Characterization of DNA-binding activity of Zα domains from poxviruses and the importance of the β-wing regions in converting B-DNA to Z-DNA

The E3L gene is essential for pathogenesis in vaccinia virus. The E3L gene product consists of an N-terminal Zα domain and a C-terminal double-stranded RNA (dsRNA) binding domain; the left-handed Z-DNA-binding activity of the Zα domain of E3L is required for viral pathogenicity in mice. E3L is highly conserved among poxviruses, including the smallpox virus, and it is likely that the orthologous Zα domains play similar roles. To better understand the biological function of E3L proteins, we have investigated the Z-DNA-binding behavior of five representative Zα domains from poxviruses. Using surface plasmon resonance (SPR), we have demonstrated that these viral Zα domains bind Z-DNA tightly. Ability of Zα[subscript E3L] converting B-DNA to Z-DNA was measured by circular dichroism (CD). The extents to which these Zαs can stabilize Z-DNA vary considerably. Mutational studies demonstrate that residues in the loop of the β-wing play an important role in this stabilization. Notably the Zα domain of vaccinia E3L acquires ability to convert B-DNA to Z-DNA by mutating amino acid residues in this region. Differences in the host cells of the various poxviruses may require different abilities to stabilize Z-DNA; this may be reflected in the observed differences in behavior in these Zα proteins.Korean Science and Engineering Foundation (National Research Laboratory Program (NRL-2006-02287))Korean Science and Engineering Foundation (Ubiquitome Research Program (M10533010002-06N3301-00210))Korean Science and Engineering Foundation (21C Frontier Functional Proteomics Program (FPR06B2-120))National Institutes of Health (U.S.)Ellison Medical FoundationKorea (South). Ministry of Science and Technology (National Laboratory program (NRL-2006-02287)

Aromatic hydrocarbon degradation of biofilm formed by microorganisms on cellulose material at 50 litre modules

Biofilms are defined as community of microorganisms which are irreversibly or reversibly attached on solid surfaces. These microorganisms are embedded in a self-produced exopolysaccharide matrix, and exhibit different growth and bioactivity compared with planktonic cells. With their high biomass density, stability, and potential for biodegradation of recalcitrant compounds contained in oil contaminated wastewater such as aromatic hydrocarbons. Aromatic hydrocarbons are the main constituents of petroleum and its refined products. These compounds are also quantitatively the main environmental pollutants worldwide. In this report, cellulose material was used as a carrier for forming biofilm by microorganisms to remove of these components. Cellulose material is considered as inexpensive, available, sustainable, little waste production and can be recycled. As a result, the microorganisms were successful to adhere on cellulose material at 50 liter module with cell density of 4.3x108 CFU/ml after 7 day-incubation. Under the scanning electron microscope with the 1500 magnification, the microbial cells had a very high density, closely linked together and firm adhesion on the cellulose material. The mixture species biofilm attached on cellulose carrier at 50 liter module had the ability to degrade 80.1, 78.3, 60.0, 98.5 and 91.2% of anthracene, fluorene, naphthalene, phenol and pyrene after 7 days, respectively. The obtained results showed that biofilm formed by multiple bacterial strains attached on cellulose material may considerably increase the degrading efficiency of aromatic hydrocarbon compounds. The results also indicated that cellulose material is suitable carrier to choose in removal of aromatic hydrocarbon contaminated wastewater. These results are considered as new approach to apply microbial films on cellulose material to degrade oil polluted waste-water in the environment

EVALUATION OF EFFICACY OF NIBRG-14 VACCINE AGAINST HIGHLY PATHOGENIC H5N1 VIRUSES ISOLATED DURING 2011 INFLUENZA OUTBREAKS IN VIETNAM

Highly pathogenic avian  influenza (HPAI) H5N1 viruses continue to be endemic  in many Asian countries causing  lethal  infections  in human. The vaccine virus  (NIBRG-14) developed from a H5N1 virus strain (A/Vietnam/1194/2004) has been approved by WHO for use in human as  well  as  poultry  vaccine.  It  is  well-known  that  the  A/H5N1  viruses  have  diversified  both genetically  and  antigenically  allowing  them  to  escape  from  the  host  immune  surveillance system.  Therefore,  evaluation  of  the  vaccine  immunogenicity  and  its  relationship  to  newly emerging  viruses  is  crucially  important. NIBRG-14 virus particles propagated  in  embryonated chicken eggs were inactivated with formalin and adjuvanted with mineral oil to form a water-in-oil emulsion. The  resulting vaccine was  injected  subcutaneously  into chickens and ducks. The vaccinated birds were challenged with  the HPAI virus strains circulating  in Vietnam  including clade  1,  clade  2.3.2.1a  and  2.3.2.1b  at  day  21  post-vaccination  (p.  v.).  We  observed  that vaccinated birds were protected from manifestation of disease signs upon challenge with HPAI clade 1 and clade 2.3.2.1a viruses; however,  it did not confer protection against clade 2.3.2.1b challenge  andstressing  the  need  for  development  of  new  effective  vaccines  against  the  newly emerging viruses

Genetic variants of MICB and PLCE1 and associations with the laboratory features of dengue

Background: A previous genome-wide association study identified 2 susceptibility loci for severe dengue at MICB rs3132468 and PLCE1 rs3740360 and further work showed these mutations to be also associated with less severe clinical presentations. The aim of this study was to determine if these specific loci were associated with laboratory features of dengue that correlate with clinical severity with the aim of elucidating the functional basis of these genetic variants. Methods: This was a case-only analysis of laboratory-confirmed dengue patients obtained from 2 prospective cohort studies and 1 randomised clinical trial in Vietnam (Trial registration: ISRCTN ISRCTN03147572. Registered 24th July 2012). 2742 dengue cases were successfully genotyped at MICB rs3132468 and PLCE1 rs3740360. Laboratory variables were compared between genotypes and stratified by DENV serotype. Results: The analysis showed no association between MICB and PLCE1 genotype and early viraemia level, platelet nadir, white cell count nadir, or maximum haematocrit in both overall analysis and in analysis stratified by serotype. Discussion: The lack of an association between genotype and viremia level may reflect the sampling procedures within the included studies. The study findings mean that the functional basis of these mutations remains unclear. Trial registration: ISRCTN ISRCTN03147572. Registered 24th July 2012

Large-scale analysis of putative plasmids in clinical multidrug-resistant Escherichia coli isolates from Vietnamese patients

IntroductionIn the past decades, extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant (CR) Escherichia coli isolates have been detected in Vietnamese hospitals. The transfer of antimicrobial resistance (AMR) genes carried on plasmids is mainly responsible for the emergence of multidrug-resistant E. coli strains and the spread of AMR genes through horizontal gene transfer. Therefore, it is important to thoroughly study the characteristics of AMR gene-harboring plasmids in clinical multidrug-resistant bacterial isolates.MethodsThe profiles of plasmid assemblies were determined by analyzing previously published whole-genome sequencing data of 751 multidrug-resistant E. coli isolates from Vietnamese hospitals in order to identify the risk of AMR gene horizontal transfer and dissemination.ResultsThe number of putative plasmids in isolates was independent of the sequencing coverage. These putative plasmids originated from various bacterial species, but mostly from the Escherichia genus, particularly E. coli species. Many different AMR genes were detected in plasmid contigs of the studied isolates, and their number was higher in CR isolates than in ESBL-producing isolates. Similarly, the blaKPC-2, blaNDM-5, blaOXA-1, blaOXA-48, and blaOXA-181 β-lactamase genes, associated with resistance to carbapenems, were more frequent in CR strains. Sequence similarity network and genome annotation analyses revealed high conservation of the β-lactamase gene clusters in plasmid contigs that carried the same AMR genes.DiscussionOur study provides evidence of horizontal gene transfer in multidrug-resistant E. coli isolates via conjugative plasmids, thus rapidly accelerating the emergence of resistant bacteria. Besides reducing antibiotic misuse, prevention of plasmid transmission also is essential to limit antibiotic resistance

H2_{2}O2_{2} production in Lactobacillus strains isolated from the intestinal microbiome of healthy people

Lactobacillus sp. in the digestive tract are capable of producing H2O2 to inhibit the growth of harmful bacteria and balance the gut microflora. In this study, we have isolated 115 strains of Lactobacillus spp. from stool samples of healthy people in Ha Noi. Of the 50 tested Lactobacillus strains, 9 strains were capable of producing H2O2, of which the Lac.VFE-14 strain produced highly H2O2 with a concentration of 2.183 mM, followed by Lac.VFE-08 strains (2.081 mM) and Lac.VFE-04 (2.067 mM). All three strains grew well in MRS medium supplemented with bile salts or adjusted to low pH value. With 0.3% of bile salt, the survival rates of these 3 strains were 99%, 95% and 97%, respectively. At pH 3.0, after 3 hours of cultivation, the survival rates of the three strains were 98.54%, 94.15% and 95.27%, respectively. In addition, each of the cell-free culture supernatants of these three strains that inhibit the growth of S. aureus ATCC-23235. The inhibition zone diameters of the three strains were 19.0±1.0 mm, 14.0±1.0 mm and 11.7±1.3 mm, respectively. The results of 16S rRNA gene analyses showed that Lac.VFE-14, Lac.VFE-08 and Lac.VFE-04 had high similarity scores with L. plantarum ZZU 23 (100%), L. rhamnosus JCM 1136 (99%) and L. plantarum S7 (98.65%), respectively. This study indicates that all three strains have the potential to be used as probiotics in the future. 

Clinical evaluation of dengue and identification of risk factors for severe disease: protocol for a multicentre study in 8 countries

Background: The burden of dengue continues to increase globally, with an estimated 100 million clinically apparent infections occurring each year. Although most dengue infections are asymptomatic, patients can present with a wide spectrum of clinical symptoms ranging from mild febrile illness through to severe manifestations of bleeding, organ impairment, and hypovolaemic shock due to a systemic vascular leak syndrome. Clinical diagnosis of dengue and identification of which patients are likely to develop severe disease remain challenging. This study aims to improve diagnosis and clinical management through approaches designed a) to differentiate between dengue and other common febrile illness within 72 h of fever onset, and b) among patients with dengue to identify markers that are predictive of the likelihood of evolving to a more severe disease course. Method/Design: This is a prospective multi-centre observational study aiming to enrol 7–8000 participants aged ≥ 5 years presenting with a febrile illness consistent with dengue to outpatient health facilities in 8 countries across Asia and Latin America. Patients presenting within 72 h of fever onset who do not exhibit signs of severe disease are eligible for the study. A broad range of clinical and laboratory parameters are assessed daily for up to 6 days during the acute illness, and also at a follow up visit 1 week later. Discussion: Data from this large cohort of patients, enrolled early with undifferentiated fever, will be used to develop a practical diagnostic algorithm and a robust clinical case definition for dengue. Additionally, among patients with confirmed dengue we aim to identify simple clinical and laboratory parameters associated with progression to a more severe disease course. We will also investigate early virological and serological correlates of severe disease, and examine genetic associations in this large heterogeneous cohort. In addition the results will be used to assess the new World Health Organization classification scheme for dengue in practice, and to update the guidelines for “Integrated Management of Childhood Illness” used in dengue-endemic countries. Trial registration: NCT01550016. Registration Date: March 7, 201

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead