Novel insights into human respiratory syncytial virus-host factor interactions through integrated proteomics and transcriptomics analysis

<p>The lack of vaccine and limited antiviral options against respiratory syncytial virus (RSV) highlights the need for novel therapeutic strategies. One alternative is to develop drugs that target host factors required for viral replication. Several microarray and proteomics studies had been published to identify possible host factors that are affected during RSV replication. In order to obtain a comprehensive understanding of RSV-host interaction, we integrated available proteome and transcriptome datasets and used it to construct a virus-host interaction network. Then, we interrogated the network to identify host factors that are targeted by the virus and we searched for drugs from the DrugBank database that interact with these host factors, which may have potential applications in repositioning for future treatment options of RSV infection.</p

Phylogenetic analysis of the A) HA1 fragment of hemagglutinin, HA gene (885nt) and B) neuraminidase, NA gene (1,404nt) of influenza B viruses.

<p>Trees were constructed using the Neighbor-Joining method. Numbers at the nodes indicate confidence levels of bootstrap analysis with 1,000 replicates as percentage value. Amino acid substitutions that characterized a particular branch are indicated on the left side node. Vaccine strains are italicized and in red. Reference strains are boldfaced.</p

Genetic Characterization of Human Influenza Viruses in the Pandemic (2009–2010) and Post-Pandemic (2010–2011) Periods in Japan

<div><h3>Background</h3><p>Pandemic influenza A(H1N1) 2009 virus was first detected in Japan in May 2009 and continued to circulate in the 2010–2011 season. This study aims to characterize human influenza viruses circulating in Japan in the pandemic and post-pandemic periods and to determine the prevalence of antiviral-resistant viruses.</p> <h3>Methods</h3><p>Respiratory specimens were collected from patients with influenza-like illness on their first visit at outpatient clinics during the 2009–2010 and 2010–2011 influenza seasons. Cycling probe real-time PCR assays were performed to screen for antiviral-resistant strains. Sequencing and phylogenetic analysis of the HA and NA genes were done to characterize circulating strains.</p> <h3>Results and Conclusion</h3><p>In the pandemic period (2009–2010), the pandemic influenza A(H1N1) 2009 virus was the only circulating strain isolated. None of the 601 A(H1N1)pdm09 virus isolates had the H275Y substitution in NA (oseltamivir resistance) while 599/601 isolates (99.7%) had the S31N substitution in M2 (amantadine resistance). In the post-pandemic period (2010–2011), cocirculation of different types and subtypes of influenza viruses was observed. Of the 1,278 samples analyzed, 414 (42.6%) were A(H1N1)pdm09, 525 (54.0%) were A(H3N2) and 33 (3.4%) were type-B viruses. Among A(H1N1)pdm09 isolates, 2 (0.5%) were oseltamivir-resistant and all were amantadine-resistant. Among A(H3N2) viruses, 520 (99.0%) were amantadine-resistant. Sequence and phylogenetic analyses of A(H1N1)pdm09 viruses from the post-pandemic period showed further evolution from the pandemic period viruses. For viruses that circulated in 2010–2011, strain predominance varied among prefectures. In Hokkaido, Niigata, Gunma and Nagasaki, A(H3N2) viruses (A/Perth/16/2009-like) were predominant whereas, in Kyoto, Hyogo and Osaka, A(H1N1)pdm09 viruses (A/New_York/10/2009-like) were predominant. Influenza B Victoria(HA)-Yamagata(NA) reassortant viruses (B/Brisbane/60/2008-like) were predominant while a small proportion was in Yamagata lineage. Genetic variants with mutations at antigenic sites were identified in A(H1N1)pdm09, A(H3N2) and type-B viruses in the 2010–2011 season but did not show a change in antigenicity when compared with respective vaccine strains.</p> </div

Phylogenetic analysis of the A) HA1 fragment of hemagglutinin, HA gene (954nt) and B) neuraminidase, NA gene (1,388nt) of influenza A(H3N2) isolates.

<p>Trees were constructed using the Neighbor-Joining method. Numbers at the nodes indicate confidence levels of bootstrap analysis with 1,000 replicates as percentage value. Amino acid substitutions that characterized a particular branch are indicated on the left side node. Vaccine strains are italicized and in red. Reference strains are boldfaced.</p

Detection of influenza virus type, subtype and antiviral-resistance by cycling probe real time PCR.

*<p>oseltamivir-resistant (OsR): H275Y mutation in NA.</p>**<p>amantadine-resistant (AmR): S31N mutation in M2.</p><p>“-” no samples collected.</p>a<p>Percentage of antiviral resistant viruses in each season.</p

Observed mutations in the antigenic sites of HA of influenza virus isolates in Japan, 2009–2010 and 2010–2011.

<p>Three-dimensional structures of trimeric HA were downloaded from the Protein Data Bank (RCSB PDB, <a href="http://www.pdb.org" target="_blank">http://www.pdb.org</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036455#pone.0036455-Berman1" target="_blank">[44]</a> and visualized using PyMol (<a href="http:www.pymol.org" target="_blank">http:www.pymol.org</a>). (A) The amino acid differences in the antigenic sites of HA between Japanese A(H1N1)pdm09 isolates and vaccine strain, A/California/07/2009 were compared. Amino acid substitutions at G140E, A141S, I166V, G170E, S203T, R203T, D222E, E235K are located in antigenic site Ca (orange); L70F is located in antigenic site Cb (blue); K153T, K160M, K163T/N in antigenic site Sa (magenta); and S185T, A186T in antigenic site Sb (cyan). Amino acid changes outside the antigenic sites are shown in yellow. PDB entry: 3LZG. (B) HA antigenic site mutations between Japanese A(H3N2) isolates and vaccine strain, A/Perth/16/2009 were compared. N144K mutation is localized in antigenic site A (red); P162S in antigenic site B (orange); G50E/K. T212A, and E280A/S/T are localized in antigenic site C (green); I260M and R261Q are located in antigenic site E (blue). PDB entry: 1MQL (C) Amino acid substitutions in the HA antigenic sites of influenza B isolates in Japan and vaccine strain, B/Brisbane/60/2008 were compared. Mutations at A127T, V146I, and S150I are localized at antigenic site A (red); N165K/Y and K209N are located in antigenic site B (orange); and S229D is located in antigenic site D (violet). PDB entry: 2RFT.</p

Amino acid mutations differences in the NA of influenza virus isolates in Japan, 2009–2010 and 2010–2011.

<p>Three-dimensional structures of monomeric NA were downloaded from the Protein Data Bank (RCSB PDB, <a href="http://www.pdb.org" target="_blank">http://www.pdb.org</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036455#pone.0036455-Berman1" target="_blank">[44]</a> and visualized using PyMol (<a href="http:www.pymol.org" target="_blank">http:www.pymol.org</a>). The top view of the NA is shown. (A) The amino acid differences between A(H1N1)pdm09 isolates in Japan and vaccine strain, A/California/07/2009 were compared. Amino acid substitutions V241I and N369K are shown in yellow. These amino acid changes are located outside the antigenic sites but are phylogenetically relevant. PDB entry: 3NSS. (B) Antigenic site mutations between Japanese A(H3N2) isolates and vaccine strain, A/Perth/16/2009 were compared. L338F mutation is located in antigenic site F’ (olive); K369T is localized in antigenic site I’; and R400K and N402D are located in antigenic site K’. PDB entry: 1IVG (C) Amino acid substitutions in the NA antigenic sites of Japanese influenza B isolates and vaccine strain, B/Brisbane/60/2008 were compared. Mutations at N329D is localized at antigenic site F’ (olive); and D340N/D is located in antigenic site G’ (violet). PDB entry: 1INF.</p

Phylogenetic analysis of the A) HA1 fragment of hemagglutinin, HA gene (829nt) and B) neuraminidase, NA gene (1,413nt) of A(H1N1)pdm isolates.

<p>Trees were constructed using the Neighbor-Joining method. Numbers at the nodes indicate confidence levels of bootstrap analysis with 1,000 replicates as percentage value. Amino acid substitutions that characterized a particular branch are indicated on the left side node. Vaccine strains are italicized and in red. Reference strains are boldfaced. Sequences from 2009–2010 are in pink and sequences from 2010–2011 are in blue. Oseltamivir-resistant strains (OsR) are indicated with filled circles (•) and amantadine-sensitive strains (AmS) are indicated with filled triangles (▴).</p

Pengaruh Mutagen Etil Metan Sulfonat (Ems) Terhadap Pertumbuhan Kultur in Vitro Iles-iles {Amorphophallus Muelleri Blume) [Effects of Ethyl Methane Sulphonate {Ems} on Growth of I Iies-lies (Amorphophallus Muelleri Blume) in Vitro Cultures]

Amorphophallus muelleri Blume (Araceae) is one of 27 Amorphophallus species occur wild in Indonesia (Sumatera, Java, Floresand Timor). The species is valued for its glucoman content for use in food industry (heathy diet food), paper industry, pharmacyand cosmetics. The cultivation of A. muelleri is hampered by limited genetic quality of seed. The species is triploid (2n=3x=39),the seed is developed apomictically. and pollen production is low. The species is only propagated vegetatively. This may explainthat the species is difficult to breed conventionally and genetic variabillity in the exiting landaraces cultivars is rather limited.Induced mutation using ethyl methan sulfonate is one of techniques to increase genetic variation. The present research is aimed todetermine Lethal Dosage (LD) 50% and 75% of EMS and to study effects of EMS on growth of A, muelleri in vitro cultures for usein induced mutation program. Results of the experiment showed that LD-50 and LD-75 was observed at 0.875% EMS and 0.5%EMS. respectively. Number of shoot, and percentage of rooting culture were decreasing as EMS level concentration increases

Additional file 1: of Genetic characterization of measles virus in the Philippines, 2008–2011

Figure S1. Maximum clade credibility (MCC) tree of the N gene sequence of measles virus in the Philippines using the Bayesian Markov chain Monte Carlo (MCMC) method. X-axis represents the year of virus detection or isolation. Samples that were detected in 2008 are indicated by blue font color; 2009 (green); 2010 (orange); and 2011 (red). Genotype D9 MeVs are highlighted in blue box and genotype G3 viruses are highlighted in green box. Figures near the tree nodes represent posterior probability values. The scale bar represents nucleotide substitutions per site per year