Sequencing and analysis for the full-length genome RNA of foot-and-mouth disease virus China/99

The complete nucleotide sequence of genomic RNA of foot and mouth disease virus (FMDV) strain China/99 from infected bovine tongue epithelium is presented. The nucleotide sequence extending from the 5' end of the genomic RNA to the 5' end of poly (A) tail contains 8173 nucleotides (nt). Its open reading frame, which encodes a single polypeptide of 2332 amino acids, encompasses 6999 nt starting from the initiation codon AUG and terminating at the UAA codon 93 bases upstream from the 5' end of poly (A) tract. The 5' untranslated region (UTR) is composed of 1081 nt. The consensus of the 1d gene of FMDV strain China/99 compared with that of UKG/6/2001, UKG/12/2001, China/99HN4 and China/3/Tibet is over 97%. The result showed the stains belong to the members of the Pan-Asia family. There is a remarkable differentiation in the function-unknown (FUR), p2 and p3 regions between FMDV isolates from infected cattle and swine, especially in 3a gene. No deletion was found in genes /, 1a, 1b, 2a, 2c, 3b, and 3d. Thes     

Does the Genetic Code Have A Eukaryotic Origin?

In the RNA world, RNA is assumed to be the dominant macromolecule performing most, if not all, core "house-keeping" functions. The ribo-cell hypothesis suggests that the genetic code and the translation machinery may both be born of the RNA world, and the introduction of DNA to ribo-cells may take over the informational role of RNA gradually, such as a mature set of genetic code and mechanism enabling stable inheritance of sequence and its variation. In this context, we modeled the genetic code in two content variables-GC and purine contents-of protein-coding sequences and measured the purine content sensitivities for each codon when the sensitivity (% usage) is plotted as a function of GC content variation. The analysis leads to a new pattern-the symmetric pattern-where the sensitivity of purine content variation shows diagonally symmetry in the codon table more significantly in the two GC content invariable quarters in addition to the two existing patterns where the table is divided into either four GC content sensitivity quarters or two amino acid diversity halves. The most insensitive codon sets are GUN (valine) and CAN (CAR for asparagine and CAY for aspartic acid) and the most biased amino acid is valine (always over-estimated) followed by alanine (always under-estimated). The unique position of valine and its codons suggests its key roles in the final recruitment of the complete codon set of the canonical table. The distinct choice may only be attributable to sequence signatures or signals of splice sites for spliceosomal introns shared by all extant eukaryotes.     

The Role of Autophagy during Development of the Oomycete Pathogen Phytophthora infestans

Phytophthora infestans is a highly destructive plant path- ogen that causes late blight disease in plants such as potato and tomato （Fry and Goodwin, 1997）. As a typical oomycete, the primary infective propagule of P. infestans is the sporangium, which can either germinate directly or release biflagellate zoospores that encyst and germinate on the host subsequently （Grenville-Briggs et al., 2005）. Due to abundant formation of the sporangia and prolific sporulation, P. infestans can spread quickly in the host tissues and cause extensive necrosis of the infected plants （Kamoun and Smart, 2005）.     

The structure analysis and antigenicity study of the N protein of SARS-CoV

The Coronaviridae family is characterized by a nucleocapsid that is composed of the genome RNA molecule in combination with the nucleoprotein (N protein) within a virion. The most striking physiochemical feature of the N protein of SARS-CoV is that it is a typical basic protein with a high predicted pI and high hydrophilicity, which is consistent with its function of binding to the ribophosphate backbone of the RNA molecule. The predicted high extent of phosphorylation of the N protein on multiple candidate phosphorylation sites demonstrates that it would be related to important functions, such as RNA-binding and localization to the nucleolus of host cells. Subsequent study shows that there is an SR-rich region in the N protein and this region might be involved in the protein-protein interaction. The abundant antigenic sites predicted in the N protein, as well as experimental evidence with synthesized polypeptides, indicate that the N protein is one of the major antigens of the SARS-CoV. Compared with o     

The effects of detergents DDM and β-OG on the singlet excited state lifetime of the chlorophyll a in cytochrome b6f complex from spinach chloroplasts

The singlet excited state lifetime of the chlorophyll a (Chi a) in cytochrome b6f (Cyt b6f) complex was reported to be shorter than that of free Chl a in methanol, but the value was different for Cyt b6f complexes from different sources (～200 and ～600 ps are the two measured results). The present study demonstrated that the singiet excited state lifetime is associated with the detergents n-dodecyl-β-D-maltoside (DDM) and n-octyl-β-D-glucopyranoside (β-OG), but has nothing to do with the different sources of Cyt b6f complexes. Compared with the Cyt b6f dissolved in β-OG, the Cyt b6f in DDM had a lower fluorescence yield, a lower photodegradation rate of Chl a, and a shorter lifetime of Chl a excited state. In short, the singlet excited state lifetime, ～200 ps, of the Chl a in Cyt b6f complex in DDM is closer to the true in vivo.     

The effects of detergents DDM and β-OG on the singlet excited state lifetime of the chlorophyll a in cytochrome b_6f complex from spinach chloroplasts

The singlet excited state lifetime of the chlorophyll a (Chl a) in cytochrome b6f (Cyt b6f) complex was reported to be shorter than that of free Chl a in methanol, but the value was different for Cyt b6f com-plexes from different sources (~200 and ~600 ps are the two measured results). The present study demonstrated that the singlet excited state lifetime is associated with the detergents n-dodecyl-β-D- maltoside (DDM) and n-octyl-β-D-glucopyranoside (β-OG), but has nothing to do with the different sources of Cyt b6f complexes. Compared with the Cyt b6f dissolved in β-OG, the Cyt b6f in DDM had a lower fluorescence yield, a lower photodegradation rate of Chl a, and a shorter lifetime of Chl a excited state. In short, the singlet excited state lifetime, ~200 ps, of the Chl a in Cyt b6f complex in DDM is closer to the true in vivo.     

Systematics and Species Validity of the Dabieshan Pit Viper Protobothrops dabieshanensis Huang et al. 2012: Evidence from a Mitochondrial Gene Sequence Analysis

Aimed to evaluate the phylogenetic position of the recently described Protobothrops dabieshanensis Huang et al. （2012）, phylogenic relationships of 12 species within Protobothrops based on four mtDNA gene fragments （12S RNA, 16S RNA, ND4 and Cyt b） were reconstructed in our study. The result indicates a clade composed ofP dabiesha- nensis, P. jerdonii and P xiangchengsis with strong support. The genetic distance among P dabieshanensis, P jerdonii and P xiangchengsis was much lower than other congeners. Based on the data from the phylogenetic analysis and pre- viously described morphological differences, we conclude that P dabieshanensis is a valid species with close affinities to P jerdonii and P xiangchengsis.     

Identification of Nonstructural Protein 8 as the N-Terminus of the RNA-Dependent RNA Polymerase of Porcine Reproductive and Respiratory Syndrome Virus

Porcine reproductive and respiratory syndrome virus (PRRSV) is a member within the family Arteriviridae of the order Nidovirales. Replication of this positive-stranded RNA virus within the host cell involves expression of viral replicase proteins encoded by two ORFs, namely ORF1 a and ORF1 b. In particular, translation of ORF1 b depends on a-1-ribosomal frameshift strategy. Thus, nonstructural protein 9 (nsp9), the first protein within ORF1 b that specifies the function of the viral RNA-dependent RNA polymerase, is expressed as the C-terminal extension of nsp8, a small nsp that is encoded by ORF1 a. However, it has remained unclear whether the mature form of nsp9 in virus-infected cells still retains nsp8,addressing which is clearly critical to understand the biological function of nsp9. By taking advantage of specific antibodies to both nsp8 and nsp9, we report the following findings. (1) In infected cells, PRRSV nsp9 was identified as a major product with a size between 72 and 95 k Da (72–95 KDa form), which exhibited the similar mobility on the gel to the in vitro expressed nsp8–9 ORF1 b, but not the ORF1 b-coded portion (nsp9 ORF1 b). (2) The antibodies to nsp8, but not to nsp7 or nsp10, could detect a major product that had the similar mobility to the 72–95 KDa form of nsp9. Moreover, nsp9 could be co-immunoprecipitated by antibodies to nsp8, and vice versa. (3) Neither nsp4 nor nsp2 PLP2 was able to cleave nsp8–nsp9 in vitro. Together, our studies provide experimental evidence to suggest that nsp8 is an N-terminal extension of nsp9.Our findings here paves way for further charactering the biological function of PRRSV nsp9.     

RNA-binding domain of the key structural protein P7 for the Rice dwarf virus particle assembly

The Rice dwarf virus (RDV) P7 structural protein is the key protein in the RDV particle assembly. The P7 protein was digested partially or completely by Staphylococcus aureus V8 protease and/or Pseudomonasfragi Asp-N protease. The molecular mass and the N-terminal amino acid sequence of the polypeptide fragments of the P7 protein were determined by SDS-PAGE and the Edman degradation method, respectively. Then the polypeptides were located in the deduced amino acid sequence of the RDV P7 protein based on the nucleotide sequence information, with the knowledge of the specific cleavage sites of the Staphylococcus aureus V8 and Pseudomonasfragi Asp-N protease, and the two RNA-binding domains in the P7 protein were identified. Domain 1 was located in the residue 128-249 containing 122 amino acids and domain 2 was located in the residue 325-355 containing 31 amino acids. Thus, these two domains may play an important role in the virus particle assembly by contributing to the packaging of viral dsRNAs inside the particles. The two domains may be novel RNA-binding domains, because no amino acid sequences highly similar to the conservative sequences of known dsRNA-binding domains reported so far. The similarity between the motif of domain 1 and the motif of the DNA-binding protein suggests that the DNA-binding activity of the RDV P7 protein may be due to this sequence. The similarity between the motif of domain 1 and the motif of the RNA polymerase domain suggests that the P7 protein may also play a role in RNA synthesis, besides its function in the assembly and subsequent packaging of viral dsRNA into core particles.     

Physical processes and their role on the spatial and temporal variability of the spring phytoplankton bloom in the central Yellow Sea

The spatial and temporal variability of the spring phytoplankton bloom (SPB) in the central Yellow Sea is studied, using SeaWiFS surface chlorophyll remote-sensing data, AVHRR sea surface temperatures (SST), QuikSCAT sea surface wind speed (SSW) from 1998 to 2009 and the cruise survey data in 2007 and 2009. The influences of the hydrological conditions on the SPB are significant. (1) The rising SST and low SSW in spring play an important role in the development of the SPB. The SPB in the central Yellow Sea occurs primarily in April (from April 3 to April 24) and at this period the mean SST is generally greater than 10 °C, and 24 h averaged SSW is less than 5.4 m/s. The 99% of the SPB occurs when the SST is 9–14 °C and SSW is 0–7.9 m/s. (2) Specifically, the development of the SPB is from April 4 to April 7 and from April 4 to April 22 in 2007 and 2009 respectively. The longer duration of the SPB in 2009 than that in 2007 is related to the high SST in 2009, which is approximately 2 °C greater than that in 2007, and the weak SSW in 2009, which is much lower than that in 2007, which further indicate that these two factors are critical to the duration of the SPB. (3) The horizontal distribution of surface chlorophyll a in 2007 is found to be greater and located more northward than that in 2009. Comparing the spatial coverage of the SPB, the path of the Yellow Sea warm current, which is warmer and salty, and the location of maximum SST reveals that the spatial coverage of the SPB locates in the warmer temperature (>9 °C) and higher salinity (>33) waters in March and this warm and salty water was much more evident in 2007 than that in 2009 because a stronger warm current of the Yellow Sea in winter. (4) The vertical depths of the maximum chlorophyll layer (MCL) appear at three levels: surface, 10 m and 30 m in 2007, whereas the MCL occurs only at a sub-surface level in 2009 which is related to vertical stability of the water column, i.e., the water is vertically mixed in 2007 while vertically stratified in 2009.     

Physical processes and their role on the spatial and temporal variability of the spring phytoplankton bloom in the central Yellow Sea

The spatial and temporal variability of the spring phytoplankton bloom (SPB) in the central Yellow Sea is studied, using SeaWiFS surface chlorophyll remote-sensing data, AVHRR sea surface temperatures (SST), QuikSCAT sea surface wind speed (SSW) from 1998 to 2009 and the cruise survey data in 2007 and 2009. The influences of the hydrological conditions on the SPB are significant. (1) The rising SST and low SSW in spring play an important role in the development of the SPB. The SPB in the central Yellow Sea occurs primarily in April (from April 3 to April 24) and at this period the mean SST is generally greater than 10 °C, and 24 h averaged SSW is less than 5.4 m/s. The 99% of the SPB occurs when the SST is 9–14 °C and SSW is 0–7.9 m/s. (2) Specifically, the development of the SPB is from April 4 to April 7 and from April 4 to April 22 in 2007 and 2009 respectively. The longer duration of the SPB in 2009 than that in 2007 is related to the high SST in 2009, which is approximately 2 °C greater than that in 2007, and the weak SSW in 2009, which is much lower than that in 2007, which further indicate that these two factors are critical to the duration of the SPB. (3) The horizontal distribution of surface chlorophyll a in 2007 is found to be greater and located more northward than that in 2009. Comparing the spatial coverage of the SPB, the path of the Yellow Sea warm current, which is warmer and salty, and the location of maximum SST reveals that the spatial coverage of the SPB locates in the warmer temperature (>9 °C) and higher salinity (>33) waters in March and this warm and salty water was much more evident in 2007 than that in 2009 because a stronger warm current of the Yellow Sea in winter. (4) The vertical depths of the maximum chlorophyll layer (MCL) appear at three levels: surface, 10 m and 30 m in 2007, whereas the MCL occurs only at a sub-surface level in 2009 which is related to vertical stability of the water column, i.e., the water is vertically mixed in 2007 while vertically stratified in 2009.     

Morphophysiological and molecular evidence supporting the augmentative role of Piriformospora indica in mitigation of salinity in Cucumis melo L.

Salinity is one of the major limiting factors in plant growth and productivity.Cucumis melo L.is a widely cultivated plant,but its productivity is significantly influenced by the level of salinity in soil.Symbiotic colonization of plants with Piriformospora indica has shown a promotion in plants growth and tolerance against biotic stress.In this study,physiological markers such as ion analysis,antioxidant determination,proline content,electrolyte leakage and chlorophyll measurement were assessed in melon cultivar under two concentrations(100 and 200 mM)of NaCl with and without P.indica inoculation.Results showed that the endophytic inoculation consistently upregulated the level of antioxidants,enhanced plants to antagonize salinity stress.The expression level of an RNA editing factor(SLO2)which is known to participate in mitochondria electron transport chain was analyzed,and its full mRNA sequence was obtained by rapid amplification of cDNA ends(RACE).Under salinity stress,the expression level of SLO2 was increased,enhancing the plant’s capability to adapt to the stress.However,P.indica inoculation further elevated the expression level of SLO2.These findings suggested that the symbiotic association of fungi could help the plants to tolerate the salinity stress.     

Special Issue on ‘‘Ribogenomics-the study of RNA-centric molecular mechanisms and cellular processes’’

The journal Genomics Proteomics&Bioinformatics(GPB)is now inviting submissions for a special issue(to be published in spring of 2014)on the topic of‘‘The Ribogenomics of Life’’.Life was born of the RNA world.The RNA world was governed by RNA-centric mechanisms and processes in single cells.These operationally defined cells became more complex and heterogeneous:some were robust against changes but lost potential for diversity and others became complex but more opportunistic.Proteins w