Protein Subcellular Localization Prediction and Genomic Polymorphism Analysis of the SARS Coronaviru

The cause of severe acute respiratory syndrome (SARS) has been identified as a new coronavirus (CoV). Several sequences of the complete genome of SARS-CoV have been determined. The subcellular localization (SubLocation) of annotated open-reading frames of the SARS-CoV genome was predicted using a support vector machine. Several gene products were predicted to locate in the Golgi body and cell nucleus. The SubLocation information was combined with predicted transmembrane information to develop a model of the viral life cycle. The results show that this information can be used to predict the functions of genes and even the virus pathogenesis. In addition, the entire SARS viral genome sequences currentlyav ailable in GenBank were compared to identify the sequence variations among different isolates. Some variations in the Hong Kong strains may be related to the special clinical manifestations and provide clues for understanding the relationship between gene functions and evolution. These variations reflect the evolution of the SARS virus in human populations and may help development of a vaccine.     

Study of Nozzle and Vent Locations on Die Casting Filling Process

The casting nozzle location plays an important role in die casting. Improper location results in defects, such as cold shut, air cavity, shrinkage, etc. Therefore, it‘s sure that the molten metal full fills the mould cavity before it solidifies. And, it‘s to be wished that no vortex occur during the filling process, because the vortex is a main source that induces gas entrapment. To get the high quality and performance product, the inlet and outlet locations must be set properly. This paper, an optimal desi...     

Design and application of 60mer oligonucleotide microarray in SARS coronavirus detection

In April 2003, a novel coronavirus[1,2] which was associated with cases of Severe Acute Respiratory Syn-drome (SARS) was first isolated and sequenced in Canada. The genome of SARS coronavirus (SARS-CoV) is 29727[3] nucleotides in length and has 11 known open reading frames (ORFs). Although the genome organiza-tion of this virus is similar to that of other coronaviruses, phylogenetic analyses and sequence alignment show that SARS-CoV is not closely related to any of the previously ch…     

Phylogeny of SARS-CoV as inferred from complete genome comparison

SARS-CoV, as the pathogeny of severe acute respiratory syndrome (SARS), is a mystery that the origin of the virus is still unknown even a few isolates of the virus were completely sequenced. To explore the genesis of SARS-CoV,the FDOD method previously developed by us was applied to comparing complete genomes from 12 SARS-CoV isolates to those from 12 previously identified coronaviruses and an unrooted phyiogenetic tree was constructed. Our results show that all SARS-CoV isolates were clustered into a clique and previously identified coronaviruses formed the other clique. Meanwhile, the three groups of coronaviruses depart from each other clearly in our tree that is consistent with the results of prevenient papers. Differently, from the topology of the phylogenetic tree we found that SARS-CoV is more close to group 1 within genus coronavirus. The topology map also shows that the 12 SARS-CoV isolates may be divided into two groups determined by the association with the SARS-CoV from the Hotel M in Hong Kong that may give some information about the infectious relationship of the SARS.     

Genome sequence variation analysis of two SARS coronavirus isolates after passage in Vero cell culture

SARS coronavirus is an RNA virus whose replication is error-prone, which provides possibility for escape of host defenses, and even leads to evolution of new viral strains during the passage or the transmission. Lots of variations have been detected among different SARS-CoV strains. And a study on these variations is helpful for development of efficient vaccine. Moreover, the test of nucleic acid characterization and genetic stability of SARS-CoV is important in the research of inactivated vaccine. The whole genome sequences of two SARS coronavirus strains after passage in Vero cell culture were determined and were compared with those of early passages, respectively. Results showed that both SAPS coronavirus strains have high genetic stability, although nearly 10 generations were passed. Four nucleotide variations were observed between the second passage and the llth passage of Sinol strain for identification of SARS inactivated vaccine. Moreover, only one nucleotide was different between the third passage and the 10th passage of Sino3 strain for SARS inactivated vaccine. Therefore, this study suggested it was possible to develop inactivated vaccine against SARS-CoV in the future.     

Experimental investigation on upstream-injection interaction with a scramjet cavity flameholder

The study has evaluated the coherent structures and the velocity field of gaseous transverse jet upstream of a scramjet flameholder in a supersonic turbulent flow. The high spatiotemporal resolution coherent structures of the jet plume/wakes and the cavity shear layer were obtained by utilizing the nanoparticle-based planar laser scattering technique. Compared to the no upstream injection case, the cavity shear layer downstream of the jet shows significant mass exchange with mainstream. The particle image veloc- imetry velocity field and the velocity profiles demonstrated that the interaction intensity of the cavity shear layer with the upstream injection is further enhanced as the injection stagnation pressure increases.     

Bioinformatical study on the proteomics and evolution of SARS-CoV

A novel coronavirus has been identified as the causative agent of the severe acute respiratory syndrome (SARS). For all the SARS-CoV associated proteins derivated from the SARS-CoV genome, the physiochemical properties such as the molecular weight, isoelectric point and extinction coefficient of each protein were calculated. The transmembrane segments and subeellular localization (SubLoeation) prediction and conserved protein motifs search against database were employed to analyze the function of SARS-CoV proteins. Also, the homology protein sequence alignment and evolutionary distance matrix calculation between SARS-CoV associated proteins and the corresponding proteins of other coronaviruses were employed to identify the classification and phylogenetic relationship between SARS-CoV and other coronaviruses. The results showed that SARS-CoV is a novel coronavirus which is different from any of the three previously known groups of coronviruses, but it is closer to BoCoV and MHV than to other coronaviruses. This study is in aid of experimental determination of SARS-CoV proteomics and the development of antiviral vaccine.     

Molecular phylogeny of coronaviruses including human SARS-CoV

Phylogenetic tree of coronaviruses (CoVs) including the human SARS-associated virus is reconstructed from complete genomes by using our newly developed Kstring composition approach. The relation of the human SARS-CoV to other coronaviruses, i.e. the rooting of the tree is suggested by choosing an appropriate outgroup.SARS-CoV makes a separate group closer but still distant from G2 (CoVs in mammalian host). The relation between different isolates of the human SARS virus is inferred by first constructing an ultrametric distance matrix from counting sequence variations in the genomes. The resulting tree is consistent with clinic relations between the SARS-CoV isolates. In addition to a larger variety of coronavirus genomes these results provide phylogenetic knowledge based on independent novel methodology as compared to recent phylogenetic studies on SARS-CoV.     

A complete sequence and comparative analysis of a SARS-associated virus （Isolate BJO1）

The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-assoclated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs.We report the complete genome sequence and comparative analysis of an isolate (B J01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 20RFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS-associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to be involved in the immunoreactions between the virus and its host.Two amino acid changes have been detected in the M protein,which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides no evidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of other possible SARS-related pathogen(s).     

Genome sequencing and characterization analysis of a Beijing isolate of chicken coronavirus infectious bronchitis virus

Avian infectious bronchitis virus (AIBV) is classified as a member of the genus coronavirus in the family coronaviridae. The enveloped virus has a positive-sense, single-stranded RNA genome of approximately 28 kilo-bases,which has a 5‘ cap structure and 3‘ polyadenylation tract.The complete genome sequence of infectious bronchitis virus (IBV), Beijing isolate, was determined by cloning sequencing and primer walking. The whole genome is 27733 nucleotides in length, has ten open reading frames:5′-orfla-orflab-s-3a-3b-e-m- 6a-6b-n-3′. Alignments of the genome sequence of IBV Beijing isolate with those of two AIBV strains and one SARS coronavirus were performed respectively. The genome sequence of IBV Beijing isolate compared with that of the IBV strain LX4 (uncompleted, 19440 bp in size) was 91.2% similarity. However, the full-length genome sequence of IBV Beijing isolate was 85.2% identity to that of IBV Strain Beaudette, and was only 50.8% homology to that of SARS coronavirus. The results showed that the genome of IBV has remarkable variation. And IBV Beijing isolate is not closely related to SARS coronavirus. Phylogenetic analyses based on the whole genome sequence, S protein, M protein and N protein, also showed that AIBV Bering isolate is lone virus in group Ⅲ and is distant from SARS coronavirus. In conclusion, this study will contribute to the studies of diagnosis and diseases control on IBV in China.     

Infection of SARS-CoV on juvenile and adult Brandt’s vole Microtus brandtii

In the spring of 2003, severe acute respiratory syndrome (SARS) suddenly broke out in many countries of the world, especially China. About 8400 probable cases of SARS were identified worldwide and about 800 patients died. SARS not only caused severe panic all over the world, but also brought huge losses to global economy. SARS is recognized as a new kind of respiratory disease, caused by a novel coranovirus, SARS-CoV. It is characterized by pneumonic infection and pathological change.…     

Molecular phylogeny of coronaviruses including human SARS-CoV

The outbreak of SARS sets an urgent task to reveal the origin of human SARS-CoV, i.e. its relation to other known species of coronavirus, and to trace the genetic variation in the spreading process of SARS. Partial answer to the problem may be obtained from phylogenetic analy-sis of available genomes. We call a phylogenetic tree of different species of coronavirus including the human SARS-Cov a CoV Tree and that of different isolates of SARS-CoV a SARS Tree. CoV trees have been c…     

An Overlay Network for Monitoring Activities of Computer Viruses

To accurately track computer viruses, an overlay network that monitors the activities of viruses is constructed. Identifying and locating nodes infected by virus on network is achieved by a naming system in which a node in the network is mapped to a unique serial number of the hard -drive. By carefully monitoring and recording sensitive commu- nication between local system and remote nodes on the network, and suspicious operations on files that originate from remote nodes and entered via some form of file transfer, activities of viruses in both local and network level are recorded and ready for future analysis. These data can also be used in analysis of the mechanism of a computer virus as well as its spreading mode and pattern.     

A complete sequence and comparative analysis of a SARS-associated virus(Isolate BJ01)

Severe Acute Respiratory Syndrome (SARS) is a newly identified infectious disease[1—5]. The global outbreak of SARS has been threatening the health of people worldwide and has killed 353 people and infected more than 5462 in 27 countries, as reported by WHO on April 29, 2003 (http://www.who.int/csr/sarscountry/en). Although it has been recognized that a variant of virus from the family of coronavirus might be the candidate pathogen of SARS[1—5], its identity as the unique pathogen sti…     

Use of flow cytometry to investigate the cytokine response pattern in infants with respiratory syncytial virus infection and bronchiolitis

Objective:To investigate the cytokine response pattern(IL-4/IFN-γ)in infants with RSV infections and bronchiolitis during the acute phase,Methods:Four-color flow cytometry was used to measure intracellular IL-4 and IFN-γ expressions in peripheral blood CD3 and CD* lymphocytes from RSV-infected and bronchiolitis infants.Serum IL-4 and INF-γ levels were also determined.Results:RSV-infected and bronchiolitis infants showed no statistical differences from not-RSV-infected or pneumonia infants and control in the frequency of IL-4 and INF-γ levels were also determined.Results;RSV-infected and bronchiolitis infants showed no statistical differences from not-RSV-infected or pneumonia infants and control in the frequency of IL-4 and IFN-γ expressions in CD3 CD8- lymphocytes,showed no obvious Th1/Th2 imbalance,while IFN-γ was expressed much more frequently in CD3 CD* lymphocytes.Systematically,RSV-infected and bronchiolitis infants showed moch lower levels of serum IL-4 and IL-4/INF-γ ratios and much higher serum IFN-γ levels than control.Howerver,there were no statistical differences in the above three indices between RSV-infected and not-RSV infected infants or between bronchiolitis and pneumonia infants,except that bronchiolitis infants had a higher level of serum INF-γ than pneumonia infants statistically .Conclusions:There is no type-2 cytokine response predominance in the acute thase of RSV infection and bronchilitis.IL-4 productioin is suppressed and IFN-γ production upregulated,the latter being most prominent in bronchiolitis infants.     

Efficient generation of Bell and W-type states in cavity QED

Two generation schemes for Bell and W-type states of single-photon in cavity QED are proposed. The proposed schemes are simple and efficient in the sense that it requires no measurements on the particles.     

The outbreak pattern of the SARS cases in Asia

The severe acute respiratory syndrome (SARS) caused tremendous damage to many Asia countries, especially China. The transmission process and outbreak pattern of SARS is still not well understood. This study aims to find a simple model to describe the outbreak pattern of SARS cases by using SARS case data commonly released by governments. The outbreak pattern of cumulative SARS cases is expected to be a logistic type because the infection will be slowed down due to the increasing control effort by people and/or due to depletion of susceptible individuals. The increase rate of SARS cases is expected to decrease with the cumulative SARS cases, as described by the traditional logistical model, which is widely used in population dynamic studies. The instantaneous rate of increases were significantly and negatively correlated with the cumulative SARS cases in mainland of China (including Beijing, Hebei, Tianjin, Shanxi,the Autonomous Region of Inner Mongolia) and Singapore. The basic reproduction number R0 in Asia ranged from 2.0 to 5.6 (except for Taiwan, China). The R0 of Hebei and Tianjin were much higher than that of Singapore, Hongkong, Beijing, Shanxi, Inner Mongolia, indicating SARS virus might have originated differently or new mutations occurred during transmission. We demonstrated that the outbreaks of SARS in many regions of Asia were wall described by the logistic model, and the control measures implemented by governments are effective. The maximum instantaneous rate of increase, basic reproductive number, and maximum cumulative SARS cases were also calculated by using the logistic model.     

Coat protein gene and 3′ non-coding region of tobacco mosaic virus and tomato mosaic virus are associated with viral pathogenesis in Nicotiana tabacum

The camellia isolate of tomato mosaic virus (ToMV-TL) can induce local necrotic lesions on the inoculated leaves in Nicotiana tabacum, whereas the broad bean isolate of tobacco mosaic virus (TMV-B) produces the mosaic symptom on systemic leaves. To examine viral determinant for differential infection phenotype in N. tabacum, the coat protein gene and the 3′ non-coding region of TMV was replaced with that of ToMV, the chimeric virus induced similar local necrotic lesions to that induced by ToMV. The results indicate that the coat protein gene and the 3′ non-coding region of TMV and ToMV influence the virus-induced pathogenesis in N. tabacum.     

Genome evolution of novel influenza A （H1N1 ） viruses in humans

The epidemic situation of A H1N1 flu arose in North America in April 2009, which rapidly expanded to three continents of Europe, Asia and Africa, with the risk ranking up to 5. Until May 13th, the flu virus of A H1N1 had spread into 33 countries and regions, with a laboratory confirmed case number of 5728, including 61 deaths. Based on IRV and EpiFluDB database, 425 parts of A H1N1 flu virus sequence were achieved, followed by sequenced comparison and evolution analysis. The results showed that the current predominant A H1N1 flu virus was a kind of triple reassortment A flu virus： （i） HA, NA, MP, NP and NS originated from swine influenza virus; PB2 and PA originated from bird influenza virus; PB1 originated from human influenza virus. （ii） The origin of swine influenza virus could be subdivided as follows： HA, NP and NS originated from classic swine influenza virus of H1N1 subtype; NA and MP originated from bird origin swine influenza virus of H1N1 subtype. （iii） A H1N1 flu virus experienced no significant mutation during the epidemic spread, accompanied with no reassortment of the virus genome. In the paper, the region of the representative strains for sequence analysis （A/California/04/2009 （H1N1） and A/Mexico/4486/2009 （H1N1）） included USA and Mexico and was relatively wide, which suggested that the analysis results were convincing.     

Southern rice black-streaked dwarf virus: A new proposed <Emphasis Type="Italic">Fijivirus</Emphasis> species in the family <Emphasis Type="Italic">Reoviridae</Emphasis>

For the past several years, a novel dwarf disease has been observed on rice （Oryza sativa） in some regions of Guangdong Province and Hainan Province, southern China. Infected plants showed stunting, dark leaf and small enations on stem and leaf back. Typical Fijivirus viroplasma containing crystalline arrayed spherical virons approximately 70--75 nm in diameter and tubular structures were detected in ultrathin sections by an electron microscope in parenchyma phloem cells of the infected plants. The virus was transmitted to rice seedlings by white-backed planthoppers, Sogatella furcifera （Hemiptera： Delphacidae）, collected in the diseased fields. Analysis of dsRNA extracts from infected plants revealed ten linear segments, which were similar to the electrophoretic profile of Rice black-streaked dwarf virus （RBSDV）. RT-PCR with a single primer which matched to a linker sequence ligated to both 3＇ ends of the viral genomic dsRNAs resulted in amplification of genome segments 9 （S9） and 10 （S10） cDNA products. The complete nucleotide sequences of S9 and S10 were obtained from clones of the RT-PCR amplicon exhibited characteristic properties of Fijivirus including low GC content （34.5% and 35.6%）, genus conserved 5＇ and 3＇ termini sequences and similar genome organization. Blast searches indicated that the sequences of S9 and S10 shared 68.8%--74.9% and 67.1% --77.4% nucleotide identities with those of viruses in the Fijivirus group 2, respectively. These values were similar to those among other viruses in the Fijivirus group 2 and considerably lower than those among RBSDV isolates. Phylogenetic trees based on S9 and S10 nucleotide sequences and their putative amino acid sequences showed that this virus represented a separate branch among other Fijiviruses. The virus was also detected by a nested RT-PCR assay in corn （Zea mays）, barnyard grass （Echinochloa crusgalll）, Juncellus serotinus and flaccidgrass （Pennisetum flaccidum） in and/or adjacent to the infected rice fields. I