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author:("Li, wenjing")
1.  Metabolic engineering of indole pyruvic acid biosynthesis in Escherichia coli with tdiD 
Background
Indole pyruvic acid (IPA) is a versatile platform intermediate and building block for a number of high-value products in the pharmaceutical and food industries. It also has a wide range of applications, such as drugs for the nervous system, cosmetics, and luminophores. Chemical synthesis of IPA is a complicated and costly process. Moreover, through the biosynthesis route employing l-amino acid oxidase, the byproduct hydrogen peroxide leads the degradation of IPA. TdiD, identified as a specific tryptophan aminotransferase, could be an alternative solution for efficient IPA biosynthesis.
Results
Escherichia coli strain W3110, which demonstrates basic production when supplied with tryptophan, was engineered for IPA biosynthesis. Several strategies were implemented to improve IPA production. First, through incorporating the codon-optimized tdiD into W3110, IPA levels increased from 41.54 ± 1.26 to 52.54 ± 2.08 mg/L. Second, after verifying the benefit of an increased phenylpyruvate pool, a YL03 strain was constructed based on a previously reported mutant strain of W3110 with a plasmid carrying aroF fbr and pheA fbr to further improve IPA production. The recombinant YL03 strain accumulated IPA at 158.85 ± 5.36 mg/L, which was 3.82-fold higher than that of the wild-type W3110 strain. Third, optimization of tdiD co expression was carried out by replacing the Trc promoter with a series of constitutively active promoters along with increasing the plasmid copy numbers. The highest IPA production was observed in YL08, which achieved 236.42 ± 17.66 mg/L and represented a greater than 5-fold increase as compared to W3110. Finally, the effects of deletion and overexpression of tnaA on IPA biosynthesis were evaluated. The removal of tnaA led to slightly reduced IPA levels, whereas the overexpression of tnaA resulted in a considerable decline in production.
Conclusions
This study illustrates the feasibility of IPA biosynthesis in E. coli through tdiD. An efficient IPA producing strain, YL08, was developed, which provides a new possibility for biosynthesis of IPA. Although the final production was limited, this study demonstrates a convenient method of IPA synthesis.
Electronic supplementary material
The online version of this article (doi:10.1186/s12934-016-0620-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s12934-016-0620-6
PMCID: PMC5209907  PMID: 28049530
Indole pyruvic acid; tdiD; Aminotransferase; tnaA
2.  Complete Genome Sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04) 
Beijing has been one of the epicenters attacked most severely by the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) since the first patient was diagnosed in one of the city’s hospitals. We now report complete genome sequences of the BJ Group, including four isolates (Isolates BJ01, BJ02, BJ03, and BJ04) of the SARS-CoV. It is remarkable that all members of the BJ Group share a common haplotype, consisting of seven loci that differentiate the group from other isolates published to date. Among 42 substitutions uniquely identified from the BJ group, 32 are non-synonymous changes at the amino acid level. Rooted phylogenetic trees, proposed on the basis of haplotypes and other sequence variations of SARS-CoV isolates from Canada, USA, Singapore, and China, gave rise to different paradigms but positioned the BJ Group, together with the newly discovered GD01 (GD-Ins29) in the same clade, followed by the H-U Group (from Hong Kong to USA) and the H-T Group (from Hong Kong to Toronto), leaving the SP Group (Singapore) more distant. This result appears to suggest a possible transmission path from Guangdong to Beijing/Hong Kong, then to other countries and regions.
doi:10.1016/S1672-0229(03)01023-4
PMCID: PMC5172409  PMID: 15629030
SARS; SARS-CoV; haplotype; substitution; phylogeny
3.  Long non-coding RNAs regulate effects of β-crystallin B2 on mouse ovary development 
Molecular Medicine Reports  2016;14(5):4223-4231.
β-crystallin B2 (CRYBB2) knockout mice exhibit morphological and functional abnormalities in the ovary. Long non-coding RNAs (lncRNAs) regulate gene transcription and translation, and epigenetic modification of genomic DNA. The present study investigated the role of lncRNAs in mediating the effects of CRYBB2 in the regulation of ovary development in mice. In the current study, ovary tissues from wild-type (WT) and CRYBB2 knockout mice were subjected to lncRNA and mRNA microarray profiling. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to group the differentially expressed lncRNAs into regulated gene pathways and functions. The correlation matrix method was used to establish a network of lncRNA and mRNA co-expression. Quantitative reverse transcription-polymerase chain reaction (RT-qPCR) was used to verify expression of a number of these differentially expressed lncRNAs and mRNAs. There were 157 differentially expressed lncRNAs and 1,085 differentially expressed mRNAs between ovary tissues from WT and CRYBB2 knockout mice. The GO and KEGG analyses indicated that these differentially expressed lncRNAs and mRNAs were important in Ca2+ signaling and ligand and receptor interactions. The correlation matrix method established an lncRNA and mRNA co-expression network, consisting of 53 lncRNAs and 45 mRNAs with 98 nodes and 75 connections. RT-qPCR confirmed downregulation of lncRNA A-30-P01019163 expression, which further downregulated its downstream gene purinergic receptor P2X, ligand-gated ion channel, 7 (P2rx7) expression in ovary tissues from CRYBB2 knockout mice. In conclusion, CRYBB2 regulates expression of different lncRNAs to influence ovary development. lncRNA A-30-P01019163 may affect ovarian cell cycle and proliferation by regulating P2rx7 expression in the ovary.
doi:10.3892/mmr.2016.5761
PMCID: PMC5101957  PMID: 27666820
β-crystallin B2; long non-coding RNAs; ovary development; signal transduction
4.  Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level 
Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea’s genetic data sources.
doi:10.3389/fmicb.2016.00998
PMCID: PMC4921485  PMID: 27446038
comparative genomics; streptomycete; pan-genomics; genome dynamics; marine environment adaptation
5.  Calcitonin gene-related peptide is a key factor in the homing of transplanted human MSCs to sites of spinal cord injury 
Scientific Reports  2016;6:27724.
Mesenchymal stem cells (MSCs) can be used to treat many diseases, including spinal cord injury (SCI). Treatment relies mostly on the precise navigation of cells to the injury site for rebuilding the damaged spinal cord. However, the key factors guiding MSCs to the epicenter of SCI remain unknown. Here, we demonstrated that calcitonin gene-related peptide (CGRP), a neural peptide synthesized in spinal cord, can dramatically aid the homing of human umbilical cord mesenchymal stem cells (HUMSCs) in spinal cord-transected SCI rats. First, HUMSCs exhibited chemotactic responses in vitro to CGRP. By time-lapse video analysis, increased chemotactic index (CMI), forward migration index (FMI) and speed contributed to this observed migration. Then, through enzyme immunoassay, higher CGRP concentrations at the lesion site were observed after injury. The release of CGRP directed HUMSCs to the injury site, which was suppressed by CGRP 8–37, a CGRP antagonist. We also verified that the PI3K/Akt and p38MAPK signaling pathways played a critical role in the CGRP-induced chemotactic migration of HUMSCs. Collectively, our data reveal that CGRP is a key chemokine that helps HUMSCs migrate to the lesion site and thereby can be used as a model molecule to study MSCs homing after SCI.
doi:10.1038/srep27724
PMCID: PMC4906351  PMID: 27296555
6.  The Description of Shale Reservoir Pore Structure Based on Method of Moments Estimation 
PLoS ONE  2016;11(3):e0151631.
Shale has been considered as good gas reservoir due to its abundant interior nanoscale pores. Thus, the study of the pore structure of shale is of great significance for the evaluation and development of shale oil and gas. To date, the most widely used approaches for studying the shale pore structure include image analysis, radiation and fluid invasion methods. The detailed pore structures can be studied intuitively by image analysis and radiation methods, but the results obtained are quite sensitive to sample preparation, equipment performance and experimental operation. In contrast, the fluid invasion method can be used to obtain information on pore size distribution and pore structure, but the relative simple parameters derived cannot be used to evaluate the pore structure of shale comprehensively and quantitatively. To characterize the nanoscale pore structure of shale reservoir more effectively and expand the current research techniques, we proposed a new method based on gas adsorption experimental data and the method of moments to describe the pore structure parameters of shale reservoir. Combined with the geological mixture empirical distribution and the method of moments estimation principle, the new method calculates the characteristic parameters of shale, including the mean pore size (x¯), standard deviation (σ), skewness (Sk) and variation coefficient (c). These values are found by reconstructing the grouping intervals of observation values and optimizing algorithms for eigenvalues. This approach assures a more effective description of the characteristics of nanoscale pore structures. Finally, the new method has been applied to analyze the Yanchang shale in the Ordos Basin (China) and Longmaxi shale from the Sichuan Basin (China). The results obtained well reveal the pore characteristics of shale, indicating the feasibility of this new method in the study of the pore structure of shale reservoir.
doi:10.1371/journal.pone.0151631
PMCID: PMC4798251  PMID: 26992168
7.  De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway 
BMC Genomics  2015;16:818.
Background
The entire world is facing a deteriorating environment. Understanding the mechanisms underlying plant responses to external abiotic stresses is important for breeding stress-tolerant crops and herbages. Phytohormones play critical regulatory roles in plants in the response to external and internal cues to regulate growth and development. Medicago falcata is one of the stress-tolerant candidate leguminous species and is able to fix atmospheric nitrogen. This ability allows leguminous plants to grow in nitrogen deficient soils.
Methods
We performed Illumina sequencing of cDNA prepared from abiotic stress treated M. falcata. Sequencedreads were assembled to provide a transcriptome resource. Transcripts were annotated using BLASTsearches against the NCBI non-redundant database and gene ontology definitions were assigned. Acomparison among the three abiotic stress treated samples was carried out. The expression of transcriptswas confirmed with qRT-PCR.
Results
We present an abiotic stress-responsive M. falcata transcriptome using next-generation sequencing data from samples grown under standard, dehydration, high salinity, and cold conditions. We combined reads from all samples and de novo assembled 98,515 transcripts to build the M. falcata gene index. A comprehensive analysis of the transcriptome revealed abiotic stress-responsive mechanisms underlying the metabolism and core signalling components of major phytohormones. We identified nod factor signalling pathways during early symbiotic nodulation that are modified by abiotic stresses. Additionally, a global comparison of homology between the M. falcata and M. truncatula transcriptomes, along with five other leguminous species, revealed a high level of global sequence conservation within the family.
Conclusions
M. falcata is shown to be a model candidate for studying abiotic stress-responsive mechanisms in legumes. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to abiotic stresses. Our data provides many gene candidates that might be used for herbage and crop breeding. Additionally, FalcataBase (http://bioinformatics.cau.edu.cn/falcata/) was built for storing these data.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-2019-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-2019-x
PMCID: PMC4615886  PMID: 26481731
Medicago falcata; Transcriptome; Legume; Phytohormones; Nodule
8.  Evaluating the Quality of Cardiopulmonary Resuscitation in the Emergency Department by Real-Time Video Recording System 
PLoS ONE  2015;10(10):e0139825.
Objectives
To compare cardiopulmonary resuscitation (CPR) quality between manual CPR and miniaturized chest compressor (MCC) CPR. To improve CPR quality through evaluating the quality of our clinical work of resuscitation by real-time video recording system.
Methods
The study was a retrospective observational study of adult patients who experienced CPR at the emergency department of Shanghai Tenth People’s Hospital from March 2013 to August 2014. All the performance of CPR were checked back by the record of “digital real-time video recording system”. Average chest compression rate, actual chest compression rate, the percentage of hands-off period, time lag from patient arrival to chest compression, time lag from patient arrival to manual ventilation, time lag from patient arrival to first IV establish were compared. Causes of chest compression hands-off time were also studied.
Results
112 cases of resuscitation attempts were obtained. Average chest compression rate was over 100 compression per minute (cpm) in the majority of cases. However, indicators such as percentage of hands-off periods, time lag from patient arrival to the first manual ventilation and time lag from patient arrival to the first IV establish seemed to be worse in the manual CPR group compared to MCC CPR group. The saving of operators change time seemed to counteract the time spent on MCC equipment. Indicators such as percentage of hands-off periods, time lag between patient arrival to the first chest compression, time lag between patient arrival to the first manual ventilation and time lag from patient arrival to the first IV establish may influence the survival.
Conclusion
Our CPR quality remained to be improved. MCC may have a potentially positive role in CPR.
doi:10.1371/journal.pone.0139825
PMCID: PMC4592189  PMID: 26431420
9.  Apoptotic effect of mtrix metalloproteinases 9 in the development of diabetic retinopathy 
Objective: To explore the potential regulatory mechanism of MMP9 in the development of DR. Methods: Plasmids pcDNA-MMP9 and pcDNA-Ang2 were transfected into primary rat retinal Müller cells (RMCs) using Lipofectamine 2000. Cell viability and apoptosis were respectively determined by MTT assay and flow cytometry. Moreover, the interaction between MMP9 and Ang2 was explored. Besides, RMCs were treated with MMP-9 under normal glucose and high glucose condition for 2d. Besides, the expression levels of apoptotic proteins, like MMP9, Ang2, Bax2, Bcl2, cleaved PARP and cleaved caspase3 were determined by Western blot. Results: The cell viability of siRNA-MMP9 group was significantly increased while decreased in MMP9 overexpression group when compared to control group, respectively. The apoptotic cells in MMP9 overexpression group significantly increased while decreased in siRNA-MMP9 group when compared with control group. MMP9 expression was significantly regulated by Ang2 whereas no significant changes occurred in Ang2 expression when MMP9 expression changed. Moreover, MMP9 expression in HG group significantly increased while there were no significant differences between NG group and control group. Besides, the expression of Bax2, Bcl2, cleaved PARP and cleaved caspase3 in HG group increased while there were no significant differences between NG group and control group. Conclusion: Our findings indicate that MMP9 may play an important role via inducing cell apoptosis in the development of DR via regulating by Ang2 or targeting apoptotic proteins, such as Bax2, Bcl2, cleaved PARP and cleaved caspase3.
PMCID: PMC4637569  PMID: 26617754
Diabetic retinopathy; mtrix metalloproteinases 9; angiopoietin 2; apoptosis
10.  Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling 
BMC Genomics  2015;16(1):581.
Background
To promote the clinical application of next-generation sequencing, it is important to obtain accurate and consistent variants of target genomic regions at low cost. Ion Proton, the latest updated semiconductor-based sequencing instrument from Life Technologies, is designed to provide investigators with an inexpensive platform for human whole exome sequencing that achieves a rapid turnaround time. However, few studies have comprehensively compared and evaluated the accuracy of variant calling between Ion Proton and Illumina sequencing platforms such as HiSeq 2000, which is the most popular sequencing platform for the human genome. The Ion Proton sequencer combined with the Ion TargetSeq™ Exome Enrichment Kit together make up TargetSeq-Proton, whereas SureSelect-Hiseq is based on the Agilent SureSelect Human All Exon v4 Kit and the HiSeq 2000 sequencer.
Results
Here, we sequenced exonic DNA from four human blood samples using both TargetSeq-Proton and SureSelect-HiSeq. We then called variants in the exonic regions that overlapped between the two exome capture kits (33.6 Mb). The rates of shared variant loci called by two sequencing platforms were from 68.0 to 75.3 % in four samples, whereas the concordance of co-detected variant loci reached 99 %. Sanger sequencing validation revealed that the validated rate of concordant single nucleotide polymorphisms (SNPs) (91.5 %) was higher than the SNPs specific to TargetSeq-Proton (60.0 %) or specific to SureSelect-HiSeq (88.3 %). With regard to 1-bp small insertions and deletions (InDels), the Sanger sequencing validated rates of concordant variants (100.0 %) and SureSelect-HiSeq-specific (89.6 %) were higher than those of TargetSeq-Proton-specific (15.8 %).
Conclusions
In the sequencing of exonic regions, a combination of using of two sequencing strategies (SureSelect-HiSeq and TargetSeq-Proton) increased the variant calling specificity for concordant variant loci and the sensitivity for variant loci called by any one platform. However, for the sequencing of platform-specific variants, the accuracy of variant calling by HiSeq 2000 was higher than that of Ion Proton, specifically for the InDel detection. Moreover, the variant calling software also influences the detection of SNPs and, specifically, InDels in Ion Proton exome sequencing.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1796-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1796-6
PMCID: PMC4524363  PMID: 26242175
Exome sequencing; Variant calling; Accuracy
11.  Controlled trial of the effectiveness of community rehabilitation for patients with schizophrenia in Shanghai, China 
Shanghai Archives of Psychiatry  2015;27(3):167-174.
Background
The ‘Sunshine Soul Park’ is a network of social welfare institutions that provides communitybased rehabilitation services for individuals with mental illness.
Aims
Assess the effectiveness of the rehabilitation services provided at the ‘Sunshine Soul Park’ on the psychotic symptoms and social functioning of individuals with schizophrenia and, based on these findings, provide a theoretical model of community-based rehabilitation.
Methods
Sixty individuals with schizophrenia in the Huangpu District of Shanghai volunteered for the rehabilitation training program provided at six ‘Sunshine Soul Park’ community centers that involves day treatment, medication monitoring, biweekly rehabilitation training, and other recreational, social, and intellectual activities. A matched control group was recruited from individuals with schizophrenia registered on the Huangpu District registry of the ‘Severe Mental Illness Prevention and Rehabilitation System’. All participants continued their medication without change for the full year of follow-up. Both groups were assessed at baseline, and 3, 6, and 12 months after enrollment using the Insight and Treatment Attitude Questionnaire (ITAQ), Social Disability Screening Schedule (SDSS), Generic Quality of Life Inventory-74 (GQOLI-74), and Positive and Negative Syndrome Scale (PANSS).
Results
In the intervention group the ITAQ, SDSS, GQOLI-74, and PANSS scores showed statistically significant improvement compared to baseline at each follow-up assessment. Moreover, the trend in improvement in the interventions group is significantly faster than that in the control group.
Conclusions
The ‘Sunshine Soul Park’ rehabilitation training program enhances patients’ knowledge about their disorder and improves their social functioning and quality of life. Further studies to assess methods for up-scaling this intervention to other areas of China are warranted.
doi:10.11919/j.issn.1002-0829.215026
PMCID: PMC4526829  PMID: 26300599
schizophrenia; community rehabilitation; ‘Sunshine Soul Garden’; characteristic path length; quality of life; China
12.  Identification of a novel cognate cytosolic Hsp70 gene (MnHsc70-2) from oriental river prawn Macrobrachium nipponense and comparison of its expressions with the first cognate Hsc70 (MnHsc70-1) under different stresses 
Cell Stress & Chaperones  2014;19(6):949-961.
The 70-kDa family of heat-shock proteins (Hsp70) plays an important role in the host immunity, which is widely expressed in eukaryotic cells as a major chaperone protein. In the present study, the full-length complementary DNA (cDNA) of a second cognate cytosolic Hsp70 family member (MnHsc70-2) was cloned and characterized from Macrobrachium nipponense, which is an economically and nutritionally important crustacean. The cDNA was 2,717 bp, containing an open reading frame (ORF) of 1,950 bp, which encodes a protein of 649 amino acids with a theoretical molecular weight of 71.1 kDa and an isoelectric point of 5.27. Sequence alignment showed that the MnHsc70-2 shared 75–97 % identity with other heat-shock proteins. Compared to the previously identified cognate Hsp70 (MnHsc70-1) in M. nipponense, MnHsc70-2 showed quite different expression profiles under unstressed conditions in all tested tissues, including the hemocytes, heart, hepatopancreas, gill, intestine, nerve, and muscle. The phylogenetic analysis demonstrated that MnHsc70-2 showed the closest relationship with MnHsc70-1. Heat-inducibility assays showed that two isolated messenger RNAs (mRNAs) displayed different expression profiles in both the hepatopancreas and gill tissues. MnHsc70-1 mRNA expression level decreased at first and then increased to the normal level, whereas MnHsc70-2 mRNA level increased at first and then decreased. The expressions of two MnHsc70s showed substantial obvious heat-inducible regulation in both the hepatopancreas and gill. Under bacterial challenge by Aeromonas hydrophila, both MnHsc70-1 and MnHsc70-2 mRNA level was up-regulated moderately. The results suggested that two cognate Hsc70s may play essential functions in mediating responses to heat-shock and bacterial challenge.
doi:10.1007/s12192-014-0519-2
PMCID: PMC4389856  PMID: 24859888
Macrobrachium nipponense; Heat-shock protein; Heat-shock treatment; Aeromonas hydrophila; Immune response
13.  Association of the vitamin D binding protein polymorphisms with the risk of type 2 diabetes mellitus: a meta-analysis 
BMJ Open  2014;4(11):e005617.
Objective
Previous studies on the association between vitamin D binding protein (DBP) polymorphisms and the risk of type 2 diabetes mellitus (T2DM) have produced conflicting results. The purpose of this meta-analysis was to examine whether DBP polymorphisms are associated with the risk of T2DM.
Design
Systematic review and meta-analysis.
Methods
All eligible studies were searched and acquired from the Cochrane, Pubmed, ISI, CNKI (Chinese) and Wanfang (Chinese) databases. ORs with corresponding 95% CIs were computed to estimate the association between DBP polymorphisms and T2DM. In addition, heterogeneity test, meta-regression and sensitivity analysis were also conducted.
Results
Six studies, which included 1191 cases and 882 controls, met the inclusion criteria and were included in the meta-analysis. The results showed that no significant associations were found between codon 416 and codon 420 polymorphisms in the DBP and the risk of T2DM in the overall analyses. In stratified analysis, significant associations between the codon 420 polymorphism and T2DM were found in Asians (allele Lys vs Thr: OR (95% CI) 1.49 (1.19 to 1.85), genotype Lys/Thr versus Thr/Thr: OR (95% CI) 1.80 (1.36 to 2.38), and Lys/Thr+Lys/Lys versus Thr/Thr: OR (95% CI) 1.81 (1.37 to 2.39), respectively) but not in Caucasians. For the codon 416, the significant association with T2DM was also detected in Asians (genotype Glu/Asp+Glu/Glu vs Asp/Asp: OR (95% CI) 1.36 (1.04 to 1.78)) but not in Caucasians.
Conclusions
This meta-analysis demonstrated that the DBP polymorphism was moderately associated with increased susceptibility to T2DM in Asians, but a similar association was not found in Caucasians. It suggested that ethnicity might be the potential factor associated with heterogeneity.
doi:10.1136/bmjopen-2014-005617
PMCID: PMC4225232  PMID: 25371416
EPIDEMIOLOGY; STATISTICS & RESEARCH METHODS
14.  T cells expressing a LMP1-specific chimeric antigen receptor mediate antitumor effects against LMP1-positive nasopharyngeal carcinoma cells in vitro and in vivo 
Journal of Biomedical Research  2014;28(6):468-475.
Abstract
T cells modified with chimeric antigen receptor are an attractive strategy to treat Epstein-Barr virus (EBV) associated malignancies. The EBV latent membrane protein 1 (LMP1) is a 66-KD integral membrane protein encoded by EBV that consists of transmembrane-spanning loops. Previously, we have identified a functional signal chain variable fragment (scFv) that specifically recognizes LMP1 through phage library screening. Here, we constructed a LMP1 specific chimeric antigen receptor containing anti-LMP1 scFv, the CD28 signalling domain, and the CD3ζ chain (HELA/CAR). We tested its functional ability to target LMP1 positive nasopharyngeal carcinoma cells. HELA/CAR cells were efficiently generated using lentivirus vector encoding the LMP1-specific chimeric antigen receptor to infect activated human CD3+ T cells. The HELA/CAR T cells displayed LMP1 specific cytolytic action and produced IFN-γ and IL-2 in response to nasopharyngeal carcinoma cells overexpressing LMP1. To demonstrate in vivo anti-tumor activity, we tested the HELA/CAR T cells in a xenograft model using an LMP1 overexpressing tumor. Intratumoral injection of anti-LMP1 HELA/CAR-T cells significantly reduced tumor growth in vivo. These results show that targeting LMP1 using HELA/CAR cells could represent an alternative therapeutic approach for patients with EBV-positive cancers.
doi:10.7555/JBR.28.20140066
PMCID: PMC4250525  PMID: 25469116
chimeric antigen receptor; LMP1; nasopharyngeal carcinoma; EBV; adoptive T cell therapy
15.  Recent Advances in Microfluidic Cell Separations 
The Analyst  2013;138(17):4714-4721.
The isolation and sorting of cells has become an increasingly important step in chemical and biological analyses. As a unit operation in more complex analyses, isolating a phenotypically pure cell population from a heterogeneous sample presents unique challenges. Microfluidic systems are ideal platforms for performing cell separations, enabling integration with other techniques and enhancing traditional separation modalities. In recent years there have been several techniques that use surface antigen affinity, physical interactions, or a combination of the two to achieve high separation purity and efficiency. This review discusses methods including magnetophoretic, acoustophoretic, sedimentation, electric, and hydrodynamic methods for physical separations. We also discuss affinity methods, including magnetic sorting, flow sorting, and affinity capture.
doi:10.1039/c3an00315a
PMCID: PMC3739304  PMID: 23778244
16.  Loss of LKB1 disrupts breast epithelial cell polarity and promotes breast cancer metastasis and invasion 
Background
LKB1, also known as STK11, is a master kinase that serves as an energy metabolic sensor and is involved in cell polarity regulation. Recent studies have indicated that LKB1 is related to breast tumorigenesis and breast cancer progression. However, little work has been done on the roles of LKB1 in cell polarity and epithelial-mesenchymal transition in breast cancer. In this study, we tried to prove that loss of LKB1 disrupts breast epithelial cell polarity and causes tumor metastasis and invasion.
Methods
The relationships of LKB1 expression to clinic-pathological parameters and epithelial markers E-cadherin and high-molecular-weight -cytokeratin (HMW-CK) were investigated in 80 clinical breast cancer tissue samples and their paired normal control breast tissue samples by using immunohistochemistry. Then, the LKB1 expressions in metastatic and non-metastatic breast cancer cell lines were compared. The roles of LKB1 in cell polarity and epithelial-mesenchymal transition in breast cancer were determined by using immunofluorescence, western blot assay, and cell migration and invasive assays. Finally, the non-transformed human breast cell line MCF-10A was cultured in three dimensions to further reveal the role of LKB1 in breast epithelial cell polarity maintenance.
Results
Histopathological analysis showed that LKB1 expression level was significantly negatively correlated with breast cancer TNM stage, and positively correlated with ER/PR status and expression levels of E-cadherin and HMW-CK. Immunofluorescence staining showed that LKB1 was co-localized with E-cadherin at adheren junctions. In vitro analysis revealed that loss of LKB1 expression enhanced migration, invasion and the acquisition of mesenchymal phenotype, while LKB1 overexpression in MDA-MB-435 s cells, which have a low basal level of LKB1 expression, promoted the acquisition of epithelial phenotype. Finally, it was found for the first time that endogenous LKB1 knockdown resulted in abnormal cell polarity in acini formed by non-transformed breast epithelial cells grown in 3D culture.
Conclusion
Our data indicated that low expression of LKB1 was significantly associated with established markers of unfavorable breast cancer prognosis, such as loss of ER/PR, E-cadherin and HMW-CK. Knockdown of endogenous LKB1 gave rise to dysregulation of cell polarity and invasive phenotype of breast cancer cells.
doi:10.1186/s13046-014-0070-0
PMCID: PMC4431490  PMID: 25178656
LKB1; Breast cancer; Cell polarity; Metastasis; Invasion
17.  Autoantibody response to a novel tumor-associated antigen p90/CIP2A in breast cancer immunodiagnosis 
There is an urgent need to identify relevant tumor markers showing high sensitivity and specificity for early immunodiagnosis of breast cancer. Autoantibodies directed against tumor-associated antigens (TAAs) have been shown to be relevant tumor markers. The purpose of this study was to evaluate whether autoantibodies to a tumor-associated antigen p90/CIP2A can be used as diagnostic markers in breast cancer. In this study, autoantibody responses to p90/CIP2A were evaluated by enzyme-linked immunosorbent assay (ELISA), western blotting, and indirect immunofluorescence assay in sera from patients with breast cancer and normal human individuals. The results have demonstrated that p90/CIP2A can induce a relatively higher frequency of autoantibody response in breast cancer (19.1 %) compared to the sera of normal individuals (2.3 %). The frequency of p90/CIP2A expression in breast cancer tissues was significantly higher than that in adjacent normal tissues (P <0.01). Our preliminary results suggest that autoantibodies against p90/CIP2A may be a useful serum biomarker for early stage breast cancer screening and diagnosis.
doi:10.1007/s13277-013-1350-6
PMCID: PMC4096571  PMID: 24399648
Breast cancer; p90/CIP2A; Immunodiagnosis; Tumor-associated antigen
18.  MicroRNA-410 Reduces the Expression of Vascular Endothelial Growth Factor and Inhibits Oxygen-Induced Retinal Neovascularization 
PLoS ONE  2014;9(4):e95665.
Retinal neovascularization (RNV) is an eye disease that can cause retinal detachment and even lead to blindness. RNV mainly occurs in the elderly population. The pathogenesis of RNV has been previously reported to be highly related to the expression of vascular endothelial growth factor A (VEGFA), basic fibroblast growth factor (bFGF) and other angiogenic factors. It has also been reported that VEGFA and other factors associated with RNV could be regulated by certain microRNAs (miRNA), a group of small non-coding RNAs which are able to regulate the expression of many genes in vivo. Here, we demonstrate that the miRNA miR-410 is highly expressed in mice within two weeks after birth. miR-410 could suppress VEGFA expression through interaction with the 3′UTR of the VEGFA messenger RNA. Overexpressing a miR-410 mimic effectively suppresses VEGFA expression in various cell lines. Further experiments on oxygen-induced retinopathy (OIR) in mice revealed that eye drops containing large amounts of miR-410 efficiently downregulate VEGFA expression, prevent retinal angiogenesis and effectively treat RNV. These results not only show the underlying mechanism of how miR-410 targets VEGFA but also provide a potential treatment strategy for RNV that might be used in the near future.
doi:10.1371/journal.pone.0095665
PMCID: PMC4002426  PMID: 24777200
19.  Humoral Autoimmune Responses to Insulin-Like Growth Factor II mRNA-Binding Proteins IMP1 and p62/IMP2 in Ovarian Cancer 
Journal of Immunology Research  2014;2014:326593.
Ovarian cancer is one of the leading causes of cancer-related deaths among women. There is an urgent need of better approaches for the identification of appropriate biomarkers in the early detection of ovarian cancer. The aim of this study was to elucidate the significance of autoantibodies against insulin-like growth factor II mRNA-binding proteins (IMPs) in patients with ovarian cancer. In this study, autoantibody responses to two members (IMP1 and p62/IMP2) of IMPs were evaluated by enzyme-linked immunosorbent assay (ELISA), western blotting, and indirect immunofluorescence assay in sera from patients with ovarian cancer and normal human individuals. The results have demonstrated that both IMP1 and p62/IMP2 can induce relatively higher frequency of autoantibody responses in patients with ovarian cancer (26.5% and 29.4%) compared to normal individuals (P < 0.01). Our preliminary data suggest that IMP1 and p62/IMP2 can stimulate autoimmune responses in ovarian cancer, and anti-IMP1 and anti-p62/IMP2 autoantibodies could be used as potential biomarkers in immunodiagnosis of ovarian cancer.
doi:10.1155/2014/326593
PMCID: PMC4020369  PMID: 24872956
20.  CMTM3 Inhibits Human Testicular Cancer Cell Growth through Inducing Cell-Cycle Arrest and Apoptosis 
PLoS ONE  2014;9(2):e88965.
Human CMTM3 has been proposed as a putative tumor suppressor gene. The loss of CMTM3 has been found in several carcinomas. However, the regulation of CMTM3 expression and its function in tumor progression remain largely unknown. Here, we investigated the regulation of CMTM3 expression, function and molecular mechanism in human testicular cancer cells. CMTM3 was frequently downregulated or silenced in testicular cancer cell lines and tumor tissues but highly expressed in normal testis tissues. The re-expression of CMTM3 significantly suppressed the colony formation, proliferation, and migration capacity of testicular cancer cells by inducing a G2 cell cycle arrest and apoptosis. Moreover, the re-expression of CMTM3 activated the transcription of p53, induced p53 accumulation, up-regulated the expression of p21, and increased the cleavage of caspase 9, 8, 3, and PARP. The downregulation of CMTM3 in clinical tumor tissues was associated with the methylation of a single CpG site located within the Sp1/Sp3-responsive region of the core promoter. These results indicate that CMTM3 can function as tumor suppressor through the induction of a G2 cell cycle arrest and apoptosis. CMTM3 is thus involved in testicular cancer pathogenesis, and it is frequently at least partially silenced by the methylation of a single, specific CpG site in tumor tissues.
doi:10.1371/journal.pone.0088965
PMCID: PMC3938458  PMID: 24586462
21.  Hemostatic gelatin sponge is a superior matrix to Matrigel for establishment of LNCaP human prostate cancer in nude mice* 
The Prostate  2012;72(15):1669-1677.
Background
Matrigels, solubilized basement membrane preparations, are often used to support tumor development in animal models. However, tumors formed by a mixture of tumor cells and Matrigel may vary significantly. The purpose of this study was to compare tumor development and growth of LNCaP human prostate cancer cells mixed with Matrigel or in gelatin sponges.
Methods
LNCaP cells were mixed with Matrigel or absorbed into VETSPON, a gelatin sponge, and inoculated into the subcutis of nude mice. Tumor incidence and growth rate were determined. Gene expression and cell growth and survival in tumor lesions were evaluated by immunohistochemistry (IHC), immunoblotting, and RT-PCR.
Results
All mice (12/12) inoculated with LNCaP cells in VETSPON produced tumors, compared to 70% (19/27) of mice injected with the cells with Matrigel. Tumor volume also varied less with VETSPON implants. No significant differences were observed in gene expression, cell growth, apoptosis, and microvessel density in tumors established from the two types of implants. However, in samples collected on days 1 and 4, more cells in Matrigel implants than those in VETSPON implants were stained positive for cleaved-caspase 3 and -PARP1. Expression of VEGF-A, HIF-1α, and Bcl-2 was elevated in the early VETSPON implants.
Conclusion
These data indicate that VETSPON promotes tumor cell survival at the early stage of implantation and suggest that the gelatin sponge is superior to Matrigel in supporting development and progression of human prostate cancer in nude mice. This model should be useful for preclinical studies in nude mice using LNCaP cells.
doi:10.1002/pros.22520
PMCID: PMC3445655  PMID: 22473906
Prostate cancer; Matrigel; hemostatic gelatin sponge; VETSPON; animal model
22.  Optimal dose of zinc supplementation for preventing aluminum-induced neurotoxicity in rats 
Neural Regeneration Research  2013;8(29):2754-2762.
Zinc supplementation can help maintain learning and memory function in rodents. In this study, we hypothesized that zinc supplementation could antagonize the neurotoxicity induced by aluminum in rats. Animals were fed a diet containing different doses of zinc (50, 100, 200 mg/kg) for 9 weeks, and orally administered aluminum chloride (300 mg/kg daily) from the third week for 7 consecutive weeks. Open-field behavioral test results showed that the number of rearings in the group given the 100 mg/kg zinc supplement was significantly increased compared with the group given the 50 mg/kg zinc supplement. Malondialdehyde content in the cerebrum was significantly decreased, while dopamine and 5-hydroxytryptamine levels were increased in the groups given the diet supplemented with 100 and 200 mg/kg zinc, compared with the group given the diet supplemented with 50 mg/kg zinc. The acetylcholinesterase activity in the cerebrum was significantly decreased in the group given the 100 mg/kg zinc supplement. Hematoxylin-eosin staining revealed evident pathological damage in the hippocampus of rats in the group given the diet supplemented with 50 mg/kg zinc, but the damage was attenuated in the groups given the diet supplemented with 100 and 200 mg/kg zinc. Our findings suggest that zinc is a potential neuroprotective agent against aluminum-induced neurotoxicity in rats, and the optimal dosages are 100 and 200 mg/kg.
doi:10.3969/j.issn.1673-5374.2013.29.007
PMCID: PMC4145991  PMID: 25206586
neural regeneration; brain injury; aluminum; zinc; trace elements; behavior; pathology; cerebrum; malondialdehyde; superoxide dismutase; acetylcholinesterase; dopamine; grants-supported paper; neuroregeneration
23.  Chikungunya virus with E1-A226V mutation causing two outbreaks in 2010, Guangdong, China 
Virology Journal  2013;10:174.
Background
CHIKV is a mosquito-borne emerging pathogen that has a major health impact in humans in tropical zones around the globe. A new variant of the virus, E1-A226V caused a large outbreak in the Indian Ocean islands and India from 2004–2007. CHIKV outbreak was initially reported in Dongguan region of Guangdong in 2010 in China, another smaller CHIKV outbreak was found in Yangjiang region of Guangdong two weeks later. The viral agent causing the two outbreaks was inferred to be the new E1-A226V variant and Yangjiang CHIKV might be introduced from Dongguan. To confirm the hypothesis and determine the origin of CHIKV causing the outbreaks, we described Yangjiang outbreak in this study, and the molecular characterization of CHIKV from Yangjiang and Dongguang outbreaks were analyzed.
Results
27 clinical cases of CHIK fever were reported in outbreak in Yangjiang region. Sera sample from 12 clinical cases were collected from the outbreak, and nucleic acid and antibody tests for CHIKV were performed using Real-time RT-PCR and indirect immunofluorescence. Positive samples of Real-time RT-PCR were subjected to viral isolation. The results showed 3/12 samples positive for Real-time RT-PCR. 7/12 and 4/12 samples were positive for IgM and IgG against CHIKV respectively, two virus strains were isolated. Four viral genomes from Dongguan and Yangjiang were sequenced, characterized and phylogeneticly analyzed. Phylogenetic analysis revealed that the four seqeunced viruses had the closest relationship (99.4~99.6% identify) with the Singapore 2008 isolate belonging to the Indian ocean clade. A common mutation at the site of the E1-A226V was observed among four viruses. Four and three aa substitutions were detected in the CHIKV sequence from the Dongguan and Yangjiang outbreak strains respectively.
Conclusion
CHIKV with an E1-A226V mutation that originated from Southeast Asia isolates caused two outbreaks in China in 2010, and originated from two different infectious sources.
doi:10.1186/1743-422X-10-174
PMCID: PMC3691762  PMID: 23725047
Chikungunya virus; Chikungunya fever; Phylogenetic analysis; Molecular epidemiology
24.  NAC changes the course of cerebral small vessel disease in SHRSP and reveals new insights for the meaning of stases - a randomized controlled study 
Background
N-Acetylcystein (NAC) reduces the reperfusion injury and infarct size in experimental macroangiopathic stroke. Here we now investigate the impact of NAC on the development of the histopathology of microangiopathic cerebrovascular disease including initial intravasal erythrocyte accumulations, blood–brain-barrier (BBB)-disturbances, microbleeds and infarcts.
Methods
Spontaneously Hypertensive Stroke-Prone Rats (SHRSP) were treated with NAC (12 mg/kg body weight, daily oral application for three to 30 weeks) and compared to untreated SHRSP. In all rats the number of microbleeds, thromboses, infarcts and stases were quantified by HE-staining. Exemplary brains were stained against von Willebrand factor (vWF), IgG, Glutathione and GFAP.
Results
NAC animals exhibited significant more microbleeds, a greater number of vessels with BBB-disturbances, but also an elevation of Glutathione-levels in astrocytes surrounding small vessels. NAC-treatment reduced the numbers of thromboses, infarcts and arteriolar stases.
Conclusions
NAC reduces the frequency of thromboses and infarcts to the expense of an increase of small microbleeds in a rat model of microangiopathic cerebrovascular disease. We suppose that NAC acts via an at least partial inactivation of vWF resulting in an insufficient sealing of initial endothelial injury leading to more small microbleeds. By elevating Glutathione-levels NAC most likely exerts a radical scavenger function and protects small vessels against extended ruptures and subsequent infarcts. Finally, it reveals that stases are mainly caused by endothelial injuries and restricted thromboses.
doi:10.1186/2040-7378-5-5
PMCID: PMC3661381  PMID: 23587288
Animal model; Blood–brain barrier; Cerebral microbleed; Cerebral small vessel disease; von Willebrand factor
25.  Expression of protein tyrosine kinase 6 (PTK6) in nonsmall cell lung cancer and their clinical and prognostic significance 
OncoTargets and therapy  2013;6:183-188.
Aim:
The aim of the study was to validate the expression of protein tyrosine kinase 6 (PTK6) in nonsmall cell lung cancer (NSCLC), and to evaluate its clinicopathological and prognostic significance.
Methods:
We first conducted a meta-analysis on the mRNA profiling data sets of NSCLC in the Oncomine database. Then, one of the most significantly upregulated tyrosine kinase targets, PTK6, was further validated by immunohistochemistry in 104 primary NSCLC tumors. Furthermore the association between PTK6 expression, the clinical parameters, and overall survival was further analyzed.
Results:
Using the Oncomine database, we identified a list of tyrosine kinase genes related to NSCLC, among which PTK6 was the second most overexpressed gene (median rank = 915, P = 2.9 × 10−5). We further confirmed that NSCLC tumors had a higher expression level of PTK6 than normal pulmonary tissues. Moreover, high PTK6 expression correlated positively with shorter overall survival time, but not with other clinicopathological characteristics. In the multivariate Cox regression model, high PTK6 expression was demonstrated to be an independent prognostic factor for NSCLC patients.
Conclusion:
Our results validated that PTK6 was found to be overexpressed in a proportion of NSCLC samples, and was associated with a poor prognosis, suggesting that this subgroup of NSCLC patients might benefit from PTK6 inhibitors in the future.
doi:10.2147/OTT.S41283
PMCID: PMC3596122  PMID: 23525678
nonsmall cell lung cancer; tyrosine kinase; PTK6; target; prognosis

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