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  1. Fulltext Characterization and Transcriptome Studies of Autoinducer Synthase Gene from Multidrug Resistant Acinetobacter baumannii Strain 863
    Ng CK, How KY, Tee KK, Chan KG
    Genes (Basel), 2019 04 08;10(4).
    PMID: 30965610 DOI: 10.3390/genes10040282
    Quorum sensing (QS) is a cell-to-cell communication system that uses autoinducers as signaling molecules to enable inter-species and intra-species interactions in response to external stimuli according to the population density. QS allows bacteria such as Acinetobacter baumannii to react rapidly in response to environmental changes and hence, increase the chances of survival. A. baumannii is one of the causative agents in hospital-acquired infections and the number of cases has increased remarkably in the past decade. In this study, A. baumannii strain 863, a multidrug-resistant pathogen, was found to exhibit QS activity by producing N-acyl homoserine lactone. We identified the autoinducer synthase gene, which we named abaI, by performing whole genome sequencing analysis of A. baumannii strain 863. Using high resolution tandem triple quadrupole mass spectrometry, we reported that abaI of A. baumannii strain 863 produced 3-hydroxy-dodecanoyl-homoserine lactone. A gene deletion mutant was constructed, which confirmed the functionality of abaI. A growth defect was observed in the QS-deficient mutant strain. Transcriptome profiling was performed to determine the possible genes regulated by QS. Four groups of genes that showed differential expression were discovered, namely those involved in carbon source metabolism, energy production, stress response and the translation process.
    Matched MeSH terms: Recombination, Genetic/genetics
  2. Fulltext Comparing photoelectrochemical water oxidation, recombination kinetics and charge trapping in the three polymorphs of TiO2
    Moss B, Lim KK, Beltram A, Moniz S, Tang J, Fornasiero P, et al.
    Sci Rep, 2017 06 07;7(1):2938.
    PMID: 28592816 DOI: 10.1038/s41598-017-03065-5
    In this article we present the first comparative study of the transient decay dynamics of photo-generated charges for the three polymorphs of TiO2. To our knowledge, this is the first such study of the brookite phase of TiO2 over timescales relevant to the kinetics of water splitting. We find that the behavior of brookite, both in the dynamics of relaxation of photo-generated charges and in energetic distribution, is similar to the anatase phase of TiO2. Moreover, links between the rate of recombination of charge carriers, their energetic distribution and the mode of transport are made in light of our findings and used to account for the differences in water splitting efficiency observed across the three polymorphs.
    Matched MeSH terms: Recombination, Genetic
  3. Identification of new sub-genotypes of virulent Newcastle disease virus with potential panzootic features
    Miller PJ, Haddas R, Simanov L, Lublin A, Rehmani SF, Wajid A, et al.
    Infect Genet Evol, 2015 Jan;29:216-29.
    PMID: 25445644 DOI: 10.1016/j.meegid.2014.10.032
    Virulent Newcastle disease virus (NDV) isolates from new sub-genotypes within genotype VII are rapidly spreading through Asia and the Middle East causing outbreaks of Newcastle disease (ND) characterized by significant illness and mortality in poultry, suggesting the existence of a fifth panzootic. These viruses, which belong to the new sub-genotypes VIIh and VIIi, have epizootic characteristics and do not appear to have originated directly from other genotype VII NDV isolates that are currently circulating elsewhere, but are related to the present and past Indonesian NDV viruses isolated from wild birds since the 80s. Viruses from sub-genotype VIIh were isolated in Indonesia (2009-2010), Malaysia (2011), China (2011), and Cambodia (2011-2012) and are closely related to the Indonesian NDV isolated in 2007, APMV1/Chicken/Karangasem, Indonesia (Bali-01)/2007. Since 2011 and during 2012 highly related NDV isolates from sub-genotype VIIi have been isolated from poultry production facilities and occasionally from pet birds, throughout Indonesia, Pakistan and Israel. In Pakistan, the viruses of sub-genotype VIIi have replaced NDV isolates of genotype XIII, which were commonly isolated in 2009-2011, and they have become the predominant sub-genotype causing ND outbreaks since 2012. In a similar fashion, the numbers of viruses of sub-genotype VIIi isolated in Israel increased in 2012, and isolates from this sub-genotype are now found more frequently than viruses from the previously predominant sub-genotypes VIId and VIIb, from 2009 to 2012. All NDV isolates of sub-genotype VIIi are approximately 99% identical to each other and are more closely related to Indonesian viruses isolated from 1983 through 1990 than to those of genotype VII, still circulating in the region. Similarly, in addition to the Pakistani NDV isolates of the original genotype XIII (now called sub-genotype XIIIa), there is an additional sub-genotype (XIIIb) that was initially detected in India and Iran. This sub-genotype also appears to have as an ancestor a NDV strain from an Indian cockatoo isolated in 1982. These data suggest the existence of a new panzootic composed of viruses of subgenotype VIIi and support our previous findings of co-evolution of multiple virulent NDV genotypes in unknown reservoirs, e.g. as recorded with the virulent NDV identified in Dominican Republic in 2008. The co-evolution of at least three different sub-genotypes reported here and the apparent close relationship of some of those genotypes from ND viruses isolated from wild birds, suggests that identifying wild life reservoirs may help predict new panzootics.
    Matched MeSH terms: Recombination, Genetic
  4. Fulltext Two-Dimensional, Hierarchical Ag-Doped TiO2 Nanocatalysts: Effect of the Metal Oxidation State on the Photocatalytic Properties
    Md Saad SK, Ali Umar A, Ali Umar MI, Tomitori M, Abd Rahman MY, Mat Salleh M, et al.
    ACS Omega, 2018 Mar 31;3(3):2579-2587.
    PMID: 31458546 DOI: 10.1021/acsomega.8b00109
    This paper reports the synthesis of two-dimensional, hierarchical, porous, and (001)-faceted metal (Ag, Zn, and Al)-doped TiO2 nanostructures (TNSs) and the study of their photocatalytic activity. Two-dimensional metal-doped TNSs were synthesized using the hydrolysis of ammonium hexafluorotitanate in the presence of hexamethylenetetramine and metal precursors. Typical morphology of metal-doped TNSs is a hierarchical nanosheet that is composed of randomly stacked nanocubes (dimensions of up to 5 μm and 200 nm in edge length and thickness, respectively) and has dominant (001) facets exposed. Raman analysis and X-ray photoelectron spectroscopy results indicated that the Ag doping, compared to Zn and Al, much improves the crystallinity degree and at the same time dramatically lowers the valence state binding energy of the TNS and provides an additional dopant oxidation state into the system for an enhanced electron-transfer process and surface reaction. These are assumed to enhance the photocatalytic of the TNS. In a model of photocatalytic reaction, that is, rhodamine B degradation, the AgTNS demonstrates a high photocatalytic activity by converting approximately 91% of rhodamine B within only 120 min, equivalent to a rate constant of 0.018 m-1 and ToN and ToF of 94 and 1.57 min-1, respectively, or 91.1 mmol mg-1 W-1 degradation when normalized to used light source intensity, which is approximately 2 times higher than the pristine TNS and several order higher when compared to Zn- and Al-doped TNSs. Improvement of the crystallinity degree, decrease in the defect density and the photogenerated electron and hole recombination, and increase of the oxygen vacancy in the AgTNS are found to be the key factors for the enhancement of the photocatalytic properties. This work provides a straightforward strategy for the preparation of high-energy (001) faceted, two-dimensional, hierarchical, and porous Ag-doped TNSs for potential use in photocatalysis and photoelectrochemical application.
    Matched MeSH terms: Recombination, Genetic
  5. Fulltext Changes in the EV-A71 Genome through Recombination and Spontaneous Mutations: Impact on Virulence
    Mandary MB, Poh CL
    Viruses, 2018 06 12;10(6).
    PMID: 29895721 DOI: 10.3390/v10060320
    Enterovirus 71 (EV-A71) is a major etiological agent of hand, foot and mouth disease (HFMD) that mainly affects young children less than five years old. The onset of severe HFMD is due to neurological complications bringing about acute flaccid paralysis and pulmonary oedema. In this review, we address how genetic events such as recombination and spontaneous mutations could change the genomic organization of EV-A71, leading to an impact on viral virulence. An understanding of the recombination mechanism of the poliovirus and non-polio enteroviruses will provide further evidence of the emergence of novel strains responsible for fatal HFMD outbreaks. We aim to see if the virulence of EV-A71 is contributed solely by the presence of fatal strains or is due to the co-operation of quasispecies within a viral population. The phenomenon of quasispecies within the poliovirus is discussed to reflect viral fitness, virulence and its implications for EV-A71. Ultimately, this review gives an insight into the evolution patterns of EV-A71 by looking into its recombination history and how spontaneous mutations would affect its virulence.
    Matched MeSH terms: Recombination, Genetic*
  6. Fulltext Enhancing Photocurrent Performance Based on Photoanode Thickness and Surface Plasmon Resonance Using Ag-TiO2 Nanocomposites in Dye-Sensitized Solar Cells
    Lokman MQ, Shafie S, Shaban S, Ahmad F, Jaafar H, Mohd Rosnan R, et al.
    Materials (Basel), 2019 Jun 30;12(13).
    PMID: 31262020 DOI: 10.3390/ma12132111
    This study investigated the different thicknesses of TiO2 photoanode films and the effect of surface plasmon resonance (SPR) of Ag-TiO2 nanocomposites on the current-voltage (I-V) performance of dye-sensitized solar cells (DSSC). The TiO2 layer was deposited using the doctor blade technique and the thickness of the TiO2 films was controlled by using a different number of Scotch tape layers. The silver nanoparticles (AgNP) were synthesised using a chemical reduction method and the concentration of sodium citrate as a reducing agent was varied from 4 to 12 mM to study the effect of citrate ion on the size of the nanoparticles. Ag-TiO2 nanopowder was prepared by adding pure anatase TiO2 powder into AgNP colloidal solution. The mixture was left to dry for 24 h to obtain Ag-TiO2 powder for paste preparation. The three-layer Scotch tape, with thickness of 14.38 µm, achieved a high efficiency of 4.14%. This results showed that three layers was the optimal thickness to improve dye loading and to reduce the charge recombination rate. As for the Ag-TiO2 nanocomposites, 10 mM of AgNP, with a mean diameter of 65.23 nm and high efficiency of 6.92%, proved that SPR can enhance the absorption capability of dye and improve the photon-to-electron generation.
    Matched MeSH terms: Recombination, Genetic
  7. Fulltext Boosting Photovoltaic Performance of Dye-Sensitized Solar Cells Using Silver Nanoparticle-Decorated N,S-Co-Doped-TiO2 Photoanode
    Lim SP, Pandikumar A, Lim HN, Ramaraj R, Huang NM
    Sci Rep, 2015;5:11922.
    PMID: 26146362 DOI: 10.1038/srep11922
    A silver nanoparticle-decorated N,S-co-doped TiO2 nanocomposite was successfully prepared and used as an efficient photoanode in high-performance dye-sensitized solar cells (DSSCs) with N719 dye. The DSSCs assembled with the N,S-TiO2@Ag-modified photoanode demonstrated an enhanced solar-to-electrical energy conversion efficiency of 8.22%, which was better than that of a DSSC photoanode composed of unmodified TiO2 (2.57%) under full sunlight illumination (100 mWcm(-2), AM 1.5 G). This enhanced efficiency was mainly attributed to the reduced band gap energy, improved interfacial charge transfer, and retarded charge recombination process. The influence of the Ag content on the overall efficiency was also investigated, and the optimum Ag content with N,S-TiO2 was found to be 20 wt%. Because of the enhanced solar energy conversion efficiency of the N,S-TiO2@Ag nanocomposite, it should be considered as a potential photoanode for high-performance DSSCs.
    Matched MeSH terms: Recombination, Genetic
  8. Fulltext Cloning and expression of Toxoplasma gondii dense granular protein 4 (GRA4) in Pichia pastoris
    Lau YL, Hasan MT, Thiruvengadam G, Idris MM, Init I
    Trop Biomed, 2010 Dec;27(3):525-33.
    PMID: 21399595
    GRA4 of Toxoplasma gondii has been shown to prompt IgG, IgM and IgA responses in previous studies and is thus considered one of the major immunogenic proteins from T. gondii that can be used for both diagnostics purposes and vaccine development. This study seeks to clone and express the GRA4 in Pichia pastoris, which has numerous advantages over other systems for expression of eukaryotic proteins. In order to achieve this, the gene was cloned into the pPICZα A expression vector, which was then incorporated into the P. pastoris genome via insertional integration for expression of the recombinant protein, under the AOX1 promoter. The antigen was expressed along with the prepro sequence of the α-factor of yeast so that it could be excreted out of the P. pastoris cells and obtained from the medium. Upon SDS-PAGE analysis it was found that the recombinant protein was expressed optimally as a 40 kDa protein after 96 hours of induction with 0.75% of methanol. The expressed GRA4 protein showed discrepancy in size with the calculated molecular mass. This may be attributed to the various posttranslational modifications including glycosylation and phosphorylation. Despite the difference in molecular weight, the recombinant protein was able to detect toxoplasmosis in Western blot format. The recombinant GRA4 was expressed with an intact polyhistidine-tag, which could be used for future purification of the antigen.
    Matched MeSH terms: Recombination, Genetic
  9. Evidence for possible biological advantages of the newly emerging HIV-1 circulating recombinant form from Malaysia - CRF33_01B in comparison to its progenitors - CRF01_AE and subtype B
    Lau KA, Wang B, Miranda-Saksena M, Boadle R, Kamarulzaman A, Ng KP, et al.
    Curr. HIV Res., 2010 Apr;8(3):259-71.
    PMID: 20214658
    In Malaysia, co-circulation of CRF01_AE and subtype B has resulted in the emergence of the second generation derivative; CRF33_01B in approximately 20% of its HIV-1 infected individuals. Our objective was to identify possible biological advantages that CRF33_01B possesses over its progenitors. Biological and molecular comparisons of CRF33_01B against its parental subtypes clearly show that CRF33_01B replicated better in activated whole peripheral blood mononuclear cells (PBMCs) and CD4+ T-lymphocytes, but not monocyte-derived macrophages (MDMs). Also, its acquired fitness was greater than CRF01_AE but not subtype B. Moreover, CRF33_01B has higher rate of apoptotic cell death and syncytia induction compared to subtype B. These adaptive and survival abilities could have been acquired by CRF33_01B due to the incorporation of subtype B fragments into the gag-RT region of its full-length genome. Our studies confirm the previously held belief that HIV-1 strains may harbor enhanced biological fitness upon recombination. We therefore estimate a possible gradual replacement of the current predominance of CRF01_AE, as well as wider dissemination of CRF33_01B, together with the identification of other new CRF01_AE/B inter-subtype recombinants in Malaysia.
    Matched MeSH terms: Recombination, Genetic
  10. Continuous crossover(s) events of HIV-1 CRF01_AE and B subtype strains in Malaysia: evidence of rapid and extensive HIV-1 evolution in the region
    Lau KA, Wang B, Kamarulzaman A, Ngb KP, Saksena NK
    Curr. HIV Res., 2008 Mar;6(2):108-16.
    PMID: 18336258
    The Asian HIV epidemic appears to be complex, characterized by the prevalence of multiple subtypes and circulating recombinant forms with gradual replacement of pure HIV-1 subtypes in several geographical regions. The main objectives of the present study are to identify and analyse the full-length viral genomes of three unique recombinant forms (URFs); the HIV-1 isolates 07MYKLD47, 07MYKLD48 and 07MYKLD49 from Malaysia. Long-range polymerase chain reaction (PCR) amplification of seven overlapping reading frames was used to derive near full-length HIV-1 genomes. Detailed phylogenetic and bootscanning analyses were performed to determine phylogenetic associations and subtypic assignments. We further confirmed the mosaic composition of these CRF01_AE/B inter-subtype recombinant forms, which are composed of B-subtype fragment(s) in the backbone of CRF01_AE. Both 07MYKLD47 and 07MYKLD48 have an insertion of B subtype (880 bp and 532 bp) in the gag-pol and gp41-env gene regions, respectively. Whereas the isolate 07MYKLD49 has three B-subtype fragments inserted in different gene region along the genome; one each in the gag-pol (1862 bp) and pol-vif (1935 bp) regions, and a short B-subtype insertion (541 bp) in the 5' LTR-gag region. This highlights the public health relevance of newly emerging second generation HIV-1 recombinant forms and their dispersal, along with their rapid and continuous evolution in the region.
    Matched MeSH terms: Recombination, Genetic*
  11. Near full-length sequence analysis of a Unique CRF01_AE/B recombinant from Kuala Lumpur, Malaysia
    Lau KA, Wang B, Kamarulzaman A, Ng KP, Saksena NK
    AIDS Res Hum Retroviruses, 2007 Sep;23(9):1139-45.
    PMID: 17919110
    A new HIV-1 circulating recombinant form (CRF), CRF33_01B, has been identified in Malaysia. Concurrently we found a unique recombinant form (URF), that is, the HIV-1 isolate 06MYKLD46, in Kuala Lumpur, Malaysia. It is composed of B or a Thai variant of the B subtype (B') and CRF01_AE. Here, we determined the near full-length genome of the isolate 06MYKLD46 and performed detailed phylogenetic and bootscanning analyses to characterize its mosaic composition and to further confirm the subtype assignments. Although the majority of the 06MYKLD46 genome is CRF01_AE, we found three short fragments of B or B' subtype inserted along the genome. These B or B' subtype regions were 716 and 335 bp, respectively, in the protease-reverse transcriptase (PR-RT) region, similar to those found in CRF33_01B, as well as an extra 590 bp in the env gene region. Thus we suggest that 06MYKLD46 is a possible second-generation HIV-1 recombinant derived from CRF33_01B.
    Matched MeSH terms: Recombination, Genetic*
  12. Fulltext Characterization of the key aroma compounds in three types of bagels by means of the sensomics approach
    Lasekan O, Dabaj F, Muniandy M, Juhari NH, Lasekan A
    BMC Chem, 2021 Mar 13;15(1):16.
    PMID: 33714268 DOI: 10.1186/s13065-021-00743-4
    BACKGROUND: To evaluate the impact of cold fermentation time on bagel rolls, the key aroma-active compounds in the volatile fractions obtained from three different bagel rolls through solvent assisted flavor evaporation (SAFE) were sequentially characterized by an aroma extract dilution analysis (AEDA), quantified by stable isotope dilution and analyzed by odor activity values (OAVs) respectively.

    RESULTS: Findings revealed 40 aroma-active compounds with flavor dilution (FD) factor ranges of 2-1024. Of these, 22 compounds (FD ≥ 16) were quantified by stable isotope dilution assays (SIDA). Subsequent analysis of the 22 compounds by odor activity values (OAVs) revealed 14 compounds with OAVs ≥ 1 and the highest concentrations were obtained for 2,3-butanedione, 2-phenylethanol, 3-methylbutanal and acetoin respectively. Two recombination models of the bagels (i.e. 24 h and 48 h bagels) showed similarity to the corresponding bagels. Omission tests confirmed that 2,3-butanedione (buttery), acetoin (buttery), 2-acetyl-1-pyrroline (roasty), 5-methyl-2-furanmethanol (bread-like), (Z)-4-heptenal (biscuit-like) and 4-hydroxy-2,5-dimethyl-3(2H)-furanone, were the key aroma compounds. Additionally, acetic acid, butanoic acid, 2-phenylethanol (honey-like), 3-methylbutanoic acid, 2/3-methylbutanal, vanillin, 3-methylbutanol, methional were also important odorants of the bagel.

    CONCLUSION: Whilst the long, cold fermented bagels exhibited roasty, malty, buttery, baked potato-like, smoky and biscuit-like notes, the control bagels produced similar but less intense odor notes.

    Matched MeSH terms: Recombination, Genetic
  13. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins
    Lam TT, Jia N, Zhang YW, Shum MH, Jiang JF, Zhu HC, et al.
    Nature, 2020 07;583(7815):282-285.
    PMID: 32218527 DOI: 10.1038/s41586-020-2169-0
    The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-21. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection2. Although bats are probable reservoir hosts for SARS-CoV-2, the identity of any intermediate host that may have facilitated transfer to humans is unknown. Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity in the receptor-binding domain to SARS-CoV-2. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission.
    Matched MeSH terms: Recombination, Genetic
  14. Controlled Synthesis of Well-Aligned and Highly Ordered TiO₂ Nanotubes Without Bundling for Enhanced Solar-Powered Photoelectrochemical Responses
    Lai CW, Lau KS, Chou PM
    J Nanosci Nanotechnol, 2019 Dec 01;19(12):7934-7942.
    PMID: 31196312 DOI: 10.1166/jnn.2019.16777
    Using solar-powered water electrolysis systems for hydrogen generation is a key decision for the development of a sustainable hydrogen economy. A facile approach is presented in the present investigation to improve the solar-powered photoelectrochemical performance of water electrolysis systems by synthesising well-aligned and highly ordered TiO₂ nanotube films without bundling through the electrochemical anodisation technique. Herein, geometrical calculations were conducted for all synthesised TiO₂ nanotubes, and determination of the aspect ratio (AR) and geometric surface area factor (G) was achieved. On the basis of the collected data, well-aligned TiO₂ nanotubes with an AR of approximately 60 and G of approximately 400 m² ·g-1 were successfully formed in an electrolyte mixture of ethylene glycol with 0.3 wt% NH4F and 5 wt% H₂O₂ at 40 V for 60 min. The nanotubes were subsequently annealed at 400 °C to form anatase-phase TiO₂ nanotube films. The resultant well-aligned and highly ordered TiO₂ nanotube films exhibited a photocurrent density of 1.5 mA · cm-2 due to a large number of photo-induced electrons moving along the tube axis and perpendicular to the Ti substrate, which greatly reduces interfacial recombination losses.
    Matched MeSH terms: Recombination, Genetic
  15. Visible light photoelectrochemical performance of W-loaded TiO2 nanotube arrays: structural properties
    Lai CW, Sreekantan S
    J Nanosci Nanotechnol, 2012 Apr;12(4):3170-4.
    PMID: 22849082
    Well aligned TiO2 nanotubes were successfully synthesized by anodization of Ti foil at 60 V in a fluorinated bath comprised of ethylene glycol with 5 wt% of NH4F and 5 wt% of H2O2. In order to enhance the visible light absorption and photoelectrochemical response of pure TiO2 nanotube arrays, a mixed oxide system (W-TiO2) was investigated. W-TiO2 nanotube arrays were prepared using radio-frequency (RF) sputtering to incorporate the W into the lattice of TiO2 nanotube arrays. The W atoms occupy the substitutional position within the vacancies of TiO2 nanotube arrays. The as-anodized TiO2 is amorphous in nature while the annealed TiO2 is anatase phase. The mixed oxide (W-TiO2) system in suitable TiO2 phase plays important roles in efficient electron transfers due to the reduction in electron-hole recombination. In this article, the effect of the sputtered W into the as-anodized/annealed TiO2 nanotube arrays on the photoelectrochemical response was presented.
    Matched MeSH terms: Recombination, Genetic
  16. Fulltext Engineering integrative vectors based on phage site-specific recombination mechanism for Lactococcus lactis
    Koko I, Song AA, Masarudin MJ, Abdul Rahim R
    BMC Biotechnol, 2019 11 27;19(1):82.
    PMID: 31775775 DOI: 10.1186/s12896-019-0575-x
    BACKGROUND: Site-specific integration system allows foreign DNA to be integrated into the specific site of the host genome, enabling stable expression of heterologous protein. In this study, integrative vectors for secretion and surface display of proteins were constructed based on a lactococcal phage TP901-1 integrating system.

    RESULTS: The constructed integration system comprises of a lactococcal promoter (PnisA or P170), phage attachment site (attP) from bacteriophage TP901-1, a signal peptide (USP45 or SPK1) for translocation of the target protein, and a PrtP344 anchor domain in the case of the integrative vectors for surface display. There were eight successfully constructed integrative vectors with each having a different combination of promoter and signal peptide; pS1, pS2, pS3 and pS4 for secretion, and pSD1, pSD2, pSD3 and pSD4 for surface display of desired protein. The integration of the vectors into the host genome was assisted by a helper vector harbouring the integrase gene. A nuclease gene was used as a reporter and was successfully integrated into the L. lactis genome and Nuc was secreted or displayed as expected. The signal peptide SPK1 was observed to be superior to USP45-LEISSTCDA fusion in the secretion of Nuc. As for the surface display integrative vector, all systems developed were comparable with the exception of the combination of P170 promoter with USP45 signal peptide which gave very low signals in whole cell ELISA.

    CONCLUSION: The engineered synthetic integrative vectors have the potential to be used for secretion or surface display of heterologous protein production in lactococcal expression system for research or industrial purposes, especially in live vaccine delivery.

    Matched MeSH terms: Recombination, Genetic*
  17. Two more coronaviruses may infect people
    King A
    Science, 2021 05 28;372(6545):893.
    PMID: 34045334 DOI: 10.1126/science.372.6545.893
    Matched MeSH terms: Recombination, Genetic
  18. Molecular Epidemiology of a novel re-assorted epidemic strain of equine influenza virus in Pakistan in 2015-16
    Khan A, Mushtaq MH, Ahmad MUD, Nazir J, Farooqi SH, Khan A
    Virus Res, 2017 08 15;240:56-63.
    PMID: 28757141 DOI: 10.1016/j.virusres.2017.07.022
    BACKGROUND: A widespread epidemic of equine influenza (EI) occurred in nonvaccinated equine population across multiple districts in Khyber Pakhtunkhwa Province of Pakistan during 2015-2016.

    OBJECTIVES AND METHODS: An epidemiological surveillance study was conducted from Oct 2015 to April 2016 to investigate the outbreak. EI virus strains were isolated in embryonated eggs from suspected equines swab samples and were subjected to genome sequencing using M13 tagged segment specific primers. Phylogenetic analyses of the nucleotide sequences were concluded using Geneious. Haemagglutinin (HA), Neuraminidase (NA), Matrix (M) and nucleoprotein (NP) genes nucleotide and amino acid sequences of the isolated viruses were aligned with those of OIE recommended, FC-1, FC-2, and contemporary isolates of influenza A viruses from other species.

    RESULTS: HA and NA genes amino acid sequences were very similar to Tennessee/14 and Malaysia/15 of FC-1 and clustered with the contemporary isolates recently reported in the USA. Phylogenetic analysis showed that these viruses were mostly identical (with 99.6% and 97.4% nucleotide homology) to, and were reassortants containing chicken/Pakistan/14 (H7N3) and Canine/Beijing/10 (H3N2) like M and NP genes. Genetic analysis indicated that A/equine/Pakistan/16 viruses were most probably the result of several re-assortments between the co-circulating avian and equine viruses, and were genetically unlike the other equine viruses due to the presence of H7N3 or H3N2 like M and NP genes.

    CONCLUSION: Epidemiological data analysis indicated the potential chance of mixed, and management such as mixed farming system by keeping equine, canine and backyard poultry together in confined premises as the greater risk factors responsible for the re-assortments. Other factors might have contributed to the spread of the epidemic, including low awareness level, poor control of equine movements, and absence of border control disease strategies.

    Matched MeSH terms: Recombination, Genetic*
  19. Construction of an infectious molecular clone of Japanese encephalitis virus genotype V and its derivative subgenomic replicon capable of expressing a foreign gene
    Ishikawa T, Abe M, Masuda M
    Virus Res, 2015 Jan 2;195:153-61.
    PMID: 25451067 DOI: 10.1016/j.virusres.2014.10.010
    Japanese encephalitis virus (JEV) genotype V was originally isolated in Malaysia in 1952 and has long been restricted to the area. In 2009, sudden emergence of the genotype V in China and Korea was reported, suggesting expansion of its geographical distribution. Although studies on the genotype V are becoming more important, they have been limited partly due to lack of its infectious molecular clone. In this study, a plasmid carrying cDNA corresponding to the entire genome of JEV Muar strain, which belongs to genotype V, in the downstream of T7 promoter was constructed. Electroporation of viral RNA transcribed by T7 RNA polymerase (T7RNAP) in vitro from the plasmid led to production of progeny viruses both in mammalian and mosquito cells. Also, transfection of the infectious clone plasmid into mammalian cells expressing T7RNAP transiently or stably was demonstrated to generate infectious progenies. When the viral structural protein genes were partially deleted from the full-length cDNA, the subgenomic RNA transcribed in vitro from the modified plasmid was shown to replicate itself in mammalian cells as a replicon. The replicon carrying the firefly luciferase gene in place of the deleted structural protein genes was also shown to efficiently replicate itself and express luciferase in mammalian cells. Compared with the replicon derived from JEV genotype III (Nakayama strain), the genotype V-derived replicon appeared to be more tolerant to introduction of a foreign gene. The infectious clone and the replicons constructed in this study may serve as useful tools for characterizing JEV genotype V.
    Matched MeSH terms: Recombination, Genetic*
  20. Fulltext Genetic Characterization of a Panel of Diverse HIV-1 Isolates at Seven International Sites
    Hora B, Keating SM, Chen Y, Sanchez AM, Sabino E, Hunt G, et al.
    PLoS One, 2016;11(6):e0157340.
    PMID: 27314585 DOI: 10.1371/journal.pone.0157340
    HIV-1 subtypes and drug resistance are routinely tested by many international surveillance groups. However, results from different sites often vary. A systematic comparison of results from multiple sites is needed to determine whether a standardized protocol is required for consistent and accurate data analysis. A panel of well-characterized HIV-1 isolates (N = 50) from the External Quality Assurance Program Oversight Laboratory (EQAPOL) was assembled for evaluation at seven international sites. This virus panel included seven subtypes, six circulating recombinant forms (CRFs), nine unique recombinant forms (URFs) and three group O viruses. Seven viruses contained 10 major drug resistance mutations (DRMs). HIV-1 isolates were prepared at a concentration of 107 copies/ml and compiled into blinded panels. Subtypes and DRMs were determined with partial or full pol gene sequences by conventional Sanger sequencing and/or Next Generation Sequencing (NGS). Subtype and DRM results were reported and decoded for comparison with full-length genome sequences generated by EQAPOL. The partial pol gene was amplified by RT-PCR and sequenced for 89.4%-100% of group M viruses at six sites. Subtyping results of majority of the viruses (83%-97.9%) were correctly determined for the partial pol sequences. All 10 major DRMs in seven isolates were detected at these six sites. The complete pol gene sequence was also obtained by NGS at one site. However, this method missed six group M viruses and sequences contained host chromosome fragments. Three group O viruses were only characterized with additional group O-specific RT-PCR primers employed by one site. These results indicate that PCR protocols and subtyping tools should be standardized to efficiently amplify diverse viruses and more consistently assign virus genotypes, which is critical for accurate global subtype and drug resistance surveillance. Targeted NGS analysis of partial pol sequences can serve as an alternative approach, especially for detection of low-abundance DRMs.
    Matched MeSH terms: Recombination, Genetic
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