Peng Z

References (14)

Title : OsLDDT1, encoding a transmembrane structural DUF726 family protein, is essential for tapetum degradation and pollen formation in rice - Sun_2023_Plant.Sci__111596
Author(s) : Sun Z , Liu K , Chen C , Chen D , Peng Z , Zhou R , Liu L , He D , Duan W , Chen H , Huang C , Ruan Z , Zhang Y , Cao L , Zhan X , Cheng S , Sun L
Ref : Plant Sci , :111596 , 2023
Abstract : Formation of the pollen wall, which is mainly composed of lipid substances secreted by tapetal cells, is important to ensure pollen development in rice. Although several regulatory factors related to lipid biosynthesis during pollen wall formation have been identified in rice, the molecular mechanisms controlling lipid biosynthesis are unclear. We isolated the male-sterile rice mutant oslddt1 (leaked and delayed degraded tapetum 1). oslddt1 plants show complete pollen abortion resulting from delayed degradation of the tapetum and blocked formation of Ubisch bodies and pollen walls. OsLDDT1 (LOC_Os03g02170) encodes a DUF726 containing protein of unknown functionwith highly conserved transmembrane and alpha/beta Hydrolase domains. OsLDDT1 localizes to the endoplasmic reticulum and the gene is highly expressed in rice panicles. Genes involved in regulating fatty acid synthesis and formation of sporopollenin and pollen exine during anther developmentshowed significantly different expression patterns in oslddt1 plants. Interestingly, the wax and cutin contents in mature oslddt1-1 anthers were decreased by 74.07% and 72.22% compared to WT, indicating that OsLDDT1 is involved in fatty acid synthesis and affects formation of the anther epidermis. Our results provide as deeper understanding of the role of OsLDDT1 in regulating male sterility and also provide materials for hybrid rice breeding.
ESTHER : Sun_2023_Plant.Sci__111596
PubMedSearch : Sun_2023_Plant.Sci__111596
PubMedID: 36657664
Gene_locus related to this paper: orysj-q10ss2

Title : Screening models combining maternal characteristics and multiple markers for the early prediction of preeclampsia in pregnancy: a nested case-control study - Chen_2022_J.Obstet.Gynaecol__1
Author(s) : Chen L , Pi Y , Chang K , Luo S , Peng Z , Chen M , Yu L
Ref : J Obstet Gynaecol , :1 , 2022
Abstract : To identify maternal laboratory markers to predict the risk of preeclampsia (PE) in different stages of pregnancy, we analysed 67, 25, and 73, pregnancies developing PE at 11-13, 16-20, and 24-28 wks, respectively. Routine laboratory markers were measured in whole blood or serum and binary logistic regression analysis was used to identify predictive models. At 11-13 wks of gestation, patients who went on to develop PE showed significantly higher concentrations of alanine aminotransferase, aspartate aminotransferase, alpha-L-fucosidase, 5'-nucleotidase, glutamyl transpeptidase, cholinesterase, and uric acid; plateletcrit was also higher. At 16-20 wks, inhibin A concentration and plateletcrit were significantly elevated. At 24-28 wks, platelets, plateletcrit, and glucose concentration were significantly elevated. Logistic regression analysis showed that an elevation in 5'-nucleotidase was independently associated with PE at 11-13 wks. The combination of inhibin A, diastolic blood pressure, and body mass index was a significant predictor for PE at 16-20 wks, while the combination of glucose and systolic blood pressure was a significant predictor for PE at 24-28 wks. In conclusion, when combined with maternal characteristics, the measurement of 5'-nucleotidase, inhibin A, and glucose levels, represents a potentially valuable risk assessment for PE.Impact statementWhat is already known on this subject? Preeclampsia (PE) may be viewed as a spectrum of disorders with a severity that is reflected in the levels of specific biomarkers. Consequently, there is a clear need for additional biomarkers that can be used to stratify pregnancies as high or low risk soon after conception.What do the results of this study add? At 11-13 wks of gestation, maternal assays for platelets, plateletcrit, alanine aminotransferase, aspartate aminotransferase, alpha-L-fucosidase, 5'-nucleotidase, glutamyl transpeptidase, cholinesterase, and uric acid, demonstrated significantly higher values in patients with PE when compared with normal controls. Furthermore, assay results for inhibin A and platelets showed increased values at 16-20 wks of gestation. Assays performed at 24-28 wks of gestation revealed elevated levels of platelets, plateletcrit, and glucose. Our analysis indicated that increases in the levels of 5'-nucleotidase, inhibin A, and glucose, are effective and significant biomarkers that could be used in combination with maternal characteristics to screen for PE at 11-13, 16-20, and 24-28 wks of gestation, respectively. These findings provide a new basis for our understanding of the aetiology underlying PE.What are the implications of these findings for clinical practice and/or further research? Further studies that consider the entire population are now needed and should include the investigation of laboratory markers across different stages of pregnancy. Long-term follow up would also be necessary if we are to explore the full role of laboratory markers in the pathophysiology of PE.
ESTHER : Chen_2022_J.Obstet.Gynaecol__1
PubMedSearch : Chen_2022_J.Obstet.Gynaecol__1
PubMedID: 35634766

Title : Graphitic-phase C(3)N(4) nanosheets combined with MnO(2) nanosheets for sensitive fluorescence quenching detection of organophosphorus pesticides - Liu_2022_J.Environ.Sci.Health.B__1
Author(s) : Liu B , Chen J , Peng Y , Xiao W , Peng Z , Qiu P
Ref : J Environ Sci Health B , :1 , 2022
Abstract : In this study, we have developed a sensitive approach to measure organophosphorus pesticides (OPs) using graphitic-phase C(3)N(4) nanosheets (g-C(3)N(4)) combined with a nanomaterial-based quencher, MnO(2) nanosheets (MnO(2) NS). Since MnO(2) NS can quench the fluorescence of g-C(3)N(4) via the inner-filter effect (IFE), enzymatic hydrolysate (thiocholine, TCh) can efficiently trigger the decomposition of MnO(2) nanosheets in the presence of acetylcholinesterase (AChE) and acetylthiocholine (ATCh), resulting in the fluorescence recovery of g-C(3)N(4). OPs, as inhibitors to AChE activity, can prevent the generation of TCh and decomposition of MnO(2) nanosheets while exhibiting fluorescence quenching. Therefore, the AChE-ATCh-MnO(2)-g-C(3)N(4) system can be utilized to quantitatively detect OPs based on g-C(3)N(4) fluorescence. Under optimal conditions, the linear ranges for the determination of parathion-methyl (PM) and 2,2-dichlorovinyl dimethyl phosphate (DDVP) were found to be 0.1-2.1 ng/mL and 0.5-16 ng/mL, respectively, with limits of detection of 0.069 ng/mL and 0.20 ng/mL, respectively. The advantages of this assay are user-friendliness, ease of use, and cost effectiveness compared to other more sophisticated analytical instruments.
ESTHER : Liu_2022_J.Environ.Sci.Health.B__1
PubMedSearch : Liu_2022_J.Environ.Sci.Health.B__1
PubMedID: 35414329

Title : Development of a pH-Responsive, SO(4)(2-)-loaded Fe and N co-doped carbon quantum dots-based fluorescent method for highly sensitive detection of glyphosate - Peng_2022_Anal.Chim.Acta_1221_340110
Author(s) : Peng Z , Zeng M , Wu S , Yan Z , Rui J , Qiu P , Wang X
Ref : Anal Chim Acta , 1221 :340110 , 2022
Abstract : A novel sulfate-loaded iron-nitrogen co-doped carbon quantum dots (SO(4)(2-)-CQDs)-based fluorescent method was synthesized by the facile and environmentally friendly pyrolysis of persimmon frost (carbon source) and (NH(4))(2)Fe(SO(4))(2).6H(2)O. After SMMC-7721 cells were incubated with the SO(4)(2-)-CQDs for 24 h, more than 95% of the cells remained viable, even at a high concentration of the SO(4)(2-)-CQDs, indicating excellent biocompatibility and low toxicity. In addition, it was able to be taken up by the cells to emit their bright blue fluorescence after excitation at 365 nm, indicating suitable cell permeability. The SO(4)(2-)-CQDs also exhibited a unique response to changes in pH, which was applied in the detection of OPs by relying on the production of acetic acid from the hydrolysis of acetylcholine (ACh) by acetylcholinesterase (AChE), which decreased the pH and engendered an increase in the fluorescence of the SO(4)(2-)-CQDs; however, the inhibition of AChE by glyphosate resulted in little influence on fluorescence intensity due to the lack of acetic acid produced. This mechanism was the basis for the development of a sensitive assay for the detection of glyphosate. The resulting assay had a limit of detection of 0.066 ng/mL. Furthermore, the method was successfully applied for the precise and accurate monitoring of the concentration, distribution, and variation of glyphosate residues in chives and cultivated soil. Therefore, the proposed method was anticipated to provide a promising alternative for other detection methods to enable the reliable analysis of OPs in food products.
ESTHER : Peng_2022_Anal.Chim.Acta_1221_340110
PubMedSearch : Peng_2022_Anal.Chim.Acta_1221_340110
PubMedID: 35934352

Title : Ferulic acid regulates miR-17\/PTEN axis to inhibit LPS-induced pulmonary microvascular endothelial cells apoptosis through activation of PI3K\/Akt pathway - Zhang_2022_J.Toxicol.Sci_47_61
Author(s) : Zhang Q , Wang Z , Zhu J , Peng Z , Tang C
Ref : Journal of Toxicological Sciences , 47 :61 , 2022
Abstract : Acute lung injury (ALI) is mainly mediated by the damage of pulmonary microvascular endothelial cells (PMVECs). LPS is one of the pathogenic factors leading to microcirculatory abnormalities of ALI. Ferulic acid (FA) exhibits therapeutic eects against various diseases. During lipopolysaccharide-induced acute respiratory distress syndrome, FA, when given beforehand, could depress inflammation and oxidative stress. However, the concrete role and underlying mechanism of FA in ALI have not been well characterized. Ten microg/mL Lipopolysaccharide (LPS) was used to treat rat PMVECs for 24 hr. qRT-PCR was used to detect the level of miR-17 and phosphatase and tensin homolog deleted on chromosome ten (PTEN). Western blot was used to analyze the associated proteins in the PI3K/Akt pathway, and the apoptosis-related proteins. Flow cytometric analysis was performed to detect the apoptosis of PMVECs. MTT assay was constructed to detect the cell viability. Luciferase assay was conducted to detect the target gene of miR-17 and PTEN. A cell model for in vitro studying the role of FA in ALI was established using PMVECs. Our data demonstrate that FA up-regulates miR-17 and declines apoptosis induced by LPS. FA inhibits apoptosis mediated by up-regulating miR-17. Furthermore, we found miR-17 targeted PTEN negatively. FA inhibits cleaved caspase-3 and Bax expression through the PI3K/Akt pathway mediated by up-regulating miR-17. Over-expression of PTEN could contribute to the similar expression trend of the PI3K/Akt signal pathway protein compared to miR-17 inhibitor transfected cells. FA inhibits PMVECs apoptosis induced by LPS via miR-17/PTEN to further regulate the activation of the PI3K/Akt pathway in ALI. We anticipate that our data will provoke additional studies for ALI clinical therapy.
ESTHER : Zhang_2022_J.Toxicol.Sci_47_61
PubMedSearch : Zhang_2022_J.Toxicol.Sci_47_61
PubMedID: 35110471

Title : Monitoring of parathion methyl using a colorimetric gold nanoparticle-based acetylcholinesterase assay - Liu_2021_Spectrochim.Acta.A.Mol.Biomol.Spectrosc__120665
Author(s) : Liu B , Wu L , Peng Z , Wu S , Qiu P
Ref : Spectrochim Acta A Mol Biomol Spectrosc , :120665 , 2021
Abstract : A colorimetric gold nanoparticles (AuNPs)-based acetylcholinesterase (AChE) assay was designed for the first time to measure the concentration of parathion-methyl (PM) in lake water samples. In this assay, the analyte PM inhibited the hydrolysis of acetylthiocholine (ATCh) by AChE, preventing the formation of thiocholine (TCh) that would otherwise react with the AuNPs catalyst and deactivate the catalyst. Therefore, in the presence of PM, the AuNPs catalyzed the oxidation of the 3,3',5,5'-tetramethylbenzidine (TMB) colorimetric indicator to oxTMB, inducing a visual color change from colorless to blue. However, in the absence of PM, AChE hydrolyzed ATCh to TCh, which then reacted with the AuNPs, preventing the oxidation of TMB to oxTMB and rendering the solution colorless. Therefore, the change in the color of the analyte solution indicated the presence of PM, and the absorbance of the resulting solution was measured by UV-Vis spectroscopy to calculate the concentration of PM after generation of a calibration curve. This method was then employed using the smartphone app Color Picker, which converted the color information from the photos of the solution into digital red (R), green (G), and blue (B) values. The ratio of green (G) to blue (B) (G/B) was then plotted against the corresponding concentration to calculate the standard curve, whose regression equation was expressed by y = -0.012x + 1.02 (ng/mL), and the coefficient of determination (R(2)) was 0.97. In addition, this method was also used to determine the amount of PM in real lake water samples with recovery of 90.2-133.3%.
ESTHER : Liu_2021_Spectrochim.Acta.A.Mol.Biomol.Spectrosc__120665
PubMedSearch : Liu_2021_Spectrochim.Acta.A.Mol.Biomol.Spectrosc__120665
PubMedID: 34865979

Title : Development of a whole-cell biocatalyst for diisobutyl phthalate degradation by functional display of a carboxylesterase on the surface of Escherichia coli - Ding_2020_Microb.Cell.Fact_19_114
Author(s) : Ding J , Zhou Y , Wang C , Peng Z , Mu Y , Tang X , Huang Z
Ref : Microb Cell Fact , 19 :114 , 2020
Abstract : BACKGROUND: Phthalic acid esters (PAEs) are widely used as plasticizers or additives during the industrial manufacturing of plastic products. PAEs have been detected in both aquatic and terrestrial environments due to their overuse. Exposure of PAEs results in human health concerns and environmental pollution. Diisobutyl phthalate is one of the main plasticizers in PAEs. Cell surface display of recombinant proteins has become a powerful tool for biotechnology applications. In this current study, a carboxylesterase was displayed on the surface of Escherichia coli cells, for use as whole-cell biocatalyst in diisobutyl phthalate biodegradation. RESULTS: A carboxylesterase-encoding gene (carEW) identified from Bacillus sp. K91, was fused to the N-terminal of ice nucleation protein (inpn) anchor from Pseudomonas syringae and gfp gene, and the fused protein was then cloned into pET-28a(+) vector and was expressed in Escherichia coli BL21(DE3) cells. The surface localization of INPN-CarEW/or INPN-CarEW-GFP fusion protein was confirmed by SDS-PAGE, western blot, proteinase accessibility assay, and green fluorescence measurement. The catalytic activity of the constructed E. coli surface-displayed cells was determined. The cell-surface-displayed CarEW displayed optimal temperature of 45 degrees C and optimal pH of 9.0, using p-NPC2 as substrate. In addition, the whole cell biocatalyst retained ~ 100% and ~ 200% of its original activity per OD600 over a period of 23 days at 45 degrees C and one month at 4 degrees C, exhibiting the better stability than free CarEW. Furthermore, approximately 1.5 mg/ml of DiBP was degraded by 10 U of surface-displayed CarEW cells in 120 min. CONCLUSIONS: This work provides a promising strategy of cost-efficient biodegradation of diisobutyl phthalate for environmental bioremediation by displaying CarEW on the surface of E. coli cells. This approach might also provide a reference in treatment of other different kinds of environmental pollutants by displaying the enzyme of interest on the cell surface of a harmless microorganism.
ESTHER : Ding_2020_Microb.Cell.Fact_19_114
PubMedSearch : Ding_2020_Microb.Cell.Fact_19_114
PubMedID: 32471417
Gene_locus related to this paper: bacsu-pnbae

Title : A sensitive fluorescent assay for the determination of parathion-methyl using AHNSA probe with MnO(2) nanosheets - Liu_2020_Spectrochim.Acta.A.Mol.Biomol.Spectrosc_247_119146
Author(s) : Liu B , Peng Z , Wu S , He T , Qiu P
Ref : Spectrochim Acta A Mol Biomol Spectrosc , 247 :119146 , 2020
Abstract : In this paper, a novel fluorescence assay has been constructed for the determination of parathion-methyl (PM) by using 4-amino-3-hydroxy-1-naphthalenesulfonic acid (AHNSA) as probe. MnO(2) nanosheets (MnO(2) NS) could quench the fluorescence of AHNSA, while Mn(2+), the reduction product of MnO(2) NS, has no influence on it, resulting in fluorescence recovery. This is because that MnO(2) NS have oxidized characteristic, and they can react with choline (TCh), which is the product of acetylthiocholine (ATCh) catalyzed by acetylcholinesterase (AChE). In the presence of OPs, the activity of AChE was inhibited, accompanied by the restraint of the redox reaction of MnO(2) NS, therefore the fluorescence of AHNSA was quenched. Under the optimized experimental conditions, a linear range of PM was determined to be 0.4-40 ng/mL (R(2) = 0.997) by the proposed method with the limit of detection for 0.18 ng/mL (S/N = 3). The assay was successfully applied to the determination of PM in lake water, which average recoveries were between 86.5% and 114.4%.
ESTHER : Liu_2020_Spectrochim.Acta.A.Mol.Biomol.Spectrosc_247_119146
PubMedSearch : Liu_2020_Spectrochim.Acta.A.Mol.Biomol.Spectrosc_247_119146
PubMedID: 33186817

Title : Targeted label-free approach for quantification of epoxide hydrolase and glutathione transferases in microsomes - Song_2015_Anal.Biochem_478_8
Author(s) : Song W , Yu L , Peng Z
Ref : Analytical Biochemistry , 478 :8 , 2015
Abstract : The aim of this study was to investigate the expression and organ distribution of cytochrome P450 (CYP450) enzymes, microsomal epoxide hydrolase (MEH), and microsomal glutathione-S-transferase (MGST 1, 2, 3) in human liver, lung, intestinal, and kidney microsomes by targeted peptide-based quantification using nano liquid chromatography-tandem multiple reaction monitoring (nano LC-MRM). Applying this method, we analyzed 16 human liver microsomes and pooled lung, kidney, and intestine microsomes. Nine of the CYP450s (CYP1A2, 2B6, 2C8, 2C9, 2C19, 2D6, 2E1, 3A4, 3A5) could be quantified in liver. Except for CYP3A4 and 3A5 existing in intestine, other CYP450s had little content (<0.1pmol/mg protein) in extrahepatic tissues. MEH and MGSTs could be quantified both in hepatic and in extrahepatic tissues. The highest concentrations of MEH and MGST 1, 2 were found in liver; conversely MGST 3 was abundant in human kidney and intestine compared to liver. The targeted proteomics assay described here can be broadly and efficiently utilized as a tool for investigating the targeted proteins. The method also provides novel CYP450s, MEH, and MGSTs expression data in human hepatic and extrahepatic tissues that will benefit rational approaches to evaluate metabolism in drug development.
ESTHER : Song_2015_Anal.Biochem_478_8
PubMedSearch : Song_2015_Anal.Biochem_478_8
PubMedID: 25769418

Title : Sequencing, annotation, and characterization of the influenza ferret infectome - Leon_2013_J.Virol_87_1957
Author(s) : Leon AJ , Banner D , Xu L , Ran L , Peng Z , Yi K , Chen C , Xu F , Huang J , Zhao Z , Lin Z , Huang SH , Fang Y , Kelvin AA , Ross TM , Farooqui A , Kelvin DJ
Ref : J Virol , 87 :1957 , 2013
Abstract : Ferrets have become an indispensable tool in the understanding of influenza virus virulence and pathogenesis. Furthermore, ferrets are the preferred preclinical model for influenza vaccine and therapeutic testing. Here we characterized the influenza infectome during the different stages of the infectious process in ferrets with and without prior specific immunity to influenza. RNA from lung tissue and lymph nodes from infected and naive animals was subjected to next-generation sequencing, followed by de novo data assembly and annotation of the resulting sequences; this process generated a library comprising 13,202 ferret mRNAs. Gene expression profiles during pandemic H1N1 (pdmH1N1) influenza virus infection were analyzed by digital gene expression and solid support microarrays. As expected during primary infection, innate immune responses were triggered in the lung tissue; meanwhile, in the lymphoid tissue, genes encoding antigen presentation and maturation of effector cells of adaptive immunity increased dramatically. After 5 days postinfection, the innate immune gene expression was replaced by the adaptive immune response, which correlates with viral clearance. Reinfection with homologous pandemic influenza virus resulted in a diminished innate immune response, early adaptive immune gene regulation, and a reduction in clinical severity. The fully annotated ferret infectome will be a critical aid to the understanding of the molecular events that regulate disease severity and host-influenza virus interactions among seasonal, pandemic, and highly pathogenic avian influenzas.
ESTHER : Leon_2013_J.Virol_87_1957
PubMedSearch : Leon_2013_J.Virol_87_1957
PubMedID: 23236062
Gene_locus related to this paper: muspf-m1ejm3 , muspf-m3xwe4 , muspf-m3y1u3 , muspf-m3y1w0 , muspf-m3yex5 , muspf-m3ywm4 , muspf-m3yzl3 , muspf-g9kcw3 , muspf-m1efe2 , muspf-g9kdq4 , muspf-m3z0x2 , muspf-g9khi6 , muspf-m3yaj5 , muspf-g9k8i1 , muspf-m3xnu7 , muspf-m3yi69 , muspf-m3ywu1 , muspf-m3yy03 , muspf-g9l4j3 , muspf-m1ejz6

Title : Gap2 promotes the formation of a stable protein complex required for mature Fap1 biogenesis - Echlin_2013_J.Bacteriol_195_2166
Author(s) : Echlin H , Zhu F , Li Y , Peng Z , Ruiz T , Bedwell GJ , Prevelige PE, Jr. , Wu H
Ref : Journal of Bacteriology , 195 :2166 , 2013
Abstract : Serine-rich repeat glycoproteins (SRRPs) are important bacterial adhesins conserved in streptococci and staphylococci. Fap1, a SRRP identified in Streptococcus parasanguinis, is the major constituent of bacterial fimbriae and is required for adhesion and biofilm formation. An 11-gene cluster is required for Fap1 glycosylation and secretion; however, the exact mechanism of Fap1 biogenesis remains a mystery. Two glycosylation-associated proteins within this cluster--Gap1 and Gap3--function together in Fap1 biogenesis. Here we report the role of the third glycosylation-associated protein, Gap2. A gap2 mutant exhibited the same phenotype as the gap1 and gap3 mutants in terms of Fap1 biogenesis, fimbrial assembly, and bacterial adhesion, suggesting that the three proteins interact. Indeed, all three proteins interacted with each other independently and together to form a stable protein complex. Mechanistically, Gap2 protected Gap3 from degradation by ClpP protease, and Gap2 required the presence of Gap1 for expression at the wild-type level. Gap2 augmented the function of Gap1 in stabilizing Gap3; this function was conserved in Gap homologs from Streptococcus agalactiae. Our studies demonstrate that the three Gap proteins work in concert in Fap1 biogenesis and reveal a new function of Gap2. This insight will help us elucidate the molecular mechanism of SRRP biogenesis in this bacterium and in pathogenic species.
ESTHER : Echlin_2013_J.Bacteriol_195_2166
PubMedSearch : Echlin_2013_J.Bacteriol_195_2166
PubMedID: 23475979
Gene_locus related to this paper: 9stre-e7s950

Title : The oyster genome reveals stress adaptation and complexity of shell formation - Zhang_2012_Nature_490_49
Author(s) : Zhang G , Fang X , Guo X , Li L , Luo R , Xu F , Yang P , Zhang L , Wang X , Qi H , Xiong Z , Que H , Xie Y , Holland PW , Paps J , Zhu Y , Wu F , Chen Y , Wang J , Peng C , Meng J , Yang L , Liu J , Wen B , Zhang N , Huang Z , Zhu Q , Feng Y , Mount A , Hedgecock D , Xu Z , Liu Y , Domazet-Loso T , Du Y , Sun X , Zhang S , Liu B , Cheng P , Jiang X , Li J , Fan D , Wang W , Fu W , Wang T , Wang B , Zhang J , Peng Z , Li Y , Li N , Chen M , He Y , Tan F , Song X , Zheng Q , Huang R , Yang H , Du X , Chen L , Yang M , Gaffney PM , Wang S , Luo L , She Z , Ming Y , Huang W , Huang B , Zhang Y , Qu T , Ni P , Miao G , Wang Q , Steinberg CE , Wang H , Qian L , Liu X , Yin Y
Ref : Nature , 490 :49 , 2012
Abstract : The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.
ESTHER : Zhang_2012_Nature_490_49
PubMedSearch : Zhang_2012_Nature_490_49
PubMedID: 22992520
Gene_locus related to this paper: cragi-k1qzk7 , cragi-k1rad0 , cragi-k1p6v9 , cragi-k1pa46 , cragi-k1pga2 , cragi-k1pp63 , cragi-k1pwa8 , cragi-k1q0b1.1 , cragi-k1q0b1.2 , cragi-k1q1h2 , cragi-k1q2z6 , cragi-k1qaj8 , cragi-k1qaw5 , cragi-k1qhl5 , cragi-k1qly1 , cragi-k1qqb1.1 , cragi-k1qqb1.2 , cragi-k1qs61 , cragi-k1qs99 , cragi-k1qwl6 , cragi-k1r068 , cragi-k1r0n3.1 , cragi-k1r0n3.2 , cragi-k1r0r4 , cragi-k1r1i9 , cragi-k1r8q9 , cragi-k1rgi1 , cragi-k1rig4 , cragi-k1s0a7.1 , cragi-k1s0a7.2 , cragi-k1s0a7.3 , cragi-k1q6q0 , cragi-k1rru1 , cragi-k1qfi4 , cragi-k1qvm5 , cragi-k1qq58 , cragi-k1qdc0 , cragi-k1r754 , cragi-k1pje5 , cragi-k1qca6 , cragi-k1qdt5 , cragi-k1qkz7 , cragi-k1rgd2 , cragi-k1puh6 , cragi-k1raz4 , cragi-k1qqj4 , cragi-k1rbs1

Title : Genome sequence of Acinetobacter calcoaceticus PHEA-2, isolated from industry wastewater - Zhan_2011_J.Bacteriol_193_2672
Author(s) : Zhan Y , Yan Y , Zhang W , Yu H , Chen M , Lu W , Ping S , Peng Z , Yuan M , Zhou Z , Elmerich C , Lin M
Ref : Journal of Bacteriology , 193 :2672 , 2011
Abstract : Genome analysis of Acinetobacter calcoaceticus PHEA-2 was undertaken because of the importance of this bacterium for bioremediation of phenol-polluted water and because of the close phylogenetic relationship of this species with the human pathogen Acinetobacter baumannii. To our knowledge, this is the first strain of A. calcoaceticus whose genome has been sequenced.
ESTHER : Zhan_2011_J.Bacteriol_193_2672
PubMedSearch : Zhan_2011_J.Bacteriol_193_2672
PubMedID: 21441526
Gene_locus related to this paper: aciad-q6fc40 , aciba-d0c992 , aciba-q76hj1 , acibt-a3m5r6 , acibt-a3m5t3 , acibt-a3m5x2 , acica-d0ryi9 , acica-d0ryx6 , acicp-f0kgu1 , acicp-f0kh68 , acicp-f0khy0 , acicp-f0kj61 , aciba-w3svn7 , aciba-a0a009wzt4

Title : Functional and evolutionary insights from the genomes of three parasitoid Nasonia species - Werren_2010_Science_327_343
Author(s) : Werren JH , Richards S , Desjardins CA , Niehuis O , Gadau J , Colbourne JK , Beukeboom LW , Desplan C , Elsik CG , Grimmelikhuijzen CJ , Kitts P , Lynch JA , Murphy T , Oliveira DC , Smith CD , van de Zande L , Worley KC , Zdobnov EM , Aerts M , Albert S , Anaya VH , Anzola JM , Barchuk AR , Behura SK , Bera AN , Berenbaum MR , Bertossa RC , Bitondi MM , Bordenstein SR , Bork P , Bornberg-Bauer E , Brunain M , Cazzamali G , Chaboub L , Chacko J , Chavez D , Childers CP , Choi JH , Clark ME , Claudianos C , Clinton RA , Cree AG , Cristino AS , Dang PM , Darby AC , de Graaf DC , Devreese B , Dinh HH , Edwards R , Elango N , Elhaik E , Ermolaeva O , Evans JD , Foret S , Fowler GR , Gerlach D , Gibson JD , Gilbert DG , Graur D , Grunder S , Hagen DE , Han Y , Hauser F , Hultmark D , Hunter HCt , Hurst GD , Jhangian SN , Jiang H , Johnson RM , Jones AK , Junier T , Kadowaki T , Kamping A , Kapustin Y , Kechavarzi B , Kim J , Kiryutin B , Koevoets T , Kovar CL , Kriventseva EV , Kucharski R , Lee H , Lee SL , Lees K , Lewis LR , Loehlin DW , Logsdon JM, Jr. , Lopez JA , Lozado RJ , Maglott D , Maleszka R , Mayampurath A , Mazur DJ , McClure MA , Moore AD , Morgan MB , Muller J , Munoz-Torres MC , Muzny DM , Nazareth LV , Neupert S , Nguyen NB , Nunes FM , Oakeshott JG , Okwuonu GO , Pannebakker BA , Pejaver VR , Peng Z , Pratt SC , Predel R , Pu LL , Ranson H , Raychoudhury R , Rechtsteiner A , Reese JT , Reid JG , Riddle M , Robertson HM , Romero-Severson J , Rosenberg M , Sackton TB , Sattelle DB , Schluns H , Schmitt T , Schneider M , Schuler A , Schurko AM , Shuker DM , Simoes ZL , Sinha S , Smith Z , Solovyev V , Souvorov A , Springauf A , Stafflinger E , Stage DE , Stanke M , Tanaka Y , Telschow A , Trent C , Vattathil S , Verhulst EC , Viljakainen L , Wanner KW , Waterhouse RM , Whitfield JB , Wilkes TE , Williamson MS , Willis JH , Wolschin F , Wyder S , Yamada T , Yi SV , Zecher CN , Zhang L , Gibbs RA , Williamson M
Ref : Science , 327 :343 , 2010
Abstract : We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.
ESTHER : Werren_2010_Science_327_343
PubMedSearch : Werren_2010_Science_327_343
PubMedID: 20075255
Gene_locus related to this paper: nasvi-ACHE1 , nasvi-ACHE2 , nasvi-k7in31 , nasvi-k7iwl9 , nasvi-k7iyk8 , nasvi-k7jlv1 , nasvi-k7in32 , nasvi-k7ind2 , nasvi-k7inh0 , nasvi-k7inh1 , nasvi-k7inh2 , nasvi-k7inp9 , nasvi-k7iun7 , nasvi-k7iv21 , nasvi-k7ivn5 , nasvi-k7ivn6 , nasvi-k7iw29 , nasvi-k7iwk5 , nasvi-k7iwl8 , nasvi-k7iz24 , nasvi-k7izb4 , nasvi-k7j5u6 , nasvi-k7j6y1 , nasvi-k7j6y2 , nasvi-k7j6y4 , nasvi-k7j718 , nasvi-k7j755 , nasvi-k7j756 , nasvi-k7j757 , nasvi-k7j7k5 , nasvi-k7j7n7 , nasvi-k7j7r8 , nasvi-k7j7s8 , nasvi-k7j7s9 , nasvi-k7j811 , nasvi-k7iny8 , nasvi-k7izf2 , nasvi-k7iwe2 , nasvi-k7j6w4 , nasvi-k7izl9 , nasvi-k7jf39 , nasvi-k7izl8 , nasvi-k7irf1 , nasvi-k7j7l1