Author Report for: Xu QNo contact information in database for Xu Q
Zhao Z, Liu Y, Liu C, Xu Q, Song M, Yan H Ref: 3 Biotech, 13:329, 2023 : PubMed ESTHER: Zhao_2023_3.Biotech_13_329 PubMedSearch: Zhao 2023 3.Biotech 13 329 PubMedID: 37670801 Abstract Extensive use of phthalic acid esters (PAEs) as plasticizer causes diffusion into the environment, which posed a great threat to mankind. It was reported that Comamonas sp. was a potentially robust aromatic biodegrader. Although the biodegradation of several PAEs by Comamonas sp. was studies, the comprehensive genomic analysis of Comamonas sp. was few reported. In the present study, one promising bacterial strain for biodegrading diethyl phthalate (DEP) was successfully isolated from activated sludge and characterized as Comamonas sp. USTBZA1 based on the 16S rRNA sequence analysis. The results showed that pH 7.5, 30 degreesC and inoculum volume ratio of 6% were optimal for biodegradation. Initial DEP of 50 mg/L could be completely biodegrade by strain USTBZA1 within 24 h which conformed to the Gompertz model. Based on the Q-TOF LC/MS analysis, monoethyl phthalate (MEP) and phthalic acid (PA) were identified as the metabolic products of DEP biodegradation by USTBZA1. Furthermore, the whole genome of Comamonas sp. USTBZA1 was analyzed to clarify the molecular mechanism for PAEs biodegradation by USTBZA1. There were 3 and 41 genes encoding esterase/arylesterase and hydrolase, respectively, and two genes regions (pht34512 and pht4253) were responsible for the conversion of PA to protocatechuate (PCA), and two genes regions (ligCBAIKJ) were involved in PCA metabolism in USTBZA1. These results substantiated that Comamonas sp. USTBZA1 has potential application in the DEP bioremediation. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03736-3. Title: Neurexin-beta Mediates the Synaptogenic Activity of Amyloid Precursor Protein Cvetkovska V, Ge Y, Xu Q, Li S, Zhang P, Craig AM Ref: Journal of Neuroscience, :, 2022 : PubMed ESTHER: Cvetkovska_2022_J.Neurosci__ PubMedSearch: Cvetkovska 2022 J.Neurosci PubMedID: 36261284 Abstract In addition to its role in Alzheimer's disease, amyloid precursor protein (APP) has physiological roles in synapse development and function. APP induces presynaptic differentiation when presented to axons but the mechanism is unknown. Here we show that APP binds neurexin to mediate this synaptogenic activity. APP specifically binds beta not alpha neurexins modulated by splice site 4. Binding to neurexin heparan sulfate glycan and LNS protein domains is required for high affinity interaction and for full-length APP to recruit axonal neurexin. The synaptogenic activity of APP is abolished by triple knockdown of neurexins in hippocampal neurons pooled from male and female rats. Based on these and previous results, our model is that a dendritic-axonal trans dimer of full-length APP binds to axonal neurexin-beta to promote synaptic differentiation and function. Furthermore, soluble sAPPs also bind neurexin-beta and inhibit its interaction with neuroligin-1, raising the possibility that disruption of neurexin function by altered levels of full-length APP and its cleavage products may contribute to early synaptic deficits in Alzheimer's disease.SIGNIFICANCE STATEMENT:The prevailing model for the basis of Alzheimer's disease is the amyloid cascade triggered by altered cleavage of amyloid precursor protein (APP). APP also has physiological roles at the synapse but the molecular basis for its synaptic functions are not well understood. Here, we show that APP binds the presynaptic organizing protein neurexin-beta and that neurexin is essential for the synaptogenic activity of APP. Furthermore, soluble APP forms generated by APP cleavage also bind neurexin-beta and can block interaction with transmembrane synaptogenic ligands of neurexin. These findings reveal a role for neurexin-APP interaction in synapse development and raise the possibility that disruptions of neurexin function may contribute to synaptic and cognitive deficits in the critical early stage of Alzheimer's disease. Title: Transcriptome-wide association study reveals cholesterol metabolism gene Lpl is a key regulator of cognitive dysfunction Hu W, Liu J, Hu Y, Xu Q, Deng T, Wei M, Lu L, Mi J, Bergquist J and Tian G <1 more author(s)> Hu W, Liu J, Hu Y, Xu Q, Deng T, Wei M, Lu L, Mi J, Bergquist J, Xu F, Tian G (- 1) Ref: Front Mol Neurosci, 15:1044022, 2022 : PubMed ESTHER: Hu_2022_Front.Mol.Neurosci_15_1044022 PubMedSearch: Hu 2022 Front.Mol.Neurosci 15 1044022 PubMedID: 36590920 Abstract Cholesterol metabolism in the brain plays a crucial role in normal physiological function, and its aberrations are associated with cognitive dysfunction. The present study aimed to determine which cholesterol-related genes play a vital role in cognitive dysfunction and to dissect its underlying molecular mechanisms using a systems genetics approach in the BXD mice family. We first systematically analyzed the association of expression of 280 hippocampal genes related to cholesterol metabolism with cognition-related traits and identified lipoprotein lipase (Lpl) as a critical regulator. This was further confirmed by phenome-wide association studies that indicate Lpl associated with hippocampus volume residuals and anxiety-related traits. By performing expression quantitative trait locus mapping, we demonstrate that Lpl is strongly cis-regulated in the BXD hippocampus. We also identified -3,300 genes significantly (p < 0.05) correlated with the Lpl expression. Those genes are mainly involved in the regulation of neuron-related traits through the MAPK signaling pathway, axon guidance, synaptic vesicle cycle, and NF-kappa B signaling pathway. Furthermore, a protein-protein interaction network analysis identified several direct interactors of Lpl, including Rab3a, Akt1, Igf1, Crp, and Lrp1, which indicates that Lpl involves in the regulation of cognitive dysfunction through Rab3a-mediated synaptic vesicle cycle and Akt1/Igf1/Crp/Lrp1-mediated MAPK signaling pathway. Our findings demonstrate the importance of the Lpl, among the cholesterol-related genes, in regulating cognitive dysfunction and highlighting the potential signaling pathways, which may serve as novel therapeutic targets for the treatment of cognitive dysfunction. Title: Synthesis and Characterization of Epoxidized Silkworm Pupae Oil and Its Application as Polyvinyl Chloride Ji Y, Xu L, Xu Q, Liu X, Lin S, Liao S, Wang W, Lan D Ref: Appl Biochem Biotechnol, 194:1290, 2022 : PubMed ESTHER: Ji_2022_Appl.Biochem.Biotechnol_194_1290 PubMedSearch: Ji 2022 Appl.Biochem.Biotechnol 194 1290 PubMedID: 34677760 Gene_locus related to this paper: malgo-a8puy1 Abstract More and more industries demand environmental friendliness. Silkworm pupae oil (SPO), extracted from the desilked silkworm pupae, can serve as a promising substrate alternative to use in plasticization. This study aimed to prepare epoxidized silkworm pupae oil (ESPO) and investigate their effects on the thermal stability and plasticization of polyvinyl chloride (PVC) films. A chemo-enzymatic method of ESPO was developed in the presence of Lipase SMG1-F278N and H(2)O(2) in natural deep eutectic solvents (DESs). Lipase SMG1-F278N could initiate the epoxidation reaction effectively at room temperature with a negligible loss of activities 10 batches. A maximum oxirane value of 6.94% was obtained. The formation of oxirane ring in ESPO was confirmed by FTIR and (13)C NMR spectra. Moreover, ESPO showed a better thermal stability and lower freezing point than epoxidized soybean oil (ESO). It was demonstrated that ESPO had a good frost resistance. In addition, ESPO showed a significantly improved plasticizing effect on flexible polyvinyl chloride (PVC). Compared with ESO, ESPO could increase the tensile elongation at break effectively. A significantly lower migration rate of plasticizer was observed in PVC plasticized with ESPO. Title: In Situ Formation of o-Phenylenediamine Cascade Polymers Mediated by Metal-Organic Framework Nanozymes for Fluorescent and Photothermal Dual-Mode Assay of Acetylcholinesterase Activity Li S, Wei Z, Xiong L, Xu Q, Yu L, Xiao Y Ref: Analytical Chemistry, :, 2022 : PubMed ESTHER: Li_2022_Anal.Chem__ PubMedSearch: Li 2022 Anal.Chem PubMedID: 36463539 Abstract A fluorescent and photothermal dual-mode assay method was established for the detection of acetylcholinesterase (AChE) activity based on in situ formation of o-phenylenediamine (oPD) cascade polymers. First, copper metal-organic frameworks of benzenetricarboxylic acid (Cu-BTC) were screened out as nanozymes with excellent oxidase-like activity and confinement catalysis effect. Then, an ingenious oPD cascade polymerization strategy was proposed. That is, oPD was oxidized by Cu-BTC to oPD oligomers with strong yellow fluorescence, and oPD oligomers were further catalyzed to generate J-aggregation, which promotes the formation of oPD polymer nanoparticles with a high photothermal effect. By utilizing thiocholine (enzymolysis product of acetylthiocholine) to inhibit the Cu-BTC catalytic effect, AChE activity was detected through the fluorescence-photothermal dual-signal change of oPD oligomers and polymer nanoparticles. Both assay modes have low detection limitation (0.03 U L(-1) for fluorescence and 0.05 U L(-1) for photothermal) and can accurately detect the AChE activity of human serum (recovery 85.0-111.3%). The detection results of real serum samples by fluorescent and photothermal dual modes are consistent with each other (relative error >= 5.2%). It is worth emphasizing that this is the first time to report the high photothermal effect of oPD polymers and the fluorescence-photothermal dual-mode assay of enzyme activity. Title: Pesticide Residues in Commonly Consumed Vegetables in Henan Province of China in 2020 Ma C, Wei D, Liu P, Fan K, Nie L, Song Y, Wang M, Wang L, Xu Q and Zeng X <10 more author(s)> Ma C, Wei D, Liu P, Fan K, Nie L, Song Y, Wang M, Wang L, Xu Q, Wang J, Shi J, Geng J, Zhao M, Jia Z, Huan C, Huo W, Wang C, Mao Z, Huang S, Zeng X (- 10) Ref: Front Public Health, 10:901485, 2022 : PubMed ESTHER: Ma_2022_Front.Public.Health_10_901485 PubMedSearch: Ma 2022 Front.Public.Health 10 901485 PubMedID: 35757605 Abstract BACKGROUND: Pesticides are widely used in agricultural production to control insect pests and regulate plant growth in China, which may result in the presence of some pesticide residues in the vegetables. However, few studies of monitoring pesticides have been conducted in Henan Province. The aim of this study was to evaluate the level of pesticide residues in commonly consumed vegetables in the regions of Henan Province. METHODS: In this study, we collected 5,576 samples of 15 different vegetables in 17 areas from Henan Province during 2020. Eight kinds of pesticides were analyzed by gas chromatography-mass spectrometry (GC-MS), including procymidone, lambda-cyhalothrin, cypermethrin, pendimethalin, isocarbophos, isazophos, fenthion and deltamethrin. The chi-square test was used to compare the detection rates of pesticide residues in different regions. RESULTS: Of all the pesticides above, procymidone, lambda-cyhalothrin, cypermethrin, pendimethalin and isocarbophos were detected in vegetables, the detection rates were 27.0%, 16.2%, 11.4%, 3.5%, and 1.9%, respectively. However, isazophos, fenthion, and deltamethrin were not detected. In addition, procymidone, lambda-cyhalothrin, and cypermethrin were detected in urban areas, while pendimethalin was detected in rural areas. The detection rates of cypermethrin and pendimethalin in rural were 19.8% and 5.4%, respectively, which in urban were at relatively lower levels (13.7% and 1.9%, respectively) (P < 0.05). Compared the differences of pesticide detection rates among five areas of Henan province, we found that there were statistical differences in the detection rates of procymidone, cypermethrin and lambda-cyhalothrin in different regions (all P < 0.05). CONCLUSION: The results have revealed that the pesticide residues are present. Higher detection rates and more types of pesticides were found in rural areas than urban areas. In addition, there were higher detection rates in Eastern Henan. The findings provided valuable information on the current pesticide residues status, which can be a reference of pesticide supervision and management. Title: Pharmacological agents targeting autophagy and their effects on lipolysis in human adipocytes Xu Q, Mariman EC, Blaak EE, Jocken JW Ref: Mol Cell Endocrinol, 544:111555, 2022 : PubMed ESTHER: Xu_2022_Mol.Cell.Endocrinol_544_111555 PubMedSearch: Xu 2022 Mol.Cell.Endocrinol 544 111555 PubMedID: 35031432 Abstract Adipose tissue of metabolically compromised humans with obesity is often characterized by impaired regulation of autophagy pathway. However, data on the role of autophagy in human adipocyte lipid catabolism is scarce. Therefore, we investigated the effect of pharmacological agents (including 3-methyladenine (3MA), bafilomycin A1 (BAF), chloroquine (CQ) and lalistat-2 (L-stat), that target different stages of the autophagy pathway on lipid hydrolysis in differentiated human multipotent adipose-derived stem cells (hMADs). Glycerol and fatty acid release were measured as marker of lipid hydrolysis following starvation and beta-adrenergic stimulation. Microtubule-associated protein light chain 3 ratio (LC3II/LC3I) and HSL phosphorylation (pHSL) were analyzed by Western blot. Our data indicate that pharmacological inhibition of the autophagy pathway reduced lipid hydrolysis in human adipocytes, although to a limited extent (10-15%). However, further research is needed to reveal the exact mechanism of action of these pharmacological agents and their interplay with cytosolic lipid breakdown in human adipocytes. Title: Activation of cholinergic basal forebrain neurons improved cognitive functions in adult-onset hypothyroid mice Xu YX, Wang C, Li XD, Guo WL, Liu GY, Zhang HB, Sun Y, Zhu DF, Xu Q Ref: Biomed Pharmacother, 153:113495, 2022 : PubMed ESTHER: Xu_2022_Biomed.Pharmacother_153_113495 PubMedSearch: Xu 2022 Biomed.Pharmacother 153 113495 PubMedID: 36076509 Abstract Cognitive dysfunction is common in hypothyroid patients, even after undergoing sufficient levothyroxine (LT4) replacement therapy for euthyroid. Our previous studies indicated that cholinergic neurons might contribute to the decline of cognition in adult-onset hypothyroidism. Nevertheless, the role of the cellular and neural control of basal forebrain (BF) cholinergic neurons in hypothyroidism-induced cognitive impairments is unknown. Using transgenic mice that specifically expressed chemogenetic activators in their BF cholinergic neurons, we systematically investigated the role of BF cholinergic neurons in hypothyroidism-induced cognitive dysfunction by the combined approaches of patch clamp electrophysiology, behavioral testing, and immunohistochemistry. The results showed that LT4 treatment in the adult-onset hypothyroid mice reversed only 78 % of the BF cholinergic neurons to their normal values of electrophysiological properties. LT4 monotherapy did not rehabilitate cognitive function in the hypothyroid mice. Chemogenetic selective activation of the BF cholinergic neurons combined with LT4 treatment significantly improved learning and memory functions in the hypothyroid mice. In addition, chemogenetic activation of the cholinergic neurons induced the robust expression of c-Fos protein in the BF, prefrontal cortex (PFC), and hippocampus. This indicated that the BF cholinergic neurons improved learning and memory functions in the hypothyroid mice via the BF-PFC and BF-hippocampus pathways. In the hypothyroid C57BL/6 J mice, combined treatment via LT4 and donepezil, a cholinesterase inhibitor, significantly increased cognitive functions. The results suggested that the BF cholinergic neurons are critical for regulating learning and memory and reveal a novel pathophysiological mechanism for hypothyroidism-induced cognitive impairments. Title: Genome-Wide Detection of Copy Number Variations and Evaluation of Candidate Copy Number Polymorphism Genes Associated With Complex Traits of Pigs Zhang C, Zhao J, Guo Y, Xu Q, Liu M, Cheng M, Chao X, Schinckel AP, Zhou B Ref: Front Vet Sci, 9:909039, 2022 : PubMed ESTHER: Zhang_2022_Front.Vet.Sci_9_909039 PubMedSearch: Zhang 2022 Front.Vet.Sci 9 909039 PubMedID: 35847642 Abstract Copy number variation (CNV) has been considered to be an important source of genetic variation for important phenotypic traits of livestock. In this study, we performed whole-genome CNV detection on Suhuai (SH) (n = 23), Chinese Min Zhu (MZ) (n = 11), and Large White (LW) (n = 12) pigs based on next-generation sequencing data. The copy number variation regions (CNVRs) were annotated and analyzed, and 10,885, 10,836, and 10,917 CNVRs were detected in LW, MZ, and SH pigs, respectively. Some CNVRs have been randomly selected for verification of the variation type by real-time PCR. We found that SH and LW pigs are closely related, while MZ pigs are distantly related to the SH and LW pigs by CNVR-based genetic structure, PCA, V(ST), and QTL analyses. A total of 14 known genes annotated in CNVRs were unique for LW pigs. Among them, the cyclin T2 (CCNT2) is involved in cell proliferation and the cell cycle. The FA Complementation Group M (FANCM) is involved in defective DNA repair and reproductive cell development. Ten known genes annotated in 47 CNVRs were unique for MZ pigs. The genes included glycerol-3-phosphate acyltransferase 3 (GPAT3) is involved in fat synthesis and is essential to forming the glycerol triphosphate. Glutathione S-transferase mu 4 (GSTM4) gene plays an important role in detoxification. Eleven known genes annotated in 23 CNVRs were unique for SH pigs. Neuroligin 4 X-linked (NLGN4X) and Neuroligin 4 Y-linked (NLGN4Y) are involved with nerve disorders and nerve signal transmission. IgLON family member 5 (IGLON5) is related to autoimmunity and neural activities. The unique characteristics of LW, MZ, and SH pigs are related to these genes with CNV polymorphisms. These findings provide important information for the identification of candidate genes in the molecular breeding of pigs. Title: The impact of ABCB1 and CES1 polymorphisms on dabigatran pharmacokinetics and pharmacodynamics in patients with atrial fibrillation Ji Q, Zhang C, Xu Q, Wang Z, Li X, Lv Q Ref: British Journal of Clinical Pharmacology, 87:2247, 2021 : PubMed ESTHER: Ji_2021_Br.J.Clin.Pharmacol_87_2247 PubMedSearch: Ji 2021 Br.J.Clin.Pharmacol 87 2247 PubMedID: 33179295 Abstract AIMS: Our study aimed to determine the impact of genetic polymorphisms of ABCB1 and CES1 on the pharmacokinetics (PK) and pharmacodynamics (PD) of dabigatran in patients with nonvalvular atrial fibrillation (NVAF). METHODS: We conducted a prospective study and enrolled NVAF patients treated with dabigatran. Blood samples were obtained from each patient and used for genotyping and determination of plasma dabigatran concentration (PDC) and coagulation parameters including activated partial thromboplastin time (APTT) and thrombin time. Patients' demographics and clinical outcomes from scheduled follow-up visits were all recorded. Statistical analysis was performed to identify the impact of genetic polymorphisms on the PK/PD and bleeding risk of dabigatran. RESULTS: A total of 198 patients were included in analysis. For the ABCB1 polymorphisms rs4148738 and rs1045642, no significant association was found with dabigatran PK/PD. For the CES1 polymorphism rs8192935, the minor allele(C) was associated with increased trough PDCs (ANOVA: P < .001; CC vs. TT genotype, P < .001; CT vs. TT genotype, P = .014) and with APTT values at trough level (P = .015). For the CES1 polymorphism rs2244613, the minor allele(A) carriers had higher levels of trough PDC than noncarriers (ANOVA: P < .001; AA vs. CC genotype, P < .001; CA vs. CC genotype, P = .004) and increased risk for minor bleeding (P = .034; odds ratio = 2.71, 95% confidence interval 1.05-7.00). CONCLUSION: Our study indicated that the minor allele(C) on the CES1 SNP rs8192935 was associated with PDCs and APTT values at trough level. The minor allele(A) on the CES1 SNP rs2244613 was associated with increased trough PDCs and higher risk for minor bleeding in NVAF patients treated with dabigatran. Title: Mechanisms of Congenital Myasthenia Caused by Three Mutations in the COLQ Gene Luo X, Wang C, Lin L, Yuan F, Wang S, Wang Y, Wang A, Wu S, Lan X and Chen Y <9 more author(s)> Luo X, Wang C, Lin L, Yuan F, Wang S, Wang Y, Wang A, Wu S, Lan X, Xu Q, Yin R, Cheng H, Zhang Y, Xi J, Zhang J, Sun X, Yan J, Zeng F, Chen Y (- 9) Ref: Front Pediatr, 9:679342, 2021 : PubMed ESTHER: Luo_2021_Front.Pediatr_9_679342 PubMedSearch: Luo 2021 Front.Pediatr 9 679342 PubMedID: 34912755 Abstract The gene encoding collagen like tail subunit of asymmetric acetylcholinesterase (COLQ) is responsible for the transcription of three strands of collagen of acetylcholinesterase, which is attached to the endplate of neuromuscular junctions. Mutations in the COLQ gene are inherited in an autosomal-recessive manner and can lead to type V congenital myasthenia syndrome (CMS), which manifests as decreased muscle strength at birth or shortly after birth, respiratory failure, restricted eye movements, drooping of eyelids, and difficulty swallowing. Here we reported three variants within COLQ in two unrelated children with CMS. An intronic variant (c.393+1G>A) and a novel missense variant (p.Q381P) were identified as compound heterozygous in a 13-month-old boy, with the parents being carriers of each. An intragenic deletion including exons 14 and 15 was found in a homozygous state in a 12-year-old boy. We studied the relative expression of the COLQ and AChE gene in the probands' families, performed three-dimensional protein structural analysis, and analyzed the conservation of the missense mutation c.1142A>C (p.Q381P). The splicing mutation c.393+1G>A was found to affect the normal splicing of COLQ exon 5, resulting in a 27-bp deletion. The missense mutation c.1142A>C (p.Q381P) was located in a conserved position in different species. We found that homozygous deletion of COLQ exons 14-15 resulted in a 241-bp deletion, which decreased the number of amino acids and caused a frameshift translation. COLQ expression was significantly lower in the probands than in the probands' parents and siblings, while AChE expression was significantly higher. Moreover, the mutations were found to cause significant differences in the predicted three-dimensional structure of the protein. The splicing mutation c.393+1G>A, missense mutation c.1A>C (p.Q381P), and COLQ exon 14-15 deletion could cause CMS. Title: Arabidopsis Carboxylesterase 20 Binds Strigolactone and Increases Branches and Tillers When Ectopically Expressed in Arabidopsis and Maize Roesler K, Lu C, Thomas J, Xu Q, Vance P, Hou Z, Williams RW, Liu L, Owens MA, Habben JE Ref: Front Plant Sci, 12:639401, 2021 : PubMed ESTHER: Roesler_2021_Front.Plant.Sci_12_639401 PubMedSearch: Roesler 2021 Front.Plant.Sci 12 639401 PubMedID: 33986761 Gene_locus related to this paper: arath-AT5G62180 Abstract Severe drought stress can delay maize silk emergence relative to the pollen shedding period, resulting in poor fertilization and reduced grain yield. Methods to minimize the delay in silking could thus improve yield stability. An Arabidopsis enhancer-tagged carboxylesterase 20 (AtCXE20) line was identified in a drought tolerance screen. Ectopic expression of AtCXE20 in Arabidopsis and maize resulted in phenotypes characteristic of strigolactone (SL)-deficient mutants, including increased branching and tillering, decreased plant height, delayed senescence, hyposensitivity to ethylene, and reduced flavonols. Maize silk growth was increased by AtCXE20 overexpression, and this phenotype was partially complemented by exogenous SL treatments. In drought conditions, the transgenic maize plants silked earlier than controls and had decreased anthesis-silking intervals. The purified recombinant AtCXE20 protein bound SL in vitro, as indicated by SL inhibiting AtCXE20 esterase activity and altering AtCXE20 intrinsic fluorescence. Homology modeling of the AtCXE20 three-dimensional (3D) protein structure revealed a large hydrophobic binding pocket capable of accommodating, but not hydrolyzing SLs. The AtCXE20 protein concentration in transgenic maize tissues was determined by mass spectrometry to be in the micromolar range, well-above known endogenous SL concentrations. These results best support a mechanism where ectopic expression of AtCXE20 with a strong promoter effectively lowers the concentration of free SL by sequestration. This study revealed an agriculturally important role for SL in maize silk growth and provided a new approach for altering SL levels in plants. Title: Characterization and genomic analysis of an efficient dibutyl phthalate degrading bacterium Microbacterium sp. USTB-Y Zhao Z, Liu C, Xu Q, Ahmad S, Zhang H, Pang Y, Aikemu A, Liu Y, Yan H Ref: World J Microbiol Biotechnol, 37:212, 2021 : PubMed ESTHER: Zhao_2021_World.J.Microbiol.Biotechnol_37_212 PubMedSearch: Zhao 2021 World.J.Microbiol.Biotechnol 37 212 PubMedID: 34738191 Gene_locus related to this paper: 9mico-DpeH, 9mico-MpeH Inhibitor(s) related to this paper: Phthalate Abstract A promising bacterial strain for biodegrading dibutyl phthalate (DBP) was successfully isolated from activated sludge and characterized as a potential novel Microbacterium sp. USTB-Y based on 16S rRNA sequence analysis and whole genome average nucleotide identity (ANI). Initial DBP of 50 mg/L could be completely biodegraded by USTB-Y both in mineral salt medium and in DBP artificially contaminated soil within 12 h at the optimal culture conditions of pH 7.5 and 30 degC, which indicates that USTB-Y has a strong ability in DBP biodegradation. Phthalic acid (PA) was identified as the end-product of DBP biodegraded by USTB-Y using GC/MS. The draft genome of USTB-Y was sequenced by Illumina NovaSeq and 29 and 188 genes encoding for putative esterase/carboxylesterase and hydrolase/alpha/beta hydrolase were annotated based on NR (non redundant protein sequence database) analysis, respectively. Gene3781 and gene3780 from strain USTB-Y showed 100% identity with dpeH and mpeH from Microbacterium sp. PAE-1. But no phthalate catabolic gene (pht) cluster was found in the genome of strain USTB-Y. The results in the present study are valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs biodegrading Microbacterium sp. strains. Title: Two birds with one stone: The detection of nerve agents and AChE activity with an ICT-ESIPT-based fluorescence sensor Meng W, Pei Z, Wang Y, Sun M, Xu Q, Cen J, Guo K, Xiao K, Li Z Ref: J Hazard Mater, 410:124811, 2020 : PubMed ESTHER: Meng_2020_J.Hazard.Mater_410_124811 PubMedSearch: Meng 2020 J.Hazard.Mater 410 124811 PubMedID: 33450470 Abstract Nerve agents are among the world's deadliest poisons, and the target enzyme is acetylcholinesterase (AChE). To better diagnosis nerve agent poisonings, a reliable diagnostic method for both nerve agents and AChE is desirable. Herein, we synthesized a series of fluorescent sensors for both real nerve agents and acetylcholinesterase activity detection. Among these sensors, HBQ-AE exhibited a fast response rate (within 10 s for nerve agent and 8 min for AChE), good sensitivity (the limit of detection is 6 nM and 0.2 U/mL) and a high off/on contrast. To the best of our knowledge, HBQ-AE is the first fluorescence sensor for nerve agents and AChE activity detection. The fluorescent change of HBQ-AE from nonfluorescence to blue fluorescence (nerve agent) or orange fluorescence (AChE) by excitation at 365 nm can be easily observed with the naked eye. HBQ-AE was successfully applied to image nerve agents and AChE activity in living cells. Moreover, HBQ-AE is the vital member to construct a test paper that can be employed to detect and diagnose chemical warfare agents. Title: Significant improvement of the enantioselectivity of a halohydrin dehalogenase for asymmetric epoxide ring opening reactions by protein engineering Xue F, Zhang LH, Xu Q Ref: Applied Microbiology & Biotechnology, 104:2067, 2020 : PubMed ESTHER: Xue_2020_Appl.Microbiol.Biotechnol_104_2067 PubMedSearch: Xue 2020 Appl.Microbiol.Biotechnol 104 2067 PubMedID: 31932896 Abstract Halohydrin dehalogenases (HHDHs) have attracted much attention due to their ability to synthesize enantiomerically enriched epoxides and beta-haloalcohols. However, most of the HHDHs exhibit low enantioselectivity. Here, a HHDH from the alphaproteobacteria isolate 46_93_T64 (AbHHDH), which shows only poor enantioselectivity in the catalytic resolution of rac-PGE (E = 9.9), has been subjected to protein engineering to enhance its enantioselectivity. Eight mutants (R89K, R89Y, V137I, P178A, N179Q, N179L, F187L, F187A) showed better enantioselectivity than the wild type. The best single mutant N179L (E = 93.0) showed a remarkable 9.4-fold increase in the enantioselectivity. Then, the single mutations were combined to produce the double, triple, quadruple, and quintuple mutants. Among the combinational mutants, the best variant (R89Y/N179L) showed an increased E value of up to 48. The E values of the variants N179L and R89Y/N179L for other epoxides 2-7 were 12.2 to > 200, which showed great improvement compared to 1.2 to 10.5 for the wild type. Using the variant N179L, enantiopure (R)-PGE with > 99% ee could be readily prepared, affording a high yield and a high concentration. Title: Protective role of phenylethanoid glycosides, Torenoside B and Savatiside A, in Alzheimer's disease Ji S, Li S, Zhao X, Kang N, Cao K, Zhu Y, Peng P, Fan J, Xu Q and Liu Y <1 more author(s)> Ji S, Li S, Zhao X, Kang N, Cao K, Zhu Y, Peng P, Fan J, Xu Q, Yang S, Liu Y (- 1) Ref: Exp Ther Med, 17:3755, 2019 : PubMed ESTHER: Ji_2019_Exp.Ther.Med_17_3755 PubMedSearch: Ji 2019 Exp.Ther.Med 17 3755 PubMedID: 30988761 Abstract The current study assessed the efficacy of two phenylethanoid glycosides (PhGs), Torenoside B (TB) and Savatiside A (SA), in the treatment of Alzheimer's disease (AD). The effects of TB and SA compounds were first assessed following amyloid beta (Abeta)25-35 induction in SH-SY5Y cells at a range of concentrations. Their effects on cell viability and reactive oxygen species (ROS) were determined by performing MTT and dichlorofluorescin diacetate assays, respectively. The concentration of intracellular Ca(2+) was determined using Fluo-3AM to stain SH-SY5Y cells. SA and TB treatments were also assessed in Abeta25-35-induced mice. Y-maze and Morris water maze methods were utilized to assess murine learning and memory capability. The pathological changes of murine hippocampi was determined using H&E and Nissl staining. In addition, biochemical parameters associated with intracellular reactive oxygen pathways including Maleic dialdehyde (MDA), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), acetylcholinesterase (AChE) and Calnexin were also assessed. TB and SA treatment in Abeta25-35-induced SH-SY5Y cells resulted in the restoration of cell morphology, an increase of SOD and GSH-Px activity, a decrease in ROS, Ca(2+) and MDA content, and a decrease in Calnexin expression. Furthermore, SA or TB treatment administered to Abeta25-35-induced mice improved their spatial/non-spatial learning and memory capabilities. The efficacy of treatment was also supported by a marked change in the morphological structure of pyramidal neurons in the CA1 areas of murine hippocampi, as well as an increase of SOD and GSH-Px activity. Treatment also resulted in a decrease in MDA content, AchE activity and Calnexin expression in murine hippocampal tissue. As potential AD treatment drugs, SA and TB compounds have been demonstrated to alleviate the oxidative stress induced by Abeta25-35 via the regulation of intracellular calcium homeostasis and Calnexin, preventing AD development. Title: Chemical composition and biological activities of an essential oil from the aerial parts of Artemisia Gmelinii weber ex Stechm Xu Q, Zhang L, Yu S, Xia G, Zhu J, Zang H Ref: Nat Prod Res, :1, 2019 : PubMed ESTHER: Xu_2019_Nat.Prod.Res__1 PubMedSearch: Xu 2019 Nat.Prod.Res 1 PubMedID: 31177847 Abstract The aerial parts of Artemisia gmelinii Weber ex Stechm were collected from the northeast of China. The essential oil was obtained by hydrodistillation and analysed by GC-MS. A set of 66 compounds were identified representing 99.1% of the oil composition. The major compounds in the oil were cyclobutaneethanol, endo-borneol, germacrene D, eucalyptol, selin-6-en-4alpha-ol, bisabolone oxide A, caryophyllene and terpinen-4-ol. Moreover, the essential oil was evaluated for its antioxidant, antidiabetic, and anticholinesterase activities in vitro. Additionally, the antioxidant potential of the oil was evaluated using DPPH and ABTS assays. The oil showed good antidiabetic activity with an IC50 of 63.2 microg/mL, which was similar to that of the positive control acarbose, and weak anticholinesterase activities. These findings demonstrated that the essential oil of Artemisia gmelinii may be a good natural antidiabetic. Title: Regioselectivity Engineering of Epoxide Hydrolase: Near-Perfect Enantioconvergence through a Single Site Mutation Li FL, Kong XD, Chen Q, Zheng YC, Xu Q, Chen FF, Fan LQ, Lin GQ, Zhou J and Xu JH <1 more author(s)> Li FL, Kong XD, Chen Q, Zheng YC, Xu Q, Chen FF, Fan LQ, Lin GQ, Zhou J, Yu HL, Xu JH (- 1) Ref: ACS Catal, 8:8314, 2018 : PubMed ESTHER: Li_2018_ACS.Catal_8_8314 PubMedSearch: Li 2018 ACS.Catal 8 8314 Gene_locus related to this paper: vigra-Vreh3 Abstract An epoxide hydrolase from Vigna radiata (VrEH2) affords partial enantioconvergence (84% ee) in the enzymatic hydrolysis of racemic p-nitrostyrene oxide (pNSO), mainly due to insufficient regioselectivity for the (S)-enantiomer (rS = alphaS/betaS = 7.3). To improve the (S)-pNSO regioselectivity, a small but smart library of VrEH2 mutants was constructed by substituting each of four key residues lining the substrate binding site with a simplified amino acid alphabet of Val, Asn, Phe, and Trp. Among the mutants, M263N attacked almost exclusively at Calpha in the (S)-epoxide ring with satisfactory regioselectivity (rS = 99.0), without compromising the original high regioselectivity for the (R)-epoxide (rR = 99.0), resulting in near-perfect enantioconvergence (>99% analytical yield, 98% ee). Structural and conformational analysis showed that the introduced Asn263 formed additional hydrogen bonds with the nitro group in substrate, causing a shift in the substrate binding pose. This shift increased the difference in attacking distances between Calpha and Cbeta, leading to an improved regiopreference toward (S)-pNSO and affording near-perfect enantioconvergence. Title: Genome Mining and Comparative Biosynthesis of Meroterpenoids from Two Phylogenetically Distinct Fungi Zhang X, Wang TT, Xu QL, Xiong Y, Zhang L, Han H, Xu K, Guo WJ, Xu Q and Ge HM <1 more author(s)> Zhang X, Wang TT, Xu QL, Xiong Y, Zhang L, Han H, Xu K, Guo WJ, Xu Q, Tan RX, Ge HM (- 1) Ref: Angew Chem Int Ed Engl, 57:8184, 2018 : PubMed ESTHER: Zhang_2018_Angew.Chem.Int.Ed.Engl_57_8184 PubMedSearch: Zhang 2018 Angew.Chem.Int.Ed.Engl 57 8184 PubMedID: 29797385 Gene_locus related to this paper: necsz-ntng, artsz-atng Abstract Two homologous meroterpenoid gene clusters consisting of contiguous genes encoding polyketide synthase (PKS), prenyltransferase (PT), terpenoid cyclase (TC) and other tailoring enzymes were identified from two phylogenetically distinct fungi through computational analysis. Media optimization guided by reverse-transcription PCR (RT-PCR) enabled two strains to produce eight new and two known meroterpenoids (1-10). Using gene inactivation, heterologous expression, and biochemical analyses, we revealed a new polyketide-terpenoid assembly line that utilizes a pair of PKSs to synthesize 2,4-dihydroxy-6-alkylbenzoic acid, followed by oxidative decarboxylation, farnesyl transfer, and terpene cyclization to construct the meroterpenoid scaffold. In addition, two of the isolated meroterpenoids (3 and 17 d) showed immunosuppressive bioactivity. Our work reveals a new strategy for meroterpenoid natural products discovery, and reveals the biosynthetic pathway for compounds 1-10. Title: MicroRNA31-NDRG3 regulation axes are essential for hepatocellular carcinoma survival and drug resistance Du Z, Niu S, Xu X, Xu Q Ref: Cancer Biomark, 19:221, 2017 : PubMed ESTHER: Du_2017_Cancer.Biomark_19_221 PubMedSearch: Du 2017 Cancer.Biomark 19 221 PubMedID: 28269758 Abstract BACKGROUNDS: Hepatocellular carcinoma (HCC) is an epithelial cancer that originates from hepatocytes and it is the most common primary malignant tumor of the liver. Till now the prognosis of HCC patients is generally poor. The molecular mechanism giving rise to HCC development and recurrence is still largely unknown. MicroRNA-31 (miR-31) is among the most commonly altered microRNAs in human cancers, and alternations of miR-31 expression were reported to play pivotal roles in tumorigenesis and tumor progression. METHODS: In this work, the primary biological function of miR-31 in HCC tumorigenesis was investigated. RESULTS: Our data showed that overexpression of miR-31 induced markedly inhibition of HCC cell proliferation, migration in vitro and inhibited xenograft tumor growth in vivo. One target gene of miR-31, NDRG3, was also demonstrated indispensable for HCC cell survival. Furthermore, miR-31 and NDRG3 were both essential for HCC cell drug resistance in adriamycin. CONCLUSIONS: We conclude that miR-31 is a crucial regulator in hepatocellular carcinoma, miR-31 and its target gene NDRG3 may be potential therapeutic targets for HCC treatment in the future. Title: Design, synthesis and evaluation of novel ferulic acid-O-alkylamine derivatives as potential multifunctional agents for the treatment of Alzheimer's disease Sang Z, Pan W, Wang K, Ma Q, Yu L, Yang Y, Bai P, Leng C, Xu Q and Liu W <2 more author(s)> Sang Z, Pan W, Wang K, Ma Q, Yu L, Yang Y, Bai P, Leng C, Xu Q, Li X, Tan Z, Liu W (- 2) Ref: Eur Journal of Medicinal Chemistry, 130:379, 2017 : PubMed ESTHER: Sang_2017_Eur.J.Med.Chem_130_379 PubMedSearch: Sang 2017 Eur.J.Med.Chem 130 379 PubMedID: 28279845 Abstract A series of novel ferulic acid-O-alkylamines derivatives were designed, synthesized, and evaluated as multitarget-directed ligands against Alzheimer's disease. In vitro studies displayed that all the synthesized target compounds showed impressive inhibitory activity against butyrylcholinesterase (BuChE), significant inhibition/disaggregation of self-induced beta-amyloid (Abeta) aggregation and acted as potential antioxidants. Particularly, compound 7f, one of the most potent BuChE inhibitor (IC50 value of 0.021 muM for equine serum BuChE, 8.63 muM for ratBuChE and 0.07 muM for human serum BuChE), was found to be a good acetylcholinesterase (AChE) inhibitor (IC50 = 2.13 muM for electric eel AChE, 1.8 muM for ratAChE and 3.82 muM for human erythrocytes AChE), and the result of molecular docking provided an explanation for its selective BuChE inhibitory activity. Compound 7f also had noteworthy inhibitory effects on self-induced Abeta1-42 aggregation (50.8 +/- 0.82%) and was found to disaggregate self-induced Abeta1-42 aggregation (38.7 +/- 0.65%), which was further elucidated by the transmission electron microscopy. Meanwhile, compound 7f showed the modest antioxidant activity (0.55 eq of Trolox), good protective effect against H2O2-induced PC12 cell injury, with low toxicity. Moreover, compound 7f could cross the blood-brain barrier (BBB) in vitro. Significantly, compound 7f did not exhibit any acute toxicity in mice at doses up to 1000 mg/kg, and the step-down passive avoidance test showed this compound significantly reversed scopolamine-induced memory deficit in mice. Taken together, the results indicated that compound 7f is a very promising multifunctional agent in the treatment of Alzheimer's disease, particularly the advanced stages of AD. Title: The Apostasia genome and the evolution of orchids Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q and Liu ZJ <25 more author(s)> Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q, Chen LJ, Yoshida K, Fujiwara S, Wang ZW, Zhang YQ, Mitsuda N, Wang M, Liu GH, Pecoraro L, Huang HX, Xiao XJ, Lin M, Wu XY, Wu WL, Chen YY, Chang SB, Sakamoto S, Ohme-Takagi M, Yagi M, Zeng SJ, Shen CY, Yeh CM, Luo YB, Tsai WC, Van de Peer Y, Liu ZJ (- 25) Ref: Nature, 549:379, 2017 : PubMed ESTHER: Zhang_2017_Nature_549_379 PubMedSearch: Zhang 2017 Nature 549 379 PubMedID: 28902843 Gene_locus related to this paper: 9aspa-a0a2i0b2l6, 9aspa-a0a2i0w093, 9aspa-a0a2i0asr1, 9aspa-a0a2i0vyy1, 9aspa-a0a2i0a218, 9aspa-a0a2i0x5j6, 9aspa-a0a2i0aji0, 9aspa-a0a2i0a3k8, 9aspa-a0a2i0win6, 9aspa-a0a2i0vg82, 9aspa-a0a2h9zyy3 Abstract Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms. Title: Functional Analysis of Esterase TCE2 Gene from Tetranychus cinnabarinus (Boisduval) involved in Acaricide Resistance Shi L, Wei P, Wang X, Shen G, Zhang J, Xiao W, Xu Z, Xu Q, He L Ref: Sci Rep, 6:18646, 2016 : PubMed ESTHER: Shi_2016_Sci.Rep_6_18646 PubMedSearch: Shi 2016 Sci.Rep 6 18646 PubMedID: 26725309 Gene_locus related to this paper: 9acar-q5s1p7, tetur-t1kx09 Abstract The carmine spider mite, Tetranychus cinnabarinus is an important pest of crops and vegetables worldwide, and it has the ability to develop resistance against acaricides rapidly. Our previous study identified an esterase gene (designated TCE2) over-expressed in resistant mites. To investigate this gene's function in resistance, the expression levels of TCE2 in susceptible, abamectin-, fenpropathrin-, and cyflumetofen-resistant strains were knocked down (65.02%, 63.14%, 57.82%, and 63.99%, respectively) via RNA interference. The bioassay data showed that the resistant levels to three acaricides were significantly decreased after the down-regulation of TCE2, indicating a correlation between the expression of TCE2 and the acaricide-resistance in T. cinnabarinus. TCE2 gene was then re-engineered for heterologous expression in Escherichia coli. The recombinant TCE2 exhibited alpha-naphthyl acetate activity (483.3 +/- 71.8 nmol/mg pro. min(-1)), and the activity of this enzyme could be inhibited by abamectin, fenpropathrin, and cyflumetofen, respectively. HPLC and GC results showed that 10 mug of the recombinant TCE2 could effectively decompose 21.23% fenpropathrin and 49.70% cyflumetofen within 2 hours. This is the first report of a successful heterologous expression of an esterase gene from mites. This study provides direct evidence that TCE2 is a functional gene involved in acaricide resistance in T. cinnabarinus. Title: The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution Zhang GQ, Xu Q, Bian C, Tsai WC, Yeh CM, Liu KW, Yoshida K, Zhang LS, Chang SB and Liu ZJ <26 more author(s)> Zhang GQ, Xu Q, Bian C, Tsai WC, Yeh CM, Liu KW, Yoshida K, Zhang LS, Chang SB, Chen F, Shi Y, Su YY, Zhang YQ, Chen LJ, Yin Y, Lin M, Huang H, Deng H, Wang ZW, Zhu SL, Zhao X, Deng C, Niu SC, Huang J, Wang M, Liu GH, Yang HJ, Xiao XJ, Hsiao YY, Wu WL, Chen YY, Mitsuda N, Ohme-Takagi M, Luo YB, Van de Peer Y, Liu ZJ (- 26) Ref: Sci Rep, 6:19029, 2016 : PubMed ESTHER: Zhang_2016_Sci.Rep_6_19029 PubMedSearch: Zhang 2016 Sci.Rep 6 19029 PubMedID: 26754549 Gene_locus related to this paper: 9aspa-a0a2i0w093, 9aspa-a0a2i0vyy1, 9aspa-a0a2i0x5j6, 9aspa-a0a2i0win6, 9aspa-a0a2i0vg82 Abstract Orchids make up about 10% of all seed plant species, have great economical value, and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes, and find evidence of a whole genome duplication shared with Phalaenopsis. We observed the expansion of many resistance-related genes, suggesting a powerful immune system responsible for adaptation to a wide range of ecological niches. We also discovered extensive duplication of genes involved in glucomannan synthase activities, likely related to the synthesis of medicinal polysaccharides. Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC(*), involved in the regulation of development and growth, suggests that these expansions are associated with the astonishing diversity of plant architecture in the genus Dendrobium. On the contrary, members of the type I MADS box gene family are missing, which might explain the loss of the endospermous seed. The findings reported here will be important for future studies into polysaccharide synthesis, adaptations to diverse environments and flower architecture of Orchidaceae. Title: Proteomic analysis of ubiquitinated proteins from deltamethrin-resistant and susceptible strains of the diamondback moth, Plutella Xylostella L Cheng L, Du Y, Hu J, Jiao D, Li J, Zhou Z, Xu Q, Li F Ref: Archives of Insect Biochemistry & Physiology, 90:70, 2015 : PubMed ESTHER: Cheng_2015_Arch.Insect.Biochem.Physiol_90_70 PubMedSearch: Cheng 2015 Arch.Insect.Biochem.Physiol 90 70 PubMedID: 25983007 Abstract Ubiquitin, a small protein consisting of 76 amino acids, acts in protein degradation, DNA repair, signal transduction, transcriptional regulation, and receptor control through endocytosis. Using proteomics, we compared the differentially ubiquitinated proteins between a deltamethrin-resistant (DR) strain and a deltamethrin-sensitive (DS) strain in third-instar larvae of the diamondback moth. We used polyubiquitin affinity beads to enrich ubiquitinated proteins and then performed one-dimensional SDS-PAGE separation and mass spectrometric identification. In the DR strain, We found 17 proteins that were upregulated (relative to the DS strain), including carbonic anhydrase family members, ADP ribosylation factor 102F CG11027-PA, protein kinase 61C, phospholipase A2 , dihydrolipoamide dehydrogenase, tyrosine hydroxylase, and heat shock proteins, and five proteins that were downregulated in the DS strain, including carboxylesterase and DNA cytosine-5 methyltransferase. These results were also verified by qPCR. The differentially ubiquitinated proteins/enzymes were mainly responsible for protein binding, catalytic activity, and molecular transducer activity. These results improve our understanding of the relationship between protein ubiquitination and the deltamethrin stress response. Title: Effects of electroacupuncture on recovery of the electrophysiological properties of the rabbit gastrocnemius after contusion: an in vivo animal study Liu S, Wang R, Luo D, Xu Q, Xiao C, Lin P, Yu Z, Zhao X, Cai R and Wang Y <2 more author(s)> Liu S, Wang R, Luo D, Xu Q, Xiao C, Lin P, Yu Z, Zhao X, Cai R, Ma J, Zhang Q, Wang Y (- 2) Ref: BMC Complement Altern Med, 15:69, 2015 : PubMed ESTHER: Liu_2015_BMC.Complement.Altern.Med_15_69 PubMedSearch: Liu 2015 BMC.Complement.Altern.Med 15 69 PubMedID: 25887510 Abstract BACKGROUND: Our preliminary studies indicated that electroacupuncture (EA) at the ST36 and Ashi acupoints could promote regeneration of the rabbit gastrocnemius (GM) by improving microcirculation perfusion, promoting the recovery of myofiber structures, and inhibiting excessive fibrosis. However, the effects of EA on recovery of the electrophysiological properties of the GM after contusion are not yet clear. Thus, the purpose of this study was to investigate the effects of EA at the Zusanli (ST36) and Ashi acupoints with regard to recovery of the electrophysiological properties of the rabbit GM after contusion. Title: Identification of the genes regulated by Wnt-4, a critical signal for commitment of the ovary Naillat F, Yan W, Karjalainen R, Liakhovitskaia A, Samoylenko A, Xu Q, Sun Z, Shen B, Medvinsky A and Vainio SJ <1 more author(s)> Naillat F, Yan W, Karjalainen R, Liakhovitskaia A, Samoylenko A, Xu Q, Sun Z, Shen B, Medvinsky A, Quaggin S, Vainio SJ (- 1) Ref: Experimental Cell Research, 332:163, 2015 : PubMed ESTHER: Naillat_2015_Exp.Cell.Res_332_163 PubMedSearch: Naillat 2015 Exp.Cell.Res 332 163 PubMedID: 25645944 Abstract The indifferent mammalian embryonic gonad generates an ovary or testis, but the factors involved are still poorly known. The Wnt-4 signal represents one critical female determinant, since its absence leads to partial female-to-male sex reversal in mouse, but its signalling is as well implicated in the testis development. We used the Wnt-4 deficient mouse as a model to identify candidate gonadogenesis genes, and found that the Notum, Phlda2, Runx-1 and Msx1 genes are typical of the wild-type ovary and the Osr2, Dach2, Pitx2 and Tacr3 genes of the testis. Strikingly, the expression of these latter genes becomes reversed in the Wnt-4 knock-out ovary, suggesting a role in ovarian development. We identified the transcription factor Runx-1 as a Wnt-4 signalling target gene, since it is expressed in the ovary and is reduced upon Wnt-4 knock-out. Consistent with this, introduction of the Wnt-4 signal into early ovary cells ex vivo induces Runx-1 expression, while conversely Wnt-4 expression is down-regulated in the absence of Runx-1. We conclude that the Runx-1 gene can be a Wnt-4 signalling target, and that Runx-1 and Wnt-4 are mutually interdependent in their expression. The changes in gene expression due to the absence of Wnt-4 in gonads reflect the sexually dimorphic role of this signal and its complex gene network in mammalian gonad development. Title: Pictet-Spengler reaction-based biosynthetic machinery in fungi Yan W, Ge HM, Wang G, Jiang N, Mei YN, Jiang R, Li SJ, Chen CJ, Jiao RH and Tan RX <2 more author(s)> Yan W, Ge HM, Wang G, Jiang N, Mei YN, Jiang R, Li SJ, Chen CJ, Jiao RH, Xu Q, Ng SW, Tan RX (- 2) Ref: Proc Natl Acad Sci U S A, 111:18138, 2014 : PubMed ESTHER: Yan_2014_Proc.Natl.Acad.Sci.U.S.A_111_18138 PubMedSearch: Yan 2014 Proc.Natl.Acad.Sci.U.S.A 111 18138 PubMedID: 25425666 Abstract The Pictet-Spengler (PS) reaction constructs plant alkaloids such as morphine and camptothecin, but it has not yet been noticed in the fungal kingdom. Here, a silent fungal Pictet-Spenglerase (FPS) gene of Chaetomium globosum 1C51 residing in Epinephelus drummondhayi guts is described and ascertained to be activable by 1-methyl-L-tryptophan (1-MT). The activated FPS expression enables the PS reaction between 1-MT and flavipin (fungal aldehyde) to form "unnatural" natural products with unprecedented skeletons, of which chaetoglines B and F are potently antibacterial with the latter inhibiting acetylcholinesterase. A gene-implied enzyme inhibition (GIEI) strategy has been introduced to address the key steps for PS product diversifications. In aggregation, the work designs and validates an innovative approach that can activate the PS reaction-based fungal biosynthetic machinery to produce unpredictable compounds of unusual and novel structure valuable for new biology and biomedicine. Title: Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima Levisson M, Han GW, Deller MC, Xu Q, Biely P, Hendriks S, Ten Eyck LF, Flensburg C, Roversi P and Wilson IA <9 more author(s)> Levisson M, Han GW, Deller MC, Xu Q, Biely P, Hendriks S, Ten Eyck LF, Flensburg C, Roversi P, Miller MD, McMullan D, von Delft F, Kreusch A, Deacon AM, Van der Oost J, Lesley SA, Elsliger MA, Kengen SW, Wilson IA (- 9) Ref: Proteins, 80:1545, 2012 : PubMed ESTHER: Levisson_2012_Proteins_80_1545 PubMedSearch: Levisson 2012 Proteins 80 1545 PubMedID: 22411095 Gene_locus related to this paper: thema-TM0077 Inhibitor(s) related to this paper: Paraoxon Abstract TM0077 from Thermotoga maritima is a member of the carbohydrate esterase family 7 and is active on a variety of acetylated compounds, including cephalosporin C. TM0077 esterase activity is confined to short-chain acyl esters (C2-C3), and is optimal around 100degC and pH 7.5. The positional specificity of TM0077 was investigated using 4-nitrophenyl--D-xylopyranoside monoacetates as substrates in a -xylosidase-coupled assay. TM0077 hydrolyzes acetate at positions 2, 3, and 4 with equal efficiency. No activity was detected on xylan or acetylated xylan, which implies that TM0077 is an acetyl esterase and not an acetyl xylan esterase as currently annotated. Selenomethionine-substituted and native structures of TM0077 were determined at 2.1 and 2.5 resolution, respectively, revealing a classicalpha/beta-hydrolase fold. TM0077 assembles into a doughnut-shaped hexamer with small tunnels on either side leading to an inner cavity, which contains the six catalytic centers. Structures of TM0077 with covalently bound phenylmethylsulfonyl fluoride and paraoxon were determined to 2.4 and 2.1 , respectively, and confirmed that both inhibitors bind covalently to the catalytic serine (Ser188). Upon binding of inhibitor, the catalytic serine adopts an altered conformation, as observed in other esterase and lipases, and supports a previously proposed catalytic mechanism in which Ser hydroxyl rotation prevents reversal of the reaction and allows access of a water molecule for completion of the reaction. Title: Complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and ribavirin Zhang G, Deng A, Xu Q, Liang Y, Chen N, Wen T Ref: Journal of Bacteriology, 193:3142, 2011 : PubMed ESTHER: Zhang_2011_J.Bacteriol_193_3142 PubMedSearch: Zhang 2011 J.Bacteriol 193 3142 PubMedID: 21515778 Gene_locus related to this paper: baca2-a7z811 Abstract Here, we report the complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and synthesis of ribavirin by assimilation of formamide. Comparison of its genome sequence with those of strains DSM7 and FZB42 revealed horizontal gene transfer represented by unique prophages and restriction-modification systems and indicated significant accumulation of guanosine. Title: Smoking duration, intensity, and risk of Parkinson disease Chen H, Huang X, Guo X, Mailman RB, Park Y, Kamel F, Umbach DM, Xu Q, Hollenbeck A and Blair A <1 more author(s)> Chen H, Huang X, Guo X, Mailman RB, Park Y, Kamel F, Umbach DM, Xu Q, Hollenbeck A, Schatzkin A, Blair A (- 1) Ref: Neurology, 74:878, 2010 : PubMed ESTHER: Chen_2010_Neurology_74_878 PubMedSearch: Chen 2010 Neurology 74 878 PubMedID: 20220126 Abstract OBJECTIVE: To evaluate the relative importance of smoking duration vs intensity in reducing the risk of Parkinson disease (PD). Title: Depression and the subsequent risk of Parkinson's disease in the NIH-AARP Diet and Health Study Fang F, Xu Q, Park Y, Huang X, Hollenbeck A, Blair A, Schatzkin A, Kamel F, Chen H Ref: Movement Disorders, 25:1157, 2010 : PubMed ESTHER: Fang_2010_Mov.Disord_25_1157 PubMedSearch: Fang 2010 Mov.Disord 25 1157 PubMedID: 20310050 Abstract We conducted a case-control study to examine the association between depression and Parkinson's disease (PD). Participants included 992 PD cases diagnosed after 2,000 and 279,958 individuals without PD from the NIH-AARP Diet and Health Study follow-up survey. Physician-diagnosed depression and PD were self-reported with information on the year of diagnosis in the following categories: before 1985, 1985-1994, 1995-1999, and 2000-present. Only PD cases diagnosed after 2000 were included in the analysis. Odds ratios (ORs) and 95% confidence intervals (CIs) were derived from logistic regression models, adjusted for age, gender, educational level, marital status, smoking, and coffee drinking. Individuals with depression diagnosed after 2000 were more likely to report a concurrent diagnosis of PD than those without depression (OR = 4.7, 95% CI = 3.9, 5.7). Depression diagnosed before 2000 was also associated with higher odds of PD diagnosed after 2000 (OR = 2.0, 95% CI = 1.6, 2.4). This association was stronger for depression diagnosed in 1995-1999 (OR = 2.7, 95% CI = 2.0, 3.6), but was also noted for depression diagnosed in 1985-1994 (OR = 1.6, 95% CI = 1.1, 2.3) or even before 1985 (OR = 1.7, 95% CI = 1.3, 2.3). This association was not modified by other factors and persisted in an analysis excluding participants who reported poor health status. The results suggest that depression may either be a very early symptom of PD or share common etiological factors with PD. Title: A catalog of reference genomes from the human microbiome Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E and Zhu D <73 more author(s)> Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, Fitzgerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D (- 73) Ref: Science, 328:994, 2010 : PubMed ESTHER: Nelson_2010_Science_328_994 PubMedSearch: Nelson 2010 Science 328 994 PubMedID: 20489017 Gene_locus related to this paper: strp2-q04l35, strpn-AXE1, strpn-pepx Abstract The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented. Title: Emergence of a new multidrug-resistant serotype X variant in an epidemic clone of Shigella flexneri Ye C, Lan R, Xia S, Zhang J, Sun Q, Zhang S, Jing H, Wang L, Li Z and Xu J <11 more author(s)> Ye C, Lan R, Xia S, Zhang J, Sun Q, Zhang S, Jing H, Wang L, Li Z, Zhou Z, Zhao A, Cui Z, Cao J, Jin D, Huang L, Wang Y, Luo X, Bai X, Wang P, Xu Q, Xu J (- 11) Ref: J Clin Microbiol, 48:419, 2010 : PubMed ESTHER: Ye_2010_J.Clin.Microbiol_48_419 PubMedSearch: Ye 2010 J.Clin.Microbiol 48 419 PubMedID: 19955273 Gene_locus related to this paper: shifl-AES, shifl-BIOH, shifl-entf, shifl-FES, shifl-PLDB, shifl-PTRB, shifl-S2753, shifl-SF1808, shifl-SF3046, shifl-SF3908, shifl-yafa, shifl-YBFF, shifl-YCDJ, shifl-ycfp, shifl-YFBB, shifl-YHET, shifl-YJFP, shifl-YPFH, shiss-yqia Abstract Shigella spp. are the causative agent of shigellosis with Shigella flexneri serotype 2a being the most prevalent in developing countries. Epidemiological surveillance in China found that a new serotype of S. flexneri appeared in 2001 and replaced serotype 2a in 2003 as the most prevalent serotype in Henan Province. The new serotype also became the dominant serotype in 7 of the 10 other provinces under surveillance in China by 2007. The serotype was identified as a variant of serotype X. It differs from serotype X by agglutination to the monovalent anti-IV type antiserum and the group antigen-specific monoclonal antibody MASF IV-I. Genome sequencing of a serotype X variant isolate, 2002017, showed that it acquired a Shigella serotype conversion island, also as an SfX bacteriophage, containing gtr genes for type X-specific glucosylation. Multilocus sequence typing of 15 genes from 37 serotype X variant isolates and 69 isolates of eight other serotypes, 1a, 2a, 2b, 3a, 4a, 5b, X, and Y, found that all belong to a new sequence type (ST), ST91. Pulsed-field gel electrophoresis revealed 154 pulse types with 655 S. flexneri isolates analyzed and identified 57 serotype switching events. The data suggest that S. flexneri epidemics in China have been caused by a single epidemic clone, ST91, with frequent serotype switching to evade infection-induced immunity to serotypes to which the population was exposed previously. The clone has also acquired resistance to multiple antibiotics. These findings underscore the challenges to the current vaccine development and control strategies for shigellosis. Title: Bicyclic cyanothiazolidines as novel dipeptidyl peptidase 4 inhibitors Betancort JM, Winn DT, Liu R, Xu Q, Liu J, Liao W, Chen SH, Carney D, Hanway D and Campbell DA <3 more author(s)> Betancort JM, Winn DT, Liu R, Xu Q, Liu J, Liao W, Chen SH, Carney D, Hanway D, Schmeits J, Li X, Gordon E, Campbell DA (- 3) Ref: Bioorganic & Medicinal Chemistry Lett, 19:4437, 2009 : PubMed ESTHER: Betancort_2009_Bioorg.Med.Chem.Lett_19_4437 PubMedSearch: Betancort 2009 Bioorg.Med.Chem.Lett 19 4437 PubMedID: 19482472 Abstract The synthesis and biochemical evaluation of novel cyanothiazolidine inhibitors of dipeptidyl peptidase 4 (DPP4) is described. Their main structural feature is a constrained bicyclic core that prevents the intramolecular formation of inactive cyclic species. The inhibitors show good to moderate biochemical potency against DPP4 and display distinct selectivity profiles towards DPP7, DPP8 and DPP9 depending on their substitution. Title: Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution Zubieta C, Krishna SS, McMullan D, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL and Wilson IA <33 more author(s)> Zubieta C, Krishna SS, McMullan D, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, Deller M, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kumar A, Marciano D, Morse AT, Nigoghossian E, Oommachen S, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA (- 33) Ref: Proteins, 68:999, 2007 : PubMed ESTHER: Zubieta_2007_Proteins_68_999 PubMedSearch: Zubieta 2007 Proteins 68 999 PubMedID: 17546672 Gene_locus related to this paper: bacce-BC4730 Title: Catalytic role of proton transfers in the formation of a tetrahedral adduct in a serine carboxyl peptidase Guo H, Wlodawer A, Nakayama T, Xu Q Ref: Biochemistry, 45:9129, 2006 : PubMed ESTHER: Guo_2006_Biochemistry_45_9129 PubMedSearch: Guo 2006 Biochemistry 45 9129 PubMedID: 16866358 Abstract Quantum mechanical/molecular mechanical molecular dynamics and 2D free energy simulations are performed to study the formation of a tetrahedral adduct by an inhibitor N-acetyl-isoleucyl-prolyl-phenylalaninal (AcIPF) in a serine-carboxyl peptidase (kumamolisin-As) and elucidate the role of proton transfers during the nucleophilic attack by the Ser278 catalytic residue. It is shown that although the serine-carboxyl peptidases have a fold resembling that of subtilisin, the proton transfer processes during the nucleophilic attack by the Ser residue are likely to be more complex for these enzymes compared to the case in classical serine proteases. The computer simulations demonstrate that both general base and acid catalysts are required for the formation and stabilization of the tetrahedral adduct. The 2D free energy maps further demonstrate that the proton transfer from Ser278 to Glu78 (the general base catalyst) is synchronous with the nucleophilic attack, whereas the proton transfer from Asp164 (the general acid catalyst) to the inhibitor is not. The dynamics of the protons at the active site in different stages of the nucleophilic attack as well as the motions of the corresponding functional groups are also studied. It is found that the side chain of Glu78 is generally rather flexible, consistent with its possible multifunctional role during catalysis. The effects of proton shuffling from Asp82 to Glu78 and from Glu32 to Asp82 are examined, and the results indicate that such proton shuffling may not play an important role in the stabilization of the tetrahedral intermediate analogue. Title: The importance of dynamics in substrate-assisted catalysis and specificity Xu Q, Guo H, Wlodawer A Ref: Journal of the American Chemical Society, 128:5994, 2006 : PubMed ESTHER: Xu_2006_J.Am.Chem.Soc_128_5994 PubMedSearch: Xu 2006 J.Am.Chem.Soc 128 5994 PubMedID: 16669642 Abstract The QM/MM MD and free energy simulations show that the dynamics involving a His residue at the P1 site of the substrate may play an important role in substrate-assisted catalysis and specificity for a serine-carboxyl peptidase. Title: Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution Arndt JW, Schwarzenbacher R, Page R, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X and Wilson IA <43 more author(s)> Arndt JW, Schwarzenbacher R, Page R, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Klock HE, Koesema E, Kreusch A, Kuhn P, Jaroszewski L, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Nigoghossian E, Ouyang J, Peti WS, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, White A, Wolf G, Xu Q, Zagnitko O, Hodgson KO, Wooley J, Wilson IA (- 43) Ref: Proteins, 58:755, 2005 : PubMed ESTHER: Arndt_2005_Proteins_58_755 PubMedSearch: Arndt 2005 Proteins 58 755 PubMedID: 15624212 Gene_locus related to this paper: yeast-YDR428C Title: The genome of the social amoeba Dictyostelium discoideum Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K and Kuspa A <87 more author(s)> Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A (- 87) Ref: Nature, 435:43, 2005 : PubMed ESTHER: Eichinger_2005_Nature_435_43 PubMedSearch: Eichinger 2005 Nature 435 43 PubMedID: 15875012 Gene_locus related to this paper: dicdi-abhd, dicdi-ACHE, dicdi-apra, dicdi-cinbp, dicdi-CMBL, dicdi-crysp, dicdi-DPOA, dicdi-P90528, dicdi-ppme1, dicdi-Q8MYE7, dicdi-q54cf7, dicdi-q54cl7, dicdi-q54cm0, dicdi-q54ct5, dicdi-q54cu1, dicdi-q54d54, dicdi-q54d66, dicdi-q54dj5, dicdi-q54dy7, dicdi-q54ek1, dicdi-q54eq6, dicdi-q54et1, dicdi-q54et7, dicdi-q54f01, dicdi-q54g24, dicdi-q54g47, dicdi-q54gi7, dicdi-q54gw5, dicdi-q54gx3, dicdi-q54h23, dicdi-q54h73, dicdi-q54i38, dicdi-q54ie5, dicdi-q54in4, dicdi-q54kz1, dicdi-q54l36, dicdi-q54li1, dicdi-q54m29, dicdi-q54n21, dicdi-q54n35, dicdi-q54n85, dicdi-q54qe7, dicdi-q54qi3, dicdi-q54qk2, dicdi-q54rl3, dicdi-q54rl8, dicdi-q54sy6, dicdi-q54sz3, dicdi-q54t49, dicdi-q54t91, dicdi-q54th2, dicdi-q54u01, dicdi-q54vc2, dicdi-q54vw1, dicdi-q54xe3, dicdi-q54xl3, dicdi-q54xu1, dicdi-q54xu2, dicdi-q54y48, dicdi-q54yd0, dicdi-q54ye0, dicdi-q54yl1, dicdi-q54yr8, dicdi-q54z90, dicdi-q55bx3, dicdi-q55d01, dicdi-q55d81, dicdi-q55du6, dicdi-q55eu1, dicdi-q55eu8, dicdi-q55fk4, dicdi-q55gk7, dicdi-Q54ZA6, dicdi-q86h82, dicdi-Q86HC9, dicdi-Q86HM5, dicdi-Q86HM6, dicdi-q86iz7, dicdi-q86jb6, dicdi-Q86KU7, dicdi-q550s3, dicdi-q552c0, dicdi-q553t5, dicdi-q555e5, dicdi-q555h0, dicdi-q555h1, dicdi-q557k5, dicdi-q558u2, dicdi-Q869Q8, dicdi-u554, dicdi-y9086, dicdi-q54r44, dicdi-f172a Abstract The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi. Title: Chlorpyrifos resistance in mosquito Culex quinquefasciatus Liu H, Xu Q, Zhang L, Liu N Ref: Journal of Medical Entomology, 42:815, 2005 : PubMed ESTHER: Liu_2005_J.Med.Entomol_42_815 PubMedSearch: Liu 2005 J.Med.Entomol 42 815 PubMedID: 16363165 Inhibitor(s) related to this paper: Diethyl-maleate, Tribufos Abstract Two mosquito strains of Culex quinquefasciatus Say, MAmCq and HAmCq, were collected from Mobile and Huntsville, AL, respectively, after the control of mosquitoes with insecticides proved difficult. A synergism study showed that resistance to chlorpyrifos in MAmCq and HAmCq was not suppressed by piperonyl butoxide (PBO) and S,S,S,-tributylphosphorotrithioate (DEF), suggesting that P450 monooxygenase- and hydrolase-mediated detoxication does not contribute to chlorpyrifos resistance in either strain. Diethyl maleate (DEM) did not cause any significant change in the level of chlorpyrifos toxicity to HAmCq. However, DEM enhanced toxicity of chlorpyrifos to MAmCq 2.5-fold, indicating that glutathione S-transferase (GST)-mediated detoxication may play a minor role in the resistance of MAmCq. An inhibition study of acetylcholinesterase (AChE) by chlorpyrifos showed that bimolecular rate constants (Ki) of chlorpyrifos for the inhibition of AChE in adults and larvae of the susceptible S-Lab strain were 2.2- and 1.9-fold higher, respectively, than in the HAmCq strain and 3.4- and 3.8-fold higher than in the MAmCq strain. The single mutation, G119S, resulting from a single nucleotide polymorphism (SNP), G to A, in ace-1 acetylcholinesterase gene was present in HAmCq and MAmCq mosquitoes. The frequency of the heterozygote for the G119S mutant allele in the HAmCq and MAmCq mosquito populations was 0.25 and 0.45, respectively, and no individuals in either of these mosquito strains were homozygous for the A allele. It thus seems likely that the presence of heterozygous individuals for the G119S allele in HAmCq and MAmCq populations may be a response to the insensitivity of AChE observed in these two mosquito strains. Title: Transfer in SDS of biotinylated proteins from acrylamide gels to an avidin-coated membrane filter Karlin A, Wang C, Li J, Xu Q Ref: Biotechniques, 36:1010, 2004 : PubMed ESTHER: Karlin_2004_Biotechniques_36_1010 PubMedSearch: Karlin 2004 Biotechniques 36 1010 PubMedID: 15211752 Abstract Avidin was covalently linked to aldehyde-derivatized polyethersulfone membrane filters. These filters were used in Western blot analysis of proteins reacted with biotinylation reagents and electrophoresed in sodium dodecyl sulfate (SDS) on polyacrylamide gels. Electrophoretic transfer from the gels to these filters was in 0.1% SDS, in which the covalently bound avidin retained its biotin-binding capacity. We compared Western blots on avidin-coated membrane filters of biotinylated and nonbiotinylated forms of mouse immunoglobulin G (IgG), mouse IgG heavy chain, muscle-type acetylcholine receptor alpha subunit, and fused alpha and beta subunits of receptor. Biotinylated proteins were captured with high specificity compared to their nonbiotinylated counterparts and sensitively detected on the avidin-coated membranes. Title: Multiplex sequencing of 1.5 Mb of the Mycobacterium leprae genome Smith DR, Richterich P, Rubenfield M, Rice PW, Butler C, Kirst S, Gundersen K, Abendschan K, Xu Q and Safer H <13 more author(s)> Smith DR, Richterich P, Rubenfield M, Rice PW, Butler C, Kirst S, Gundersen K, Abendschan K, Xu Q, Chung M, Deloughery C, Maher J, Lundstrom R, Tulig C, Falls K, Imrich J, Torrey D, Engelstein M, Nietupski R, Seitz B, Connelly S, McDougall S, Safer H (- 13) Ref: Genome Res, 7:802, 1997 : PubMed ESTHER: Smith_1997_Genome.Res_7_802 PubMedSearch: Smith 1997 Genome.Res 7 802 PubMedID: 9267804 Abstract The nucleotide sequence of 1.5 Mb of genomic DNA from Mycobacterium leprae was determined using computer-assisted multiplex sequencing technology. This brings the 2.8-Mb M. leprae genome sequence to approximately 66% completion. The sequences, derived from 43 recombinant cosmids, contain 1046 putative protein-coding genes, 44 repetitive regions, 3 tRNAs, and 15 tRNAs. The gene density of one per 1.4 kb is slightly lower than that of Mycoplasma (1.2 kb). Of the protein coding genes, 44% have significant matches to genes with well-defined functions. Comparison of 1157 M. leprae and 1564 Mycobacterium tuberculosis proteins shows a complex mosaic of homologous genomic blocks with up to 22 adjacent proteins in conserved map order. Matches to known enzymatic, antigenic, membrane, cell wall, cell division, multidrug resistance, and virulence proteins suggest therapeutic and vaccine targets. Unusual features of the M. leprae genome include large polyketide synthase (pks) operons, inteins, and highly fragmented pseudogenes. | |||||||
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