Ren L

References (17)

Title : Mechanisms of biochar assisted di-2-ethylhexyl phthalate (DEHP) biodegradation in tomato rhizosphere by metabolic and metagenomic analysis - Lin_2024_Chemosphere__141520
Author(s) : Lin Z , Wu W , Yang C , Yang G , Wei T , Huang F , Li H , Ren L , Liang Y , Zhang D , Li Z , Zhen Z
Ref : Chemosphere , :141520 , 2024
Abstract : The intensive accumulation of di-2-ethylhexyl phthalate (DEHP) in agricultural soils has resulted in severe environmental pollution that endangers ecosystem and human health. Biochar is an eco-friendly material that can help in accelerating organic pollutant degradation; nevertheless, its roles in enhancing DEHP removal in rhizosphere remain unclear. This work investigated the impacts of biochar dosage (0%-2.0%) on DEHP degradation performance in tomato rhizosphere by comprehensively exploring the change in DEHP metabolites, bacterial communities and DEHP-degrading genes. Our results showed a significant increase of rhizosphere pH, organic matter and humus by biochar amendment, which achieved a satisfactorily higher DEHP removal efficiency, maximally 77.53% in treatments with 1.0% of biochar. Biochar addition also remarkably changed rhizosphere bacterial communities by enriching some potential DEHP degraders of Nocardioides, Sphingomonas, Bradyrhizobium and Rhodanobacter. The abundance of genes encoding key enzymes (hydrolase, esterase and cytochrome P450) and DEHP-degrading genes (pht3, pht4, pht5, benC-xylZ and benD-xylL) were increased after biochar amendment, leading to the change in DEHP degradation metabolism, primarily from benzoic acid pathway to protocatechuic acid pathway. Our findings evidenced that biochar amendment could accelerate DEHP degradation by altering rhizosphere soil physicochemical variables, bacterial community composition and metabolic genes, providing clues for the mechanisms of biochar-assisted DEHP degradation in organic contaminated farmland soils.
ESTHER : Lin_2024_Chemosphere__141520
PubMedSearch : Lin_2024_Chemosphere__141520
PubMedID: 38395368

Title : Light-accelerating oxidase-mimicking activity of black phosphorus quantum dots for colorimetric detection of acetylcholinesterase activity and inhibitor screening - Ren_2021_Analyst_145_8022
Author(s) : Ren L , Li H , Liu M , Du J
Ref : Analyst , 145 :8022 , 2021
Abstract : A feasible and sensitive colorimetric platform was established for the assay of acetylcholinesterase (AChE) activity and evaluation of its inhibitor screening, based upon the light-accelerating oxidase-mimicking activity of black phosphorus quantum dots (BP QDs). The BP QDs were synthesized through a thermal exfoliation method and characterized using various techniques. The BP QDs exhibit oxidase-mimicking catalytic activity on dissolved oxygen-mediating oxidation of 3,3',5,5'-tetramethylbenzidine, a typical substrate of oxidase. This results in a transformation of 3,3',5,5'-tetramethylbenzidine into its blue oxidized product, which has a visible absorption peak at 652 nm. The exposure of 365 nm light irradiation significantly accelerates the oxidase-mimicking activity of the BP QDs and speeds up the reaction efficiency. AChE can specifically catalyze the decomposition of its substrate acetylthiocholine chloride to thiocholine. Thiocholine has reducing capacity and can thus reduce the oxidase-mimicking activity of the BP QDs. As a result, the oxidation of 3,3',5,5'-tetramethylbenzidine is hindered and the blue solution becomes paler. This gives a linear response for AChE ranging from 0.5 to 10.0 mU mL-1 and a detection limit of 0.17 mU mL-1. The assay was successfully applied to evaluate inhibitor screening with neostigmine as the model.
ESTHER : Ren_2021_Analyst_145_8022
PubMedSearch : Ren_2021_Analyst_145_8022
PubMedID: 33057486

Title : Indirect cholinergic activation slows down pancreatic cancer growth and tumor-associated inflammation - Pfitzinger_2020_J.Exp.Clin.Cancer.Res_39_289
Author(s) : Pfitzinger PL , Fangmann L , Wang K , Demir E , Gurlevik E , Fleischmann-Mundt B , Brooks J , D'Haese JG , Teller S , Hecker A , Jesinghaus M , Jger C , Ren L , Istvanffy R , Kuhnel F , Friess H , Ceyhan GO , Demir IE
Ref : J Exp Clin Cancer Research , 39 :289 , 2020
Abstract : BACKGROUND: Nerve-cancer interactions are increasingly recognized to be of paramount importance for the emergence and progression of pancreatic cancer (PCa). Here, we investigated the role of indirect cholinergic activation on PCa progression through inhibition of acetylcholinesterase (AChE) via clinically available AChE-inhibitors, i.e. physostigmine and pyridostigmine. METHODS: We applied immunohistochemistry, immunoblotting, MTT-viability, invasion, flow-cytometric-cell-cycle-assays, phospho-kinase arrays, multiplex ELISA and xenografted mice to assess the impact of AChE inhibition on PCa cell growth and invasiveness, and tumor-associated inflammation. Survival analyses were performed in a novel genetically-induced, surgically-resectable mouse model of PCa under adjuvant treatment with gemcitabine+/-physostigmine/pyridostigmine (n = 30 mice). Human PCa specimens (n = 39) were analyzed for the impact of cancer AChE expression on tumor stage and survival. RESULTS: We discovered a strong expression of AChE in cancer cells of human PCa specimens. Inhibition of this cancer-cell-intrinsic AChE via pyridostigmine and physostigmine, or administration of acetylcholine (ACh), diminished PCa cell viability and invasion in vitro and in vivo via suppression of pERK signaling, and reduced tumor-associated macrophage (TAM) infiltration and serum pro-inflammatory cytokine levels. In the novel genetically-induced, surgically-resectable PCa mouse model, adjuvant co-therapy with AChE blockers had no impact on survival. Accordingly, survival of resected PCa patients did not differ based on tumor AChE expression levels. Patients with higher-stage PCa also exhibited loss of the ACh-synthesizing enzyme, choline-acetyltransferase (ChAT), in their nerves. CONCLUSION: For future clinical trials of PCa, direct cholinergic stimulation of the muscarinic signaling, rather than indirect activation via AChE blockade, may be a more effective strategy.
ESTHER : Pfitzinger_2020_J.Exp.Clin.Cancer.Res_39_289
PubMedSearch : Pfitzinger_2020_J.Exp.Clin.Cancer.Res_39_289
PubMedID: 33357230

Title : Suppression of inflammation and fibrosis using soluble epoxide hydrolase inhibitors enhances cardiac stem cell-based therapy - Sirish_2020_Stem.Cells.Transl.Med_9_1570
Author(s) : Sirish P , Thai PN , Lee JH , Yang J , Zhang XD , Ren L , Li N , Timofeyev V , Lee KSS , Nader CE , Rowland DJ , Yechikov S , Ganaga S , Young N , Lieu DK , Yamoah EN , Hammock BD , Chiamvimonvat N
Ref : Stem Cells Transl Med , 9 :1570 , 2020
Abstract : Stem cell replacement offers a great potential for cardiac regenerative therapy. However, one of the critical barriers to stem cell therapy is a significant loss of transplanted stem cells from ischemia and inflammation in the host environment. Here, we tested the hypothesis that inhibition of the soluble epoxide hydrolase (sEH) enzyme using sEH inhibitors (sEHIs) to decrease inflammation and fibrosis in the host myocardium may increase the survival of the transplanted human induced pluripotent stem cell derived-cardiomyocytes (hiPSC-CMs) in a murine postmyocardial infarction model. A specific sEHI (1-trifluoromethoxyphenyl-3-(1-propionylpiperidine-4-yl)urea [TPPU]) and CRISPR/Cas9 gene editing were used to test the hypothesis. TPPU results in a significant increase in the retention of transplanted cells compared with cell treatment alone. The increase in the retention of hiPSC-CMs translates into an improvement in the fractional shortening and a decrease in adverse remodeling. Mechanistically, we demonstrate a significant decrease in oxidative stress and apoptosis not only in transplanted hiPSC-CMs but also in the host environment. CRISPR/Cas9-mediated gene silencing of the sEH enzyme reduces cleaved caspase-3 in hiPSC-CMs challenged with angiotensin II, suggesting that knockdown of the sEH enzyme protects the hiPSC-CMs from undergoing apoptosis. Our findings demonstrate that suppression of inflammation and fibrosis using an sEHI represents a promising adjuvant to cardiac stem cell-based therapy. Very little is known regarding the role of this class of compounds in stem cell-based therapy. There is consequently an enormous opportunity to uncover a potentially powerful class of compounds, which may be used effectively in the clinical setting.
ESTHER : Sirish_2020_Stem.Cells.Transl.Med_9_1570
PubMedSearch : Sirish_2020_Stem.Cells.Transl.Med_9_1570
PubMedID: 32790136

Title : The Effect of Longwave Ultraviolet Light Radiation on Dendrolimus tabulaeformis Antioxidant and Detoxifying Enzymes - Wang_2019_Insects_11_
Author(s) : Wang W , Gao C , Ren L , Luo Y
Ref : Insects , 11 : , 2019
Abstract : Longwave ultraviolet (UVA) light, in the range of 315-400 nm, has been widely used as a light source in the light trapping of insect pests. Previous studies have demonstrated the oxidative stress and lethal effect of UV radiation on insects. In this study, we evaluated the influence of UVA radiation on the antioxidant and detoxifying enzymes of Dendrolimus tabulaeformis. We tested the contents of malondialdehyde (MDA), hydroxyl radical (.OH), hydrogen peroxide (H2O2), reduced glutathione (GSH), and oxidized glutathione (GSSH) following different exposure time periods of UVA light irradiation on D. tabulaeformis adults. In addition, we investigated how the activities of antioxidant and detoxifying enzymes responded to UVA radiation by determining the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), polyphenol oxidase (PPO), glutathione S-transferase (GST), glutathione reductase (GR), acetylcholinesterase (AChE), carboxylesterase (CarE), alkaline phosphatase (ALP), and acid phosphatase (ACP). Adults were exposed to UVA light for different time periods (0, 5, 15, 30, 60, and 120 min). We found that exposure to UVA light for 5 min resulted in rapid variation in the activities of the antioxidant and detoxification enzyme systems. However, the antioxidant capacity of females was incongruous with that of males following UVA irradiation. Our results confirmed that UVA light irradiation increased the level of oxidative stress and disturbed physiological detoxification in D. tabulaeformis adults. Based on the above results, we anticipated that further research of the mechanism of UVA irradiation on the antioxidant and detoxifying enzymes of D. tabulaeformis would gain more importance, allowing to develop and use new, less toxic and environmentally friendly pesticides.
ESTHER : Wang_2019_Insects_11_
PubMedSearch : Wang_2019_Insects_11_
PubMedID: 31861292

Title : Clinical analysis of Chinese anti-low-density-lipoprotein-receptor-associated protein 4 antibodies in patients with myasthenia gravis - Li_2019_Eur.J.Neurol_26_1296
Author(s) : Li M , Han J , Zhang Y , Lv J , Zhang J , Zhao X , Ren L , Fang H , Yang J , Cui X , Zhang Q , Li Q , Du Y , Gao F
Ref : Eur Journal of Neurology , 26 :1296 , 2019
Abstract : BACKGROUND AND PURPOSE: Low-density-lipoprotein-receptor-associated protein 4 (LRP4) autoantibodies have recently been detected in myasthenia gravis (MG), but little is known about the clinical characteristics associated with this serological type. In this study, the clinical features of Chinese patients with anti-LRP4 antibody-positive MG were characterized. METHODS: A total of 2172 MG serum samples were collected from patients in various parts of China. An enzyme-linked immunosorbent assay was used to detect acetylcholine receptor (AChR) antibody and titin antibody, and cell-based assays were used to detect muscle-specific kinase antibody and LRP4 antibody. Clinical data for patients with MG were collected from different provinces in China. RESULTS: In total, 16 (0.8%) patients with LRP4-MG were found amongst 2172 total patients, including three patients with AChR/LRP4-MG. Additionally, 13 (2.9%) patients with LRP4-MG were found amongst 455 patients with double seronegative MG. The ratio of males to females for these 13 patients was 1:1.6, and 53.8% patients were children. A total of 91.7% of cases exhibited initial ocular involvement, and 58.3% of cases exhibited simple eye muscle involvement. Responses to acetylcholinesterase inhibitors and prednisone were observed. CONCLUSION: The expanded sample confirmed that the positive rate of LRP4 antibodies in China is lower than that in western countries. Our results highlighted the differences between LRP4-MG and other antibody groups. Children and female patients with LRP4-MG have a higher prevalence, often involving the ocular muscles and limb muscles. The clinical symptoms are mild, and satisfactory responses to treatment are often achieved.
ESTHER : Li_2019_Eur.J.Neurol_26_1296
PubMedSearch : Li_2019_Eur.J.Neurol_26_1296
PubMedID: 31050101

Title : Hydrolysis mechanism of carbendazim hydrolase from the strain Microbacterium sp. djl-6F - Lei_2017_J.Environ.Sci.(China)_54_171
Author(s) : Lei J , Wei S , Ren L , Hu S , Chen P
Ref : J Environ Sci (China) , 54 :171 , 2017
Abstract : The carbendazim (MBC) hydrolyzing enzyme gene was cloned and heterologously expressed in Escherichia coli BL21 (DE3) from a newly isolated MBC-degrading bacterium strain Microbacterium sp. strain djl-6F. High performance liquid chromatography-mass spectrometry (HPLC-MS) analysis revealed that purified MheI-6F protein catalyzes direct hydrolysis of MBC into 2-aminobenzimidazole (2-AB) with a high turnover rate and moderate affinity (K(m) of 6.69micromol/L and k(cat) of 160.88/min) without the need for any cofactors. The optimal catalytic condition of MheI-6F was identified as 45 degreesC, pH7.0. The enzymatic activity of MheI-6F was found to be diminished by metal ions, and strongly inhibited by sodium dodecyl sulfate (SDS). Through generating amino acid mutations in MheI-6F, Cys16 and Cys222 were identified as the catalytic groups that are essential for the hydrolysis of MBC. This is the first report on the biodegradation of MBC at the enzymatice level.
ESTHER : Lei_2017_J.Environ.Sci.(China)_54_171
PubMedSearch : Lei_2017_J.Environ.Sci.(China)_54_171
PubMedID: 28391926
Gene_locus related to this paper: 9acto-c8cp46

Title : Meta-analyses of four polymorphisms of lipoprotein lipase associated with the risk of Alzheimer's disease - Ren_2016_Neurosci.Lett_619_73
Author(s) : Ren L , Ren X
Ref : Neuroscience Letters , 619 :73 , 2016
Abstract : AIMS: We evaluated the contributions of four polymorphisms of the lipoprotein lipase (LPL) gene to the risk of Alzheimer's disease (AD).
METHODS: Through a comprehensive literature search for genetic variants of LPL involved in AD association studies, we found four polymorphisms for the current meta-analyses. These polymorphisms were Asn291Ser(rs268), PvuII(rs285), HindIII(rs320) and Ser447Ter(rs328).
RESULTS: In total, eight studies with 5064 cases and 5016 controls were retrieved for the meta-analyses of the four genetic variants. The analyses showed that Asn291Ser(rs268) (OR=2.34, 95% CI=1.05-5.25, P=0.04), HindIII(rs320) (OR=1.44, 95% CI=1.17-1.78, P=0.0006), and Ser447Ter(rs328) (OR=0.80, 95% CI=0.66-0.98, P=0.03) were significantly associated with a risk of AD. No association was found between the PvuII(rs285) polymorphism and the risk of AD.
CONCLUSIONS: Our results showed that Asn291Ser(rs268), HindIII(rs320) and Ser447Ter(rs328) polymorphisms of LPL were associated with a risk of AD. Asn291Ser(rs268) and HindIII(rs320) were predisposing factors of AD, whereas Ser447Ter(rs328) showed a protective effect for AD.
ESTHER : Ren_2016_Neurosci.Lett_619_73
PubMedSearch : Ren_2016_Neurosci.Lett_619_73
PubMedID: 26975783

Title : Developmental exposure of zebrafish larvae to organophosphate flame retardants causes neurotoxicity - Sun_2016_Neurotoxicol.Teratol_55_16
Author(s) : Sun L , Xu W , Peng T , Chen H , Ren L , Tan H , Xiao D , Qian H , Fu Z
Ref : Neurotoxicology & Teratology , 55 :16 , 2016
Abstract : With the gradual ban on brominated flame retardants (FRs), the application of organophosphate flame retardants (OPFRs) has increased remarkably. Considering the structural similarity between OPFRs and organophosphate pesticides, hypotheses that OPFRs may interfere with neurodevelopment as organophosphate pesticides are reasonable. In this study, the neurotoxicity of three OPFRs, including tri-n-butyl phosphate (TNBP), tris (2-butoxyethyl) phosphate (TBOEP) and tris (2-chloroethyl) phosphate (TCEP), was evaluated in zebrafish larvae and then compared with the neurotoxicity of organophosphate pesticide chlorpyrifos (CPF). The results showed that similar to CPF, exposure to OPFRs for 5days resulted in significant changes in locomotor behavior, either in free swimming or in photomotor response. However, given the transcriptional changes that occur in nervous system genes in response to OPFRs and CPF, as well as the altered enzyme activity of AChE and its mRNA level, the underlying mechanisms for neurotoxicity among these organophosphate chemicals might be varied. In summary, the results confirm the potential neurodevelopmental toxicity of OPFRs and underscore the importance of identifying the mechanistic targets of the OPFRs with specific moieties. Furthermore, as the neurobehavioral responses are well conserved among vertebrates and the exposure of children to OPFRs is significant, a thorough assessment of the risk of OPFRs exposure during early development should be highly emphasized in future studies.
ESTHER : Sun_2016_Neurotoxicol.Teratol_55_16
PubMedSearch : Sun_2016_Neurotoxicol.Teratol_55_16
PubMedID: 27018022

Title : Antifeedant Activity of Ginkgo biloba Secondary Metabolites against Hyphantria cunea Larvae: Mechanisms and Applications - Pan_2016_PLoS.One_11_e0155682
Author(s) : Pan L , Ren L , Chen F , Feng Y , Luo Y
Ref : PLoS ONE , 11 :e0155682 , 2016
Abstract : Ginkgo biloba is a typical relic plant that rarely suffers from pest hazards. This study analyzed the pattern of G. biloba pest hazards in Beijing; tested the antifeedant activity of G. biloba extracts, including ginkgo flavonoids, ginkgolide, and bilobalide, against Hyphantria cunea larvae; determined the activities of glutathione transferase (GSTs), acetylcholinesterase (AChE), carboxylesterase (CarE) and mixed-functional oxidase (MFO), in larvae after feeding on these G. biloba secondary metabolites; and screened for effective botanical antifeedants in the field. In this study, no indicators of insect infestation were found for any of the examined leaves of G. biloba; all tested secondary metabolites showed significant antifeedant activity and affected the activity of the four larval detoxifying enzymes. Ginkgolide had the highest antifeedant activity and the most significant effect on the detoxifying enzymes (P<0.05). Spraying leaves with G. biloba extracts or ginkgolide both significantly repelled H. cunea larvae in the field (P<0.05), although the former is more economical and practical. This study investigated the antifeedant activity of G. biloba secondary metabolites against H. cunea larvae, and the results provide new insights into the mechanism of G. biloba pest resistance. This study also developed new applications of G. biloba secondary metabolites for effective pest control.
ESTHER : Pan_2016_PLoS.One_11_e0155682
PubMedSearch : Pan_2016_PLoS.One_11_e0155682
PubMedID: 27214257

Title : The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut - Bertioli_2016_Nat.Genet_48_438
Author(s) : Bertioli DJ , Cannon SB , Froenicke L , Huang G , Farmer AD , Cannon EK , Liu X , Gao D , Clevenger J , Dash S , Ren L , Moretzsohn MC , Shirasawa K , Huang W , Vidigal B , Abernathy B , Chu Y , Niederhuth CE , Umale P , Araujo AC , Kozik A , Kim KD , Burow MD , Varshney RK , Wang X , Zhang X , Barkley N , Guimaraes PM , Isobe S , Guo B , Liao B , Stalker HT , Schmitz RJ , Scheffler BE , Leal-Bertioli SC , Xun X , Jackson SA , Michelmore R , Ozias-Akins P
Ref : Nat Genet , 48 :438 , 2016
Abstract : Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of -2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.
ESTHER : Bertioli_2016_Nat.Genet_48_438
PubMedSearch : Bertioli_2016_Nat.Genet_48_438
PubMedID: 26901068
Gene_locus related to this paper: aradu-a0a6p4dix2 , aradu-a0a6p4dpj0 , aradu-a0a6p4dix7

Title : Enzymatic preparation of optically pure (+)-2-azabicyclo[2.2.1]hept-5-en-3-one by (-)-gamma-lactamase from Bradyrhizobium japonicum USDA 6 - Zhu_2014_Bioorg.Med.Chem.Lett_24_4899
Author(s) : Zhu S , Ren L , Yu S , Gong C , Song D , Zheng G
Ref : Bioorganic & Medicinal Chemistry Lett , 24 :4899 , 2014
Abstract : Whole cells of Bradyrhizobium japonicum USDA 6 showed both (+)-gamma-lactamase activity and (-)-gamma-lactamase activity. Insight into the genome of B. japonicum USDA 6 revealed two potential gamma-lactamases: a type I (+)-gamma-lactamase and a (-)-gamma-lactamase, making it the first strain to contain two totally different enantioselective lactamases. Both recombinant enzymes could easily be used to prepare either optically pure (+)-gamma-lactam ((+)-2-azabicyclo[2.2.1]hept-5-en-3-one) or optically pure (-)-gamma-lactam ((-)-2-azabicyclo[2.2.1]hept-5-en-3-one), which are versatile synthetic building blocks for the synthesis of various carbocyclic nucleosides and carbocyclic sugar analogues. Bioinformatic analysis showed that the type I (+)-gamma-lactamase belongs to the amidase signature family, with 504 amino acids; the (-)-gamma-lactamase, which consists of 274 amino acids, belongs to the hydrolase family. Here, we report that B. japonicum USDA contains a (-)-gamma-lactamase in addition to a (+)-gamma-lactamase, and it is the (-)-gamma-lactamase from this strain that is examined in detail in this Letter. Enzymatic synthesis of optically pure (+)-gamma-lactam with nearly 50% isolated yield and >99% ee was achieved.
ESTHER : Zhu_2014_Bioorg.Med.Chem.Lett_24_4899
PubMedSearch : Zhu_2014_Bioorg.Med.Chem.Lett_24_4899
PubMedID: 25240615
Gene_locus related to this paper: brajp-BAL06612

Title : Complete Genome Sequence of Marinobacter sp. BSs20148 - Song_2013_Genome.Announc_1_E00236
Author(s) : Song L , Ren L , Li X , Yu D , Yu Y , Wang X , Liu G
Ref : Genome Announc , 1 : , 2013
Abstract : Marinobacter sp. BSs20148 was isolated from marine sediment collected from the Arctic Ocean at a water depth of 3,800 m. Here we report the complete genome sequence of Marinobacter sp. BSs20148. This genomic information will facilitate the study of the physiological metabolism, ecological roles, and evolution of the Marinobacter species.
ESTHER : Song_2013_Genome.Announc_1_E00236
PubMedSearch : Song_2013_Genome.Announc_1_E00236
PubMedID: 23682144
Gene_locus related to this paper: 9alte-m1faq0 , 9alte-m1fkf6 , 9alte-m1fib0

Title : The duck genome and transcriptome provide insight into an avian influenza virus reservoir species - Huang_2013_Nat.Genet_45_776
Author(s) : Huang Y , Li Y , Burt DW , Chen H , Zhang Y , Qian W , Kim H , Gan S , Zhao Y , Li J , Yi K , Feng H , Zhu P , Li B , Liu Q , Fairley S , Magor KE , Du Z , Hu X , Goodman L , Tafer H , Vignal A , Lee T , Kim KW , Sheng Z , An Y , Searle S , Herrero J , Groenen MA , Crooijmans RP , Faraut T , Cai Q , Webster RG , Aldridge JR , Warren WC , Bartschat S , Kehr S , Marz M , Stadler PF , Smith J , Kraus RH , Ren L , Fei J , Morisson M , Kaiser P , Griffin DK , Rao M , Pitel F , Wang J , Li N
Ref : Nat Genet , 45 :776 , 2013
Abstract : The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 virus. Further, we show how the duck's defense mechanisms against influenza infection have been optimized through the diversification of its beta-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses.
ESTHER : Huang_2013_Nat.Genet_45_776
PubMedSearch : Huang_2013_Nat.Genet_45_776
PubMedID: 23749191
Gene_locus related to this paper: anapl-BCHE , anapl-r0lw36 , anapl-r0m5n4 , anapl-thioe , anapl-u3iqr9 , anapl-r0l4n7 , anapl-u3j4v8 , anapl-u3icy5 , anapl-u3ivv9 , anapl-u3j4g1 , anapl-u3j4i2 , anapl-u3j4v5 , anapl-r0kv25 , anapl-u3ild2 , anapl-u3imh5 , anapl-b6dzk9 , anapl-u3imp7 , anapl-u3i5h5 , anapl-u3id17 , anapl-r0m1y3 , anapl-r0lhc4 , anapl-r0ktn0 , anapl-r0l8l1 , anapl-r0lin6 , anapl-r0jhf3

Title : Genome of Helicobacter pylori strain XZ274, an isolate from a tibetan patient with gastric cancer in China - Guo_2012_J.Bacteriol_194_4146
Author(s) : Guo Y , Wang H , Li Y , Song Y , Chen C , Liao Y , Ren L , Guo C , Tong W , Shen W , Chen M , Mao X , Guo G , Zou Q
Ref : Journal of Bacteriology , 194 :4146 , 2012
Abstract : The infection rate of Helicobacter pylori is high all over the world, especially in the Chinese Tibetan Plateau. Here, we report the genome sequence of Helicobacter pylori strain XZ274 isolated from a Tibetan patient with gastric cancer. The strain contains 1,634,138 bp with 1,654 coding sequences and a pXZ274 plasmid of 22,406 bp with 26 coding sequences. This is the first complete genome sequence of Helicobacter pylori from the Tibetan Plateau in China.
ESTHER : Guo_2012_J.Bacteriol_194_4146
PubMedSearch : Guo_2012_J.Bacteriol_194_4146
PubMedID: 22815458
Gene_locus related to this paper: helpy-o25061

Title : The B73 maize genome: complexity, diversity, and dynamics - Schnable_2009_Science_326_1112
Author(s) : Schnable PS , Ware D , Fulton RS , Stein JC , Wei F , Pasternak S , Liang C , Zhang J , Fulton L , Graves TA , Minx P , Reily AD , Courtney L , Kruchowski SS , Tomlinson C , Strong C , Delehaunty K , Fronick C , Courtney B , Rock SM , Belter E , Du F , Kim K , Abbott RM , Cotton M , Levy A , Marchetto P , Ochoa K , Jackson SM , Gillam B , Chen W , Yan L , Higginbotham J , Cardenas M , Waligorski J , Applebaum E , Phelps L , Falcone J , Kanchi K , Thane T , Scimone A , Thane N , Henke J , Wang T , Ruppert J , Shah N , Rotter K , Hodges J , Ingenthron E , Cordes M , Kohlberg S , Sgro J , Delgado B , Mead K , Chinwalla A , Leonard S , Crouse K , Collura K , Kudrna D , Currie J , He R , Angelova A , Rajasekar S , Mueller T , Lomeli R , Scara G , Ko A , Delaney K , Wissotski M , Lopez G , Campos D , Braidotti M , Ashley E , Golser W , Kim H , Lee S , Lin J , Dujmic Z , Kim W , Talag J , Zuccolo A , Fan C , Sebastian A , Kramer M , Spiegel L , Nascimento L , Zutavern T , Miller B , Ambroise C , Muller S , Spooner W , Narechania A , Ren L , Wei S , Kumari S , Faga B , Levy MJ , McMahan L , Van Buren P , Vaughn MW , Ying K , Yeh CT , Emrich SJ , Jia Y , Kalyanaraman A , Hsia AP , Barbazuk WB , Baucom RS , Brutnell TP , Carpita NC , Chaparro C , Chia JM , Deragon JM , Estill JC , Fu Y , Jeddeloh JA , Han Y , Lee H , Li P , Lisch DR , Liu S , Liu Z , Nagel DH , McCann MC , SanMiguel P , Myers AM , Nettleton D , Nguyen J , Penning BW , Ponnala L , Schneider KL , Schwartz DC , Sharma A , Soderlund C , Springer NM , Sun Q , Wang H , Waterman M , Westerman R , Wolfgruber TK , Yang L , Yu Y , Zhang L , Zhou S , Zhu Q , Bennetzen JL , Dawe RK , Jiang J , Jiang N , Presting GG , Wessler SR , Aluru S , Martienssen RA , Clifton SW , McCombie WR , Wing RA , Wilson RK
Ref : Science , 326 :1112 , 2009
Abstract : We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.
ESTHER : Schnable_2009_Science_326_1112
PubMedSearch : Schnable_2009_Science_326_1112
PubMedID: 19965430
Gene_locus related to this paper: maize-b4ffc7 , maize-b6u7e1 , maize-c0pcy5 , maize-c0pgf7 , maize-c0pgw1 , maize-c0pfl3 , maize-b4fpr7 , maize-k7vy73 , maize-a0a096swr3 , maize-k7v3i9 , maize-b6u9v9 , maize-a0a3l6e780 , maize-b4fv80 , maize-a0a1d6nse2 , maize-c4j9a1 , maize-k7uba1

Title : Influences of Cu or Cd on the neurotoxicity induced by petroleum hydrocarbons in ragworm Perinereis aibuhitensis - Zhang_2008_J.Environ.Sci.(China)_20_364
Author(s) : Zhang Q , Zhou Q , Wang J , Sun S , Hua T , Ren L
Ref : J Environ Sci (China) , 20 :364 , 2008
Abstract : The ecotoxicological effects of heavy metals and petroleum hydrocarbons (PHCs) on ragworms are still vague. The relationships between toxicological indices (mortality and acetylcholinesterase (AChE) activity) and concentrations of toxicants (Cu, Cd, and PHCs) were examined in the estuary keystone species Perinereis aibuhitensis in laboratory conditions. The results of single toxicant indicated that three toxicants had potentially physiological toxicity to P. aibuhitensis. The estimated 4-d and 10-d LC50 for Cu, Cd, and PHCs was derived from the relationships between mortality and toxicants concentrations. Notable changes in the morphological signs and symptoms of P. aibuhitensis exposed to PHCs were observed. The AChE activity of P. aibuhitensis was more sensitive to the toxicity of PHCs than the others. The results of combined toxicants implied that the combined toxicity of Cu or Cd and PHCs to P. aibuhitensis was related to the concentration combination of toxicants. Compared to single PHCs treatment, the addition of Cu or Cd significantly mitigated the neurotoxicity of PHCs to AChE activity in P. aibuhitensis, which showed an antagonistic effect.
ESTHER : Zhang_2008_J.Environ.Sci.(China)_20_364
PubMedSearch : Zhang_2008_J.Environ.Sci.(China)_20_364
PubMedID: 18595406