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Search Results: 1 - 10 of 126823 matches for " Shisheng Li "
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Implication of Posttranslational Histone Modifications in Nucleotide Excision Repair
Shisheng Li
International Journal of Molecular Sciences , 2012, DOI: 10.3390/ijms131012461
Abstract: Histones are highly alkaline proteins that package and order the DNA into chromatin in eukaryotic cells. Nucleotide excision repair (NER) is a conserved multistep reaction that removes a wide range of generally bulky and/or helix-distorting DNA lesions. Although the core biochemical mechanism of NER is relatively well known, how cells detect and repair lesions in diverse chromatin environments is still under intensive research. As with all DNA-related processes, the NER machinery must deal with the presence of organized chromatin and the physical obstacles it presents. A huge catalogue of posttranslational histone modifications has been documented. Although a comprehensive understanding of most of these modifications is still lacking, they are believed to be important regulatory elements for many biological processes, including DNA replication and repair, transcription and cell cycle control. Some of these modifications, including acetylation, methylation, phosphorylation and ubiquitination on the four core histones (H2A, H2B, H3 and H4) or the histone H2A variant H2AX, have been found to be implicated in different stages of the NER process. This review will summarize our recent understanding in this area.
Two Glycosylation Sites in H5N1 Influenza Virus Hemagglutinin That Affect Binding Preference by Computer-Based Analysis
Wentian Chen, Shisheng Sun, Zheng Li
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0038794
Abstract: Increasing numbers of H5N1 influenza viruses (IVs) are responsible for human deaths, especially in North Africa and Southeast Asian. The binding of hemagglutinin (HA) on the viral surface to host sialic acid (SA) receptors is a requisite step in the infection process. Phylogenetic analysis reveals that H5N1 viruses can be divided into 10 clades based on their HA sequences, with most human IVs centered from clade 1 and clade 2.1 to clade 2.3. Protein sequence alignment in various clades indicates the high conservation in the receptor-binding domains (RBDs) is essential for binding with the SA receptor. Two glycosylation sites, 158N and 169N, also participate in receptor recognition. In the present work, we attempted to construct a serial H5N1 HA models including diverse glycosylated HAs to simulate the binding process with various SA receptors in silico. As the SA-α-2,3-Gal and SA-α-2,6-Gal receptor adopted two distinctive topologies, straight and fishhook-like, respectively, the presence of N-glycans at 158N would decrease the affinity of HA for all of the receptors, particularly SA-α-2,6-Gal analogs. The steric clashes of the huge glycans shown at another glycosylation site, 169N, located on an adjacent HA monomer, would be more effective in preventing the binding of SA-α-2,3-Gal analogs.
Double Cladding Seven-core Photonic Crystal Fiber  [PDF]
Gelin Zhang, Fengfei Xing, Peiguang Yan, Huifeng Wei, Huiquan Li, Shisheng Huang, Rongyong Lin, Kangkang Chen
Optics and Photonics Journal (OPJ) , 2013, DOI: 10.4236/opj.2013.32B011

A double cladding seven-core PCF was presented for high power supercontinuum generation. The calculated zero dispersion wavelength is located at 912 nm, which has a good agreement with the measurement. The attenuation is measured 6 dB/km at 1590 nm and lower than 14.5 dB/km at 1060 nm, the water-loss peak at 1380 nm is about 134 dB/km; Supercontinuum spanning over more than 1500 nm was generated when the designed seven-core PCF was pumped by a gain-switching Yetterbium-doped fiber laser. These results will be helpful in the future design of multicore photonic crystal fibers (MCPCF) with proper guidance properties for high power supercontinuum generation.

Prediction of Biological Functions on Glycosylation Site Migrations in Human Influenza H1N1 Viruses
Shisheng Sun, Qinzhe Wang, Fei Zhao, Wentian Chen, Zheng Li
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0032119
Abstract: Protein glycosylation alteration is typically employed by various viruses for escaping immune pressures from their hosts. Our previous work had shown that not only the increase of glycosylation sites (glycosites) numbers, but also glycosite migration might be involved in the evolution of human seasonal influenza H1N1 viruses. More importantly, glycosite migration was likely a more effectively alteration way for the host adaption of human influenza H1N1 viruses. In this study, we provided more bioinformatics and statistic evidences for further predicting the significant biological functions of glycosite migration in the host adaptation of human influenza H1N1 viruses, by employing homology modeling and in silico protein glycosylation of representative HA and NA proteins as well as amino acid variability analysis at antigenic sites of HA and NA. The results showed that glycosite migrations in human influenza viruses have at least five possible functions: to more effectively mask the antigenic sites, to more effectively protect the enzymatic cleavage sites of neuraminidase (NA), to stabilize the polymeric structures, to regulate the receptor binding and catalytic activities and to balance the binding activity of hemagglutinin (HA) with the release activity of NA. The information here can provide some constructive suggestions for the function research related to protein glycosylation of influenza viruses, although these predictions still need to be supported by experimental data.
The Evolutionary Pattern of Glycosylation Sites in Influenza Virus (H5N1) Hemagglutinin and Neuraminidase
Wentian Chen, Yaogang Zhong, Yannan Qin, Shisheng Sun, Zheng Li
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049224
Abstract: Two glycoproteins, hemagglutinin (HA) and neuraminidase (NA), on the surface of influenza viruses play crucial roles in transfaunation, membrane fusion and the release of progeny virions. To explore the distribution of N-glycosylation sites (glycosites) in these two glycoproteins, we collected and aligned the amino acid sequences of all the HA and NA subtypes. Two glycosites were located at HA0 cleavage sites and fusion peptides and were strikingly conserved in all HA subtypes, while the remaining glycosites were unique to their subtypes. Two to four conserved glycosites were found in the stalk domain of NA, but these are affected by the deletion of specific stalk domain sequences. Another highly conserved glycosite appeared at the top center of tetrameric global domain, while the others glycosites were distributed around the global domain. Here we present a detailed investigation of the distribution and the evolutionary pattern of the glycosites in the envelope glycoproteins of IVs, and further focus on the H5N1 virus and conclude that the glycosites in H5N1 have become more complicated in HA and less influential in NA in the last five years.
Rpb1 Sumoylation in Response to UV Radiation or Transcriptional Impairment in Yeast
Xuefeng Chen, Baojin Ding, Danielle LeJeune, Christine Ruggiero, Shisheng Li
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0005267
Abstract: Covalent modifications of proteins by ubiquitin and the Small Ubiquitin-like MOdifier (SUMO) have been revealed to be involved in a plethora of cellular processes, including transcription, DNA repair and DNA damage responses. It has been well known that in response to DNA damage that blocks transcription elongation, Rpb1, the largest subunit of RNA polymerase II (Pol II), is ubiquitylated and subsequently degraded in mammalian and yeast cells. However, it is still an enigma regarding how Pol II responds to damaged DNA and conveys signal(s) for DNA damage-related cellular processes. We found that Rpb1 is also sumoylated in yeast cells upon UV radiation or impairment of transcription elongation, and this modification is independent of DNA damage checkpoint activation. Ubc9, an E2 SUMO conjugase, and Siz1, an E3 SUMO ligase, play important roles in Rpb1 sumoylation. K1487, which is located in the acidic linker region between the C-terminal domain and the globular domain of Rpb1, is the major sumoylation site. Rpb1 sumoylation is not affected by its ubiquitylation, and vice versa, indicating that the two processes do not crosstalk. Abolishment of Rpb1 sumoylation at K1487 does not affect transcription elongation or transcription coupled repair (TCR) of UV-induced DNA damage. However, deficiency in TCR enhances UV-induced Rpb1 sumoylation, presumably due to the persistence of transcription-blocking DNA lesions in the transcribed strand of a gene. Remarkably, abolishment of Rpb1 sumoylation at K1487 causes enhanced and prolonged UV-induced phosphorylation of Rad53, especially in TCR-deficient cells, suggesting that the sumoylation plays a role in restraining the DNA damage checkpoint response caused by transcription-blocking lesions. Our results demonstrate a novel covalent modification of Rpb1 in response to UV induced DNA damage or transcriptional impairment, and unravel an important link between the modification and the DNA damage checkpoint response.
Glycosylation Site Alteration in the Evolution of Influenza A (H1N1) Viruses
Shisheng Sun, Qinzhe Wang, Fei Zhao, Wentian Chen, Zheng Li
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0022844
Abstract: Influenza virus typically alters protein glycosylation in order to escape immune pressure from hosts and hence to facilitate survival in different host environments. In this study, the patterns and conservation of glycosylation sites on HA and NA of influenza A/H1N1 viruses isolated from various hosts at different time periods were systematically analyzed, by employing a new strategy combining genome-based glycosylation site prediction and 3D modeling of glycoprotein structures, for elucidation of the modes and laws of glycosylation site alteration in the evolution of influenza A/H1N1 viruses. The results showed that influenza H1N1 viruses underwent different alterations of protein glycosylation in different hosts. Two alternative modes of glycosylation site alteration were involved in the evolution of human influenza virus: One was an increase in glycosylation site numbers, which mainly occurred with high frequency in the early stages of evolution. The other was a change in the positional conversion of the glycosylation sites, which was the dominating mode with relatively low frequency in the later evolutionary stages. The mechanisms and possibly biological functions of glycosylation site alteration for the evolution of influenza A/H1N1 viruses were also discussed. Importantly, the significant role of positional alteration of glycosylation sites in the host adaptation of influenza virus was elucidated. Although the results still need to be supported by experimental data, the information here may provide some constructive suggestions for research into the glycosylation of influenza viruses as well as even the design of surveillance and the production of viral vaccines.
Degradation kinetics and bioavailability of pentachlorophenol in paddy soil-rice plant ecosystem

Li depeng,wang shisheng,

生态学报 , 2011,
Abstract: The in situ microcosm experiment was set up in the four long-term fertilization field experiments, the degradation kinetics and bioaccumulation characteristics of pentachlorophenol (PCP) with initial concentration of 85 mg/kg in paddy soil-rice plant ecosystem were investigated. The long-term fertilization field experiment employed was in the Experimental Station of Red Soil, the Chinese Academy of Sciences, located in Yingtan, Jiangxi Province, China. The four long-term fertilization treatments included (1) no fertilizer (the control, CK), (2) application of urea (N), (3) application of organic fertilizer (OM), and (4) mixed organic fertilizer and urea (N+OM), and no addition of PCP as control was also set up for any treatment. The results showed that carbon dioxide release in OM and N+OM was both higher than that in CK, but no significant difference was observed between CK and N, indicating that long-term fertilization of organic fertilizer or mixed organic fertilizer and urea increased microbial activities in paddy soil, but no effect on microbial activity was showed under long-term fertilization of urea. PCP residue in paddy soil gradually decreased with time increasing in four treatments. After the rice plant was harvested, the final PCP residue in N+OM was the least, was 8.7 mg/kg, and the highest PCP residue was in N, was 30.9 mg/kg. It could be found that PCP degradation followed one-order kinetics equation in four treatments, and the fitting degrees were 97.7%, 78.8%, 89.5%, 91.7% for CK, N, OM and N+OM,respectively. According to one-order kinetics equation, the half-lives calculated of PCP degradation were 27.7, 35.2, 24.8 and 22.4 days for CK, N, OM and N+OM,respectively. The results observed indicated that long-term fertilization of organic fertilizer or mixed organic fertilizer and urea accelerated PCP degradation, but long-term fertilization of urea inhibited PCP degradation. As for no addition of PCP in four treatments, the air-dried shoot and grain biomass of rice plant in N+OM and OM was significantly higher than those in CK, and no significant difference was displayed between N and CK, suggesting that long-term fertilization of organic fertilizer or mixed organic fertilizer and urea increased soil fertility, but the soil fertility did not increase under long-term fertilization of urea. In the presence of PCP, the average shoot and grain biomass was remarkably smaller when compared with no addition of PCP. The average shoot biomass decreased by 40.7%, 43.9%, 58.1%, 50.6% for CK, N, OM, N+OM, respectively, and 80.2%, 88.2%, 86.5%, 72.9% of grain biomass decreased was observed for CK, N, OM, N+OM, respectively. It suggested that higher PCP concentration had a severe damage to rice plant aboveground part growth. Beyond understanding, the root biomass did not decrease in four treatments. No significant difference in PCP concentration in grain was observed among four treatments, the average concentration in grain was 0.51 mg/kg, and b
Physiological responses and detoxific mechanisms to Pb, Zn, Cu and Cd in young seedlings of Paulownia fortunei

Jiang Wang,Weihua Li,Chongbang Zhang,Shisheng Ke,

环境科学学报(英文版) , 2010,
Abstract: Paulownia fortunei has been successfully used in the phytoremediation of many Pb/Zn mine tailings. However, seed germination and young seedlings of P. fortunei rarely occurred in these mine tailings. The physiological responses and detoxific mechanisms of P. fortunei young seedling to Pb, Zn, Cu and Cd stress were investigated. The germinated rate, shoot length, chlorophyll and carotenoid contents in leaves of young seedlings had a great reduction under Zn and Cu treatments, but had little decrease under Pb and Cd treatments. The production rate of O2 .??, H2O2 and malondialdehyde (MDA) contents significantly increased in response to added Zn and Cu indicating great oxidative stress for young seedlings, but they had no significant change to added Pb and Cd. Young seedlings had e ective detoxific mechanism to Pb and Cd, as antioxidant enzymes activities, phytochelatins (PCs-SH) and proline contents increased with increasing rates of added Pb and Cd. However, young seedlings had un-e ective detoxific mechanisms to Zn and Cu stress. Results revealed the heavy metals (such as Cu) that present at low concentrations in mine tailings may be major constraint for the survival of young seedlings.
Atomically thin spherical shell-shaped superscatterers based on Bohr model
Rujiang Li,Xiao Lin,Shisheng Lin,Xu Liu,Hongsheng Chen
Physics , 2015, DOI: 10.1088/0957-4484/26/43/435201
Abstract: Graphene monolayers can be used for atomically thin three-dimensional shell-shaped superscatterer designs. Due to the excitation of the first-order resonance of transverse magnetic (TM) graphene plasmons, the scattering cross section of the bare subwavelength dielectric particle is enhanced significantly by five orders of magnitude. The superscattering phenomenon can be intuitively understood and interpreted with Bohr model. Besides, based on the analysis of Bohr model, it is shown that contrary to the TM case, superscattering is hard to occur by exciting the resonance of transverse electric (TE) graphene plasmons due to their poor field confinements.
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