duan_2016_Biotechnol.Lett_38_2127
PubMedSearch : Duan_2016_Biotechnol.Lett_38_2127
PubMedID: 27640008

Title : Insights into Adaptations to a Near-Obligate Nematode Endoparasitic Lifestyle from the Finished Genome of Drechmeria coniospora - Zhang_2016_Sci.Rep_6_23122
Author(s) : Zhang L , Zhou Z , Guo Q , Fokkens L , Miskei M , Pocsi I , Zhang W , Chen M , Wang L , Sun Y , Donzelli BG , Gibson DM , Nelson DR , Luo JG , Rep M , Liu H , Yang S , Wang J , Krasnoff SB , Xu Y , Molnar I , Lin M
Ref : Sci Rep , 6 :23122 , 2016
Abstract : Nematophagous fungi employ three distinct predatory strategies: nematode trapping, parasitism of females and eggs, and endoparasitism. While endoparasites play key roles in controlling nematode populations in nature, their application for integrated pest management is hindered by the limited understanding of their biology. We present a comparative analysis of a high quality finished genome assembly of Drechmeria coniospora, a model endoparasitic nematophagous fungus, integrated with a transcriptomic study. Adaptation of D. coniospora to its almost completely obligate endoparasitic lifestyle led to the simplification of many orthologous gene families involved in the saprophytic trophic mode, while maintaining orthologs of most known fungal pathogen-host interaction proteins, stress response circuits and putative effectors of the small secreted protein type. The need to adhere to and penetrate the host cuticle led to a selective radiation of surface proteins and hydrolytic enzymes. Although the endoparasite has a simplified secondary metabolome, it produces a novel peptaibiotic family that shows antibacterial, antifungal and nematicidal activities. Our analyses emphasize the basic malleability of the D. coniospora genome: loss of genes advantageous for the saprophytic lifestyle; modulation of elements that its cohort species utilize for entomopathogenesis; and expansion of protein families necessary for the nematode endoparasitic lifestyle.
ESTHER : Zhang_2016_Sci.Rep_6_23122
PubMedSearch : Zhang_2016_Sci.Rep_6_23122
PubMedID: 26975455
Gene_locus related to this paper: 9hypo-a0a151ga75 , 9hypo-a0a151gbh5 , 9hypo-a0a151gd50 , 9hypo-a0a151ggb9 , 9hypo-a0a151gjd5 , 9hypo-a0a151gtv2 , 9hypo-a0a151gxh2 , 9hypo-a0a151gaw8 , 9hypo-a0a151gia2

Title : Surface display of the thermophilic lipase Tm1350 on the spore of Bacillus subtilis by the CotB anchor protein - Chen_2015_Extremophiles_19_799
Author(s) : Chen H , Tian R , Ni Z , Zhang Q , Zhang T , Chen Z , Chen K , Yang S
Ref : Extremophiles , 19 :799 , 2015
Abstract : Lipases expressed in microbial hosts have great commercial value, but their applications are restricted by the high costs of production and harsh conditions used in industrial processes, such as high temperature and alkaline environment. In this study, an Escherichia coli-Bacillus subtilis shuttle vector (pHS-cotB-Tm1350) was constructed for the spore surface display of the lipase Tm1350 from hyperthermophilic bacterium Thermotoga maritima MSB8. Successful display of the CotB-Tm1350 fusion protein on spore surface was confirmed by Western blot analysis and activity measurements. The optimal catalytic temperature and pH of the spore surface-displayed Tm1350 were 80 degreesC and 9, respectively, which were higher than non-immobilized Tm1350 (70 degreesC and pH 7.5). Analysis of thermal and pH stability showed that spore surface-displayed Tm1350 retained 81 or 70 % of its original activity after 8 h of incubation at pH 8 or pH 9 (70 degreesC), which were 18 % higher than the retained activity of the non-immobilized Tm1350 under the same conditions. Meanwhile, recycling experiments showed that the recombinant spores could be used for up to three reaction cycles without a significant decrease in the catalytic rate (84 %). These results suggested that enzyme display on the surface of the B. subtilis spore could serve as an effective approach for enzyme immobilization, which has potential applications in the harsh biochemical industry.
ESTHER : Chen_2015_Extremophiles_19_799
PubMedSearch : Chen_2015_Extremophiles_19_799
PubMedID: 26026992

Title : Expression and Characterization of a New Thermostable Esterase from Clostridium thermocellum - Zhang_2015_Appl.Biochem.Biotechnol_177_1437
Author(s) : Zhang T , Chen H , Ni Z , Tian R , Jia J , Chen Z , Yang S
Ref : Appl Biochem Biotechnol , 177 :1437 , 2015
Abstract : The thermostable esterase from the thermophilic bacterium Clostridium thermocellum DSM 1313 was expressed in Escherichia coli and purified by Ni(2+) affinity chromatography. Its molecular weight was approximately 35 kDa according to 12 % sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. The enzyme exhibited the highest specific activity with p-nitrophenyl butyrate (285 s(-1) mM(-1)). The activity of the esterase was greatest at 65 degrees C, and the esterase maintained residual activity levels of 70 and 50 % after 3 h incubation at 65 and 70 degrees C, respectively. Its activity was optimal at pH 7.0, was enhanced in the presence of Ca(2+) and Mg(2+), and was inhibited by Ni(2+) and Cu(2+). The addition of surfactants, such as Tween-20, Tween-80, Triton X-100, and SDS, at concentrations of 5 % (v/v) significantly inhibited the lipolytic action of the esterase. Enzyme activity was relatively stable in 10 % methanol, and 50 % residual activity was seen in 10 % DMSO, demonstrating its potential in biodiesel production and industrial applications.
ESTHER : Zhang_2015_Appl.Biochem.Biotechnol_177_1437
PubMedSearch : Zhang_2015_Appl.Biochem.Biotechnol_177_1437
PubMedID: 26373940
Gene_locus related to this paper: clotm-q4cf59

Title : Expression and display of a novel thermostable esterase from Clostridium thermocellum on the surface of Bacillus subtilis using the CotB anchor protein - Chen_2015_J.Ind.Microbiol.Biotechnol_42_1439
Author(s) : Chen H , Zhang T , Jia J , Vastermark A , Tian R , Ni Z , Chen Z , Chen K , Yang S
Ref : J Ind Microbiol Biotechnol , 42 :1439 , 2015
Abstract : Esterases expressed in microbial hosts are commercially valuable, but their applications are limited due to high costs of production and harsh industrial processes involved. In this study, the esterase-DSM (from Clostridium thermocellum) was expressed and successfully displayed on the spore surface, and the spore-associated esterase was confirmed by western blot analysis and activity measurements. The optimal temperature and pH of spore surface-displayed DSM was 60 and 8.5 degrees C, respectively. It also demonstrates a broad temperature and pH optimum in the range of 50-70, 7-9.5 degrees C. The spore surface-displayed esterase-DSM retained 78, 68 % of its original activity after 5 h incubation at 60 and 70 degrees C, respectively, which was twofold greater activity than that of the purified DSM. The recombinant spores has high activity and stability in DMSO, which was 49 % higher than the retained activity of the purified DSM in DMSO (20 % v/v), and retained 65.2 % of activity after 7 h of incubation in DMSO (20 % v/v). However, the recombinant spores could retain 77 % activity after 3 rounds of recycling. These results suggest that enzyme displayed on the surface of the Bacillus subtilis spore could serve as an effective approach for enzyme immobilization.
ESTHER : Chen_2015_J.Ind.Microbiol.Biotechnol_42_1439
PubMedSearch : Chen_2015_J.Ind.Microbiol.Biotechnol_42_1439
PubMedID: 26318029

Title : Expression and Characterization of a Novel Thermo-Alkalistable Lipase from Hyperthermophilic Bacterium Thermotoga maritima - Tian_2015_Appl.Biochem.Biotechnol_176_1482
Author(s) : Tian R , Chen H , Ni Z , Zhang Q , Zhang Z , Zhang T , Zhang C , Yang S
Ref : Appl Biochem Biotechnol , 176 :1482 , 2015
Abstract : A gene coding for lipase (Tm1350) from the hyperthermophilic bacterium Thermotoga maritima MSB8 was cloned and overexpressed by Escherichia coli. The enzyme can degrade substrates with both short and long acyl chain lengths. The apparent Km and Vmax values for p-nitrophenyl butyrate were 8 mM and 333 U/mg, respectively. The enzyme displayed optimal activity at pH 7.5 and 70 degrees C, maintained 66 % of the original activity after 8 h of incubation, and its half-lives at pHs 9 and 10 were 8 and 1 h. The activity of Tm1350 was stimulated up to 131 or 151 % of the original activity by incubating with 4 M urea or 20 % (v/v) methanol, and 90.1 or 70.2 % of the activity was maintained after 8 h incubation of the enzyme in 20 or 75 % (v/v) of the methanol, showing potential for biodiesel production. The activity of the enzyme without cysteine residue was stimulated up to 618 and 550 % of the original activity by incubating with dithiothreitol (DTT) and reduced glutathione (GSH) at a concentration of 1 mM. However, the circular dichroism spectra of the enzyme have no obvious change after DTT treatment. It is speculated that DTT interacts with potential residues in some key active sites without influence of structure.
ESTHER : Tian_2015_Appl.Biochem.Biotechnol_176_1482
PubMedSearch : Tian_2015_Appl.Biochem.Biotechnol_176_1482
PubMedID: 25957275

Title : Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei - Yang_2015_J.Lipid.Res_56_1616
Author(s) : Yang S , Qin Z , Duan X , Yan Q , Jiang Z
Ref : J Lipid Res , 56 :1616 , 2015
Abstract : Two hormone-sensitive lipase (HSL) family esterases (RmEstA and RmEstB) from the thermophilic fungus Rhizomucor miehei, exhibiting distinct substrate specificity, have been recently reported to show great potential in industrial applications. In this study, the crystal structures of RmEstA and RmEstB were determined at 2.15 A and 2.43 A resolutions, respectively. The structures of RmEstA and RmEstB showed two distinctive domains, a catalytic domain and a cap domain, with the classical alpha/beta-hydrolase fold. Catalytic triads consisting of residues Ser161, Asp262, and His292 in RmEstA, and Ser164, Asp261, and His291 in RmEstB were found in the respective canonical positions. Structural comparison of RmEstA and RmEstB revealed that their distinct substrate specificity might be attributed to their different substrate-binding pockets. The aromatic amino acids Phe222 and Trp92, located in the center of the substrate-binding pocket of RmEstB, blocked this pocket, thus narrowing its catalytic range for substrates (C2-C8). Two mutants (F222A and W92F in RmEstB) showing higher catalytic activity toward long-chain substrates further confirmed the hypothesized interference. This is the first report of HSL family esterase structures from filamentous fungi.jlr The information on structure-function relationships could open important avenues of exploration for further industrial applications of esterases.
ESTHER : Yang_2015_J.Lipid.Res_56_1616
PubMedSearch : Yang_2015_J.Lipid.Res_56_1616
PubMedID: 26108223
Gene_locus related to this paper: rhimi-RmEstB , rhimi-v5j5w4

Title : Characterization of an acidic cold-adapted cutinase from Thielavia terrestris and its application in flavor ester synthesis - Xu_2015_Food.Chem_188_439
Author(s) : Xu H , Yan Q , Duan X , Yang S , Jiang Z
Ref : Food Chem , 188 :439 , 2015
Abstract : An acidic cutinase (TtcutB) from Thielavia terrestris CAU709 was purified to apparent homogeneity with 983Umg(-1) specific activity. The molecular mass of the enzyme was estimated to be 27.3 and 27.9kDa by SDS-PAGE and gel filtration, respectively. A peptide sequence homology search revealed no homologous cutinases from T. terrestris, except for one putative cutinase gene (XP003656017.1), indicating that TtcutB is a novel enzyme. TtcutB exhibited an acidic pH optimum of 4.0, and stability at pH 2.5-10.5. Optimal activity was at 55 degrees C, it was stable up to 65 degrees C, and retained over 30% activity at 0 degrees C. Km values toward p-nitrophenyl (pNP) acetate, pNP-butyrate and pNP-caproate were 8.3, 1.1 and 0.88mM, respectively. The cutinase exhibited strong synthetic activity on flavor ester butyl butyrate under non-aqueous environment, and the highest esterification efficiency of 95% was observed under the optimized reaction conditions. The enzyme's unique biochemical properties suggest great potential in flavor esters-producing industries.
ESTHER : Xu_2015_Food.Chem_188_439
PubMedSearch : Xu_2015_Food.Chem_188_439
PubMedID: 26041215
Gene_locus related to this paper: thite-g2rae6

Title : Homozygous missense mutation in the LIPH gene causing autosomal recessive hypotrichosis simplex in a Chinese patient -
Author(s) : Liu LH , Wang JW , Chen G , Chang RX , Zhou Y , Tang HY , Zhu J , Wang PG , Yang S , Zhang XJ
Ref : J Dermatol , 41 :105 , 2014
PubMedID: 24354445

Title : Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei - Zhou_2014_BMC.Genomics_15_294
Author(s) : Zhou P , Zhang G , Chen S , Jiang Z , Tang Y , Henrissat B , Yan Q , Yang S , Chen CF , Zhang B , Du Z
Ref : BMC Genomics , 15 :294 , 2014
Abstract : BACKGROUND: The zygomycete fungi like Rhizomucor miehei have been extensively exploited for the production of various enzymes. As a thermophilic fungus, R. miehei is capable of growing at temperatures that approach the upper limits for all eukaryotes. To date, over hundreds of fungal genomes are publicly available. However, Zygomycetes have been rarely investigated both genetically and genomically.
RESULTS: Here, we report the genome of R. miehei CAU432 to explore the thermostable enzymatic repertoire of this fungus. The assembled genome size is 27.6-million-base (Mb) with 10,345 predicted protein-coding genes. Even being thermophilic, the G + C contents of fungal whole genome (43.8%) and coding genes (47.4%) are less than 50%. Phylogenetically, R. miehei is more closerly related to Phycomyces blakesleeanus than to Mucor circinelloides and Rhizopus oryzae. The genome of R. miehei harbors a large number of genes encoding secreted proteases, which is consistent with the characteristics of R. miehei being a rich producer of proteases. The transcriptome profile of R. miehei showed that the genes responsible for degrading starch, glucan, protein and lipid were highly expressed.
CONCLUSIONS: The genome information of R. miehei will facilitate future studies to better understand the mechanisms of fungal thermophilic adaptation and the exploring of the potential of R. miehei in industrial-scale production of thermostable enzymes. Based on the existence of a large repertoire of amylolytic, proteolytic and lipolytic genes in the genome, R. miehei has potential in the production of a variety of such enzymes.
ESTHER : Zhou_2014_BMC.Genomics_15_294
PubMedSearch : Zhou_2014_BMC.Genomics_15_294
PubMedID: 24746234

Title : Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes - You_2014_Nat.Commun_5_5594
Author(s) : You X , Bian C , Zan Q , Xu X , Liu X , Chen J , Wang J , Qiu Y , Li W , Zhang X , Sun Y , Chen S , Hong W , Li Y , Cheng S , Fan G , Shi C , Liang J , Tom Tang Y , Yang C , Ruan Z , Bai J , Peng C , Mu Q , Lu J , Fan M , Yang S , Huang Z , Jiang X , Fang X , Zhang G , Zhang Y , Polgar G , Yu H , Li J , Liu Z , Ravi V , Coon SL , Yang H , Venkatesh B , Shi Q
Ref : Nat Commun , 5 :5594 , 2014
Abstract : Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers' tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates.
ESTHER : You_2014_Nat.Commun_5_5594
PubMedSearch : You_2014_Nat.Commun_5_5594
PubMedID: 25463417
Gene_locus related to this paper: 9gobi-a0a3b4bh68 , 9gobi-a0a3b4bmj6 , 9gobi-a0a3b4alj9 , 9gobi-a0a3b4biy6 , 9gobi-a0a3b4ah01 , 9gobi-a0a3b3z8m7 , 9gobi-a0a3b4aaj5 , 9gobi-a0a3b4b6y7

Title : Characterization of a novel hormone-sensitive lipase family esterase from Rhizomucor miehei with tertiary alcohol hydrolysis activity - Yan_2014_J.Mol.Catal.B.Enzym_109_76
Author(s) : Yan Q , Yang S , Duan X , Xu H , Liu Y , Jiang Z
Ref : J Mol Catal B Enzym , 109 :76 , 2014
Abstract : A novel esterase gene (designated RmEstB) from the thermophilic fungus Rhizomucor miehei was cloned and functionally expressed in Escherichia coli. Sequence analysis revealed a 960-bp open reading frame encoding a protein of 319 amino acids. The deduced protein sequence contained an HGGG motif, suggesting that the enzyme is a hormone-sensitive lipase (HSL) family esterase. It showed highest identity of 52% with the esterase from Pseudomonas mandelii. The recombinant esterase was purified to homogeneity at 5.1-fold purification with a recovery yield of 85%. The molecular mass of RmEstB was estimated to be 37 kDa by SDS-PAGE. RmEstB was most active at pH 7.5 and 50 C. The enzyme was highly stable in the presence of 30% ethanol, methanol, acetone, isopropanol, dimethyl sulfoxide and acetonitrile. RmEstB showed a broad range of substrate specificities toward various p-nitrophenol (pNP) esters (C2-C10) and triglycerides (C2-C6), with the highest specific activities obtained for pNP acetate (255 U/mg) and triacetin (1330 U/mg), respectively. In addition, RmEstB efficiently catalyzed the hydrolysis of sterically hindered esters of tertiary alcohols. This study presents a novel fungal HSL family esterase with potential for some industrial applications.
ESTHER : Yan_2014_J.Mol.Catal.B.Enzym_109_76
PubMedSearch : Yan_2014_J.Mol.Catal.B.Enzym_109_76
Gene_locus related to this paper: rhimi-RmEstB

Title : Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization - Qin_2014_Proc.Natl.Acad.Sci.U.S.A_111_5135
Author(s) : Qin C , Yu C , Shen Y , Fang X , Chen L , Min J , Cheng J , Zhao S , Xu M , Luo Y , Yang Y , Wu Z , Mao L , Wu H , Ling-Hu C , Zhou H , Lin H , Gonzalez-Morales S , Trejo-Saavedra DL , Tian H , Tang X , Zhao M , Huang Z , Zhou A , Yao X , Cui J , Li W , Chen Z , Feng Y , Niu Y , Bi S , Yang X , Cai H , Luo X , Montes-Hernandez S , Leyva-Gonzalez MA , Xiong Z , He X , Bai L , Tan S , Liu D , Liu J , Zhang S , Chen M , Zhang L , Zhang Y , Liao W , Wang M , Lv X , Wen B , Liu H , Luan H , Yang S , Wang X , Xu J , Li X , Li S , Wang J , Palloix A , Bosland PW , Li Y , Krogh A , Rivera-Bustamante RF , Herrera-Estrella L , Yin Y , Yu J , Hu K , Zhang Z
Ref : Proc Natl Acad Sci U S A , 111 :5135 , 2014
Abstract : As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded approximately 0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of approximately 81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.
ESTHER : Qin_2014_Proc.Natl.Acad.Sci.U.S.A_111_5135
PubMedSearch : Qin_2014_Proc.Natl.Acad.Sci.U.S.A_111_5135
PubMedID: 24591624
Gene_locus related to this paper: capch-q75qh4 , capan-a0a1u8fuf5 , capan-a0a1u8gmz3 , capan-a0a1u8f879 , capan-a0a1u8ftr2 , capan-a0a1u8g8s6

Title : Biochemical characterization of a first fungal esterase from Rhizomucor miehei showing high efficiency of ester synthesis - Liu_2013_PLoS.One_8_e77856
Author(s) : Liu Y , Xu H , Yan Q , Yang S , Duan X , Jiang Z
Ref : PLoS ONE , 8 :e77856 , 2013
Abstract : BACKGROUND: Esterases with excellent merits suitable for commercial use in ester production field are still insufficient. The aim of this research is to advance our understanding by seeking for more unusual esterases and revealing their characterizations for ester synthesis. METHODOLOGY/PRINCIPAL FINDINGS: A novel esterase-encoding gene from Rhizomucor miehei (RmEstA) was cloned and expressed in Escherichia coli. Sequence analysis revealed a 975-bp ORF encoding a 324-amino-acid polypeptide belonging to the hormone-sensitive lipase (HSL) family IV and showing highest similarity (44%) to the Paenibacillus mucilaginosus esterase/lipase. Recombinant RmEstA was purified to homogeneity: it was 34 kDa by SDS-PAGE and showed optimal pH and temperature of 6.5 and 45 degrees C, respectively. The enzyme was stable to 50 degrees C, under a broad pH range (5.0-10.6). RmEstA exhibited broad substrate specificity toward p-nitrophenol esters and short-acyl-chain triglycerols, with highest activities (1,480 U mg(-1) and 228 U mg(-1)) for p-nitrophenyl hexanoate and tributyrin, respectively. RmEstA efficiently synthesized butyl butyrate (92% conversion yield) when immobilized on AOT-based organogel. CONCLUSION: RmEstA has great potential for industrial applications. RmEstA is the first reported esterase from Rhizomucor miehei.
ESTHER : Liu_2013_PLoS.One_8_e77856
PubMedSearch : Liu_2013_PLoS.One_8_e77856
PubMedID: 24204998
Gene_locus related to this paper: rhimi-v5j5w4

Title : A low molecular mass cutinase of Thielavia terrestris efficiently hydrolyzes poly(esters) - Yang_2013_J.Ind.Microbiol.Biotechnol_40_217
Author(s) : Yang S , Xu H , Yan Q , Liu Y , Zhou P , Jiang Z
Ref : J Ind Microbiol Biotechnol , 40 :217 , 2013
Abstract : A low molecular mass cutinase (designated TtcutA) from Thielavia terrestris was purified and biochemically characterized. The thermophilic fungus T. terrestris CAU709 secreted a highly active cutinase (90.4 U ml(-1)) in fermentation broth containing wheat bran as the carbon source. The cutinase was purified 19-fold with a recovery yield of 4.8 %. The molecular mass of the purified TtcutA was determined as 25.3 and 22.8 kDa using SDS-PAGE and gel filtration, respectively. TtcutA displayed optimal activity at pH 4.0 and 50 degrees C. It was highly stable up to 65 degrees C and in the broad pH range 2.5-10.5. Extreme stability in high concentrations (80 %, v/v) of solvents such as methanol, ethanol, acetone, acetonitrile, isopropanol, and dimethyl sulfoxide was observed for the enzyme. The K (m) values for this enzyme towards p-nitrophenyl (pNP) acetate, pNP butyrate, and pNP caproate were 7.7, 1.0, and 0.52 mM, respectively. TtcutA was able to efficiently degrade various ester polymers, including cutin, polyethylene terephthalate (PET), polycaprolactone (PCL), and poly(butylene succinate) (PBS) at hydrolytic rates of 3 mumol h(-1) mg(-1) protein, 1.1 mg h(-1) mg(-1) protein, 203.6 mg h(-1) mg(-1) protein, and 56.4 mg h(-1) mg(-1) protein, respectively. Because of these unique biochemical properties, TtcutA of T. terrestris may be useful in various industrial applications in the future.
ESTHER : Yang_2013_J.Ind.Microbiol.Biotechnol_40_217
PubMedSearch : Yang_2013_J.Ind.Microbiol.Biotechnol_40_217
PubMedID: 23271406

Title : Modulated dye retention for the signal-on fluorometric determination of acetylcholinesterase inhibitor - Liao_2013_Anal.Chem_85_4968
Author(s) : Liao S , Han W , Ding H , Xie D , Tan H , Yang S , Wu Z , Shen G , Yu R
Ref : Analytical Chemistry , 85 :4968 , 2013
Abstract : A novel fluorometric assay method based on target-induced signal on was developed for acetylcholinesterase (AChE) inhibitor with obviously improved detection sensitivity. In this method, the AChE molecules catalyzed the hydrolysis of acetylthiocholine (ATCl) to form thiocholine, which in turn can specifically react with fluorescent squaraine derivative, a specific chemodosimeter for thiol-containing compounds, resulting in fluorescence quenching and offering a low fluorometric background for the further detection of AChE inhibitor. In the presence of AChE inhibitor, the catalytic hydrolysis of ATCl is blocked, and then the squaraine derivative remains intact and shows signal-on fluorescence. The amount of the remaining fluorescent squaraine derivative is positively correlated with that of the AChE inhibitor in solution. This new designed sensing system shows an obviously improved sensitivity toward target with a detection limit of 5 pg mL(-1) (0.018 nM) for the AChE inhibitor, comparing favorably with previously reported fluorometric methods. To our best knowledge, this new method is the first example of fluorometric enzymatic assay for AChE inhibitors based on such a signal-on principle and using a specific reaction, which has potential to offer an effective strategy for the detection of AChE inhibitors.
ESTHER : Liao_2013_Anal.Chem_85_4968
PubMedSearch : Liao_2013_Anal.Chem_85_4968
PubMedID: 23597308

Title : De novo Assembly and Characterization of the Global Transcriptome for Rhyacionia leptotubula Using Illumina Paired-End Sequencing - Zhu_2013_PLoS.One_8_e81096
Author(s) : Zhu JY , Li YH , Yang S , Li QW
Ref : PLoS ONE , 8 :e81096 , 2013
Abstract : BACKGROUND: The pine tip moth, Rhyacionia leptotubula (Lepidoptera: Tortricidae) is one of the most destructive forestry pests in Yunnan Province, China. Despite its importance, less is known regarding all aspects of this pest. Understanding the genetic information of it is essential for exploring the specific traits at the molecular level. Thus, we here sequenced the transcriptome of R. leptotubula with high-throughput Illumina sequencing. METHODOLOGY/PRINCIPAL FINDINGS: In a single run, more than 60 million sequencing reads were generated. De novo assembling was performed to generate a collection of 46,910 unigenes with mean length of 642 bp. Based on Blastx search with an E-value cut-off of 10(-5), 22,581 unigenes showed significant similarities to known proteins from National Center for Biotechnology Information (NCBI) non-redundant (Nr) protein database. Of these annotated unigenes, 10,360, 6,937 and 13,894 were assigned to Gene Ontology (GO), Clusters of Orthologous Group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. A total of 5,926 unigenes were annotated with domain similarity derived functional information, of which 55 and 39 unigenes respectively encoding the insecticide resistance related enzymes, cytochrome P450 and carboxylesterase. Using the transcriptome data, 47 unigenes belonging to the typical "stress" genes of heat shock protein (Hsp) family were retrieved. Furthermore, 1,450 simple sequence repeats (SSRs) were detected; 3.09% of the unigenes contained SSRs. Large numbers of SSR primer pairs were designed and out of randomly verified primer pairs 80% were successfully yielded amplicons. CONCLUSIONS/SIGNIFICANCE: A large of putative R. leptotubula transcript sequences has been obtained from the deep sequencing, which extensively increases the comprehensive and integrated genomic resources of this pest. This large-scale transcriptome dataset will be an important information platform for promoting our investigation of the molecular mechanisms from various aspects in this species.
ESTHER : Zhu_2013_PLoS.One_8_e81096
PubMedSearch : Zhu_2013_PLoS.One_8_e81096
PubMedID: 24278383

Title : Predictions of BCHE Inhibitors Using Support Vector Machine and Naive Bayesian Classification Techniques in Drug Discovery - Fang_2013_J.Chem.Inf.Model_53_3009
Author(s) : Fang J , Yang R , Gao L , Zhou D , Yang S , Liu AL , Du GH
Ref : J Chem Inf Model , 53 :3009 , 2013
Abstract : Butyrylcholinesterase (BCHE, EC is an important pharmacological target for Alzheimer's disease (AD) treatment. However, the currently available BCHE inhibitor screening assays are expensive, labor-intensive, and compound-dependent. It is necessary to develop robust in silico methods to predict the activities of BCHE inhibitors for the lead identification. In this investigation, support vector machine (SVM) models and naive Bayesian models were built to discriminate BCHE inhibitors (BCHEIs) from the noninhibitors. Each molecule was initially represented in 1870 structural descriptors (1235 from ADRIANA.Code, 334 from MOE, and 301 from Discovery studio). Correlation analysis and stepwise variable selection method were applied to figure out activity-related descriptors for prediction models. Additionally, structural fingerprint descriptors were added to improve the predictive ability of models, which were measured by cross-validation, a test set validation with 1001 compounds and an external test set validation with 317 diverse chemicals. The best two models gave Matthews correlation coefficient of 0.9551 and 0.9550 for the test set and 0.9132 and 0.9221 for the external test set. To demonstrate the practical applicability of the models in virtual screening, we screened an in-house data set with 3601 compounds, and 30 compounds were selected for further bioactivity assay. The assay results showed that 10 out of 30 compounds exerted significant BCHE inhibitory activities with IC50 values ranging from 0.32 to 22.22 muM, at which three new scaffolds as BCHE inhibitors were identified for the first time. To our best knowledge, this is the first report on BCHE inhibitors using machine learning approaches. The models generated from SVM and naive Bayesian approaches successfully predicted BCHE inhibitors. The study proved the feasibility of a new method for predicting bioactivities of ligands and discovering novel lead compounds.
ESTHER : Fang_2013_J.Chem.Inf.Model_53_3009
PubMedSearch : Fang_2013_J.Chem.Inf.Model_53_3009
PubMedID: 24144102

Title : Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937 - Glasner_2011_J.Bacteriol_193_2076
Author(s) : Glasner JD , Yang CH , Reverchon S , Hugouvieux-Cotte-Pattat N , Condemine G , Bohin JP , Van Gijsegem F , Yang S , Franza T , Expert D , Plunkett G, 3rd , San Francisco MJ , Charkowski AO , Py B , Bell K , Rauscher L , Rodriguez-Palenzuela P , Toussaint A , Holeva MC , He SY , Douet V , Boccara M , Blanco C , Toth I , Anderson BD , Biehl BS , Mau B , Flynn SM , Barras F , Lindeberg M , Birch PR , Tsuyumu S , Shi X , Hibbing M , Yap MN , Carpentier M , Dassa E , Umehara M , Kim JF , Rusch M , Soni P , Mayhew GF , Fouts DE , Gill SR , Blattner FR , Keen NT , Perna NT
Ref : Journal of Bacteriology , 193 :2076 , 2011
Abstract : Dickeya dadantii is a plant-pathogenic enterobacterium responsible for the soft rot disease of many plants of economic importance. We present here the sequence of strain 3937, a strain widely used as a model system for research on the molecular biology and pathogenicity of this group of bacteria.
ESTHER : Glasner_2011_J.Bacteriol_193_2076
PubMedSearch : Glasner_2011_J.Bacteriol_193_2076
PubMedID: 21217001
Gene_locus related to this paper: dicd3-e0scu7 , dicd3-e0sjp0 , erwch-INDC , dicd3-e0sgk0 , dicze-c6cmc7 , 9entr-u6zcq0 , dicd3-e0sg49

Title : Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018 - Hu_2011_BMC.Genomics_12_93
Author(s) : Hu S , Zheng H , Gu Y , Zhao J , Zhang W , Yang Y , Wang S , Zhao G , Yang S , Jiang W
Ref : BMC Genomics , 12 :93 , 2011
Abstract : BACKGROUND: Clostridium acetobutylicum, a gram-positive and spore-forming anaerobe, is a major strain for the fermentative production of acetone, butanol and ethanol. But a previously isolated hyper-butanol producing strain C. acetobutylicum EA 2018 does not produce spores and has greater capability of solvent production, especially for butanol, than the type strain C. acetobutylicum ATCC 824.
RESULTS: Complete genome of C. acetobutylicum EA 2018 was sequenced using Roche 454 pyrosequencing. Genomic comparison with ATCC 824 identified many variations which may contribute to the hyper-butanol producing characteristics in the EA 2018 strain, including a total of 46 deletion sites and 26 insertion sites. In addition, transcriptomic profiling of gene expression in EA 2018 relative to that of ATCC824 revealed expression-level changes of several key genes related to solvent formation. For example, spo0A and adhEII have higher expression level, and most of the acid formation related genes have lower expression level in EA 2018. Interestingly, the results also showed that the variation in CEA_G2622 (CAC2613 in ATCC 824), a putative transcriptional regulator involved in xylose utilization, might accelerate utilization of substrate xylose.
CONCLUSIONS: Comparative analysis of C. acetobutylicum hyper-butanol producing strain EA 2018 and type strain ATCC 824 at both genomic and transcriptomic levels, for the first time, provides molecular-level understanding of non-sporulation, higher solvent production and enhanced xylose utilization in the mutant EA 2018. The information could be valuable for further genetic modification of C. acetobutylicum for more effective butanol production.
ESTHER : Hu_2011_BMC.Genomics_12_93
PubMedSearch : Hu_2011_BMC.Genomics_12_93
PubMedID: 21284892
Gene_locus related to this paper: cloab-CAC2917 , cloab-q97db4 , cloac-CAC0719 , cloac-CAC1022 , cloac-CAC1962 , cloac-CAC2246 , cloac-CAC3407 , cloac-CAP0071 , cloac-pnbae

Title : Genome sequence and analysis of the tuber crop potato - Xu_2011_Nature_475_189
Author(s) : Xu X , Pan S , Cheng S , Zhang B , Mu D , Ni P , Zhang G , Yang S , Li R , Wang J , Orjeda G , Guzman F , Torres M , Lozano R , Ponce O , Martinez D , De la Cruz G , Chakrabarti SK , Patil VU , Skryabin KG , Kuznetsov BB , Ravin NV , Kolganova TV , Beletsky AV , Mardanov AV , Di Genova A , Bolser DM , Martin DM , Li G , Yang Y , Kuang H , Hu Q , Xiong X , Bishop GJ , Sagredo B , Mejia N , Zagorski W , Gromadka R , Gawor J , Szczesny P , Huang S , Zhang Z , Liang C , He J , Li Y , He Y , Xu J , Zhang Y , Xie B , Du Y , Qu D , Bonierbale M , Ghislain M , Herrera Mdel R , Giuliano G , Pietrella M , Perrotta G , Facella P , O'Brien K , Feingold SE , Barreiro LE , Massa GA , Diambra L , Whitty BR , Vaillancourt B , Lin H , Massa AN , Geoffroy M , Lundback S , DellaPenna D , Buell CR , Sharma SK , Marshall DF , Waugh R , Bryan GJ , Destefanis M , Nagy I , Milbourne D , Thomson SJ , Fiers M , Jacobs JM , Nielsen KL , Sonderkaer M , Iovene M , Torres GA , Jiang J , Veilleux RE , Bachem CW , De Boer J , Borm T , Kloosterman B , van Eck H , Datema E , Hekkert B , Goverse A , van Ham RC , Visser RG
Ref : Nature , 475 :189 , 2011
Abstract : Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.
ESTHER : Xu_2011_Nature_475_189
PubMedSearch : Xu_2011_Nature_475_189
PubMedID: 21743474
Gene_locus related to this paper: soltu-q2tqv0 , soltu-q4h433 , soltu-m0zl00 , soltu-m1aw23 , soltu-m0zxh5 , soltu-m1d3q4 , soltu-m1bz14 , soltu-m1d3q6 , sollc-k4b1g3 , soltu-m0zzn8 , soltu-m1ba60 , sollc-k4bf33 , soltu-m1c8d8 , soltu-m1ced9 , soltu-m1a385 , soltu-m1bz15 , soltu-m1a7s9 , soltu-m1bc84 , soltu-m1bpd1 , sollc-k4bm34 , soltu-m1a487 , soltu-m1a5u0 , soltu-m1cjx7 , soltu-m1bvq8 , soltu-m1baq1 , soltu-m1cfh4 , soltu-m1azl4 , soltu-m0ztj0 , soltu-m1d6d0 , soltu-m1cap1 , soltu-m1a7m1 , soltu-m1d3s6

Title : The Arabidopsis LSD1 gene plays an important role in the regulation of low temperature-dependent cell death - Huang_2010_New.Phytol_187_301
Author(s) : Huang X , Li Y , Zhang X , Zuo J , Yang S
Ref : New Phytol , 187 :301 , 2010
Abstract : SUMMARY: In higher plants, the crosstalk between cold stress responses and reactive oxygen species (ROS) signaling is not well understood. *Two chilling-sensitive mutants, chs4-1 and chs4-3, were characterized genetically and molecularly. *The CHS4 gene, identified by map-based cloning, was found to be identical to lesion simulating disease resistance 1 (LSD1). We therefore renamed these two alleles lsd1-3 and lsd1-4, respectively. These two mutants exhibited an extensive cell death phenotype under cold stress conditions. Consistently, lsd1-3 plants exposed to cold showed up-regulation of the PR1 and PR2 genes, and increased accumulation of salicylic acid. These results indicate that low temperature is another trigger of cell death in lsd1 mutants. Furthermore, lsd1-3 plants accumulated higher concentrations of H(2)O(2) and total glutathione under cold conditions than wild-type plants. Genetic analysis revealed that PAD4 and EDS1, two key signaling regulators mediating resistance responses, are required for the chilling-sensitive phenotype of lsd1-3. *These findings reveal a role of LSD1 in regulating cell death trigged by cold stress and a link between cold stress responses and ROS-associated signaling.
ESTHER : Huang_2010_New.Phytol_187_301
PubMedSearch : Huang_2010_New.Phytol_187_301
PubMedID: 20456049

Title : The genome of the cucumber, Cucumis sativus L - Huang_2009_Nat.Genet_41_1275
Author(s) : Huang S , Li R , Zhang Z , Li L , Gu X , Fan W , Lucas WJ , Wang X , Xie B , Ni P , Ren Y , Zhu H , Li J , Lin K , Jin W , Fei Z , Li G , Staub J , Kilian A , van der Vossen EA , Wu Y , Guo J , He J , Jia Z , Tian G , Lu Y , Ruan J , Qian W , Wang M , Huang Q , Li B , Xuan Z , Cao J , Asan , Wu Z , Zhang J , Cai Q , Bai Y , Zhao B , Han Y , Li Y , Li X , Wang S , Shi Q , Liu S , Cho WK , Kim JY , Xu Y , Heller-Uszynska K , Miao H , Cheng Z , Zhang S , Wu J , Yang Y , Kang H , Li M , Liang H , Ren X , Shi Z , Wen M , Jian M , Yang H , Zhang G , Yang Z , Chen R , Ma L , Liu H , Zhou Y , Zhao J , Fang X , Fang L , Liu D , Zheng H , Zhang Y , Qin N , Li Z , Yang G , Yang S , Bolund L , Kristiansen K , Li S , Zhang X , Wang J , Sun R , Zhang B , Jiang S , Du Y
Ref : Nat Genet , 41 :1275 , 2009
Abstract : Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and 'fresh green' odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system.
ESTHER : Huang_2009_Nat.Genet_41_1275
PubMedSearch : Huang_2009_Nat.Genet_41_1275
PubMedID: 19881527
Gene_locus related to this paper: cucsa-a0a0a0ktw5 , cucsa-a0a0a0lnt6 , cucsa-a0a0a0kpn7 , cucsa-a0a0a0lvt9 , cucsa-a0a0a0kdx8 , cucsa-a0a0a0m228 , cucsa-a0a0a0kz31 , cucsa-a0a0a0k5t5 , cucsa-a0a0a0kfs7 , cucsa-a0a0a0kjj7 , cucsa-a0a0a0kzs7 , cucsa-a0a0a0l0a6 , cucsa-a0a0a0l4w4 , cucsa-a0a0a0lpz0 , cucsa-a0a0a0ls66

Title : Lipidomic analysis reveals differential defense responses of Taxus cuspidata cells to two elicitors, methyl jasmonate and cerium (Ce4+) - Yang_2008_Biochim.Biophys.Acta_1781_123
Author(s) : Yang S , Lu SH , Yuan YJ
Ref : Biochimica & Biophysica Acta , 1781 :123 , 2008
Abstract : Methyl jasmonate (MeJA) and cerium (Ce(4+)) elicitation share common features of increasing taxol accumulation of Taxus cuspidata cells. Interestingly, Ce(4+) induces programmed cell death (PCD), but this phenomenon is not observed with MeJA elicitation. Here, using a lipidomic approach to measure more than 100 membrane glycerophospholipids of T. cuspidata cells quantitatively, we discovered that lysophosphatidylcholine (LysoPC), phosphatidic acid (PA) and phosphatidylcholine were three potential lipid markers that were responsible for the differences between Ce(4+)-induced cells and MeJA-induced cells. Compared with MeJA elicitation, marked increase of phospholipase D (PLD) activity was observed following Ce(4+) elicitation, suggesting that the PLD activation and high concentrations of PA production might mediate the PCD. Rapid increase of phospholipase A(2) (PLA(2)) activity caused the release of fatty acids and LysoPC following Ce(4+) elicitation, which enhanced endogenous jasmonic acid (JA) accumulation. In contrast, PLA(2) activity was poorly induced following MeJA elicitation. PLA(2) inhibitor suppressed not only JA accumulation but also taxol production, suggesting that the PLA(2) activation mediated Ce(4+)-induced taxol production partially through a JA-dependent signaling pathway. These results demonstrate that differential alternation of glycerolphospholipids caused by phospholipases constitutes an important step in cell death response to Ce(4+) and increasing taxol production.
ESTHER : Yang_2008_Biochim.Biophys.Acta_1781_123
PubMedSearch : Yang_2008_Biochim.Biophys.Acta_1781_123
PubMedID: 18179778

Title : Overexpression of Serratia marcescens lipase in Escherichia coli for efficient bioresolution of racemic ketoprofen - Long_2007_J.Mol.Catal.B.Enzym_47_105
Author(s) : Long ZD , Xu JH , Zhao LL , Pan J , Yang S , Hua L
Ref : J Mol Catal B Enzym , 47 :105 , 2007
Abstract : Lipase from Serratia marcescens ECU1010 was cloned and overexpressed in E. coli. After optimization, the maximum lipase activities reached 5000-6000 U/l and this recombinant lipase could enantioselectively hydrolyze (S)-ketoprofen esters into (S)-ketoprofen. Among six alkyl esters of racemic ketoprofen investigated, this lipase showed the best enantioselectivity for the kinetic resolution of ketoprofen ethyl ester, with an eep (enantiomeric excess of product) of 91.6% and E-value of 63 obtained at 48.2% conversion. Twelve nonionic surfactants were tested for enhancing the enantioselectivity of this lipase in the bioresolution of ketoprofen ethyl ester. A very high E-value of 1084 was achieved, with an optical purity of >99% eep and a yield of 42.6% in the presence of 3% Brij 92V. Further studies showed that the selectivity of the lipase was improved with the increase of Brij 92V concentration. The substrate (ketoprofen ethyl ester) does not inhibit the lipase activity, while the product (S)-ketoprofen inhibits the lipase activity to some extent. These results indicate that the S. marcescens lipase is very useful for biocatalytic production of chiral profens such as (S)-ketoprofen.
ESTHER : Long_2007_J.Mol.Catal.B.Enzym_47_105
PubMedSearch : Long_2007_J.Mol.Catal.B.Enzym_47_105
Gene_locus related to this paper: serma-lipasA

Title : Genome sequence, comparative analysis and haplotype structure of the domestic dog - Lindblad-Toh_2005_Nature_438_803
Author(s) : Lindblad-Toh K , Wade CM , Mikkelsen TS , Karlsson EK , Jaffe DB , Kamal M , Clamp M , Chang JL , Kulbokas EJ, 3rd , Zody MC , Mauceli E , Xie X , Breen M , Wayne RK , Ostrander EA , Ponting CP , Galibert F , Smith DR , deJong PJ , Kirkness E , Alvarez P , Biagi T , Brockman W , Butler J , Chin CW , Cook A , Cuff J , Daly MJ , Decaprio D , Gnerre S , Grabherr M , Kellis M , Kleber M , Bardeleben C , Goodstadt L , Heger A , Hitte C , Kim L , Koepfli KP , Parker HG , Pollinger JP , Searle SM , Sutter NB , Thomas R , Webber C , Baldwin J , Abebe A , Abouelleil A , Aftuck L , Ait-Zahra M , Aldredge T , Allen N , An P , Anderson S , Antoine C , Arachchi H , Aslam A , Ayotte L , Bachantsang P , Barry A , Bayul T , Benamara M , Berlin A , Bessette D , Blitshteyn B , Bloom T , Blye J , Boguslavskiy L , Bonnet C , Boukhgalter B , Brown A , Cahill P , Calixte N , Camarata J , Cheshatsang Y , Chu J , Citroen M , Collymore A , Cooke P , Dawoe T , Daza R , Decktor K , DeGray S , Dhargay N , Dooley K , Dorje P , Dorjee K , Dorris L , Duffey N , Dupes A , Egbiremolen O , Elong R , Falk J , Farina A , Faro S , Ferguson D , Ferreira P , Fisher S , FitzGerald M , Foley K , Foley C , Franke A , Friedrich D , Gage D , Garber M , Gearin G , Giannoukos G , Goode T , Goyette A , Graham J , Grandbois E , Gyaltsen K , Hafez N , Hagopian D , Hagos B , Hall J , Healy C , Hegarty R , Honan T , Horn A , Houde N , Hughes L , Hunnicutt L , Husby M , Jester B , Jones C , Kamat A , Kanga B , Kells C , Khazanovich D , Kieu AC , Kisner P , Kumar M , Lance K , Landers T , Lara M , Lee W , Leger JP , Lennon N , Leuper L , LeVine S , Liu J , Liu X , Lokyitsang Y , Lokyitsang T , Lui A , MacDonald J , Major J , Marabella R , Maru K , Matthews C , McDonough S , Mehta T , Meldrim J , Melnikov A , Meneus L , Mihalev A , Mihova T , Miller K , Mittelman R , Mlenga V , Mulrain L , Munson G , Navidi A , Naylor J , Nguyen T , Nguyen N , Nguyen C , Nicol R , Norbu N , Norbu C , Novod N , Nyima T , Olandt P , O'Neill B , O'Neill K , Osman S , Oyono L , Patti C , Perrin D , Phunkhang P , Pierre F , Priest M , Rachupka A , Raghuraman S , Rameau R , Ray V , Raymond C , Rege F , Rise C , Rogers J , Rogov P , Sahalie J , Settipalli S , Sharpe T , Shea T , Sheehan M , Sherpa N , Shi J , Shih D , Sloan J , Smith C , Sparrow T , Stalker J , Stange-Thomann N , Stavropoulos S , Stone C , Stone S , Sykes S , Tchuinga P , Tenzing P , Tesfaye S , Thoulutsang D , Thoulutsang Y , Topham K , Topping I , Tsamla T , Vassiliev H , Venkataraman V , Vo A , Wangchuk T , Wangdi T , Weiand M , Wilkinson J , Wilson A , Yadav S , Yang S , Yang X , Young G , Yu Q , Zainoun J , Zembek L , Zimmer A , Lander ES
Ref : Nature , 438 :803 , 2005
Abstract : Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
ESTHER : Lindblad-Toh_2005_Nature_438_803
PubMedSearch : Lindblad-Toh_2005_Nature_438_803
PubMedID: 16341006
Gene_locus related to this paper: canfa-1lipg , canfa-2neur , canfa-3neur , canfa-ACHE , canfa-BCHE , canfa-cauxin , canfa-CESDD1 , canfa-e2qsb1 , canfa-e2qsl3 , canfa-e2qsz2 , canfa-e2qvk3 , canfa-e2qw15 , canfa-e2qxs8 , canfa-e2qzs6 , canfa-e2r5t3 , canfa-e2r6f6 , canfa-e2r7e8 , canfa-e2r8v9 , canfa-e2r8z1 , canfa-e2r9h4 , canfa-e2r455 , canfa-e2rb70 , canfa-e2rcq9 , canfa-e2rd94 , canfa-e2rgi0 , canfa-e2rkq0 , canfa-e2rlz9 , canfa-e2rm00 , canfa-e2rqf1 , canfa-e2rss9 , canfa-f1p6w8 , canfa-f1p8b6 , canfa-f1p9d8 , canfa-f1p683 , canfa-f1pb79 , canfa-f1pgw0 , canfa-f1phd0 , canfa-f1phx2 , canfa-f1pke8 , canfa-f1pp08 , canfa-f1ppp9 , canfa-f1ps07 , canfa-f1ptf1 , canfa-f1pvp4 , canfa-f1pw93 , canfa-f1pwk3 , canfa-pafa , canfa-q1ert3 , canfa-q5jzr0 , canfa-e2rmb9 , canlf-f6v865 , canlf-e2rjg6 , canlf-e2r2h2 , canlf-f1p648 , canlf-f1pw90 , canlf-j9p8v6 , canlf-f1pcc4 , canlf-e2qxh0 , canlf-e2r774 , canlf-f1pf96 , canlf-e2rq56 , canlf-j9nwb1 , canlf-f1ptw2 , canlf-j9p8h1 , canlf-e2ree2 , canlf-f1prs1 , canlf-j9nus1 , canlf-e2rf91 , canlf-f1pg57 , canlf-f1q111

Title : Inhibition of lipase activity and lipolysis in rat islets reduces insulin secretion - Mulder_2004_Diabetes_53_122
Author(s) : Mulder H , Yang S , Winzell MS , Holm C , Ahren B
Ref : Diabetes , 53 :122 , 2004
Abstract : Lipids may serve as coupling factors in K(ATP)-independent glucose sensing in beta-cells. We have previously demonstrated that beta-cells harbor lipase activities, one of which is the hormone-sensitive lipase. Whether beta-cell lipases are critical for glucose-stimulated insulin secretion (GSIS) by providing lipid-derived signals from endogenous lipids is unknown. Therefore, using a lipase inhibitor (orlistat), we examined whether lipase inhibition reduces insulin secretion. Islet lipolysis stimulated by glucose and diglyceride lipase activity was abolished by orlistat. Incubation of rat islets with orlistat dose dependently inhibited GSIS; this inhibition was reversed by 1 mmol/l palmitate, suggesting that orlistat acts via impaired formation of an acylglyceride-derived coupling signal. Orlistat inhibited the potentiating effect of forskolin on GSIS, an effect proposed to be due to activation of a lipase. In perifused islets, orlistat attenuated mainly the second phase of insulin secretion. Because the rise in islet ATP/ADP levels in response to glucose and oxidation of the sugar were unaffected by orlistat whereas the second phase of insulin secretion was reduced, it seems likely that a lipid coupling factor involved in K(ATP)-independent glucose sensing has been perturbed. Thus, beta-cell lipase activity is involved in GSIS, emphasizing the important role of beta-cell lipid metabolism for insulin secretion.
ESTHER : Mulder_2004_Diabetes_53_122
PubMedSearch : Mulder_2004_Diabetes_53_122
PubMedID: 14693706

Title : Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution - Hillier_2004_Nature_432_695
Author(s) : Hillier LW , Miller W , Birney E , Warren W , Hardison RC , Ponting CP , Bork P , Burt DW , Groenen MA , Delany ME , Dodgson JB , Chinwalla AT , Cliften PF , Clifton SW , Delehaunty KD , Fronick C , Fulton RS , Graves TA , Kremitzki C , Layman D , Magrini V , McPherson JD , Miner TL , Minx P , Nash WE , Nhan MN , Nelson JO , Oddy LG , Pohl CS , Randall-Maher J , Smith SM , Wallis JW , Yang SP , Romanov MN , Rondelli CM , Paton B , Smith J , Morrice D , Daniels L , Tempest HG , Robertson L , Masabanda JS , Griffin DK , Vignal A , Fillon V , Jacobbson L , Kerje S , Andersson L , Crooijmans RP , Aerts J , van der Poel JJ , Ellegren H , Caldwell RB , Hubbard SJ , Grafham DV , Kierzek AM , McLaren SR , Overton IM , Arakawa H , Beattie KJ , Bezzubov Y , Boardman PE , Bonfield JK , Croning MD , Davies RM , Francis MD , Humphray SJ , Scott CE , Taylor RG , Tickle C , Brown WR , Rogers J , Buerstedde JM , Wilson SA , Stubbs L , Ovcharenko I , Gordon L , Lucas S , Miller MM , Inoko H , Shiina T , Kaufman J , Salomonsen J , Skjoedt K , Ka-Shu Wong G , Wang J , Liu B , Yu J , Yang H , Nefedov M , Koriabine M , deJong PJ , Goodstadt L , Webber C , Dickens NJ , Letunic I , Suyama M , Torrents D , von Mering C , Zdobnov EM , Makova K , Nekrutenko A , Elnitski L , Eswara P , King DC , Yang S , Tyekucheva S , Radakrishnan A , Harris RS , Chiaromonte F , Taylor J , He J , Rijnkels M , Griffiths-Jones S , Ureta-Vidal A , Hoffman MM , Severin J , Searle SM , Law AS , Speed D , Waddington D , Cheng Z , Tuzun E , Eichler E , Bao Z , Flicek P , Shteynberg DD , Brent MR , Bye JM , Huckle EJ , Chatterji S , Dewey C , Pachter L , Kouranov A , Mourelatos Z , Hatzigeorgiou AG , Paterson AH , Ivarie R , Brandstrom M , Axelsson E , Backstrom N , Berlin S , Webster MT , Pourquie O , Reymond A , Ucla C , Antonarakis SE , Long M , Emerson JJ , Betran E , Dupanloup I , Kaessmann H , Hinrichs AS , Bejerano G , Furey TS , Harte RA , Raney B , Siepel A , Kent WJ , Haussler D , Eyras E , Castelo R , Abril JF , Castellano S , Camara F , Parra G , Guigo R , Bourque G , Tesler G , Pevzner PA , Smit A , Fulton LA , Mardis ER , Wilson RK
Ref : Nature , 432 :695 , 2004
Abstract : We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
ESTHER : Hillier_2004_Nature_432_695
PubMedSearch : Hillier_2004_Nature_432_695
PubMedID: 15592404
Gene_locus related to this paper: chick-a0a1d5pmd9 , chick-b3tzb3 , chick-BCHE , chick-cb043 , chick-d3wgl5 , chick-e1bsm0 , chick-e1bvq6 , chick-e1bwz0 , chick-e1bwz1 , chick-e1byn1 , chick-e1bz81 , chick-e1c0z8 , chick-e1c7p7 , chick-f1nby4 , chick-f1ncz8 , chick-f1ndp3 , chick-f1nep4 , chick-f1nj68 , chick-f1njg6 , chick-f1njk4 , chick-f1njs4 , chick-f1njs5 , chick-f1nk87 , chick-f1nmx9 , chick-f1ntp8 , chick-f1nvg7 , chick-f1nwf2 , chick-f1p1l1 , chick-f1p3j5 , chick-f1p4c6 , chick-f1p508 , chick-fas , chick-h9l0k6 , chick-nlgn1 , chick-NLGN3 , chick-q5f3h8 , chick-q5zhm0 , chick-q5zi81 , chick-q5zij5 , chick-q5zin0 , chick-thyro , chick-f1nrq2 , chick-e1byd4 , chick-e1c2h6 , chick-a0a1d5pk92 , chick-a0a1d5pzg7 , chick-f1nbc2 , chick-f1nf25 , chick-f1nly5 , chick-f1p4h5 , chick-f1nzi7 , chick-f1p5k3 , chick-f1nm35 , chick-a0a1d5pl11 , chick-a0a1d5pj73 , chick-f1nxu6 , chick-a0a1d5nwc0 , chick-e1bxs8 , chick-f1p2g7 , chick-f1nd96

Title : Large-scale cDNA transfection screening for genes related to cancer development and progression - Wan_2004_Proc.Natl.Acad.Sci.U.S.A_101_15724
Author(s) : Wan D , Gong Y , Qin W , Zhang P , Li J , Wei L , Zhou X , Li H , Qiu X , Zhong F , He L , Yu J , Yao G , Jiang H , Qian L , Yu Y , Shu H , Chen X , Xu H , Guo M , Pan Z , Chen Y , Ge C , Yang S , Gu J
Ref : Proc Natl Acad Sci U S A , 101 :15724 , 2004
Abstract : A large-scale assay was performed by transfecting 29,910 individual cDNA clones derived from human placenta, fetus, and normal liver tissues into human hepatoma cells and 22,926 cDNA clones into mouse NIH 3T3 cells. Based on the results of colony formation in hepatoma cells and foci formation in NIH 3T3 cells, 3,806 cDNA species (8,237 clones) were found to possess the ability of either stimulating or inhibiting cell growth. Among them, 2,836 (6,958 clones) were known genes, 372 (384 clones) were previously unrecognized genes, and 598 (895 clones) were unigenes of uncharacterized structure and function. A comprehensive analysis of the genes and the potential mechanisms for their involvement in the regulation of cell growth is provided. The genes were classified into four categories: I, genes related to the basic cellular mechanism for growth and survival; II, genes related to the cellular microenvironment; III, genes related to host-cell systemic regulation; and IV, genes of miscellaneous function. The extensive growth-regulatory activity of genes with such highly diversified functions suggests that cancer may be related to multiple levels of cellular and systemic controls. The present assay provides a direct genomewide functional screening method. It offers a better understanding of the basic machinery of oncogenesis, including previously undescribed systemic regulatory mechanisms, and also provides a tool for gene discovery with potential clinical applications.
ESTHER : Wan_2004_Proc.Natl.Acad.Sci.U.S.A_101_15724
PubMedSearch : Wan_2004_Proc.Natl.Acad.Sci.U.S.A_101_15724
PubMedID: 15498874

Title : Genome sequence of the Brown Norway rat yields insights into mammalian evolution - Gibbs_2004_Nature_428_493
Author(s) : Gibbs RA , Weinstock GM , Metzker ML , Muzny DM , Sodergren EJ , Scherer S , Scott G , Steffen D , Worley KC , Burch PE , Okwuonu G , Hines S , Lewis L , DeRamo C , Delgado O , Dugan-Rocha S , Miner G , Morgan M , Hawes A , Gill R , Celera , Holt RA , Adams MD , Amanatides PG , Baden-Tillson H , Barnstead M , Chin S , Evans CA , Ferriera S , Fosler C , Glodek A , Gu Z , Jennings D , Kraft CL , Nguyen T , Pfannkoch CM , Sitter C , Sutton GG , Venter JC , Woodage T , Smith D , Lee HM , Gustafson E , Cahill P , Kana A , Doucette-Stamm L , Weinstock K , Fechtel K , Weiss RB , Dunn DM , Green ED , Blakesley RW , Bouffard GG , de Jong PJ , Osoegawa K , Zhu B , Marra M , Schein J , Bosdet I , Fjell C , Jones S , Krzywinski M , Mathewson C , Siddiqui A , Wye N , McPherson J , Zhao S , Fraser CM , Shetty J , Shatsman S , Geer K , Chen Y , Abramzon S , Nierman WC , Havlak PH , Chen R , Durbin KJ , Egan A , Ren Y , Song XZ , Li B , Liu Y , Qin X , Cawley S , Cooney AJ , D'Souza LM , Martin K , Wu JQ , Gonzalez-Garay ML , Jackson AR , Kalafus KJ , McLeod MP , Milosavljevic A , Virk D , Volkov A , Wheeler DA , Zhang Z , Bailey JA , Eichler EE , Tuzun E , Birney E , Mongin E , Ureta-Vidal A , Woodwark C , Zdobnov E , Bork P , Suyama M , Torrents D , Alexandersson M , Trask BJ , Young JM , Huang H , Wang H , Xing H , Daniels S , Gietzen D , Schmidt J , Stevens K , Vitt U , Wingrove J , Camara F , Mar Alba M , Abril JF , Guigo R , Smit A , Dubchak I , Rubin EM , Couronne O , Poliakov A , Hubner N , Ganten D , Goesele C , Hummel O , Kreitler T , Lee YA , Monti J , Schulz H , Zimdahl H , Himmelbauer H , Lehrach H , Jacob HJ , Bromberg S , Gullings-Handley J , Jensen-Seaman MI , Kwitek AE , Lazar J , Pasko D , Tonellato PJ , Twigger S , Ponting CP , Duarte JM , Rice S , Goodstadt L , Beatson SA , Emes RD , Winter EE , Webber C , Brandt P , Nyakatura G , Adetobi M , Chiaromonte F , Elnitski L , Eswara P , Hardison RC , Hou M , Kolbe D , Makova K , Miller W , Nekrutenko A , Riemer C , Schwartz S , Taylor J , Yang S , Zhang Y , Lindpaintner K , Andrews TD , Caccamo M , Clamp M , Clarke L , Curwen V , Durbin R , Eyras E , Searle SM , Cooper GM , Batzoglou S , Brudno M , Sidow A , Stone EA , Payseur BA , Bourque G , Lopez-Otin C , Puente XS , Chakrabarti K , Chatterji S , Dewey C , Pachter L , Bray N , Yap VB , Caspi A , Tesler G , Pevzner PA , Haussler D , Roskin KM , Baertsch R , Clawson H , Furey TS , Hinrichs AS , Karolchik D , Kent WJ , Rosenbloom KR , Trumbower H , Weirauch M , Cooper DN , Stenson PD , Ma B , Brent M , Arumugam M , Shteynberg D , Copley RR , Taylor MS , Riethman H , Mudunuri U , Peterson J , Guyer M , Felsenfeld A , Old S , Mockrin S , Collins F
Ref : Nature , 428 :493 , 2004
Abstract : The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
ESTHER : Gibbs_2004_Nature_428_493
PubMedSearch : Gibbs_2004_Nature_428_493
PubMedID: 15057822
Gene_locus related to this paper: rat-abhea , rat-abheb , rat-cd029 , rat-d3zaw4 , rat-dpp9 , rat-d3zhq1 , rat-d3zkp8 , rat-d3zuq1 , rat-d3zxw8 , rat-d4a4w4 , rat-d4a7w1 , rat-d4a9l7 , rat-d4a071 , rat-d4aa31 , rat-d4aa33 , rat-d4aa61 , rat-dglb , rat-f1lz91 , rat-Kansl3 , rat-nceh1 , rat-Tex30 , ratno-1hlip , ratno-1neur , ratno-1plip , ratno-2neur , ratno-3neur , ratno-3plip , ratno-ABH15 , ratno-ACHE , ratno-balip , ratno-BCHE , ratno-cauxin , ratno-Ces1d , ratno-Ces1e , ratno-Ces2f , ratno-d3ze31 , ratno-d3zp14 , ratno-d3zxi3 , ratno-d3zxq0 , ratno-d3zxq1 , ratno-d4a3d4 , ratno-d4aa05 , ratno-dpp4 , ratno-dpp6 , ratno-est8 , ratno-FAP , ratno-hyep , ratno-hyes , ratno-kmcxe , ratno-lmcxe , ratno-LOC246252 , ratno-MGLL , ratno-pbcxe , ratno-phebest , ratno-Ppgb , ratno-q4qr68 , ratno-q6ayr2 , ratno-q6q629 , ratno-SPG21 , ratno-thyro , rat-m0rc77 , rat-a0a0g2k9y7 , rat-a0a0g2kb83 , rat-d3zba8 , rat-d3zbj1 , rat-d3zcr8 , rat-d3zxw5 , rat-d4a340 , rat-f1lvg7 , rat-m0r509 , rat-m0r5d4 , rat-b5den3 , rat-d3zxk4 , rat-d4a1b6 , rat-d3zmg4 , rat-ab17c

Title : Induction of lipoprotein lipase gene expression in Chlamydia pneumoniae-infected macrophages is dependent on Ca2+ signaling events - Azenabor_2004_Biol.Chem_385_67
Author(s) : Azenabor AA , Job G , Yang S
Ref : Biol Chem , 385 :67 , 2004
Abstract : Unregulated uptake of low density lipoprotein (LDL) in macrophages is the hallmark of early atherogenic lesions, and Chlamydia pneumoniae infection of macrophages induces this process by an unknown mechanism. It was therefore aimed in this study to investigate (i) the role of C. pneumoniae in macrophage expression of the lipoprotein lipase (LpL) gene, (ii) the probable role of Ca2+ influx signals and (iii) the effect of the process on LDL uptake. Lipoprotein lipase mRNA expression and LpL activity in infected RAW-264.7 cells were significantly upregulated. A biphasic Ca2+ influx signal was observed in infected cells with a moderate influx (303 nM Ca2+) favoring optimal LpL gene expression. Also, the antagonists of L-type Ca2+ channel in macrophages significantly down-regulated LpL gene expression and the biomolecular content of C. pneumoniae responsible for the observed events was in part found to be Chlamydia lipopolysaccharide (cLPS). Investigations aimed at determining the specific relevance of Ca(2+)-dependent lipoprotein lipase gene expression in C. pneumoniae-infected macrophages showed that the condition caused enhanced uptake of LDL which was abrogated by Calphostin-C-mediated down-regulation of LpL. This discovery of a specialized Ca2+ influx signal-mediated LpL upregulation in C. pneumoniae-infected macrophages provides a mechanistic insight into early events involving C. pneumoniae in macrophage foam cell formation resulting from LDL uptake.
ESTHER : Azenabor_2004_Biol.Chem_385_67
PubMedSearch : Azenabor_2004_Biol.Chem_385_67
PubMedID: 14977048

Title : The genome sequence of Drosophila melanogaster - Adams_2000_Science_287_2185
Author(s) : Adams MD , Celniker SE , Holt RA , Evans CA , Gocayne JD , Amanatides PG , Scherer SE , Li PW , Hoskins RA , Galle RF , George RA , Lewis SE , Richards S , Ashburner M , Henderson SN , Sutton GG , Wortman JR , Yandell MD , Zhang Q , Chen LX , Brandon RC , Rogers YH , Blazej RG , Champe M , Pfeiffer BD , Wan KH , Doyle C , Baxter EG , Helt G , Nelson CR , Gabor GL , Abril JF , Agbayani A , An HJ , Andrews-Pfannkoch C , Baldwin D , Ballew RM , Basu A , Baxendale J , Bayraktaroglu L , Beasley EM , Beeson KY , Benos PV , Berman BP , Bhandari D , Bolshakov S , Borkova D , Botchan MR , Bouck J , Brokstein P , Brottier P , Burtis KC , Busam DA , Butler H , Cadieu E , Center A , Chandra I , Cherry JM , Cawley S , Dahlke C , Davenport LB , Davies P , de Pablos B , Delcher A , Deng Z , Mays AD , Dew I , Dietz SM , Dodson K , Doup LE , Downes M , Dugan-Rocha S , Dunkov BC , Dunn P , Durbin KJ , Evangelista CC , Ferraz C , Ferriera S , Fleischmann W , Fosler C , Gabrielian AE , Garg NS , Gelbart WM , Glasser K , Glodek A , Gong F , Gorrell JH , Gu Z , Guan P , Harris M , Harris NL , Harvey D , Heiman TJ , Hernandez JR , Houck J , Hostin D , Houston KA , Howland TJ , Wei MH , Ibegwam C , Jalali M , Kalush F , Karpen GH , Ke Z , Kennison JA , Ketchum KA , Kimmel BE , Kodira CD , Kraft C , Kravitz S , Kulp D , Lai Z , Lasko P , Lei Y , Levitsky AA , Li J , Li Z , Liang Y , Lin X , Liu X , Mattei B , McIntosh TC , McLeod MP , McPherson D , Merkulov G , Milshina NV , Mobarry C , Morris J , Moshrefi A , Mount SM , Moy M , Murphy B , Murphy L , Muzny DM , Nelson DL , Nelson DR , Nelson KA , Nixon K , Nusskern DR , Pacleb JM , Palazzolo M , Pittman GS , Pan S , Pollard J , Puri V , Reese MG , Reinert K , Remington K , Saunders RD , Scheeler F , Shen H , Shue BC , Siden-Kiamos I , Simpson M , Skupski MP , Smith T , Spier E , Spradling AC , Stapleton M , Strong R , Sun E , Svirskas R , Tector C , Turner R , Venter E , Wang AH , Wang X , Wang ZY , Wassarman DA , Weinstock GM , Weissenbach J , Williams SM , WoodageT , Worley KC , Wu D , Yang S , Yao QA , Ye J , Yeh RF , Zaveri JS , Zhan M , Zhang G , Zhao Q , Zheng L , Zheng XH , Zhong FN , Zhong W , Zhou X , Zhu S , Zhu X , Smith HO , Gibbs RA , Myers EW , Rubin GM , Venter JC
Ref : Science , 287 :2185 , 2000
Abstract : The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.
ESTHER : Adams_2000_Science_287_2185
PubMedSearch : Adams_2000_Science_287_2185
PubMedID: 10731132
Gene_locus related to this paper: drome-1vite , drome-2vite , drome-3vite , drome-a1z6g9 , drome-abhd2 , drome-ACHE , drome-b6idz4 , drome-BEM46 , drome-CG5707 , drome-CG5704 , drome-CG1309 , drome-CG1882 , drome-CG1986 , drome-CG2059 , drome-CG2493 , drome-CG2528 , drome-CG2772 , drome-CG3160 , drome-CG3344 , drome-CG3523 , drome-CG3524 , drome-CG3734 , drome-CG3739 , drome-CG3744 , drome-CG3841 , drome-CG4267 , drome-CG4382 , drome-CG4390 , drome-CG4572 , drome-CG4582 , drome-CG4851 , drome-CG4979 , drome-CG5068 , drome-CG5162 , drome-CG5355 , drome-CG5377 , drome-CG5397 , drome-CG5412 , drome-CG5665 , drome-CG5932 , drome-CG5966 , drome-CG6018 , drome-CG6113 , drome-CG6271 , drome-CG6283 , drome-CG6295 , drome-CG6296 , drome-CG6414 , drome-CG6431 , drome-CG6472 , drome-CG6567 , drome-CG6675 , drome-CG6753 , drome-CG6847 , drome-CG7329 , drome-CG7367 , drome-CG7529 , drome-CG7632 , drome-CG8058 , drome-CG8093 , drome-CG8233 , drome-CG8424 , drome-CG8425 , drome-CG9059 , drome-CG9186 , drome-CG9287 , drome-CG9289 , drome-CG9542 , drome-CG9858 , drome-CG9953 , drome-CG9966 , drome-CG10116 , drome-CG10163 , drome-CG10175 , drome-CG10339 , drome-CG10357 , drome-CG10982 , drome-CG11034 , drome-CG11055 , drome-CG11309 , drome-CG11319 , drome-CG11406 , drome-CG11598 , drome-CG11600 , drome-CG11608 , drome-CG11626 , drome-CG11935 , drome-CG12108 , drome-CG12869 , drome-CG13282 , drome-CG13562 , drome-CG13772 , drome-CG14034 , drome-nlg3 , drome-CG14717 , drome-CG15101 , drome-CG15102 , drome-CG15106 , drome-CG15111 , drome-CG15820 , drome-CG15821 , drome-CG15879 , drome-CG17097 , drome-CG17099 , drome-CG17101 , drome-CG17191 , drome-CG17192 , drome-CG17292 , drome-CG18258 , drome-CG18284 , drome-CG18301 , drome-CG18302 , drome-CG18493 , drome-CG18530 , drome-CG18641 , drome-CG18815 , drome-CG31089 , drome-CG31091 , drome-CG32333 , drome-CG32483 , drome-CG33174 , drome-dnlg1 , drome-este4 , drome-este6 , drome-GH02384 , drome-GH02439 , drome-glita , drome-KRAKEN , drome-lip1 , drome-LIP2 , drome-lip3 , drome-MESK2 , drome-nrtac , drome-OME , drome-q7k274 , drome-Q9VJN0 , drome-Q8IP31 , drome-q9vux3