23 results on '"Yue Zhong"'
Search Results
2. A qualitative exploration of “empathic labor” in Chinese hospice nurses
- Author
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Wang, Ya-Ling, Yang, Zi-Wei, Tang, Yue-Zhong, Li, Hui-Ling, and Zhou, Lan-Shu
- Published
- 2022
- Full Text
- View/download PDF
3. Identification of different proteins binding to Na, K-ATPase α1 in LPS-induced ARDS cell model by proteomic analysis
- Author
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Wen, Xu-Peng, Long, Guo, Zhang, Yue-Zhong, Huang, He, Liu, Tao-Hua, and Wan, Qi-Quan
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- 2022
- Full Text
- View/download PDF
4. Non-targeted proteomics of acute respiratory distress syndrome: clinical and research applications
- Author
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Wen, Xu-Peng, Zhang, Yue-Zhong, and Wan, Qi-Quan
- Published
- 2021
- Full Text
- View/download PDF
5. Engineering the acyltransferase domain of epothilone polyketide synthase to alter the substrate specificity
- Author
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Wang, Huimin, Liang, Junheng, Yue, Qianwen, Li, Long, Shi, Yan, Chen, Guosong, Li, Yue-zhong, Bian, Xiaoying, Zhang, Youming, Zhao, Guoping, and Ding, Xiaoming
- Published
- 2021
- Full Text
- View/download PDF
6. Engineering the acyltransferase domain of epothilone polyketide synthase to alter the substrate specificity
- Author
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Qianwen Yue, Yue-zhong Li, Huimin Wang, Yan Shi, Junheng Liang, Guosong Chen, Xiaoming Ding, Guoping Zhao, Long Li, Xiaoying Bian, and Youming Zhang
- Subjects
Stereochemistry ,Substrate specificity ,Bioengineering ,Epothilone ,medicine.disease_cause ,Protein Engineering ,01 natural sciences ,Applied Microbiology and Biotechnology ,Microbiology ,03 medical and health sciences ,Polyketide ,Bacterial Proteins ,Polyketide synthase ,Catalytic Domain ,medicine ,030304 developmental biology ,0303 health sciences ,Mutation ,biology ,Bacteria ,010405 organic chemistry ,Chemistry ,Research ,QR1-502 ,0104 chemical sciences ,Protein Structure, Tertiary ,Acyl carrier protein ,Acyltransferase ,Dehydratase ,biology.protein ,AT ,Domain swap ,Linker ,Polyketide Synthases ,Biotechnology ,medicine.drug - Abstract
Background Polyketide synthases (PKSs) include ketone synthase (KS), acyltransferase (AT) and acyl carrier protein (ACP) domains to catalyse the elongation of polyketide chains. Some PKSs also contain ketoreductase (KR), dehydratase (DH) and enoylreductase (ER) domains as modification domains. Insertion, deletion or substitution of the catalytic domains may lead to the production of novel polyketide derivatives or to the accumulation of desired products. Epothilones are 16-membered macrolides that have been used as anticancer drugs. The substrate promiscuity of the module 4 AT domain of the epothilone PKS (EPOAT4) results in production of epothilone mixtures; substitution of this domain may change the ratios of epothilones. In addition, there are two dormant domains in module 9 of the epothilone PKS. Removing these redundant domains to generate a simpler and more efficient assembly line is a desirable goal. Results The substitution of module 4 drastically diminished the activity of epothilone PKS. However, with careful design of the KS-AT linker and the post-AT linker, replacing EPOAT4 with EPOAT2, EPOAT6, EPOAT7 or EPOAT8 (specifically incorporating methylmalonyl-CoA (MMCoA)) significantly increased the ratio of epothilone D (4) to epothilone C (3) (the highest ratio of 4:3 = 4.6:1), whereas the ratio of 4:3 in the parental strain Schlegelella brevitalea 104-1 was 1.4:1. We also obtained three strains by swapping EPOAT4 with EPOAT3, EPOAT5, or EPOAT9, which specifically incorporate malonyl-CoA (MCoA). These strains produced only epothilone C, and the yield was increased by a factor of 1.8 compared to that of parental strain 104-1. Furthermore, mutations of five residues in the AT domain identified Ser310 as the critical factor for MMCoA recognition in EPOAT4. Then, the mutation of His308 to valine or tyrosine combined with the mutation of Phe310 to serine further altered the product ratios. At the same time, we successfully deleted the inactive module 9 DH and ER domains and fused the ΨKR domain with the KR domain through an ~ 25-residue linker to generate a productive and simplified epothilone PKS. Conclusions These results suggested that the substitution and deletion of catalytic domains effectively produces desirable compounds and that selection of the linkers between domains is crucial for maintaining intact PKS catalytic activity.
- Published
- 2021
7. Impact of concomitant tricuspid annuloplasty on right ventricular remodeling in patients with rheumatic mitral valve disease
- Author
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Yue Zhong, Li Rao, Wenjuan Bai, Hong Qian, and Hui Wang
- Subjects
lcsh:Diseases of the circulatory (Cardiovascular) system ,medicine.medical_specialty ,medicine.medical_treatment ,Disease ,030204 cardiovascular system & hematology ,Rheumatic mitral valve disease ,Cardiac Valve Annuloplasty ,Functional tricuspid regurgitation ,03 medical and health sciences ,0302 clinical medicine ,Tricuspid annuloplasty ,Internal medicine ,Mitral valve ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,030212 general & internal medicine ,Ventricular remodeling ,Angiology ,Retrospective Studies ,Ejection fraction ,Ventricular Remodeling ,business.industry ,Research ,Right ventricular remodeling ,Mitral valve replacement ,General Medicine ,medicine.disease ,medicine.anatomical_structure ,lcsh:RC666-701 ,Concomitant ,Cardiology ,Mitral Valve ,Tricuspid Valve ,Cardiology and Cardiovascular Medicine ,business ,Concomitant tricuspid valve annuloplasty - Abstract
Background Studies on the management of functional tricuspid regurgitation (TR) during mitral valve operations have drawn inconsistent conclusions. This study was designed to compare the treatment strategy of concomitant tricuspid annuloplasty (TAP) against isolated mitral valve replacement (MVR) in rheumatic mitral valve disease patients, and to assess the effect of concomitant TAP on postoperative right ventricular (RV) remodeling and function. Methods One hundred-seventy patients with rheumatic mitral valve disease receiving MVR were categorized into TAP group (n = 124) and non-TAP group (n = 46). Clinical and echocardiographic data were collected preoperatively and at 1-year follow-up. Three-dimensional echocardiographic indices of RV geometry and function were analyzed. Results At baseline, concomitant TAP group had larger RV end-diastolic volume, more decreased RV ejection fraction and RV longitudinal strain than non-TAP group (all P P P P P = 0.025). Conclusions Our results suggest that concomitant TAP could improve RV remodeling and function for rheumatic mitral valve disease patients, while those with mild preoperative functional TR who had isolated MVR might experience RV dilation and deterioration of RV function at follow-up. Concomitant surgery for functional TR could be considered for patients undergoing MVR with rheumatic mitral valve disease.
- Published
- 2021
8. Estimate of the sequenced proportion of the global prokaryotic genome
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Jinlan Wang, Yue-zhong Li, Jingjing Wang, Jianing Wang, and Zheng Zhang
- Subjects
Microbiology (medical) ,Earth, Planet ,Biome ,Earth microbiome project ,Biology ,Genome sequencing ,Microbiology ,Genome ,lcsh:Microbial ecology ,DNA sequencing ,03 medical and health sciences ,Microbial ecology ,Predominant taxa ,Databases, Genetic ,Prokaryotic biome ,Microbiome ,030304 developmental biology ,0303 health sciences ,Bacteria ,030306 microbiology ,Microbiota ,Research ,Genomics ,biology.organism_classification ,Archaea ,Taxon ,Prokaryotic Cells ,Evolutionary biology ,Earth Microbiome Project ,lcsh:QR100-130 ,Sequence Alignment ,Sequence Analysis - Abstract
Background Sequencing prokaryotic genomes has revolutionized our understanding of the many roles played by microorganisms. However, the cell and taxon proportions of genome-sequenced bacteria or archaea on earth remain unknown. This study aimed to explore this basic question using large-scale alignment between the sequences released by the Earth Microbiome Project and 155,810 prokaryotic genomes from public databases. Results Our results showed that the median proportions of the genome-sequenced cells and taxa (at 100% identities in the 16S-V4 region) in different biomes reached 38.1% (16.4–86.3%) and 18.8% (9.1–52.6%), respectively. The sequenced proportions of the prokaryotic genomes in biomes were significantly negatively correlated with the alpha diversity indices, and the proportions sequenced in host-associated biomes were significantly higher than those in free-living biomes. Due to a set of cosmopolitan OTUs that are found in multiple samples and preferentially sequenced, only 2.1% of the global prokaryotic taxa are represented by sequenced genomes. Most of the biomes were occupied by a few predominant taxa with a high relative abundance and much higher genome-sequenced proportions than numerous rare taxa. Conclusions These results reveal the current situation of prokaryotic genome sequencing for earth biomes, provide a more reasonable and efficient exploration of prokaryotic genomes, and promote our understanding of microbial ecological functions.
- Published
- 2020
9. Association of decreased serum brain-derived neurotrophic factor (BDNF) concentrations in early pregnancy with antepartum depression
- Author
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Yasmin V. Barrios, Michelle A. Williams, Karin Hevner, Qiu-Yue Zhong, Marta B. Rondon, Chunfang Qiu, Jenny Fung, Sixto E. Sanchez, and Bizu Gelaye
- Subjects
maternal serum ,0302 clinical medicine ,Neurotrophic factors ,Pregnancy ,puerperal depression ,Peru ,Prevalence ,Young adult ,reproductive and urinary physiology ,Depression (differential diagnoses) ,comparative study ,psychological rating scale ,Baby blues ,longitudinal study ,Maternal depression ,cohort analysis ,female genital diseases and pregnancy complications ,Pathophysiology ,3. Good health ,Psychiatry and Mental health ,female ,risk factor ,brain derived neurotrophic factor ,Pregnancy Trimester, Second ,disease severity ,Female ,antepartum depression ,Patient Health Questionnaire 9 ,Research Article ,Adult ,medicine.medical_specialty ,prevalence ,purl.org/pe-repo/ocde/ford#3.02.24 [https] ,first trimester pregnancy ,Enzyme-Linked Immunosorbent Assay ,Article ,Depression, Postpartum ,03 medical and health sciences ,Young Adult ,second trimester pregnancy ,blood ,Internal medicine ,medicine ,Humans ,controlled study ,human ,Risk factor ,Psychiatry ,Brain-derived neurotrophic factor ,Psychiatric Status Rating Scales ,business.industry ,Brain-Derived Neurotrophic Factor ,treatment response ,prediction ,Biomarker ,medicine.disease ,030227 psychiatry ,enzyme linked immunosorbent assay ,Endocrinology ,pregnant woman ,BDNF ,protein blood level ,business ,trend study ,030217 neurology & neurosurgery - Abstract
Background Antepartum depression is one of the leading causes of maternal morbidity and mortality in the prenatal period. There is accumulating evidence for the role of brain-derived neurotrophic factor (BDNF) in the pathophysiology of depression. The present study examines the extent to which maternal early pregnancy serum BDNF levels are associated with antepartum depression. Method A total of 968 women were recruited and interviewed in early pregnancy. Antepartum depression prevalence and symptom severity were assessed using the Patient Health Questionnaire-9 (PHQ-9) scale. Maternal serum BDNF levels were measured using a competitive enzyme-linked immunosorbent assay (ELISA). Logistic regression procedures were performed to estimate odds ratios (OR) and 95% confidence intervals (95% CI) adjusted for confounders. Results Maternal early pregnancy serum BDNF levels were significantly lower in women with antepartum depression compared to women without depression (mean ± standard deviation [SD]: 20.78 ± 5.97 vs. 21.85 ± 6.42 ng/ml, p = 0.024). Lower BDNF levels were associated with increased odds of maternal antepartum depression. After adjusting for confounding, women whose serum BDNF levels were in the lowest three quartiles (25.31 ng/ml). There was no evidence of an association of BDNF levels with depression symptom severity. Conclusions Lower maternal serum BDNF levels in early pregnancy are associated with antepartum depression. These findings may point toward new therapeutic opportunities and BDNF should be assessed as a potential biomarker for risk prediction and monitoring response to treatment for antepartum depression. Electronic supplementary material The online version of this article (doi:10.1186/s12888-015-0428-7) contains supplementary material, which is available to authorized users.
- Published
- 2015
10. CRISPR/dCas9-mediated transcriptional improvement of the biosynthetic gene cluster for the epothilone production in Myxococcus xanthus.
- Author
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Peng, Ran, Wang, Ye, Feng, Wan-wan, Yue, Xin-jing, Chen, Jiang-he, Hu, Xiao-zhuang, Li, Zhi-feng, Sheng, Duo-hong, Zhang, You-ming, and Li, Yue-zhong
- Subjects
CRISPRS ,MYXOCOCCUS xanthus ,EUKARYOTIC cells ,RNA polymerases ,MYXOBACTERALES ,SIGMA factor (Transcription factor) - Abstract
Background: The CRISPR/dCas9 system is a powerful tool to activate the transcription of target genes in eukaryotic or prokaryotic cells, but lacks assays in complex conditions, such as the biosynthesis of secondary metabolites. Results: In this study, to improve the transcription of the heterologously expressed biosynthetic genes for the production of epothilones, we established the CRISPR/dCas9-mediated activation technique in Myxococcus xanthus and analyzed some key factors involving in the CRISPR/dCas9 activation. We firstly optimized the cas9 codon to fit the M. xanthus cells, mutated the gene to inactivate the nuclease activity, and constructed the dCas9-activator system in an epothilone producer. We compared the improvement efficiency of different sgRNAs on the production of epothilones and the expression of the biosynthetic genes. We also compared the improvement effects of different activator proteins, the ω and α subunits of RNA polymerase, and the sigma factors σ54 and CarQ. By using a copper-inducible promoter, we determined that higher expressions of dCas9-activator improved the activation effects. Conclusions: Our results showed that the CRISPR/dCas-mediated transcription activation is a simple and broadly applicable technique to improve the transcriptional efficiency for the production of secondary metabolites in micro-organisms. This is the first time to construct the CRISPR/dCas9 activation system in myxobacteria and the first time to assay the CRISPR/dCas9 activations for the biosynthesis of microbial secondary metabolites. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
11. Increasing on-target cleavage efficiency for CRISPR/Cas9-induced large fragment deletion in Myxococcus xanthus.
- Author
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Yang, Ying-jie, Wang, Ye, Li, Zhi-feng, Gong, Ya, Zhang, Peng, Hu, Wen-chao, Sheng, Duo-hong, and Li, Yue-zhong
- Subjects
CRISPRS ,GENOME editing ,MYXOCOCCUS xanthus ,DNA ,TRANSFER RNA ,GRAM-negative bacteria - Abstract
Background: The CRISPR/Cas9 system is a powerful tool for genome editing, in which the sgRNA binds and guides the Cas9 protein for the sequence-specific cleavage. The protocol is employable in different organisms, but is often limited by cell damage due to the endonuclease activity of the introduced Cas9 and the potential off-target DNA cleavage from incorrect guide by the 20 nt spacer. Results: In this study, after resolving some critical limits, we have established an efficient CRISPR/Cas9 system for the deletion of large genome fragments related to the biosynthesis of secondary metabolites in Myxococcus xanthus cells. We revealed that the high expression of a codon-optimized cas9 gene in M. xanthus was cytotoxic, and developed a temporally high expression strategy to reduce the cell damage from high expressions of Cas9. We optimized the deletion protocol by using the tRNA-sgRNA-tRNA chimeric structure to ensure correct sgRNA sequence. We found that, in addition to the position-dependent nucleotide preference, the free energy of a 20 nt spacer was a key factor for the deletion efficiency. Conclusions: By using the developed protocol, we achieved the CRISPR/Cas9-induced deletion of large biosynthetic gene clusters for secondary metabolites in M. xanthus DK1622 and its epothilone-producing mutant. The findings and the proposals described in this paper were suggested to be workable in other organisms, for example, other Gram negative bacteria with high GC content. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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- View/download PDF
12. A bacterial negative transcription regulator binding on an inverted repeat in the promoter for epothilone biosynthesis.
- Author
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Xin-jing Yue, Xiao-wen Cui, Zheng Zhang, Ran Peng, Peng Zhang, Zhi-feng Li, and Yue-zhong Li
- Subjects
BIOSYNTHESIS ,MYXOBACTERALES ,METABOLISM ,ORGANIC synthesis ,BIOCHEMISTRY - Abstract
Background: Microbial secondary metabolism is regulated by a complex and mostly-unknown network of global and pathway-specific regulators. A dozen biosynthetic gene clusters for secondary metabolites have been reported in myxobacteria, but a few regulation factors have been identified. Results: We identified a transcription regulator Esi for the biosynthesis of epothilones. Inactivation of esi promoted the epothilone production, while overexpression of the gene suppressed the production. The regulation was determined to be resulted from the transcriptional changes of epothilone genes. Esi was able to bind, probably via the N-terminus of the protein, to an inverted repeat sequence in the promoter of the epothilone biosynthetic gene cluster. The Esi-homologous sequences retrieved from the RefSeq database are all of the Proteobacteria. However, the Esi regulation is not universal in myxobacteria, because the esi gene exists only in a few myxobacterial genomes. Conclusions: Esi binds to the epothilone promoter and down-regulates the transcriptional level of the whole gene cluster to affect the biosynthesis of epothilone. This is the first transcription regulator identified for epothilone biosynthesis. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
13. Cultivation to improve in vivo solubility of overexpressed arginine deiminases in Escherichia coli and the enzyme characteristics
- Author
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Yue-zhong Li and Ying Wang
- Subjects
Arginine ,Hydrolases ,Listeria ,Cultivation ,Molecular Sequence Data ,L-arginine ,medicine.disease_cause ,L-citrulline ,chemistry.chemical_compound ,Bacterial Proteins ,medicine ,Escherichia coli ,Solubilization ,Arginine deiminase ,chemistry.chemical_classification ,Growth medium ,biology ,Base Sequence ,Pseudomonas putida ,Conversion ,Hydrogen-Ion Concentration ,biology.organism_classification ,Recombinant Proteins ,Amino acid ,Enzyme ,Biochemistry ,chemistry ,Solubility ,Citrulline ,Heterologous expression ,Biotechnology ,Research Article ,Molecular Chaperones - Abstract
Background Overexpression of foreign genes in Escherichia coli cells is an efficient means to obtain recombinant proteins. The technique is, however, often hampered by misfolding, degradation, aggregation and formation in inclusion bodies of products. Results In this study, we reported that in vivo solubility of overexpressed arginine deiminases (ADI) improved by changing the cultivation conditions. ADI is enzymes that convert L-arginine to L-citrulline. After codon optimization, we synthesized the ADI gene of Pseudomonas putida and constructed it for overexpression in E. coli cells. The rADI products were mainly in inclusion body forms. We performed a series of optimization to enhance solubility of the protein. Co-expression with the GroES-GroEL chaperone team increased approximately 5-fold of the rADI activity. In addition the combination of L-arginine and D-glucose in the Luria-Bertani (LB) growth medium further increased the total activity to about 15 times. Separate L-arginine and D-glucose or the addition of other saccharides or amino acids had no such effects. The solubilization effects of the combination of L-arginine and D-glucose were further confirmed in the overexpression of another ADI from Listeria welshimeri. The enzymatic and conversion characteristics of the rADI products were further determined. Conclusions Combined addition of L-arginine and D-glucose in the LB medium significantly improved in vivo solubility of rADI proteins. The present study suggested a new strategy to increase the solubilization of overexpressed recombinant proteins in E. coli cells.
- Published
- 2014
14. The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081).
- Author
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Chen, Xiao-jing, Han, Kui, Feng, Jing, Zhuo, Li, Li, Ya-jie, and Li, Yue-zhong
- Subjects
NUCLEOTIDE sequencing ,PLASMIDS ,MYXOBACTERALES ,MYXOCOCCUS ,PHYLOGENY ,PROTEOBACTERIA ,ANIMAL social behavior ,GENETIC engineering - Abstract
Myxobacteria, phylogenetically located in the delta division of the Proteobacteria, are well known for characterized social behaviors and large genomes of more than 9 Mb in size. Myxococcus fulvus is a typical species of the genus Myxococcus in the family Myxococcaceae. M. fulvus 124B02, originally isolated from a soil sample collected in Northeast China, is the one and only presently known myxobacterial strain that harbors an endogenous autonomously replicating plasmid, named pMF1. The endogenous plasmid is of importance for understanding the genome evolution of myxobacteria, as well as for the development of genetic engineering tools in myxobacteria. Here we describe the complete genome sequence of this organism. M. fulvus 124B02 consists of a circular chromosome with a total length of 11,048,835 bp and a circular plasmid of 18,634 bp. Comparative genomic analyses suggest that pMF1 has a longstanding sustention within myxobacteria, and probably contributes to the genome expansion of myxobacteria. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
15. Allopatric integrations selectively change host transcriptomes, leading to varied expression efficiencies of exotic genes in Myxococcus xanthus.
- Author
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Li-Ping Zhu, Xin-Jing Yue, Kui Han, Zhi-Feng Li, Lian-Shuai Zheng, Xiu-Nan Yi, Hai-Long Wang, You-Ming Zhang, and Yue-Zhong Li
- Subjects
CHROMOSOMAL translocation ,CHLORAMPHENICOL ,MYXOCOCCUS xanthus ,TRANSFERASES ,BIOSYNTHESIS - Abstract
Background: Exotic genes, especially clustered multiple-genes for a complex pathway, are normally integrated into chromosome for heterologous expression. The influences of insertion sites on heterologous expression and allotropic expressions of exotic genes on host remain mostly unclear. Results: We compared the integration and expression efficiencies of single and multiple exotic genes that were inserted into Myxococcus xanthus genome by transposition and attB-site-directed recombination. While the site-directed integration had a rather stable chloramphenicol acetyl transferase (CAT) activity, the transposition produced varied CAT enzyme activities. We attempted to integrate the 56-kb gene cluster for the biosynthesis of antitumor polyketides epothilones into M. xanthus genome by site-direction but failed, which was determined to be due to the insertion size limitation at the attB site. The transposition technique produced many recombinants with varied production capabilities of epothilones, which, however, were not paralleled to the transcriptional characteristics of the local sites where the genes were integrated. Comparative transcriptomics analysis demonstrated that the allopatric integrations caused selective changes of host transcriptomes, leading to varied expressions of epothilone genes in different mutants. Conclusions: With the increase of insertion fragment size, transposition is a more practicable integration method for the expression of exotic genes. Allopatric integrations selectively change host transcriptomes, which lead to varied expression efficiencies of exotic genes. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
16. Association of decreased serum brain-derived neurotrophic factor (BDNF) concentrations in early pregnancy with antepartum depression.
- Author
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Fung, Jenny, Gelaye, Bizu, Qiu-Yue Zhong, Rondon, Marta B., Sanchez, Sixto E., Barrios, Yasmin V., Hevner, Karin, Chunfang Qiu, and Williams, Michelle A.
- Subjects
BLOOD serum analysis ,BRAIN-derived neurotrophic factor ,DIAGNOSIS of pregnancy ,PRENATAL depression ,PATHOLOGICAL physiology ,MORTALITY - Abstract
Background: Antepartum depression is one of the leading causes of maternal morbidity and mortality in the prenatal period. There is accumulating evidence for the role of brain-derived neurotrophic factor (BDNF) in the pathophysiology of depression. The present study examines the extent to which maternal early pregnancy serum BDNF levels are associated with antepartum depression. Method: A total of 968 women were recruited and interviewed in early pregnancy. Antepartum depression prevalence and symptom severity were assessed using the Patient Health Questionnaire-9 (PHQ-9) scale. Maternal serum BDNF levels were measured using a competitive enzyme-linked immunosorbent assay (ELISA). Logistic regression procedures were performed to estimate odds ratios (OR) and 95% confidence intervals (95% CI) adjusted for confounders. Results: Maternal early pregnancy serum BDNF levels were significantly lower in women with antepartum depression compared to women without depression (mean ± standard deviation [SD]: 20.78 ± 5.97 vs. 21.85 ± 6.42 ng/ml, p = 0.024). Lower BDNF levels were associated with increased odds of maternal antepartum depression. After adjusting for confounding, women whose serum BDNF levels were in the lowest three quartiles (<17.32 ng/ml) had 1.61-fold increased odds (OR = 1.61, 95% CI: 1.13, 2.30) of antepartum depression as compared with women whose BDNF levels were in the highest quartile (>25.31 ng/ml). There was no evidence of an association of BDNF levels with depression symptom severity. Conclusions: Lower maternal serum BDNF levels in early pregnancy are associated with antepartum depression. These findings may point toward new therapeutic opportunities and BDNF should be assessed as a potential biomarker for risk prediction and monitoring response to treatment for antepartum depression. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
17. Cultivation to improve in vivo solubility of overexpressed arginine deiminases in Escherichia coli and the enzyme characteristics.
- Author
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Ying Wang and Yue-Zhong Li
- Subjects
- *
ARGININE deiminase , *GENE expression , *ESCHERICHIA coli , *SOLUBILIZATION , *TILLAGE , *GLUCOSE - Abstract
Background Overexpression of foreign genes in Escherichia coli cells is an efficient means to obtain recombinant proteins. The technique is, however, often hampered by misfolding, degradation, aggregation and formation in inclusion bodies of products. Results In this study, we reported that in vivo solubility of overexpressed arginine deiminases (ADI) improved by changing the cultivation conditions. ADI is enzymes that convert L-arginine to L-citrulline. After codon optimization, we synthesized the ADI gene of Pseudomonas putida and constructed it for overexpression in E. coli cells. The rADI products were mainly in inclusion body forms. We performed a series of optimization to enhance solubility of the protein. Co-expression with the GroEL-GroES chaperone team increased approximately 5- fold of the rADI activity. In addition the combination of L-arginine and D-glucose in the Luria-Bertani (LB) growth medium further increased the total activity to about 15 times. Separate L-arginine and D-glucose or the addition of other saccharides or amino acids had no such effects. The solubilization effects of the combination of L-arginine and D-glucose were further confirmed in the overexpression of another ADI from Listeria welshimeri. The enzymatic and conversion characteristics of the rADI products were further determined. Conclusions Combined addition of L-arginine and D-glucose in the LB medium significantly improved in vivo solubility of rADI proteins. The present study suggested a new strategy to increase the solubilization of overexpressed recombinant proteins in E. coli cells. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
18. Diverse histone modifications on histone 3 lysine 9 and their relation to DNA methylation in specifying gene silencing.
- Author
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Jiejun Wu, Shu-Huei Wang, Potter, Dustin, Liu, Joseph C, Smith, Laura T, Yue-Zhong Wu, Huang, Tim H-M, and Plass, Christoph
- Subjects
HISTONES ,LYSINE ,METHYLATION ,ETHANES ,CELL lines ,GENE silencing - Abstract
Background: Previous studies of individual genes have shown that in a self-enforcing way, dimethylation at histone 3 lysine 9 (dimethyl-H3K9) and DNA methylation cooperate to maintain a repressive mode of inactive genes. Less clear is whether this cooperation is generalized in mammalian genomes, such as mouse genome. Here we use epigenomic tools to simultaneously interrogate chromatin modifications and DNA methylation in a mouse leukemia cell line, L1210. Results: Histone modifications on H3K9 and DNA methylation in L1210 were profiled by both global CpG island array and custom mouse promoter array analysis. We used chromatin immunoprecipitation microarray (ChIP-chip) to examine acetyl-H3K9 and dimethyl-H3K9. We found that the relative level of acetyl-H3K9 at different chromatin positions has a wider range of distribution than that of dimethyl-H3K9. We then used differential methylation hybridization (DMH) and the restriction landmark genome scanning (RLGS) to analyze the DNA methylation status of the same targets investigated by ChIP-chip. The results of epigenomic profiling, which have been independently confirmed for individual loci, show an inverse relationship between DNA methylation and histone acetylation in regulating gene silencing. In contrast to the previous notion, dimethyl-H3K9 seems to be less distinct in specifying silencing for the genes tested. Conclusion: This study demonstrates in L1210 leukemia cells a diverse relationship between histone modifications and DNA methylation in the maintenance of gene silencing. Acetyl-H3K9 shows an inverse relationship between DNA methylation and histone acetylation in regulating gene silencing as expected. However, dimethyl-H3K9 seems to be less distinct in relation to promoter methylation. Meanwhile, a combination of epigenomic tools is of help in understanding the heterogeneity of epigenetic regulation, which may further our vision accumulated from single-gene studies. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
19. A bacterial negative transcription regulator binding on an inverted repeat in the promoter for epothilone biosynthesis.
- Author
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Yue XJ, Cui XW, Zhang Z, Peng R, Zhang P, Li ZF, and Li YZ
- Subjects
- Multigene Family, Promoter Regions, Genetic, Proteobacteria genetics, Proteobacteria metabolism, Secondary Metabolism, Suppression, Genetic, Epothilones biosynthesis, Gene Expression Regulation, Bacterial, Inverted Repeat Sequences, Myxococcales genetics, Myxococcales metabolism, Transcription, Genetic
- Abstract
Background: Microbial secondary metabolism is regulated by a complex and mostly-unknown network of global and pathway-specific regulators. A dozen biosynthetic gene clusters for secondary metabolites have been reported in myxobacteria, but a few regulation factors have been identified., Results: We identified a transcription regulator Esi for the biosynthesis of epothilones. Inactivation of esi promoted the epothilone production, while overexpression of the gene suppressed the production. The regulation was determined to be resulted from the transcriptional changes of epothilone genes. Esi was able to bind, probably via the N-terminus of the protein, to an inverted repeat sequence in the promoter of the epothilone biosynthetic gene cluster. The Esi-homologous sequences retrieved from the RefSeq database are all of the Proteobacteria. However, the Esi regulation is not universal in myxobacteria, because the esi gene exists only in a few myxobacterial genomes., Conclusions: Esi binds to the epothilone promoter and down-regulates the transcriptional level of the whole gene cluster to affect the biosynthesis of epothilone. This is the first transcription regulator identified for epothilone biosynthesis.
- Published
- 2017
- Full Text
- View/download PDF
20. Allopatric integrations selectively change host transcriptomes, leading to varied expression efficiencies of exotic genes in Myxococcus xanthus.
- Author
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Zhu LP, Yue XJ, Han K, Li ZF, Zheng LS, Yi XN, Wang HL, Zhang YM, and Li YZ
- Subjects
- Bacterial Proteins genetics, Bacterial Proteins metabolism, Epothilones genetics, Epothilones metabolism, Gene Expression, Mutagenesis, Insertional, Myxococcus xanthus metabolism, Myxococcus xanthus genetics, Transcriptome
- Abstract
Background: Exotic genes, especially clustered multiple-genes for a complex pathway, are normally integrated into chromosome for heterologous expression. The influences of insertion sites on heterologous expression and allotropic expressions of exotic genes on host remain mostly unclear., Results: We compared the integration and expression efficiencies of single and multiple exotic genes that were inserted into Myxococcus xanthus genome by transposition and attB-site-directed recombination. While the site-directed integration had a rather stable chloramphenicol acetyl transferase (CAT) activity, the transposition produced varied CAT enzyme activities. We attempted to integrate the 56-kb gene cluster for the biosynthesis of antitumor polyketides epothilones into M. xanthus genome by site-direction but failed, which was determined to be due to the insertion size limitation at the attB site. The transposition technique produced many recombinants with varied production capabilities of epothilones, which, however, were not paralleled to the transcriptional characteristics of the local sites where the genes were integrated. Comparative transcriptomics analysis demonstrated that the allopatric integrations caused selective changes of host transcriptomes, leading to varied expressions of epothilone genes in different mutants., Conclusions: With the increase of insertion fragment size, transposition is a more practicable integration method for the expression of exotic genes. Allopatric integrations selectively change host transcriptomes, which lead to varied expression efficiencies of exotic genes.
- Published
- 2015
- Full Text
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21. Cultivation to improve in vivo solubility of overexpressed arginine deiminases in Escherichia coli and the enzyme characteristics.
- Author
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Wang Y and Li YZ
- Subjects
- Arginine metabolism, Bacterial Proteins chemistry, Bacterial Proteins genetics, Base Sequence, Citrulline metabolism, Hydrogen-Ion Concentration, Hydrolases chemistry, Hydrolases genetics, Listeria enzymology, Molecular Chaperones genetics, Molecular Chaperones metabolism, Molecular Sequence Data, Pseudomonas putida enzymology, Recombinant Proteins biosynthesis, Recombinant Proteins chemistry, Recombinant Proteins genetics, Solubility, Bacterial Proteins metabolism, Escherichia coli metabolism, Hydrolases metabolism
- Abstract
Background: Overexpression of foreign genes in Escherichia coli cells is an efficient means to obtain recombinant proteins. The technique is, however, often hampered by misfolding, degradation, aggregation and formation in inclusion bodies of products., Results: In this study, we reported that in vivo solubility of overexpressed arginine deiminases (ADI) improved by changing the cultivation conditions. ADI is enzymes that convert L-arginine to L-citrulline. After codon optimization, we synthesized the ADI gene of Pseudomonas putida and constructed it for overexpression in E. coli cells. The rADI products were mainly in inclusion body forms. We performed a series of optimization to enhance solubility of the protein. Co-expression with the GroES-GroEL chaperone team increased approximately 5-fold of the rADI activity. In addition the combination of L-arginine and D-glucose in the Luria-Bertani (LB) growth medium further increased the total activity to about 15 times. Separate L-arginine and D-glucose or the addition of other saccharides or amino acids had no such effects. The solubilization effects of the combination of L-arginine and D-glucose were further confirmed in the overexpression of another ADI from Listeria welshimeri. The enzymatic and conversion characteristics of the rADI products were further determined., Conclusions: Combined addition of L-arginine and D-glucose in the LB medium significantly improved in vivo solubility of rADI proteins. The present study suggested a new strategy to increase the solubilization of overexpressed recombinant proteins in E. coli cells.
- Published
- 2014
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22. Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.
- Author
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Smiraglia DJ, Kazhiyur-Mannar R, Oakes CC, Wu YZ, Liang P, Ansari T, Su J, Rush LJ, Smith LT, Yu L, Liu C, Dai Z, Chen SS, Wang SH, Costello J, Ioshikhes I, Dawson DW, Hong JS, Teitell MA, Szafranek A, Camoriano M, Song F, Elliott R, Held W, Trasler JM, Plass C, and Wenger R
- Subjects
- Animals, Computational Biology, DNA Methylation, Electrophoresis, Gel, Two-Dimensional, Genome, Human genetics, Humans, Intestinal Mucosa metabolism, Liver metabolism, Mice, Organ Specificity genetics, CpG Islands genetics, DNA Restriction Enzymes metabolism, Genome genetics, Genomics methods, Restriction Mapping methods
- Abstract
Background: Restriction landmark genomic scanning (RLGS) is one of the most successfully applied methods for the identification of aberrant CpG island hypermethylation in cancer, as well as the identification of tissue specific methylation of CpG islands. However, a limitation to the utility of this method has been the ability to assign specific genomic sequences to RLGS spots, a process commonly referred to as "RLGS spot cloning.", Results: We report the development of a virtual RLGS method (vRLGS) that allows for RLGS spot identification in any sequenced genome and with any enzyme combination. We report significant improvements in predicting DNA fragment migration patterns by incorporating sequence information into the migration models, and demonstrate a median Euclidian distance between actual and predicted spot migration of 0.18 centimeters for the most complex human RLGS pattern. We report the confirmed identification of 795 human and 530 mouse RLGS spots for the most commonly used enzyme combinations. We also developed a method to filter the virtual spots to reduce the number of extra spots seen on a virtual profile for both the mouse and human genomes. We demonstrate use of this filter to simplify spot cloning and to assist in the identification of spots exhibiting tissue-specific methylation., Conclusion: The new vRLGS system reported here is highly robust for the identification of novel RLGS spots. The migration models developed are not specific to the genome being studied or the enzyme combination being used, making this tool broadly applicable. The identification of hundreds of mouse and human RLGS spot loci confirms the strong bias of RLGS studies to focus on CpG islands and provides a valuable resource to rapidly study their methylation.
- Published
- 2007
- Full Text
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23. Diverse histone modifications on histone 3 lysine 9 and their relation to DNA methylation in specifying gene silencing.
- Author
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Wu J, Wang SH, Potter D, Liu JC, Smith LT, Wu YZ, Huang TH, and Plass C
- Subjects
- Acetylation, Animals, Azacitidine analogs & derivatives, Azacitidine pharmacology, Cell Line, Tumor, Chromatin Immunoprecipitation, CpG Islands genetics, DNA Modification Methylases antagonists & inhibitors, Decitabine, Gene Expression Regulation drug effects, Hydroxamic Acids pharmacology, Leukemia L1210 genetics, Leukemia L1210 metabolism, Leukemia L1210 pathology, Lysine metabolism, Methylation, Mice, Mice, Inbred DBA, Oligonucleotide Array Sequence Analysis, DNA Methylation, Gene Silencing, Histones metabolism, Protein Processing, Post-Translational
- Abstract
Background: Previous studies of individual genes have shown that in a self-enforcing way, dimethylation at histone 3 lysine 9 (dimethyl-H3K9) and DNA methylation cooperate to maintain a repressive mode of inactive genes. Less clear is whether this cooperation is generalized in mammalian genomes, such as mouse genome. Here we use epigenomic tools to simultaneously interrogate chromatin modifications and DNA methylation in a mouse leukemia cell line, L1210., Results: Histone modifications on H3K9 and DNA methylation in L1210 were profiled by both global CpG island array and custom mouse promoter array analysis. We used chromatin immunoprecipitation microarray (ChIP-chip) to examine acetyl-H3K9 and dimethyl-H3K9. We found that the relative level of acetyl-H3K9 at different chromatin positions has a wider range of distribution than that of dimethyl-H3K9. We then used differential methylation hybridization (DMH) and the restriction landmark genome scanning (RLGS) to analyze the DNA methylation status of the same targets investigated by ChIP-chip. The results of epigenomic profiling, which have been independently confirmed for individual loci, show an inverse relationship between DNA methylation and histone acetylation in regulating gene silencing. In contrast to the previous notion, dimethyl-H3K9 seems to be less distinct in specifying silencing for the genes tested., Conclusion: This study demonstrates in L1210 leukemia cells a diverse relationship between histone modifications and DNA methylation in the maintenance of gene silencing. Acetyl-H3K9 shows an inverse relationship between DNA methylation and histone acetylation in regulating gene silencing as expected. However, dimethyl-H3K9 seems to be less distinct in relation to promoter methylation. Meanwhile, a combination of epigenomic tools is of help in understanding the heterogeneity of epigenetic regulation, which may further our vision accumulated from single-gene studies.
- Published
- 2007
- Full Text
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