Song C

References (31)

Title : Structure-activity relationship of Caulerpa lentillifera polysaccharide in inhibiting lipid digestion - You_2024_Int.J.Biol.Macromol__129435
Author(s) : You Y , Song C , Fu Y , Sun Y , Wen C , Zhu B , Song S
Ref : Int J Biol Macromol , :129435 , 2024
Abstract : Caulerpa lentillifera polysaccharide (CLP) has been characterized as a sulfated polysaccharide which can effectively inhibit lipid digestion. However, little information was known regarding its inhibitory mechanisms. In the present study, desulfation and degradation were conducted to prepare the derivatives of CLP, and a series of chemical and spectroscopic methods were used to elucidate the structure-activity relationship of CLP on the inhibitory effect of lipid digestion. Results revealed that CLP possessed excellent binding capacities for sodium cholate, sodium glycocholate, and sodium taurocholate. In addition, CLP can effectively inhibit lipase activity by quenching the fluorescence intensity, changing the secondary structure, and decreasing the UV-Vis absorbance. Of note, sulfate groups in CLP took a vital role in inhibiting lipase activity, while the molecular weight of CLP showed a positive correlation with the binding activities of bile acids. Furthermore, adding CLP into the whey protein isolate (WPI) emulsion system also impeded lipid digestion, indicating that CLP can be a potential reduced-fat nutraceutical used in food emulsion systems.
ESTHER : You_2024_Int.J.Biol.Macromol__129435
PubMedSearch : You_2024_Int.J.Biol.Macromol__129435
PubMedID: 38228205

Title : On the Binding Mode and Molecular Mechanism of Enzymatic Polyethylene Terephthalate Degradations - Falkenstein_2023_ACS.Catal_13_6919
Author(s) : Falkenstein P , Zhao Z , Di Pede-Mattatelli A , Kunze G , Sommer M , Sonnendecker C , Zimmermann W , Colizzi F , Matysik J , Song C
Ref : ACS Catal , 13 :6919 , 2023
Abstract : Enzymatic degradation of polyethylene terephthlate (PET) by polyester hydrolases is currently subject to intensive research, as it is considered as a potential eco-friendly recycling method for plastic waste. However, the substrate-binding mode and the molecular mechanism of enzymatic PET hydrolysis are still under intense investigation, and controversial hypotheses have been presented. To help unravel the inherent mechanism of biocatalytic PET degradation at the atomic level, we performed solid-state NMR measurements of a cutinase from Thermobifida fusca (TfCut2) embedded in trehalose glasses together with chemically synthesized, amorphous 13C(O)-labeled oligomeric PET. The resulting ternary enzyme-PET-trehalose glassy system enabled advanced solid-state NMR methods for real-time tracking of the enzymatic PET degradation and the investigation of PET chain dynamics. Combined with enhanced-sampling molecular dynamics simulations, specific enzymesubstrate interactions during the degradation process could also be monitored. Our results demonstrate that the PET chain is first cleaved by TfCut2 in blocks of at least one repeat unit and further to terephthalic acid and ethylene glycol. Moreover, the second step (formation of final hydrolysis products) appears to be rate-limiting in such reactions. The observed dynamic changes and interfacial protein contacts of 13C-labeled PET carbonyl groups suggest that only one PET repeat unit is bound to the enzyme during the degradation process while the rest of the PET chain is only loosely confined to the active site. These results, not accessible by using conventional solution enzyme samples and small nonhydrolyzable substrates, provide a better understanding of the biocatalytic PET degradation mechanism of polyester hydrolases.
ESTHER : Falkenstein_2023_ACS.Catal_13_6919
PubMedSearch : Falkenstein_2023_ACS.Catal_13_6919
Gene_locus related to this paper: thefu-q6a0i4

Title : A Phenotypic Screen Identifies Potent DPP9 Inhibitors Capable of Killing HIV-1 Infected Cells - Moore_2022_ACS.Chem.Biol_17_2595
Author(s) : Moore KP , Schwaid AG , Tudor M , Park S , Beshore DC , Converso A , Shipe WD , Anand R , Lan P , Moningka R , Rothman DM , Sun W , Chi A , Cornella-Taracido I , Adam GC , Bahnck-Teets C , Carroll SS , Fay JF , Goh SL , Lusen J , Quan S , Rodriguez S , Xu M , Andrews CL , Song C , Filzen T , Li J , Hollenstein K , Klein DJ , Lammens A , Lim UM , Fang Z , McHale C , Li Y , Lu M , Diamond TL , Howell BJ , Zuck P , Balibar CJ
Ref : ACS Chemical Biology , 17 :2595 , 2022
Abstract : Although current antiretroviral therapy can control HIV-1 replication and prevent disease progression, it is not curative. Identifying mechanisms that can lead to eradication of persistent viral reservoirs in people living with HIV-1 (PLWH) remains an outstanding challenge to achieving cure. Utilizing a phenotypic screen, we identified a novel chemical class capable of killing HIV-1 infected peripheral blood mononuclear cells. Tool compounds ICeD-1 and ICeD-2 ("inducer of cell death-1 and 2"), optimized for potency and selectivity from screening hits, were used to deconvolute the mechanism of action using a combination of chemoproteomic, biochemical, pharmacological, and genetic approaches. We determined that these compounds function by modulating dipeptidyl peptidase 9 (DPP9) and activating the caspase recruitment domain family member 8 (CARD8) inflammasome. Efficacy of ICeD-1 and ICeD-2 was dependent on HIV-1 protease activity and synergistic with efavirenz, which promotes premature activation of HIV-1 protease at high concentrations in infected cells. This in vitro synergy lowers the efficacious cell kill concentration of efavirenz to a clinically relevant dose at concentrations of ICeD-1 or ICeD-2 that do not result in complete DPP9 inhibition. These results suggest engagement of the pyroptotic pathway as a potential approach to eliminate HIV-1 infected cells.
ESTHER : Moore_2022_ACS.Chem.Biol_17_2595
PubMedSearch : Moore_2022_ACS.Chem.Biol_17_2595
PubMedID: 36044633
Gene_locus related to this paper: human-DPP8 , human-DPP9

Title : Marine fungal metabolite butyrolactone I prevents cognitive deficits by relieving inflammation and intestinal microbiota imbalance on aluminum trichloride-injured zebrafish - Nie_2022_J.Neuroinflammation_19_39
Author(s) : Nie Y , Yang J , Zhou L , Yang Z , Liang J , Liu Y , Ma X , Qian Z , Hong P , Kalueff AV , Song C , Zhang Y
Ref : J Neuroinflammation , 19 :39 , 2022
Abstract : BACKGROUND: Mounting evidences indicate that oxidative stress, neuroinflammation, and dysregulation of gut microbiota are related to neurodegenerative disorders (NDs). Butyrolactone I (BTL-I), a marine fungal metabolite, was previously reported as an in vitro neuroprotectant and inflammation inhibitor. However, little is known regarding its in vivo effects, whereas zebrafish (Danio rerio) could be used as a convenient in vivo model of toxicology and central nervous system (CNS) diseases. METHODS: Here, we employed in vivo and in silico methods to investigate the anti-NDs potential of BTL-I. Specifically, we established a cognitive deficit model in zebrafish by intraperitoneal (i.p.) injection of aluminum trichloride (AlCl(3)) (21 microg) and assessed their behaviors in the T-maze test. The proinflammatory cytokines interleukin-1beta (IL-1beta) and tumor necrosis factor-alpha (TNF-alpha) as well as acetylcholinesterase (AChE) activity or glutathione (GSH) levels were assayed 24 h after AlCl(3) injection. The intestinal flora variation of the zebrafish was investigated by 16S rDNA high-throughput analysis. The marine fungal metabolite, butyrolactone I (BTL-I), was used to modulate zebrafish cognitive deficits evoked by AlCl(3) and evaluated about its effects on the above inflammatory, cholinergic, oxidative stress, and gut floral indicators. Furthermore, the absorption, distribution, metabolism, excretion, and toxicity (ADMET) and drug-likeness properties of BTL-I were studied by the in silico tool ADMETlab. RESULTS: BTL-I dose-dependently ameliorated AlCl(3)-induced cognitive deficits in zebrafish. While AlCl(3) treatment elevated the levels of central and peripheral proinflammatory cytokines, increased AChE activity, and lowered GSH in the brains of zebrafish, these effects, except GSH reduction, were reversed by 25-100 mg/kg BTL-I administration. Besides, 16S rDNA high-throughput sequencing of the intestinal flora of zebrafish showed that AlCl(3) decreased Gram-positive bacteria and increased proinflammatory Gram-negative bacteria, while BTL-I contributed to maintaining the predominance of beneficial Gram-positive bacteria. Moreover, the in silico analysis indicated that BTL-I exhibits acceptable drug-likeness and ADMET profiles. CONCLUSIONS: The present findings suggest that BTL-I is a potential therapeutic agent for preventing CNS deficits caused by inflammation, neurotoxicity, and gut flora imbalance.
ESTHER : Nie_2022_J.Neuroinflammation_19_39
PubMedSearch : Nie_2022_J.Neuroinflammation_19_39
PubMedID: 35130930

Title : 3D-Printed, Portable, Fluorescent-Sensing Platform for Smartphone-Capable Detection of Organophosphorus Residue Using Reaction-Based Aggregation Induced Emission Luminogens - Jiao_2021_ACS.Sens__
Author(s) : Jiao Z , Guo Z , Huang X , Yang J , Huang J , Liu Y , Liu G , Zhang P , Song C , Tang BZ
Ref : ACS Sens , : , 2021
Abstract : Development of an easy-to-use, low-cost, household device can help the consumer quickly identify an organophosphorus (OP) residue concentration level. In this work, we demonstrate a 3D-printed, portable, fluorescent-sensing platform for smartphone-capable detection of OPs in vegetables. For development of the proposed device, we utilize the smartphone for capturing the strong thiol-activated fluorescence, which was produced by hydrolysis of OPs in the presence of alkali. The thiol-responsive AIEgen (maleimide-functionalized tetraphenylethylene) was non-emissive in both solution and the solid state but could be readily lighted up by the click addition of thiol to its MI pendant. An android application "Detection" has been developed on the basis of the gray value to analyze the different concentration levels of OPs in vegetable samples. The gray value was linearly related with the concentration of five kinds of organophosphorus residue, ranging from 0 to 20 microg/mL. It was also applied for determination of OPs residue in the leaves of cowpea, celery, and Chinese cabbage. Different from acetylcholinesterase enzyme-based sensors for poor stability under high temperature, the proposed method was a direct detection method for OPs and can be used for rapid monitoring of OPs residue concentration levels before LC-MS analysis.
ESTHER : Jiao_2021_ACS.Sens__
PubMedSearch : Jiao_2021_ACS.Sens__
PubMedID: 34406746

Title : Chemical Composition and Anti-Alzheimer's Disease-related Activities of a Functional Oil from the Edible Seaweed Hizikia fusiforme - Yang_2020_Chem.Biodivers_17_e2000055
Author(s) : Yang WC , Zhang YY , Li YJ , Nie YY , Liang JY , Liu YY , Liu JS , Zhang Y , Song C , Qian ZJ
Ref : Chem Biodivers , 17 :e2000055 , 2020
Abstract : Cholinergic disorder, oxidative stress, and neuroinflammation play important roles in the pathology of Alzheimer's disease. To explore the healthy potential of the edible seaweed Hizikia fusiforme on this aspect, a functional oil (HFFO) was extracted from this alga and investigated on its constituents by gas chromatography-mass spectrometry (GC-MS) in this study. Its anti-Alzheimer's related bioactivities including acetylcholinesterase (AChE) inhibition, antioxidation, and anti-neuroinflammation were evaluated, traced, and simulated by in vitro and in silico methods. GC-MS analysis indicated that HFFO mainly contained arachidonic acid (ARA), 11,14,17-eicosatrienoic acid (ETrA), palmitic acid, phytol, etc. HFFO showed moderate AChE inhibition and antioxidant activity. Bioactivity tracing using commercial standards verified that AChE inhibition of HFFO mainly originated from ARA and ETrA, whereas antioxidant activity mainly from ARA. Lineweaver-Burk plots showed that both ARA and ETrA are noncompetitive AChE inhibitors. A molecular docking study demonstrated low CDOCKER interaction energy of -26.33 kcal/mol for ARA and -50.36 kcal/mol for ETrA when interacting with AChE and multiple interactions in the ARA (or ETrA)-AChE complex. In the anti-neuroinflammatory evaluation, HFFO showed no toxicity toward BV-2 cells at 20 mug/mL and effectively inhibited the production of nitroxide and reduced the level of reactive oxygen species in liposaccharide-induced BV-2 cells. The results indicated that HFFO could be used in functional foods for its anti-Alzheimer's disease-related activities.
ESTHER : Yang_2020_Chem.Biodivers_17_e2000055
PubMedSearch : Yang_2020_Chem.Biodivers_17_e2000055
PubMedID: 32419273

Title : Conformational fitting of a flexible oligomeric substrate does not explain the enzymatic PET degradation -
Author(s) : Wei R , Song C , Grasing D , Schneider T , Bielytskyi P , Bottcher D , Matysik J , Bornscheuer UT , Zimmermann W
Ref : Nat Commun , 10 :5581 , 2019
PubMedID: 31811142

Title : Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce - Reyes-Chin-Wo_2017_Nat.Commun_8_14953
Author(s) : Reyes-Chin-Wo S , Wang Z , Yang X , Kozik A , Arikit S , Song C , Xia L , Froenicke L , Lavelle DO , Truco MJ , Xia R , Zhu S , Xu C , Xu H , Xu X , Cox K , Korf I , Meyers BC , Michelmore RW
Ref : Nat Commun , 8 :14953 , 2017
Abstract : Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence.
ESTHER : Reyes-Chin-Wo_2017_Nat.Commun_8_14953
PubMedSearch : Reyes-Chin-Wo_2017_Nat.Commun_8_14953
PubMedID: 28401891
Gene_locus related to this paper: lacsa-a0a2j6jnd3 , lacsa-a0a2j6l6y4 , lacsa-a0a2j6mjs5 , lacsa-a0a2j6mk82 , lacsa-a0a2j6k5z4 , lacsa-a0a2j6mk08 , lacsa-a0a2j6mhc5 , lacsa-a0a2j6m8d0 , lacsa-a0a2j6mdb6 , lacsa-a0a2j6mdh6 , lacsa-a0a2j6jnf0 , lacsa-a0a2j6mji4 , lacsa-a0a2j6ke81 , lacsa-a0a2j6jip3 , lacsa-a0a2j6jir5 , lacsa-a0a2j6ksa7 , lacsa-a0a2j6l4a3

Title : Application of Chitosan, Chitooligosaccharide, and Their Derivatives in the Treatment of Alzheimer's Disease - Ouyang_2017_Mar.Drugs_15_
Author(s) : Ouyang QQ , Zhao S , Li SD , Song C
Ref : Mar Drugs , 15 : , 2017
Abstract : Classic hypotheses of Alzheimer's disease (AD) include cholinergic neuron death, acetylcholine (ACh) deficiency, metal ion dynamic equilibrium disorder, and deposition of amyloid and tau. Increased evidence suggests neuroinflammation and oxidative stress may cause AD. However, none of these factors induces AD independently, but they are all associated with the formation of Abeta and tau proteins. Current clinical treatments based on ACh deficiency can only temporarily relieve symptoms, accompanied with many side-effects. Hence, searching for natural neuroprotective agents, which can significantly improve the major symptoms and reverse disease progress, have received great attention. Currently, several bioactive marine products have shown neuroprotective activities, immunomodulatory and anti-inflammatory effects with low toxicity and mild side effects in laboratory studies. Recently, chitosan (CTS), chitooligosaccharide (COS) and their derivatives from exoskeletons of crustaceans and cell walls of fungi have shown neuroprotective and antioxidative effects, matrix metalloproteinase inhibition, anti-HIV and anti-inflammatory properties. With regards to the hypotheses of AD, the neuroprotective effect of CTS, COS, and their derivatives on AD-like changes in several models have been reported. CTS and COS exert beneficial effects on cognitive impairments via inhibiting oxidative stress and neuroinflammation. They are also a new type of non-toxic beta-secretase and AChE inhibitor. As neuroprotective agents, they could reduce the cell membrane damage caused by copper ions and decrease the content of reactive oxygen species. This review will focus on their anti-neuroinflammation, antioxidants and their inhibition of beta-amyloid, acetylcholinesterase and copper ions adsorption. Finally, the limitations and future work will be discussed.
ESTHER : Ouyang_2017_Mar.Drugs_15_
PubMedSearch : Ouyang_2017_Mar.Drugs_15_
PubMedID: 29112116

Title : Characterization of a Novel Thermo-Stable Lipasefrom Endophyte Pseudomonas putida in Pistacia chinensis Bunge - Song_2017_Appl.Biochem.Microbiol_53_524
Author(s) : Song C , Liu Z , Xie Q , Wang H , Huang Y , Ruan Y , Chen D
Ref : Applied Biochemistry and Microbiology , 53 :524 , 2017
Abstract : A novel lipolytic enzyme-producing endophytic strain PC2 was successfully isolated from the seeds of an ideal bioenergy plant Pistacia chinensis Bunge. Based on the analysis of morphology and 16S rRNA sequence, bacterial strain PC2 was identified as a subspecies of Pseudomonas putida, therefore named as P. putida PC2. Whole-genome sequencing showed PC2 contained a 1224-nucleotide lipase gene (named lip-PC2) predicted to encode a 407-amino-acid protein. Purified lipases from both the original PC2 strain and heterologously expressed Escherichia coli were nearly 50 kD with specific activity of 9.48 U/mL. LIP-PC2 displayed the maximal activity at 50C or pH 8.0, and maintained above 80% relative activity in the range of from 40 to 60degC or pH in the range of from 6.0 to 8.0, indicating thermostable and alkaline properties. Enzyme activity was enhanced by Mg2+, Na+ and Mn2+, but strongly inhibited by Cu2+, Zn2+ Co2+, EDTA as well as organic solvents and surfactants. Additionally, the analysis of amino acid sequence and structure indicated that LIP-PC2 was a novel member belonging to family I.3 of bacterial lipolytic enzymes and its catalytic triad was consisted of Ser-200, Asp-342 and His-374
ESTHER : Song_2017_Appl.Biochem.Microbiol_53_524
PubMedSearch : Song_2017_Appl.Biochem.Microbiol_53_524
Gene_locus related to this paper: psepu-a0a160gpc6

Title : Structural Effect of Thioureas on the Detection of Chemical Warfare Agent Simulants - Ha_2017_ACS.Sens_2_1146
Author(s) : Ha S , Lee M , Seo HO , Song SG , Kim KS , Park CH , Kim IH , Kim YD , Song C
Ref : ACS Sens , 2 :1146 , 2017
Abstract : The ability to rapidly detect, identify, and monitor chemical warfare agents (CWAs) is imperative for both military and civilian defense. Since most CWAs and their simulants have an organophosphonate group, which is a hydrogen (H)-bond acceptor, many H-bond donors have been developed to effectively bind to the organophosphonate group. Although thioureas have been actively studied as an organocatalyst, they are relatively less investigated in CWA detection. In addition, there is a lack of studies on the structure-property relationship for gas phase detection. In this study, we synthesized various thioureas of different chemical structures, and tested them for sensing dimethylmethylphosphonate (DMMP), a CWA simulant. Molecular interaction between DMMP and thiourea was measured by (1)H NMR titration and supported by density functional theory (DFT) calculations. Strong H-bond donor ability of thiourea may cause self-aggregation, and CH-pi interaction can play an important role in the DMMP detection. Gas-phase adsorption of DMMP was also measured using a quartz crystal microbalance (QCM) and analyzed using the simple Langmuir isotherm, showing the importance of structure-induced morphology of thioureas on the surface.
ESTHER : Ha_2017_ACS.Sens_2_1146
PubMedSearch : Ha_2017_ACS.Sens_2_1146
PubMedID: 28776366

Title : Nuclear envelope localization of LEMD2 is developmentally dynamic and lamin A\/C dependent yet insufficient for heterochromatin tethering - Thanisch_2017_Differentiation_94_58
Author(s) : Thanisch K , Song C , Engelkamp D , Koch J , Wang A , Hallberg E , Foisner R , Leonhardt H , Stewart CL , Joffe B , Solovei I
Ref : Differentiation , 94 :58 , 2017
Abstract : Peripheral heterochromatin in mammalian nuclei is tethered to the nuclear envelope by at least two mechanisms here referred to as the A- and B-tethers. The A-tether includes lamins A/C and additional unknown components presumably INM protein(s) interacting with both lamins A/C and chromatin. The B-tether includes the inner nuclear membrane (INM) protein Lamin B-receptor, which binds B-type lamins and chromatin. Generally, at least one of the tethers is always present in the nuclear envelope of mammalian cells. Deletion of both causes the loss of peripheral heterochromatin and consequently inversion of the entire nuclear architecture, with this occurring naturally in rod photoreceptors of nocturnal mammals. The tethers are differentially utilized during development, regulate gene expression in opposite manners, and play an important role during cell differentiation. Here we aimed to identify the unknown chromatin binding component(s) of the A-tether. We analyzed 10 mouse tissues by immunostaining with antibodies against 7 INM proteins and found that every cell type has specific, although differentially and developmentally regulated, sets of these proteins. In particular, we found that INM protein LEMD2 is concomitantly expressed with A-type lamins in various cell types but is lacking in inverted nuclei of rod cells. Truncation or deletion of Lmna resulted in the downregulation and mislocalization of LEMD2, suggesting that the two proteins interact and pointing at LEMD2 as a potential chromatin binding mediator of the A-tether. Using nuclei of mouse rods as an experimental model lacking peripheral heterochromatin, we expressed a LEMD2 transgene alone or in combination with lamin C in these cells and observed no restoration of peripheral heterochromatin in either case. We conclude that in contrary to the B-tether, the A-tether has a more intricate composition and consists of multiple components that presumably vary, at differing degrees of redundancy, between cell types and differentiation stages.
ESTHER : Thanisch_2017_Differentiation_94_58
PubMedSearch : Thanisch_2017_Differentiation_94_58
PubMedID: 28056360

Title : Engineering Pseudomonas putida KT2440 for simultaneous degradation of organophosphates and pyrethroids and its application in bioremediation of soil - Zuo_2015_Biodegradation_26_223
Author(s) : Zuo Z , Gong T , Che Y , Liu R , Xu P , Jiang H , Qiao C , Song C , Yang C
Ref : Biodegradation , 26 :223 , 2015
Abstract : Agricultural soils are usually co-contaminated with organophosphate (OP) and pyrethroid pesticides. To develop a stable and marker-free Pseudomonas putida for co-expression of two pesticide-degrading enzymes, we constructed a suicide plasmid with expression cassettes containing a constitutive promoter J23119, an OP-degrading gene (mpd), a pyrethroid-hydrolyzing carboxylesterase gene (pytH) that utilizes the upp gene as a counter-selectable marker for upp-deficient P. putida. By introduction of suicide plasmid and two-step homologous recombination, both mpd and pytH genes were integrated into the chromosome of a robust soil bacterium P. putida KT2440 and no selection marker was left on chromosome. Functional expression of mpd and pytH in P. putida KT2440 was demonstrated by Western blot analysis and enzyme activity assays. Degradation experiments with liquid cultures showed that the mixed pesticides including methyl parathion, fenitrothion, chlorpyrifos, permethrin, fenpropathrin, and cypermethrin (0.2 mM each) were degraded completely within 48 h. The inoculation of engineered strain (10(6) cells/g) to soils treated with the above mixed pesticides resulted in a higher degradation rate than in noninoculated soils. All six pesticides could be degraded completely within 15 days in fumigated and nonfumigated soils with inoculation. Theses results highlight the potential of the engineered strain to be used for in situ bioremediation of soils co-contaminated with OP and pyrethroid pesticides.
ESTHER : Zuo_2015_Biodegradation_26_223
PubMedSearch : Zuo_2015_Biodegradation_26_223
PubMedID: 25917649

Title : An upp-based markerless gene replacement method for genome reduction and metabolic pathway engineering in Pseudomonas mendocina NK-01 and Pseudomonas putida KT2440 - Wang_2015_J.Microbiol.Methods_113_27
Author(s) : Wang Y , Zhang C , Gong T , Zuo Z , Zhao F , Fan X , Yang C , Song C
Ref : J Microbiol Methods , 113 :27 , 2015
Abstract : A markerless gene replacement method was adapted by combining a suicide plasmid, pEX18Tc, with a counterselectable marker, the upp gene encoding uracil phosphoribosyltransferase (UPRTase), for the medium-chain length polyhydroxyalkanoates (PHAMCL)-producing strain Pseudomonas mendocina NK-01. An NK-01 5-fluorouracil (5-FU) resistant background strain was first constructed by deleting the chromosomal upp gene. The suicide plasmid pEX18Tc, carrying a functional allele of the upp gene of P. mendocina NK-01, was used to construct the vectors to delete the algA (encoding mannose-1-phosphate guanylyltransferase) and phaZ (encoding PHAMCL depolymerase) genes, and a 30kb chromosomal fragment in the 5-FU resistant background host. The genes were removed efficiently from the genome of P. mendocina NK-01 and left a markerless chromosomal mutant. In addition, two exogenous genes were inserted into the phaC1 (PHAMCL polymerase) loci of Pseudomonas putida KT-UPP simultaneously. Thus, we constructed a genetically stable and marker-free P. putida KT2440 mutant with integrated mpd (encoding methyl parathion hydrolase (MPH)) and pytH (encoding a pyrethroid-hydrolyzing carboxylesterase (PytH)) gene on the chromosome. The upp-based counterselection system could be further adapted for P. mendocina NK-01 and P. putida KT2440 and used for genome reduction and metabolic pathway engineering.
ESTHER : Wang_2015_J.Microbiol.Methods_113_27
PubMedSearch : Wang_2015_J.Microbiol.Methods_113_27
PubMedID: 25828098

Title : Protective effects of low molecular weight chondroitin sulfate on amyloid beta (Abeta)-induced damage in vitro and in vivo - Zhang_2015_Neurosci_305_169
Author(s) : Zhang Q , Li J , Liu C , Song C , Li P , Yin F , Xiao Y , Jiang W , Zong A , Zhang X , Wang F
Ref : Neuroscience , 305 :169 , 2015
Abstract : In the present study, we investigated the effects of low molecular weight chondroitin sulfate (LMWCS) on amyloid beta (Abeta)-induced neurotoxicity in vitro and in vivo. The in vitro results showed that LMWCS blocked Abeta25-35-induced cell viability loss and apoptosis, decreased intracellular calcium concentration, reactive oxygen species (ROS) levels, the mitochondrial membrane potential (MMP) depolarization, and the protein expression of Caspase-3. During in vivo experiments, LMWCS improved the cognitive impairment induced by Abeta1-40, increased the level of choline acetyltransferase (ChAT), superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px), and decreased the level of malondialdehyde (MDA) and acetylcholinesterase (AChE) in the mouse brain. Moreover, LMWCS decreased the density of pyramidal cells of CA1 regions, and suppressed the protein expression of Bax/Bcl-2 and Caspase-3, -9 in the hippocampus of mice. In conclusion, LMWCS possessed neuroprotective properties against toxic effects induced by Abeta peptides both in vitro and in vivo, which might be related to anti-apoptotic activity. LMWCS might be a useful preventive and therapeutic compound for Alzheimer's disease.
ESTHER : Zhang_2015_Neurosci_305_169
PubMedSearch : Zhang_2015_Neurosci_305_169
PubMedID: 26254241

Title : An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome - Bian_2014_J.Proteomics_96_253
Author(s) : Bian Y , Song C , Cheng K , Dong M , Wang F , Huang J , Sun D , Wang L , Ye M , Zou H
Ref : J Proteomics , 96 :253 , 2014
Abstract : UNLABELLED: Protein phosphorylation is one of the most common post-translational modifications. It plays key roles in regulating diverse biological processes of liver tissues. To better understand the role of protein phosphorylation in liver functions, it is essential to perform in-depth phosphoproteome analysis of human liver. Here, an enzyme assisted reversed-phase-reversed-phase liquid chromatography (RP-RPLC) approach with both RPLC separations operated with optimized acidic mobile phase was developed. High orthogonal separation was achieved by trypsin digestion of the Glu-C generated peptides in the fractions collected from the first RPLC separation. The phosphoproteome coverage was further improved by using two types of instruments, i.e. TripleTOF 5600 and LTQ Orbitrap Velos. A total of 22,446 phosphorylation sites, corresponding to 6526 nonredundant phosphoproteins were finally identified from normal human liver tissues. Of these sites, 15,229 sites were confidently localized with Ascore>/=13. This dataset was the largest phosphoproteome dataset of human liver. It can be a public resource for the liver research community and holds promise for further biology studies. BIOLOGICAL SIGNIFICANCE: The enzyme assisted approach enabled the two RPLC separations operated both with optimized acidic mobile phases. The identifications from TripleTOF 5600 and Orbitrap Velos are highly complementary. The largest phosphoproteome dataset of human liver was generated.
ESTHER : Bian_2014_J.Proteomics_96_253
PubMedSearch : Bian_2014_J.Proteomics_96_253
PubMedID: 24275569
Gene_locus related to this paper: human-LIPC

Title : Genome Sequence of the epsilon-Poly-l-Lysine-Producing Strain Streptomyces albulus NK660, Isolated from Soil in Gutian, Fujian Province, China - Gu_2014_Genome.Announc_2_e00532
Author(s) : Gu Y , Yang C , Wang X , Geng W , Sun Y , Feng J , Wang Y , Quan Y , Che Y , Zhang C , Gong T , Zhang W , Gao W , Zuo Z , Song C , Wang S
Ref : Genome Announc , 2 :e00532 , 2014
Abstract : We determined the complete genome sequence of a soil bacterium, Streptomyces albulus NK660. It can produce epsilon-poly-l-lysine, which has antimicrobial activity against a spectrum of microorganisms. The genome of S. albulus NK660 contains a 9,360,281-bp linear chromosome and a 12,120-bp linear plasmid.
ESTHER : Gu_2014_Genome.Announc_2_e00532
PubMedSearch : Gu_2014_Genome.Announc_2_e00532
PubMedID: 24926050
Gene_locus related to this paper: stra9-a0a059w351

Title : DNA methylation reader MECP2: cell type- and differentiation stage-specific protein distribution - Song_2014_Epigenetics.Chromatin_7_17
Author(s) : Song C , Feodorova Y , Guy J , Peichl L , Jost KL , Kimura H , Cardoso MC , Bird A , Leonhardt H , Joffe B , Solovei I
Ref : Epigenetics Chromatin , 7 :17 , 2014
Abstract : BACKGROUND: Methyl-CpG binding protein 2 (MECP2) is a protein that specifically binds methylated DNA, thus regulating transcription and chromatin organization. Mutations in the gene have been identified as the principal cause of Rett syndrome, a severe neurological disorder. Although the role of MECP2 has been extensively studied in nervous tissues, still very little is known about its function and cell type specific distribution in other tissues. RESULTS: Using immunostaining on tissue cryosections, we characterized the distribution of MECP2 in 60 cell types of 16 mouse neuronal and non-neuronal tissues. We show that MECP2 is expressed at a very high level in all retinal neurons except rod photoreceptors. The onset of its expression during retina development coincides with massive synapse formation. In contrast to astroglia, retinal microglial cells lack MECP2, similar to microglia in the brain, cerebellum, and spinal cord. MECP2 is also present in almost all non-neural cell types, with the exception of intestinal epithelial cells, erythropoietic cells, and hair matrix keratinocytes. Our study demonstrates the role of MECP2 as a marker of the differentiated state in all studied cells other than oocytes and spermatogenic cells. MECP2-deficient male (Mecp2 (-/y) ) mice show no apparent defects in the morphology and development of the retina. The nuclear architecture of retinal neurons is also unaffected as the degree of chromocenter fusion and the distribution of major histone modifications do not differ between Mecp2 (-/y) and Mecp2 (wt) mice. Surprisingly, the absence of MECP2 is not compensated by other methyl-CpG binding proteins. On the contrary, their mRNA levels were downregulated in Mecp2 (-/y) mice. CONCLUSIONS: MECP2 is almost universally expressed in all studied cell types with few exceptions, including microglia. MECP2 deficiency does not change the nuclear architecture and epigenetic landscape of retinal cells despite the missing compensatory expression of other methyl-CpG binding proteins. Furthermore, retinal development and morphology are also preserved in Mecp2-null mice. Our study reveals the significance of MECP2 function in cell differentiation and sets the basis for future investigations in this direction.
ESTHER : Song_2014_Epigenetics.Chromatin_7_17
PubMedSearch : Song_2014_Epigenetics.Chromatin_7_17
PubMedID: 25170345

Title : Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis - Wang_2014_Genome.Biol_15_R39
Author(s) : Wang L , Yu S , Tong C , Zhao Y , Liu Y , Song C , Zhang Y , Zhang X , Wang Y , Hua W , Li D , Li F , Yu J , Xu C , Han X , Huang S , Tai S , Wang J , Xu X , Li Y , Liu S , Varshney RK
Ref : Genome Biol , 15 :R39 , 2014
Abstract : BACKGROUND: Sesame, Sesamum indicum L., is considered the queen of oilseeds for its high oil content and quality, and is grown widely in tropical and subtropical areas as an important source of oil and protein. However, the molecular biology of sesame is largely unexplored. RESULTS: Here, we report a high-quality genome sequence of sesame assembled de novo with a contig N50 of 52.2 kb and a scaffold N50 of 2.1 Mb, containing an estimated 27,148 genes. The results reveal novel, independent whole genome duplication and the absence of the Toll/interleukin-1 receptor domain in resistance genes. Candidate genes and oil biosynthetic pathways contributing to high oil content were discovered by comparative genomic and transcriptomic analyses. These revealed the expansion of type 1 lipid transfer genes by tandem duplication, the contraction of lipid degradation genes, and the differential expression of essential genes in the triacylglycerol biosynthesis pathway, particularly in the early stage of seed development. Resequencing data in 29 sesame accessions from 12 countries suggested that the high genetic diversity of lipid-related genes might be associated with the wide variation in oil content. Additionally, the results shed light on the pivotal stage of seed development, oil accumulation and potential key genes for sesamin production, an important pharmacological constituent of sesame. CONCLUSIONS: As an important species from the order Lamiales and a high oil crop, the sesame genome will facilitate future research on the evolution of eudicots, as well as the study of lipid biosynthesis and potential genetic improvement of sesame.
ESTHER : Wang_2014_Genome.Biol_15_R39
PubMedSearch : Wang_2014_Genome.Biol_15_R39
PubMedID: 24576357
Gene_locus related to this paper: sesin-a0a6i9snr9

Title : Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing - Qi_2014_Nat.Commun_5_4340
Author(s) : Qi X , Li MW , Xie M , Liu X , Ni M , Shao G , Song C , Kay-Yuen Yim A , Tao Y , Wong FL , Isobe S , Wong CF , Wong KS , Xu C , Li C , Wang Y , Guan R , Sun F , Fan G , Xiao Z , Zhou F , Phang TH , Tong SW , Chan TF , Yiu SM , Tabata S , Wang J , Xu X , Lam HM
Ref : Nat Commun , 5 :4340 , 2014
Abstract : Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.
ESTHER : Qi_2014_Nat.Commun_5_4340
PubMedSearch : Qi_2014_Nat.Commun_5_4340
PubMedID: 25004933
Gene_locus related to this paper: soybn-i1k636 , soybn-i1j4c6 , glyso-a0a0b2sjw6 , soybn-a0a0r0i9y7 , soybn-a0a0r0j241 , soybn-i1kfz9 , glyso-a0a0b2rre9 , soybn-i1jx17

Title : Epigenetics of eu- and heterochromatin in inverted and conventional nuclei from mouse retina - Eberhart_2013_Chromosome.Res_21_535
Author(s) : Eberhart A , Feodorova Y , Song C , Wanner G , Kiseleva E , Furukawa T , Kimura H , Schotta G , Leonhardt H , Joffe B , Solovei I
Ref : Chromosome Res , 21 :535 , 2013
Abstract : To improve light propagation through the retina, the rod nuclei of nocturnal mammals are uniquely changed compared to the nuclei of other cells. In particular, the main classes of chromatin are segregated in them and form regular concentric shells in order; inverted in comparison to conventional nuclei. A broad study of the epigenetic landscape of the inverted and conventional mouse retinal nuclei indicated several differences between them and several features of general interest for the organization of the mammalian nuclei. In difference to nuclei with conventional architecture, the packing density of pericentromeric satellites and LINE-rich chromatin is similar in inverted rod nuclei; euchromatin has a lower packing density in both cases. A high global chromatin condensation in rod nuclei minimizes the structural difference between active and inactive X chromosome homologues. DNA methylation is observed primarily in the chromocenter, Dnmt1 is primarily associated with the euchromatic shell. Heterochromatin proteins HP1-alpha and HP1-beta localize in heterochromatic shells, whereas HP1-gamma is associated with euchromatin. For most of the 25 studied histone modifications, we observed predominant colocalization with a certain main chromatin class. Both inversions in rod nuclei and maintenance of peripheral heterochromatin in conventional nuclei are not affected by a loss or depletion of the major silencing core histone modifications in respective knock-out mice, but for different reasons. Maintenance of peripheral heterochromatin appears to be ensured by redundancy both at the level of enzymes setting the epigenetic code (writers) and the code itself, whereas inversion in rods rely on the absence of the peripheral heterochromatin tethers (absence of code readers).
ESTHER : Eberhart_2013_Chromosome.Res_21_535
PubMedSearch : Eberhart_2013_Chromosome.Res_21_535
PubMedID: 23996328

Title : Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution - Chen_2013_Nat.Commun_4_1595
Author(s) : Chen J , Huang Q , Gao D , Wang J , Lang Y , Liu T , Li B , Bai Z , Luis Goicoechea J , Liang C , Chen C , Zhang W , Sun S , Liao Y , Zhang X , Yang L , Song C , Wang M , Shi J , Liu G , Liu J , Zhou H , Zhou W , Yu Q , An N , Chen Y , Cai Q , Wang B , Liu B , Min J , Huang Y , Wu H , Li Z , Zhang Y , Yin Y , Song W , Jiang J , Jackson SA , Wing RA , Chen M
Ref : Nat Commun , 4 :1595 , 2013
Abstract : The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb de novo assembled genome sequence of Oryza brachyantha. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha. We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza.
ESTHER : Chen_2013_Nat.Commun_4_1595
PubMedSearch : Chen_2013_Nat.Commun_4_1595
PubMedID: 23481403
Gene_locus related to this paper: orysa-Q6ZDG3 , orysa-q6h415 , orysj-q6yse8 , orysa-q33aq0 , orybr-j3l7k2 , orybr-j3m138 , orybr-j3l6m8 , orybr-j3m3b3 , orybr-j3l8d1 , orybr-j3kza5 , orybr-j3mnb5 , orybr-j3n4p4 , orybr-j3lg73 , orybr-j3l342 , orybr-j3msi2 , orybr-j3nb83 , orybr-j3mpc5

Title : Glycosyl-phosphatidylinositol (GPI)-anchored membrane association of the porcine reproductive and respiratory syndrome virus GP4 glycoprotein and its co-localization with CD163 in lipid rafts - Du_2012_Virology_424_18
Author(s) : Du Y , Pattnaik AK , Song C , Yoo D , Li G
Ref : Virology , 424 :18 , 2012
Abstract : The porcine reproductive and respiratory syndrome virus (PRRSV) glycoprotein 4 (GP4) resembles a typical type I membrane protein in its structure but lacks a hydrophilic tail at the C-terminus, suggesting that GP4 may be a lipid-anchored membrane protein. Using the human decay-accelerating factor (DAF; CD55), a known glycosyl-phosphatidylinositol (GPI) lipid-anchored protein, chimeric constructs were made to substitute the GPI-anchor domain of DAF with the putative lipid-anchor domain of GP4, and their membrane association and lipase cleavage were determined in cells. The DAF-GP4 fusion protein was transported to the plasma membrane and was cleaved by phosphatidylinositol-specific phospholipase C (PI-PLC), indicating that the C-terminal domain of GP4 functions as a GPI anchor. Mutational studies for residues adjacent to the GPI modification site and characterization of respective mutant viruses generated from infectious cDNA clones show that the ability of GP4 for membrane association corresponded to virus viability and growth characteristics. The residues T158 (omega-2, where omega is the GPI moiety at E160), P159 (omega-1), and M162 (omega+2) of GP4 were determined to be important for virus replication, with M162 being of particular importance for virus infectivity. The complete removal of the peptide-anchor domain in GP4 resulted in a complete loss of virus infectivity. The depletion of cholesterol from the plasma membrane of cells reduced the virus production, suggesting a role of lipid rafts in PRRSV infection. Remarkably, GP4 was found to co-localize with CD163 in the lipid rafts on the plasma membrane. Since CD163 has been reported as a cellular receptor for PRRSV and GP4 has been shown to interact with this receptor, our data implicates an important role of lipid rafts during entry of the virus.
ESTHER : Du_2012_Virology_424_18
PubMedSearch : Du_2012_Virology_424_18
PubMedID: 22222209

Title : Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions - Loper_2012_PLoS.Genet_8_e1002784
Author(s) : Loper JE , Hassan KA , Mavrodi DV , Davis EW, 2nd , Lim CK , Shaffer BT , Elbourne LD , Stockwell VO , Hartney SL , Breakwell K , Henkels MD , Tetu SG , Rangel LI , Kidarsa TA , Wilson NL , van de Mortel JE , Song C , Blumhagen R , Radune D , Hostetler JB , Brinkac LM , Durkin AS , Kluepfel DA , Wechter WP , Anderson AJ , Kim YC , Pierson LS, 3rd , Pierson EA , Lindow SE , Kobayashi DY , Raaijmakers JM , Weller DM , Thomashow LS , Allen AE , Paulsen IT
Ref : PLoS Genet , 8 :e1002784 , 2012
Abstract : We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.
ESTHER : Loper_2012_PLoS.Genet_8_e1002784
PubMedSearch : Loper_2012_PLoS.Genet_8_e1002784
PubMedID: 22792073
Gene_locus related to this paper: psebn-f2kd12 , psefl-e2xn15 , psefs-c3k632 , psepf-q3k919 , psebn-f2k9f6 , psefl-i2br68 , psefl-i4k4a8 , 9psed-i4l6c7 , 9psed-i4xqw9 , psefl-j2epr2 , 9psed-j2ew12 , psefs-c3k813 , psefl-w2f4e5 , 9psed-s6i647 , 9psed-j2wmk3 , 9psed-i4kt90 , 9psed-a0a068aip7 , 9psed-j2nei8 , 9psed-i4kw69 , psefl-i2bvr1 , psefl-j2mu40 , 9psed-j2ync4

Title : Complete genome sequence of Bacillus amyloliquefaciens LL3, which exhibits glutamic acid-independent production of poly-gamma-glutamic acid - Geng_2011_J.Bacteriol_193_3393
Author(s) : Geng W , Cao M , Song C , Xie H , Liu L , Yang C , Feng J , Zhang W , Jin Y , Du Y , Wang S
Ref : Journal of Bacteriology , 193 :3393 , 2011
Abstract : Bacillus amyloliquefaciens is one of most prevalent Gram-positive aerobic spore-forming bacteria with the ability to synthesize polysaccharides and polypeptides. Here, we report the complete genome sequence of B. amyloliquefaciens LL3, which was isolated from fermented food and presents the glutamic acid-independent production of poly-gamma-glutamic acid.
ESTHER : Geng_2011_J.Bacteriol_193_3393
PubMedSearch : Geng_2011_J.Bacteriol_193_3393
PubMedID: 21551302
Gene_locus related to this paper: baca2-a7z811

Title : Complete genome of Pseudomonas mendocina NK-01, which synthesizes medium-chain-length polyhydroxyalkanoates and alginate oligosaccharides - Guo_2011_J.Bacteriol_193_3413
Author(s) : Guo W , Wang Y , Song C , Yang C , Li Q , Li B , Su W , Sun X , Song D , Yang X , Wang S
Ref : Journal of Bacteriology , 193 :3413 , 2011
Abstract : Pseudomonas mendocina NK-01 can synthesize medium-chain-length polyhydroxyalkanoate (PHA(MCL)) and alginate oligosaccharides (AO) simultaneously from glucose under conditions of limited nitrogen. Here, we report the complete sequence of the 5.4-Mbp genome of Pseudomonas mendocina NK-01, which was isolated from farmland soil in Tianjin, China.
ESTHER : Guo_2011_J.Bacteriol_193_3413
PubMedSearch : Guo_2011_J.Bacteriol_193_3413
PubMedID: 21551299
Gene_locus related to this paper: pseme-PHAZ , psemn-f4dpi6 , psemn-f4dyl0 , psemn-f4dqg5 , pseme-a0a081x852 , psemn-f4dv64

Title : The genome of the mesopolyploid crop species Brassica rapa - Wang_2011_Nat.Genet_43_1035
Author(s) : Wang X , Wang H , Wang J , Sun R , Wu J , Liu S , Bai Y , Mun JH , Bancroft I , Cheng F , Huang S , Li X , Hua W , Freeling M , Pires JC , Paterson AH , Chalhoub B , Wang B , Hayward A , Sharpe AG , Park BS , Weisshaar B , Liu B , Li B , Tong C , Song C , Duran C , Peng C , Geng C , Koh C , Lin C , Edwards D , Mu D , Shen D , Soumpourou E , Li F , Fraser F , Conant G , Lassalle G , King GJ , Bonnema G , Tang H , Belcram H , Zhou H , Hirakawa H , Abe H , Guo H , Jin H , Parkin IA , Batley J , Kim JS , Just J , Li J , Xu J , Deng J , Kim JA , Yu J , Meng J , Min J , Poulain J , Hatakeyama K , Wu K , Wang L , Fang L , Trick M , Links MG , Zhao M , Jin M , Ramchiary N , Drou N , Berkman PJ , Cai Q , Huang Q , Li R , Tabata S , Cheng S , Zhang S , Sato S , Sun S , Kwon SJ , Choi SR , Lee TH , Fan W , Zhao X , Tan X , Xu X , Wang Y , Qiu Y , Yin Y , Li Y , Du Y , Liao Y , Lim Y , Narusaka Y , Wang Z , Li Z , Xiong Z , Zhang Z
Ref : Nat Genet , 43 :1035 , 2011
Abstract : We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
ESTHER : Wang_2011_Nat.Genet_43_1035
PubMedSearch : Wang_2011_Nat.Genet_43_1035
PubMedID: 21873998
Gene_locus related to this paper: braol-Q8GTM3 , braol-Q8GTM4 , brarp-m4ei94 , brarp-m4c988 , brana-a0a078j4a9 , brana-a0a078e1m0 , brana-a0a078cd75 , brarp-m4dwa6 , brana-a0a078j4f0 , brana-a0a078cus4 , brana-a0a078f8c2 , brana-a0a078jql1 , brana-a0a078dgj3 , brana-a0a078hw50 , brana-a0a078cuu0 , brana-a0a078dfa9 , brana-a0a078ic91 , brarp-m4ctw3 , brana-a0a078ca65 , brana-a0a078ctc8 , brana-a0a078h021 , brana-a0a078jx23 , brarp-m4da84 , brarp-m4dwr7 , brana-a0a078dh94 , brana-a0a078h612 , brana-a0a078j2t3 , braol-a0a0d3dpb2 , braol-a0a0d3dx76 , brana-a0a078jxa8 , brana-a0a078i2k3 , brarp-m4cwq4 , brarp-m4dcj8 , brarp-m4eh17 , brarp-m4eey4 , brarp-m4dnj8 , brarp-m4ey83 , brarp-m4ey84

Title : Role of alpha7-nicotinic acetylcholine receptors in tetanic stimulation-induced gamma oscillations in rat hippocampal slices - Song_2005_Neuropharmacol_48_869
Author(s) : Song C , Murray TA , Kimura R , Wakui M , Ellsworth K , Javedan SP , Marxer-Miller S , Lukas RJ , Wu J
Ref : Neuropharmacology , 48 :869 , 2005
Abstract : Hippocampal gamma oscillations, as a form of neuronal network synchronization, are speculated to be associated with learning, memory and attention. Nicotinic acetylcholine receptor alpha7 subtypes (alpha7-nAChRs) are highly expressed in hippocampal neurons and play important roles in modulating neuronal function, synaptic plasticity, learning and memory. However, little is known about the role of alpha7-nAChRs in hippocampal gamma oscillations. Here, we examined the effects of selective alpha7- and non-alpha7-nAChR antagonists on tetanic gamma oscillations in rat hippocampal slices. We found that brief tetanic stimulation-induced gamma oscillations (30-80 Hz) and pharmacological blockade of alpha7-nAChRs using the relatively selective alpha7-nAChR antagonists, methyllycaconitine (10 or 100 nM) or alpha-bungarotoxin (10 nM), significantly reduced the frequency spectrum power, the number of spikes, and burst duration of evoked gamma oscillations. Neither mecamylamine nor dihydro-beta-erythroidine, which are selective antagonists of non-alpha7-nAChRs, demonstrated significant effects on tetanic gamma oscillations. Nicotine exposure promotes hippocampal gamma oscillations in a methyllycaconitine-sensitive manner. It is concluded that alpha7-nAChRs in hippocampal slices play important roles in regulation of gamma oscillations, thus potentially helping to explain roles of nAChRs in cognitive functions such as learning, memory and attention.
ESTHER : Song_2005_Neuropharmacol_48_869
PubMedSearch : Song_2005_Neuropharmacol_48_869
PubMedID: 15829257

Title : Investigation of the role of a second conserved serine in carboxylesterases via site-directed mutagenesis - Stok_2004_Arch.Biochem.Biophys_430_247
Author(s) : Stok JE , Goloshchapov A , Song C , Wheelock CE , Derbel MB , Morisseau C , Hammock BD
Ref : Archives of Biochemistry & Biophysics , 430 :247 , 2004
Abstract : Carboxylesterases are enzymes that catalyze the hydrolysis of ester and amide moieties. These enzymes have an active site that is composed of a nucleophile (Ser), a base (His), and an acid (Glu) that is commonly known as a catalytic triad. It has previously been observed that the majority of carboxylesterases and lipases contain a second conserved serine in their active site [Proteins, 34 (1999) 184]. To investigate whether this second serine is also involved in the catalytic mechanism, it was mutated to an alanine, a glycine or a cysteine. Site-directed mutagenesis of this conserved serine resulted in a loss of specific activity, in both the S247G and S247A mutants (5- to 15-fold), which was due to a decrease in the rate of catalysis (kcat). Due to the instability of the S247C mutant no reliable data could be attained. A carbamate inhibitor, carbaryl, was then employed to investigate whether this decrease in the kcat was due to the rate of formation of the acyl-enzyme intermediate (k2) or the rate of deacylation (k3). The S247A mutant was found only to alter k2 (2.5-fold decrease), with no effect on k3. Together with information inferred from a human carboxylesterase crystal structure, it was concluded that this serine provides an important structural support for the spatial orientation of the glutamic acid, stabilizing the catalytic triad so that it can perform the hydrolysis.
ESTHER : Stok_2004_Arch.Biochem.Biophys_430_247
PubMedSearch : Stok_2004_Arch.Biochem.Biophys_430_247
PubMedID: 15369824
Gene_locus related to this paper: ratno-Ces1d

Title : Diagnosis and management of Alzheimer's disease - Coll_2003_Conn.Med_67_505
Author(s) : Coll PP , Fortinsky RH , Kaplan R , Song C
Ref : Conn Med , 67 :505 , 2003
Abstract : Alzheimer's disease is a progressive neurological condition that usually presents with short-term memory impairment, and then progresses to profound cognitive and physical disability. The diagnosis is based primarily on clinical findings with a definitive diagnosis only being possible with pathological examination of brain tissue. Alzheimer's disease causes distress to patients, families and caregivers. Most patients with advanced Alzheimer's disease need 24-hour supervision, often provided in a long-term care setting. Although no cure is available, with a variety of treatments, modest but measurable benefits are available. Research is being conducted to find more effective treatments and hopefully in time a cure or means of prevention. All physicians whose practice includes older patients need to possess some familiarity with the diagnosis and management of Alzheimer's disease.
ESTHER : Coll_2003_Conn.Med_67_505
PubMedSearch : Coll_2003_Conn.Med_67_505
PubMedID: 14587132

Title : Effect of chronic treatment with piracetam and tacrine on some changes caused by thymectomy in the rat brain - Song_1997_Pharmacol.Biochem.Behav_56_697
Author(s) : Song C , Earley B , Leonard BE
Ref : Pharmacol Biochem Behav , 56 :697 , 1997
Abstract : Thymectomized rats, 5 weeks after surgery, showed a significant impairment in learning and memory as shown by deficits in passive avoidance and in the Morris water maze test. The behaviour of the thymectomized rats in the "open field" apparatus was largely unchanged. Following treatment for 20 days with either piracetam (500 mg/kg) or tacrine (3.0 mg/kg), the deficit in passive avoidance learning was largely reversed. Chronic treatment with tacrine also reversed the deficit in the behaviour of the thymectomized rats in the Morris water maze. The effects of thymectomy on the biogenic amines and some of their metabolites in the amygdaloid cortex, hypothalamus, striatum and olfactory bulbs were also determined. Relative to the sham-operated controls, thymectomy resulted in a reduction in the noradrenaline concentration in the amygdala, hypothalamus, and olfactory bulbs. This effect was reversed by chronic piracetam and tacrine treatments. The concentration of dopamine was also reduced in the olfactory bulbs after thymectomy whereas in the striatum the concentration of 5-hydroxytryptamine (5-HT; serotonin) was increased. The concentration of gamma amino butyric acid (GABA) was determined in amygdaloid cortex and hippocampus only. The only significant change occurred following chronic treatment of thymectomized rats with tacrine, when a significant elevation of GABA was found. Neither piracetam nor tacrine produced any change in the amines of their metabolites in the sham-operated controls. Tacrine, however, elevated the dopamine and reduced the 5-HT content of the hypothalamus and increased the 3,4-dihydroxylphenylacetic acid concentration of the striatum of thymectomized rats. Examination of the differential white blood cell count of the thymectomized rats showed that the percentage of lymphocytes was decreased, and the percentage of neutrophils increased, relative to the sham-operated controls. Chronic lacrine, but not piracetam, treatment reversed the lesion-induced changes.
ESTHER : Song_1997_Pharmacol.Biochem.Behav_56_697
PubMedSearch : Song_1997_Pharmacol.Biochem.Behav_56_697
PubMedID: 9130296