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author:("Li, pentaol")
1.  Insights into how Spt5 functions in transcription elongation and repressing transcription coupled DNA repair 
Nucleic Acids Research  2014;42(11):7069-7083.
Spt5, a transcription elongation factor, and Rpb4, a subunit of RNA polymerase II (RNAP II) that forms a subcomplex with Rpb7, play important roles in transcription elongation and repression of transcription coupled DNA repair (TCR) in eukaryotic cells. How Spt5 physically interacts with RNAP II, and if and/or how Spt5 and Rpb4/7 coordinate to achieve the distinctive functions have been enigmatic. By site-specific incorporation of the unnatural amino acid p-benzoyl-L-phenylalanine, a photoreactive cross-linker, we mapped interactions between Spt5 and RNAP II in Saccharomyces cerevisiae. Through its KOW4-5 domains, Spt5 extensively interacts with Rpb4/7. Spt5 also interacts with Rpb1 and Rpb2, two largest subunits of RNAP II, at the clamp, protrusion and wall domains. These interactions may lock the clamp to the closed conformation and enclose the DNA being transcribed in the central cleft of RNAP II. Deletion of Spt5 KOW4-5 domains decreases transcription elongation and derepresses TCR. Our findings suggest that Spt5 is a key coordinator for holding the RNAP II complex in a closed conformation that is highly competent for transcription elongation but repressive to TCR.
doi:10.1093/nar/gku333
PMCID: PMC4066765  PMID: 24813444
2.  Broad Activity against Porcine Bacterial Pathogens Displayed by Two Insect Antimicrobial Peptides Moricin and Cecropin B 
Molecules and Cells  2013;35(2):106-114.
In response to infection, insects produce a variety of antimicrobial peptides (AMPs) to kill the invading pathogens. To study their physicochemical properties and bioactivities for clinical and commercial use in the porcine industry, we chemically synthesized the mature peptides Bombyx mori moricin and Hyalophora cecropia cecropin B. In this paper, we described the antimicrobial activity of the two AMPs. Moricin exhibited antimicrobial activity on eight strains tested with minimal inhibitory concentration values (MICs) ranging between 8 and 128 μg/ml, while cecropin B mainly showed antimicrobial activity against the Gramnegative strains with MICs ranging from 0.5 to 16 μg/ml. Compared to the potent antimicrobial activity these two AMPs displayed against most of the bacterial pathogens tested, they exhibited limited hemolytic activity against porcine red blood cells. The activities of moricin and cecropin B against Haemophilus parasuis SH 0165 were studied in further detail. Transmission electron microscopy (TEM) of moricin and cecropin B treated H. parasuis SH 0165 indicated extensive damage to the membranes of the bacteria. Insights into the probable mechanism utilized by moricin and cecropin B to eliminate pathogens are also presented. The observations from this study are important for the future application of AMPs in the porcine industry.
doi:10.1007/s10059-013-2132-0
PMCID: PMC3887904  PMID: 23456332
antimicrobial peptide; cecropin B; Haemophilus parasuis SH 0165; moricin; transmission electron microscopy
3.  Computed tomography-guided core needle biopsy of lung lesions: Diagnostic yield and correlation between factors and complications 
Oncology Letters  2013;7(1):288-294.
The aim of the present study was to determine the diagnostic accuracy of computed tomography (CT)-guided core needle biopsy (CNB) and to retrospectively analyze the correlation between the factors and complications of the procedure. Between January 2009 and June 2010, CNB was performed on 345 lung lesions in 343 patients. These patients were then followed up for at least two years. The sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) of the CNB diagnoses were calculated. The correlation between factors, such as smoking, positoin and maximal diameter, and the complications of pneumothorax and hemorrhage was analyzed by χ2 test. The sensitivity, specificity, accuracy, PPV and NPV of the CNB diagnoses were 97.3, 100, 97.7, 100 and 87.7%, respectively. A statistically significant correlation was found between pneumothorax and the factors of smoking (P=0.015) and position (P<0.01) and length of the needle in the normal parenchyma (P=0.011), as well as between hemorrhage and the maximal diameter (P=0.005) and length of the needle in the normal parenchyma (P<0.01) and the frequency of needle adjustments (P<0.01). A CT-guided core needle biopsy of the lung lesions provides a high diagnostic yield. Smoking, the decubitus position and a longer length of the needle in the normal parenchyma were found to represent risk factors for a pneumothorax. In addition, a small diameter and longer length of the needle in the normal parenchyma and a more frequent adjustment of the needle were poor predictive factors of hemorrhage.
doi:10.3892/ol.2013.1680
PMCID: PMC3861590  PMID: 24348866
CT-guided; core needle biopsy; pneumothorax; hemorrhage; core needle biopsy diagnosis; final diagnosis
4.  Transcription analysis of the porcine alveolar macrophage response to porcine circovirus type 2 
BMC Genomics  2013;14:353.
Background
Porcine circovirus type 2 (PCV2) is the causal agent of postweaning multisystemic wasting syndrome (PMWS), which has severely impacted the swine industry worldwide. PCV2 triggers a weak and atypical innate immune response, but the key genes and mechanisms by which the virus interferes with host innate immunity have not yet been elucidated. In this study, genes that control the response of primary porcine alveolar macrophages (PAMs), the main target of PCV2, were profiled in vitro.
Results
PAMs were successfully infected by PCV2-WH strain, as evidenced quantitative real-time polymerase chain reaction (qPCR) and immunofluorescence assay (IFA) results. Infection-related differential gene expression was investigated using pig microarrays from the US Pig Genome Coordination Program and validated by real-time PCR and enzyme-linked immunosorbent assay (ELISA). Microarray analysis at 24 and 48 hours post-infection (HPI) revealed 266 and 175 unique genes, respectively, that were differentially expressed (false discovery rate <0.05; fold-change >2). Only six genes were differentially expressed between 24 and 48 HPI. The up-regulated genes were principally related to immune response, cytokine activity, locomotion, regulation of cell proliferation, apoptosis, cell growth arrest, and antigen procession and presentation. The down-regulated genes were mainly involved in terpenoid biosynthesis, carbohydrate metabolism, translation, proteasome degradation, signal transducer activity, and ribosomal proteins, which were representative of the reduced vital activity of PCV2-infected cells.
Conclusions
PCV2 infection of PAMs causes up-regulation of genes related to inflammation, indicating that PCV2 may induce systematic inflammation. PCV2 persistently induced cytokines, mainly through the Toll-like receptor (TLR) 1 and TLR9 pathways, which may promote high levels of cytokine secretion. PCV2 may prevent apoptosis in PAMs by up-regulating SERPINB9 expression, possibly to lengthen the duration of PCV2 replication-permissive conditions. The observed gene expression profile may provide insights into the underlying immunological response and pathological changes that occur in pigs following PCV2 infection.
doi:10.1186/1471-2164-14-353
PMCID: PMC3680065  PMID: 23711280
5.  Efficacy of single dose of an inactivated porcine circovirus type 2 (PCV2) whole-virus vaccine with oil adjuvant in piglets 
Background
Post-weaning multisystemic wasting syndrome (PMWS) associated with PCV2 is one of the most costly diseases currently faced by the swine industry. The development of effective vaccines against PCV2 infection has been accepted as an important strategy in the prophylaxis of PMWS.
Methods
In the present study, a PK-15 cell-adapted formalin-inactivated prototype vaccine candidate was prepared using a strain of PCV2 from China. Inactivation of the virus was accomplished using a standard formalin inactivation protocol. The protective properties of the inactivated PCV2 vaccine were evaluated in piglets. Ten 28-day-old pigs were randomly assigned to two groups, each with five. Group 1 was vaccinated intramuscularly with the inactivated virus preparation; Group 2 received sterile PBS as a placebo. By 28 days post-vaccination (DPV), Groups 1 and 2 were challenged intranasally and intramuscularly with 5 × 107 TCID50 of a virulent PCV2 isolate.
Results
The vaccinated pigs seroconverted to PCV2 and had high levels of serum antibodies to PCV2 at 28 days after vaccination, whereas the control pigs remained seronegative. No significant signs of clinical disease were recorded following the challenge with PCV2, but moderate amounts of PCV2 antigen were detected in most lymphoid organs of the control pigs. PCV2 was detected in two out of the five vaccinated pigs. Furthermore, pathological lesions and viremia were milder in the vaccinated group.
Conclusions
The obtained results indicate that the inactivated PCV2 virus vaccine with an oil adjuvant induce an immunological response in pigs that appears to provide protection from infection with PCV2. The vaccine, therefore, may have the potential to serve as a vaccine aimed to protect pigs from developing PMWS.
doi:10.1186/1751-0147-54-67
PMCID: PMC3539982  PMID: 23171757
Porcine circovirus type 2; Post-weaning multisystemic wasting syndrome; Single-dose immunization; Formalin-inactivated vaccine
6.  Design and Synthesis of Benzenesulfonamide Derivatives as Potent Anti-Influenza Hemagglutinin Inhibitors 
ACS Medicinal Chemistry Letters  2011;2(8):603-607.
Structural optimization of salicylamide-based hemagglutinin (HA) inhibitor 1 resulted in the identification of cis-3-(5-hydroxy-1,3,3-trimethylcyclohexylmethylamino)benzenesulfonamide 28 and its derivatives as potent anti-influenza agents. The lead compound 28 and its 2-chloro analogue 40 can effectively prevent cytopathic effects (CPE) caused by infection of influenza A/Weiss/43 strain (H1N1) with EC50 values of 210 and 86 nM, respectively. Mechanism of action studies indicate that 40 and its analogues inhibit the virus fusion with host endosome membrane by binding to HA and stabilizing the prefusion HA structure. With significantly improved metabolic stability, the reported series represents the first generation of orally bioavailable HA inhibitors that have a good selectivity window and potential for further development as novel anti-influenza agents.
doi:10.1021/ml2000627
PMCID: PMC4018120  PMID: 24900355
Anti-influenza; hemagglutinin; benzenesulfonamide; inhibitor
7.  New Variants of Porcine Epidemic Diarrhea Virus, China, 2011 
Emerging Infectious Diseases  2012;18(8):1350-1353.
In 2011, porcine epidemic diarrhea virus (PEDV) infection rates rose substantially in vaccinated swine herds. To determine the distribution profile of PEDV outbreak strains, we sequenced the full-length spike gene from samples from 9 farms where animals exhibited severe diarrhea and mortality rates were high. Three new PEDV variants were identified.
doi:10.3201/eid1808.120002
PMCID: PMC3414035  PMID: 22840964
porcine epidemic diarrhea virus; prevalence; China; phylogeny; variant strain; viruses
8.  Combination of CT-guided hookwire localization and video-assisted thoracoscopic surgery for pulmonary nodular lesions: Analysis of 103 patients 
Oncology Letters  2012;4(4):824-828.
At present, there is no standardized method for the diagnosis and management of pulmonary nodular lesions (PNLs) smaller than 3 cm. This study investigated the use of computed tomography (CT)-guided hookwire localization and video-assisted thoracoscopic surgery (VATS) for PNLs. A total of 103 patients undergoing CT-guided hook-wire localization and VATS were enrolled, and 107 lesions were collected. We assessed the localization achievement ratio, complications rate, conversion thoracotomy rate, intraoperative dislodgement rate, pathological diagnosis rate, duration of surgery and average days of hospitalization. All 107 nodules from 103 patients were successfully localized (100%), the asymptomatic pneumothorax rate was 36.9%, the asymptomatic hemorrhage rate was 40.8% and the simultaneous pneumothorax and hemorrhage rate was 8.7%. A conversion thoracotomy was required in 2 (1.9%) patients and the intraoperative dislodgement rate was 2.9%. The average time for localization was 11±4 min, and the average times for wedge resection and lobectomies were 16±2 and 95±30 min, respectively. The mean hospitalization time following the surgery was 6±3 days. All 107 nodules managed to achieve pathological diagnoses. A combination of CT-guided hook-wire localization and VATS for PNL is a safe and efficient procedure of great clinical value.
doi:10.3892/ol.2012.800
PMCID: PMC3506590  PMID: 23205107
pulmonary nodular lesions; ground-glass nodules; hookwire system; video-assisted thoracoscopic surgery
9.  Transcription analysis on response of porcine alveolar macrophages to Haemophilus parasuis 
BMC Genomics  2012;13:68.
Background
Haemophilus parasuis (H. parasuis) is the etiological agent of Glässer's disease in pigs. Currently, the molecular basis of this infection is largely unknown. The innate immune response is the first line of defense against the infectious disease. Systematical analysis on host innate immune response to the infection is important for understanding the pathogenesis of the infectious microorganisms.
Results
A total of 428 differentially expressed (DE) genes were identified in the porcine alveolar macrophages (PAMs) 6 days after H. parasuis infection. These genes were principally related to inflammatory response, immune response, microtubule polymerization, regulation of transcript and signal transduction. Through the pathway analysis, the significant pathways mainly concerned with cell adhesion molecules, cytokine-cytokine receptor interaction, complement and coagulation cascades, toll-like receptor signaling pathway, MAPK signaling pathway, suggesting that the host took different strategies to activate immune and inflammatory response upon H. parasuis infection. The global interactions network and two subnetworks of the proteins encoded by DE genes were analyzed by using STRING. Further immunostimulation analysis indicated that mRNA levels of S100 calcium-binding protein A4 (S100A4) and S100 calcium-binding protein A6 (S100A6) in porcine PK-15 cells increased within 48 h and were sustained after administration of lipopolysaccharide (LPS) and Poly (I:C) respectively. The s100a4 and s100a6 genes were found to be up-regulated significantly in lungs, spleen and lymph nodes in H. parasuis infected pigs. We firstly cloned and sequenced the porcine coronin1a gene. Phylogenetic analysis showed that poCORONIN 1A belonged to the group containing the Bos taurus sequence. Structural analysis indicated that the poCORONIN 1A contained putative domains of Trp-Asp (WD) repeats signature, Trp-Asp (WD) repeats profile and Trp-Asp (WD) repeats circular profile at the N-terminus.
Conclusions
Our present study is the first one focusing on the response of porcine alveolar macrophages to H. parasuis. Our data demonstrate a series of genes are activated upon H. parasuis infection. The observed gene expression profile could help screening the potential host agents for reducing the prevalence of H. parasuis and further understanding the molecular pathogenesis associated with H. parasuis infection in pigs.
doi:10.1186/1471-2164-13-68
PMCID: PMC3296652  PMID: 22330747
10.  Use of a radiopaque localizer grid to reduce radiation exposure 
Background
Minimally invasive spine surgery requires placement of the skin incision at an ideal location in the patient's back by the surgeon. However, numerous fluoroscopic x-ray images are sometimes required to find the site of entry, thereby exposing patients and Operating Room personnel to additional radiation. To minimize this exposure, a radiopaque localizer grid was devised to increase planning efficiency and reduce radiation exposure.
Results
The radiopaque localizer grid was utilized to plan the point of entry for minimally invasive spine surgery. Use of the grid allowed the surgeon to accurately pinpoint the ideal entry point for the procedure with just one or two fluoroscopic X-ray images.
Conclusions
The reusable localizer grid is a simple and practical device that may be utilized to more efficiently plan an entry site on the skin, thus reducing radiation exposure. This device or a modified version may be utilized for any procedure involving the spine.
doi:10.1186/1750-1164-5-6
PMCID: PMC3177900  PMID: 21827694
Radiation; Exposure; Minimally Invasive; Spine Surgery; Localization; Innovation; Grid

Results 1-10 (10)