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1.  Platelet-Derived Growth Factor Receptor Beta: A Novel Urinary Biomarker for Recurrence of Non-Muscle-Invasive Bladder Cancer 
PLoS ONE  2014;9(5):e96671.
Non-muscle-invasive bladder cancer (NMIBC) is one of the most common malignant tumors in the urological system with a high risk of recurrence, and effective non-invasive biomarkers for NMIBC relapse are still needed. The human urinary proteome can reflect the status of the microenvironment of the urinary system and is an ideal source for clinical diagnosis of urinary system diseases. Our previous work used proteomics to identify 1643 high-confidence urinary proteins in the urine from a healthy population. Here, we used bioinformatics to construct a cancer-associated protein-protein interaction (PPI) network comprising 16 high-abundance urinary proteins based on the urinary proteome database. As a result, platelet-derived growth factor receptor beta (PDGFRB) was selected for further validation as a candidate biomarker for NMIBC diagnosis and prognosis. Although the levels of urinary PDGFRB showed no significant difference between patients pre- and post-surgery (n = 185, P>0.05), over 3 years of follow-up, urinary PDGFRB was shown to be significantly higher in relapsed patients (n = 68) than in relapse-free patients (n = 117, P<0.001). The levels of urinary PDGFRB were significantly correlated with the risk of 3-year recurrence of NMIBC, and these levels improved the accuracy of a NMIBC recurrence risk prediction model that included age, tumor size, and tumor number (area under the curve, 0.862; 95% CI, 0.809 to 0.914) compared to PDGFR alone. Therefore, we surmise that urinary PDGFRB could serve as a non-invasive biomarker for predicting NMIBC recurrence.
doi:10.1371/journal.pone.0096671
PMCID: PMC4011858  PMID: 24801713
2.  Genome Sequence of the Octopine-Type Agrobacterium tumefaciens Strain Ach5 
Genome Announcements  2014;2(2):e00225-14.
We have sequenced the complete genome of the plant pathogen Agrobacterium tumefaciens strain LBA4213, a derivative of the wild-type strain A. tumefaciens Ach5 and the ancestor of A. tumefaciens strain LBA4404 used in genetic engineering. The genome consists of a circular chromosome and a linear chromosome, as well as a megaplasmid and a tumor-inducing plasmid.
doi:10.1128/genomeA.00225-14
PMCID: PMC3968341  PMID: 24675863
3.  Efficient Reprogramming of Naïve-Like Induced Pluripotent Stem Cells from Porcine Adipose-Derived Stem Cells with a Feeder-Independent and Serum-Free System 
PLoS ONE  2014;9(1):e85089.
Induced pluripotent stem cells (iPSCs) are somatic cells reprogrammed by ectopic expression of transcription factors or small molecule treatment, which resemble embryonic stem cells (ESCs). They hold great promise for improving the generation of genetically modified large animals. However, few porcine iPSCs (piPSCs) lines obtained currently can support development of cloned embryos. Here, we generated iPSCs from porcine adipose-derived stem cells (pADSCs), using drug-inducible expression of defined human factors (Oct4, Sox2, c-Myc and Klf4). Reprogramming of iPSCs from pADSCs was more efficient than from fibroblasts, regardless of using feeder-independent or feeder-dependent manners. By addition of Lif-2i medium containing mouse Lif, CHIR99021 and PD0325901 (Lif-2i), naïve-like piPSCs were obtained under feeder-independent and serum-free conditions. These successfully reprogrammed piPSCs were characterized by short cell cycle intervals, alkaline phosphatase (AP) staining, expression of Oct4, Sox2, Nanog, SSEA3 and SSEA4, and normal karyotypes. The resemblance of piPSCs to naïve ESCs was confirmed by their packed dome morphology, growth after single-cell dissociation, Lif-dependency, up-regulation of Stella and Eras, low expression levels of TRA-1-60, TRA-1-81 and MHC I and activation of both X chromosomes. Full reprogramming of naïve-like piPSCs was evaluated by the significant up-regulation of Lin28, Esrrb, Utf1 and Dppa5, differentiating into cell types of all three germ layers in vitro and in vivo. Furthermore, nuclear transfer embryos from naïve-like piPSCs could develop to blastocysts with improved quality. Thus, we provided an efficient protocol for generating naïve-like piPSCs from pADSCs in a feeder-independent and serum-free system with controlled regulation of exogenous genes, which may facilitate optimization of culture media and the production of transgenic pigs.
doi:10.1371/journal.pone.0085089
PMCID: PMC3896366  PMID: 24465482
4.  Immunization against recombinant GnRH-I alters ultrastructure of gonadotropin cell in an experimental boar model 
Background
Gonadotropin cell is the main responsible for the secretion of follicle stimulating hormone (FSH) and luteinizing hormone (LH), and immunocastration reduces the concentrations of serum FSH and LH. A few studies have reported the histological structure of gonadotropin cells obtained from immunocastration animals at the light microscopy level. However, the ultrastructure of gonadotropin cells remains largely unexplored. The aim of this study was to evaluate and to compare ultrastructure of gonadotropin cell in gonadally intact boars and immunologically castrated male animals.
Findings
In this study, serum and adenohypophysis tissue were collected from nine gonadally intact boars and nine male pigs treated with recombinant gonadotropin releasing hormone I (GnRH-I). Anti-GnRH-I antibodies in serum and the ultrastructure of gonadotropin cell in adenohypophysis were determined by enzymelinked immunosorbent assay and electron microscopy, respectively. The results demonstrated that active immunization against recombinant GnRH-I increased serum GnRH-I antibody levels (P<0.05). Ultramicroscopic analysis of gonadotropin cell revealed a decrease (P<0.05) in the number and size of the large granules and small granules in the recombinant GnRH-I immunized animals.
Conclusions
We conclude that immunization against recombinant GnRH-I induces severe atrophy of granules in gonadotropin cell of boars, possibly reflecting GnRH-I regulation of gonadotropin cell.
doi:10.1186/1477-7827-11-63
PMCID: PMC3720181  PMID: 23855561
Ultrastructure; Gonadotropin; Boar; Immunization; GnRH-I
5.  Promise of a Low Power Mobile CPU based Embedded System in Artificial Leg Control 
This paper presents the design and implementation of a low power embedded system using mobile processor technology (Intel Atom™ Z530 Processor) specifically tailored for a neural-machine interface (NMI) for artificial limbs. This embedded system effectively performs our previously developed NMI algorithm based on neuromuscular-mechanical fusion and phase-dependent pattern classification. The analysis shows that NMI embedded system can meet real-time constraints with high accuracies for recognizing the user's locomotion mode. Our implementation utilizes the mobile processor efficiently to allow a power consumption of 2.2 watts and low CPU utilization (less than 4.3%) while executing the complex NMI algorithm. Our experiments have shown that the highly optimized C program implementation on the embedded system has superb advantages over existing PC implementations on MATLAB. The study results suggest that mobile-CPU-based embedded system is promising for implementing advanced control for powered lower limb prostheses.
doi:10.1109/EMBC.2012.6347178
PMCID: PMC3676646  PMID: 23367113
Neural-machine interface; real-time system; embedded system; support vector machine; control of artificial limbs
6.  An Automatic and User-Driven Training Method for Locomotion Mode Recognition for Artificial Leg Control 
Our previously developed locomotion-mode-recognition (LMR) system has provided a great promise to intuitive control of powered artificial legs. However, the lack of fast, practical training methods is a barrier for clinical use of our LMR system for prosthetic legs. This paper aims to design a new, automatic, and user-driven training method for practical use of LMR system. In this method, a wearable terrain detection interface based on a portable laser distance sensor and an inertial measurement unit (IMU) is applied to detect the terrain change in front of the prosthesis user. The mechanical measurement from the prosthetic pylon is used to detect gait phase. These two streams of information are used to automatically identify the transitions among various locomotion modes, switch the prosthesis control mode, and label the training data with movement class and gait phase in real-time. No external device is required in this training system. In addition, the prosthesis user without assistance from any other experts can do the whole training procedure. The pilot experimental results on an able-bodied subject have demonstrated that our developed new method is accurate and user-friendly, and can significantly simplify the LMR training system and training procedure without sacrificing the system performance. The novel design paves the way for clinical use of our designed LMR system for powered lower limb prosthesis control.
doi:10.1109/EMBC.2012.6347389
PMCID: PMC3676647  PMID: 23367324
7.  A Special Purpose Embedded System for Neural Machine Interface for Artificial Legs 
This paper presents a design and implementation of a neural-machine interface (NMI) for artificial legs that can decode amputee’s intended movement in real time. The newly designed NMI integrates an FPGA chip for fast processing and a microcontroller unit (MCU) with multiple on-chip analog-to-digital converters (ADCs) for real-time data sampling. The resulting embedded system is able to sample in real time 12 EMG signals and 6 mechanical signals and execute a special complex phase-dependent classifier for accurate recognition of the user’s intended locomotion modes. The implementation and evaluation are based on Altera’s Stratix III 3S150 FPGA device coupled with Freescale’s MPC5566 MCU. The experimental results for classifying three locomotion modes (level-ground walking, stairs ascent, and stairs descent) based on data collected from an able-bodied human subject have shown acceptable performance for real-time controlling of artificial legs.
doi:10.1109/IEMBS.2011.6091288
PMCID: PMC3676650  PMID: 22255511
8.  Complete Genome Sequences of Two Newcastle Disease Virus Strains of Genotype VIII 
Genome Announcements  2013;1(1):e00180-12.
Here, the whole genome sequences of two Newcastle disease viruses (NDV) of genotype VIII, which were isolated from west China in the 1980s, were determined and characterized phylogenetically. This is the first report with respect to the complete genomic information of genotype VIII NDV strains.
doi:10.1128/genomeA.00180-12
PMCID: PMC3569313  PMID: 23409260
9.  Protection conferred by a recombinant Marek’s disease virus that expresses the spike protein from infectious bronchitis virus in specific pathogen-free chicken 
Virology Journal  2012;9:85.
Background
In many countries, the predominant field isolates of infectious bronchitis virus (IBV) have been classified as QX-like strains since 1996. However, no commercial vaccines that are specific for this type of IBV are currently available. Therefore, there is an urgent need to develop novel vaccines that prevent QX-like IBV infection.
Results
A recombinant Marek’s disease virus (MDV), rMDV-S1, that expresses the S1 subunit of the spike (S) protein from the QX-like infectious bronchitis virus (IBV) was constructed by inserting the IBV S1 gene into the genome of the CVI988/Rispens strain of MDV. Specific pathogen-free (SPF) chickens that were vaccinated with rMDV-S1 were protected when challenged with the QX-like IBV. They were observed to have mild clinical signs of disease, a short virus-shedding period and low mortality. Additionally, the rMDV-S1 conferred full protection to chickens against virulent MDV, as did the CVI988/Rispens strain.
Conclusions
Our results demonstrate that rMDV-S1 is an effective and promising recombinant vaccine for the prevention of QX-like IBV infection.
doi:10.1186/1743-422X-9-85
PMCID: PMC3447679  PMID: 22559869
Infectious bronchitis virus; Spike protein; Marek’s disease virus
10.  On Design and Implementation of Neural-Machine Interface for Artificial Legs 
The quality of life of leg amputees can be improved dramatically by using a cyber physical system (CPS) that controls artificial legs based on neural signals representing amputees’ intended movements. The key to the CPS is the neural-machine interface (NMI) that senses electromyographic (EMG) signals to make control decisions. This paper presents a design and implementation of a novel NMI using an embedded computer system to collect neural signals from a physical system - a leg amputee, provide adequate computational capability to interpret such signals, and make decisions to identify user’s intent for prostheses control in real time. A new deciphering algorithm, composed of an EMG pattern classifier and a post-processing scheme, was developed to identify the user’s intended lower limb movements. To deal with environmental uncertainty, a trust management mechanism was designed to handle unexpected sensor failures and signal disturbances. Integrating the neural deciphering algorithm with the trust management mechanism resulted in a highly accurate and reliable software system for neural control of artificial legs. The software was then embedded in a newly designed hardware platform based on an embedded microcontroller and a graphic processing unit (GPU) to form a complete NMI for real time testing. Real time experiments on a leg amputee subject and an able-bodied subject have been carried out to test the control accuracy of the new NMI. Our extensive experiments have shown promising results on both subjects, paving the way for clinical feasibility of neural controlled artificial legs.
doi:10.1109/TII.2011.2166770
PMCID: PMC3290414  PMID: 22389637
Neural-machine interface; prosthetics; high performance computer; trust management
11.  Characterization of Bovine Induced Pluripotent Stem Cells by Lentiviral Transduction of Reprogramming Factor Fusion Proteins 
Pluripotent stem cells from domesticated animals have potential applications in transgenic breeding. Here, we describe induced pluripotent stem (iPS) cells derived from bovine fetal fibroblasts by lentiviral transduction of Oct4, Sox2, Klf4 and c-Myc defined-factor fusion proteins. Bovine iPS cells showed typical colony morphology, normal karyotypes, stained positively for alkaline phosphatase (AP) and expressed Oct4, Nanog and SSEA1. The CpG in the promoter regions of Oct4 and Nanog were highly unmethylated in bovine iPS cells compared to the fibroblasts. The cells were able to differentiate into cell types of all three germ layers in vitro and in vivo. In addition, these cells were induced into female germ cells under defined culture conditions and expressed early and late female germ cell-specific genes Vasa, Dazl, Gdf9, Nobox, Zp2, and Zp3. Our data suggest that bovine iPS cells were generated from bovine fetal fibroblasts with defined-factor fusion proteins mediated by lentivirus and have potential applications in bovine transgenic breeding and gene-modified animals.
doi:10.7150/ijbs.3723
PMCID: PMC3314191  PMID: 22457605
bovine; fetal fibroblasts; iPS cells; defined-factor fusion proteins
12.  Roles of the spiA gene from Salmonella enteritidis in biofilm formation and virulence 
Microbiology  2011;157(Pt 6):1798-1805.
Salmonella enteritidis has emerged as one of the most important food-borne pathogens for humans, and the formation of biofilms by this species may improve its resistance to disadvantageous conditions. The spiA gene of Salmonella typhimurium is essential for its virulence in host cells. However, the roles of the spiA gene in biofilm formation and virulence of S. enteritidis remain unclear. In this study we constructed a spiA gene mutant with a suicide plasmid. Phenotypic and biological analysis revealed that the mutant was similar to the wild-type strain in growth rate, morphology, and adherence to and invasion of epithelial cells. However, the mutant showed reduced biofilm formation in a quantitative microtitre assay and by scanning electron microscopy, and significantly decreased curli production and intracellular proliferation of macrophages during the biofilm phase. In addition, the spiA mutant was attenuated in a mouse model in both the exponential growth and biofilm phases. These data indicate that the spiA gene is involved in both biofilm formation and virulence of S. enteritidis.
doi:10.1099/mic.0.046185-0
PMCID: PMC3167914  PMID: 21415117
13.  Dapdiamides, Tripeptide Antibiotics Formed by Unconventional Amide Ligases† 
Journal of Natural Products  2009;73(3):441-446.
Construction of a genomic DNA library from Pantoea agglomerans strain CU0119 and screening against the plant pathogen Erwinia amylovora yielded a new family of antibiotics, dapdiamides A−E (1−5). The structures were established through 2D-NMR experiments and mass spectrometry, as well as the synthesis of dapdiamide A (1). Transposon mutagenesis of the active cosmid allowed identification of the biosynthetic gene cluster. The dapdiamide family’s promiscuous biosynthetic pathway contains two unconventional amide ligases that are predicted to couple its constituent monomers.
doi:10.1021/np900685z
PMCID: PMC2846032  PMID: 20041689
14.  A Novel Genotype H9N2 Influenza Virus Possessing Human H5N1 Internal Genomes Has Been Circulating in Poultry in Eastern China since 1998 ▿ †  
Journal of Virology  2009;83(17):8428-8438.
Many novel reassortant influenza viruses of the H9N2 genotype have emerged in aquatic birds in southern China since their initial isolation in this region in 1994. However, the genesis and evolution of H9N2 viruses in poultry in eastern China have not been investigated systematically. In the current study, H9N2 influenza viruses isolated from poultry in eastern China during the past 10 years were characterized genetically and antigenically. Phylogenetic analysis revealed that these H9N2 viruses have undergone extensive reassortment to generate multiple novel genotypes, including four genotypes (J, F, K, and L) that have never been recognized before. The major H9N2 influenza viruses represented by A/Chicken/Beijing/1/1994 (Ck/BJ/1/94)-like viruses circulating in poultry in eastern China before 1998 have been gradually replaced by A/Chicken/Shanghai/F/1998 (Ck/SH/F/98)-like viruses, which have a genotype different from that of viruses isolated in southern China. The similarity of the internal genes of these H9N2 viruses to those of the H5N1 influenza viruses isolated from 2001 onwards suggests that the Ck/SH/F/98-like virus may have been the donor of internal genes of human and poultry H5N1 influenza viruses circulating in Eurasia. Experimental studies showed that some of these H9N2 viruses could be efficiently transmitted by the respiratory tract in chicken flocks. Our study provides new insight into the genesis and evolution of H9N2 influenza viruses and supports the notion that some of these viruses may have been the donors of internal genes found in H5N1 viruses.
doi:10.1128/JVI.00659-09
PMCID: PMC2738149  PMID: 19553328

Results 1-14 (14)