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  1. Fulltext Efficient Solar-Induced Photoelectrochemical Response Using Coupling Semiconductor TiO₂-ZnO Nanorod Film
    Abd Samad NA, Lai CW, Lau KS, Abd Hamid SB
    Materials (Basel), 2016 Nov 22;9(11).
    PMID: 28774068 DOI: 10.3390/ma9110937
    Efficient solar driven photoelectrochemical (PEC) response by enhancing charge separation has attracted great interest in the hydrogen generation application. The formation of one-dimensional ZnO nanorod structure without bundling is essential for high efficiency in PEC response. In this present research work, ZnO nanorod with an average 500 nm in length and average diameter of about 75 nm was successfully formed via electrodeposition method in 0.05 mM ZnCl₂ and 0.1 M KCl electrolyte at 1 V for 60 min under 70 °C condition. Continuous efforts have been exerted to further improve the solar driven PEC response by incorporating an optimum content of TiO₂ into ZnO nanorod using dip-coating technique. It was found that 0.25 at % of TiO₂ loaded on ZnO nanorod film demonstrated a maximum photocurrent density of 19.78 mA/cm² (with V vs. Ag/AgCl) under UV illumination and 14.75 mA/cm² (with V vs. Ag/AgCl) under solar illumination with photoconversion efficiency ~2.9% (UV illumination) and ~4.3% (solar illumination). This performance was approximately 3-4 times higher than ZnO film itself. An enhancement of photocurrent density and photoconversion efficiency occurred due to the sufficient Ti element within TiO₂-ZnO nanorod film, which acted as an effective mediator to trap the photo-induced electrons and minimize the recombination of charge carriers. Besides, phenomenon of charge-separation effect at type-II band alignment of Zn and Ti could further enhance the charge carrier transportation during illumination.
    Matched MeSH terms: Recombination, Genetic
  2. 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*
  3. 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
  4. Phylogenetic designation of enterovirus 71 genotypes and subgenotypes using complete genome sequences
    Chan YF, Sam IC, AbuBakar S
    Infect Genet Evol, 2010 Apr;10(3):404-12.
    PMID: 19465162 DOI: 10.1016/j.meegid.2009.05.010
    Human enterovirus 71 (EV-71) is genotyped for molecular epidemiological investigation mainly using the two structural genes, VP1 and VP4. Based on these, EV-71 is divided into three genotypes, A, B and C, and within the genotypes B and C, there are further subgenotypes, B1-B5 and C1-C5. Classification using these genes is useful but gives incomplete phylogenetic information. In the present study, the phylogenetic relationships amongst all the known EV-71 and human enterovirus A (HEV-A) isolates with complete genome sequences were examined. A different tree topology involving EV-71 isolates of subgenotypes, C4 and B5 was obtained in comparison to that drawn using VP1. The nucleotide sequence divergence of the C4 isolates was 18.11% (17-20%) when compared to other isolates of subgenotype C. However, this positions the C4 isolates within the cut-off divergence value of 17-22% used to designate the virus genotypes. Hence, it is proposed here that C4 should be designated as a new genotype D. In addition, the subgenotype B5 isolates had an average nucleotide divergence of only 6.14% (4-8%) when compared to other subgenotype B4 isolates. This places the B5 isolates within the subgenotype B4. It is proposed here that the B5 isolates to be redesignated as B4. With the newly proposed genotype D and inclusion of subgenotype B5 within B4, the average nucleotide divergence between genotypes was 18.99% (17-22%). Inter- and intra-subgenotype average divergences were 12.02% (10-14%) and 3.92% (1-10%), respectively. A phylogenetic tree built using the full genome sequences is robust as it takes into consideration changes in the sequences of both the structural and non-structural genes. Similar nucleotide similarities, however, were obtained if only VP1 and 3D RNA polymerase genes were used. Furthermore, addition of 3D RNA polymerase sequences will also show recombination events. Hence, in the absence of full genome sequences, it is proposed here that a combination of VP1 and 3D RNA polymerase gene sequences be used for initial genotyping of EV-71 isolates.
    Matched MeSH terms: Recombination, Genetic
  5. Phylogenetic evidence for inter-typic recombination in the emergence of human enterovirus 71 subgenotypes
    Yoke-Fun C, AbuBakar S
    BMC Microbiol, 2006 Aug 30;6:74.
    PMID: 16939656
    BACKGROUND: Human enterovirus 71 (EV-71) is a common causative agent of hand, foot and mouth disease (HFMD). In recent years, the virus has caused several outbreaks with high numbers of deaths and severe neurological complications. Several new EV-71 subgenotypes were identified from these outbreaks. The mechanisms that contributed to the emergence of these subgenotypes are unknown.

    RESULTS: Six EV-71 isolates from an outbreak in Malaysia, in 1997, were sequenced completely. These isolates were identified as EV-71 subgenotypes, B3, B4 and C2. A phylogenetic tree that correlated well with the present enterovirus classification scheme was established using these full genome sequences and all other available full genome sequences of EV-71 and human enterovirus A (HEV-A). Using the 5' UTR, P2 and P3 genomic regions, however, isolates of EV-71 subgenotypes B3 and C4 segregated away from other EV-71 subgenotypes into a cluster together with coxsackievirus A16 (CV-A16/G10) and EV-71 subgenotype C2 clustered with CV-A8. Results from the similarity plot analyses supported the clustering of these isolates with other HEV-A. In contrast, at the same genomic regions, a CV-A16 isolate, Tainan5079, clustered with EV-71. This suggests that amongst EV-71 and CV-A16, only the structural genes were conserved. The 3' end of the virus genome varied and consisted of sequences highly similar to various HEV-A viruses. Numerous recombination crossover breakpoints were identified within the non-structural genes of some of these newer EV-71 subgenotypes.

    CONCLUSION: Phylogenetic evidence obtained from analyses of the full genome sequence supports the possible occurrence of inter-typic recombination involving EV-71 and various HEV-A, including CV-A16, the most common causal agent of HFMD. It is suggested that these recombination events played important roles in the emergence of the various EV-71 subgenotypes.

    Matched MeSH terms: Recombination, Genetic/genetics*
  6. Recombinant human enterovirus 71 in hand, foot and mouth disease patients
    Chan YF, AbuBaker S
    Emerg Infect Dis, 2004 Aug;10(8):1468-70.
    PMID: 15496251
    Hand, foot and mouth disease (HFMD) is a common illness of infants and young children <10 years of age. It is characterized by fever, ulcers in the oral cavity, and rashes with blisters that appear on the palm and sole. The most common causal agents of HFMD are coxsackievirus A16 (CV-A16) and human enterovirus 71 (HEV71), but other enteroviruses, including CV-A5 and CV-A10, can also cause it. When caused by CV-A16 infection, it is usually a mild disease, and patients normally recover without requiring any special medical attention.
    Matched MeSH terms: Recombination, Genetic*
  7. 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
  8. Photoluminescence Investigation of Carrier Localization in Colloidal PbS and PbS/MnS Quantum Dots
    Zaini MS, Liew JYC, Alang Ahmad SA, Mohmad AR, Ahmad Kamarudin M
    ACS Omega, 2020 Dec 08;5(48):30956-30962.
    PMID: 33324803 DOI: 10.1021/acsomega.0c03768
    The existence of surface organic capping ligands on quantum dots (QDs) has limited the potential in QDs emission properties and energy band gap structure alteration as well as the carrier localization. This drawback can be addressed via depositing a thin layer of a semiconductor material on the surface of QDs. Herein, we report on the comparative study for photoluminescent (PL) properties of PbS and PbS/MnS QDs. The carrier localization effect due to the alteration of energy band gap structure and carrier recombination mechanism in the QDs were investigated via PL measurements in a temperature range of 10-300 K with the variation of the excitation power from 10 to 200 mW. For PbS QDs, the gradient of integrated PL intensity (IPL) as a function of excitation power density graph was less than unity. When the MnS shell layer was deposited onto the PbS core, the PL emission exhibited a blue shift, showing dominant carrier recombination. It was also found that the full width half-maximum showed a gradual broadening with the increasing temperature, affirming the electron-phonon interaction.
    Matched MeSH terms: Recombination, Genetic
  9. Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships
    Cabauatan PQ, Melcher U, Ishikawa K, Omura T, Hibino H, Koganezawa H, et al.
    J Gen Virol, 1999 Aug;80 ( Pt 8):2229-37.
    PMID: 10466823
    The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.
    Matched MeSH terms: Recombination, Genetic
  10. Fulltext Genetic diversity of Japanese encephalitis virus isolates obtained from the Indonesian archipelago between 1974 and 1987
    Schuh AJ, Guzman H, Tesh RB, Barrett AD
    Vector Borne Zoonotic Dis, 2013 Jul;13(7):479-88.
    PMID: 23590316 DOI: 10.1089/vbz.2011.0870
    Five genotypes (GI-V) of Japanese encephalitis virus (JEV) have been identified, all of which have distinct geographical distributions and epidemiologies. It is thought that JEV originated in the Indonesia-Malaysia region from an ancestral virus. From that ancestral virus GV diverged, followed by GIV, GIII, GII, and GI. Genotype IV appears to be confined to the Indonesia-Malaysia region, as GIV has been isolated in Indonesia from mosquitoes only, while GV has been isolated on three occasions only from a human in Malaysia and mosquitoes in China and South Korea. In contrast, GI-III viruses have been isolated throughout Asia and Australasia from a variety of hosts. Prior to this study only 13 JEV isolates collected from the Indonesian archipelago had been studied genetically. Therefore the sequences of the envelope (E) gene of 24 additional Indonesian JEV isolates, collected throughout the archipelago between 1974 and 1987, were determined and a series of molecular adaptation analyses were performed. Phylogenetic analysis indicated that over a 14-year time span three genotypes of JEV circulated throughout Indonesia, and a statistically significant association between the year of virus collection and genotype was revealed: isolates collected between 1974 and 1980 belonged to GII, isolates collected between 1980 and 1981 belonged to GIV, and isolates collected in 1987 belonged to GIII. Interestingly, three of the GII Indonesian isolates grouped with an isolate that was collected during the JE outbreak that occurred in Australia in 1995, two of the GIII Indonesian isolates were closely related to a Japanese isolate collected 40 years previously, and two Javanese GIV isolates possessed six amino acid substitutions within the E protein when compared to a previously sequenced GIV isolate collected in Flores. Several amino acids within the E protein of the Indonesian isolates were found to be under directional evolution and/or co-evolution. Conceivably, the tropical climate of the Indonesia/Malaysia region, together with its plethora of distinct fauna and flora, may have driven the emergence and evolution of JEV. This is consistent with the extensive genetic diversity seen among the JEV isolates observed in this study, and further substantiates the hypothesis that JEV originated in the Indonesia-Malaysia region.
    Matched MeSH terms: Recombination, Genetic
  11. 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
  12. 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
  13. Energy Band Gap Modulation in Nd-Doped BiFeO3/SrRuO3 Heteroepitaxy for Visible Light Photoelectrochemical Activity
    Tan KH, Chen YW, Van CN, Wang H, Chen JW, Lim FS, et al.
    ACS Appl Mater Interfaces, 2019 Jan 09;11(1):1655-1664.
    PMID: 30561192 DOI: 10.1021/acsami.8b17758
    The ability of band offsets at multiferroic/metal and multiferroic/electrolyte interfaces in controlling charge transfer and thus altering the photoactivity performance has sparked significant attention in solar energy conversion applications. Here, we demonstrate that the band offsets of the two interfaces play the key role in determining charge transport direction in a downward self-polarized BFO film. Electrons tend to move to BFO/electrolyte interface for water reduction. Our experimental and first-principle calculations reveal that the presence of neodymium (Nd) dopants in BFO enhances the photoelectrochemical performance by reduction of the local electron-hole pair recombination sites and modulation of the band gap to improve the visible light absorption. This opens a promising route to the heterostructure design by modulating the band gap to promote efficient charge transfer.
    Matched MeSH terms: Recombination, Genetic
  14. Fulltext Genetic diversity of geographically distinct Streptococcus dysgalactiae isolates from fish
    Abdelsalam M, Eissa AE, Chen SC
    J Adv Res, 2015 Mar;6(2):233-8.
    PMID: 25750757 DOI: 10.1016/j.jare.2013.12.003
    Streptococcus dysgalactiae is an emerging pathogen of fish. Clinically, infection is characterized by the development of necrotic lesions at the caudal peduncle of infected fishes. The pathogen has been recently isolated from different fish species in many countries. Twenty S. dysgalactiae isolates collected from Japan, Taiwan, Malaysia and Indonesia were molecularly characterized by biased sinusoidal field gel electrophoresis (BSFGE) using SmaI enzyme, and tuf gene sequencing analysis. DNA sequencing of ten S. dysgalactiae revealed no genetic variation in the tuf amplicons, except for three strains. The restriction patterns of chromosomal DNA measured by BSFGE were differentiated into six distinct types and one subtype among collected strains. To our knowledge, this report gives the first snapshot of S. dysgalactiae isolates collected from different countries that are localized geographically and differed on a multinational level. This genetic unrelatedness among different isolates might suggest a high recombination rate and low genetic stability.
    Matched MeSH terms: Recombination, Genetic
  15. 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
  16. Fulltext Isolation and Identification of Inter-Species Enterovirus Recombinant Genomes
    Bentley K, Tee HK, Pearson A, Lowry K, Waugh S, Jones S, et al.
    Viruses, 2021 11 29;13(12).
    PMID: 34960659 DOI: 10.3390/v13122390
    Positive-strand RNA virus evolution is partly attributed to the process of recombination. Although common between closely genetically related viruses, such as within species of the Enterovirus genus of the Picornaviridae family, inter-species recombination is rarely observed in nature. Recent studies have shown recombination is a ubiquitous process, resulting in a wide range of recombinant genomes and progeny viruses. While not all recombinant genomes yield infectious progeny virus, their existence and continued evolution during replication have critical implications for the evolution of the virus population. In this study, we utilised an in vitro recombination assay to demonstrate inter-species recombination events between viruses from four enterovirus species, A-D. We show that inter-species recombinant genomes are generated in vitro with polymerase template-switching events occurring within the virus polyprotein coding region. However, these genomes did not yield infectious progeny virus. Analysis and attempted recovery of a constructed recombinant cDNA revealed a restriction in positive-strand but not negative-strand RNA synthesis, indicating a significant block in replication. This study demonstrates the propensity for inter-species recombination at the genome level but suggests that significant sequence plasticity would be required in order to overcome blocks in the virus life cycle and allow for the production of infectious viruses.
    Matched MeSH terms: Recombination, Genetic*
  17. 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*
  18. Fulltext Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
    Barnett R, Westbury MV, Sandoval-Velasco M, Vieira FG, Jeon S, Zazula G, et al.
    Curr Biol, 2020 Dec 21;30(24):5018-5025.e5.
    PMID: 33065008 DOI: 10.1016/j.cub.2020.09.051
    Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6-8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11-14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.
    Matched MeSH terms: Recombination, Genetic
  19. Simulation on the roles of the number of quantum well and doping in Inx Ga1-xN multiple quantum wells LEDs
    Zainal N, Azimah E, Hassan Z, Abu Hassan H, Hashim M
    Sains Malaysiana, 2014;43:1557-1564.
    In this work, the emission efficiency of InxGa1-xN based light emitting diodes (LEDs) had been numerically investigated with the variation of the number of quantum well. From our calculation, we found that non-uniformity of carriers distribution (especially electron) in the wells leads to serious inhomogeneity of radiative recombination distribution that would degrade the efficiency of the LED with more wells. However, the problem was minimized when the selected quantum barriers were doped with a reasonable doping level. Comparison with other reported experimental works were also included. At the end of this work, we proposed several types of preferable LEDs designs with optimum structural parameters.
    Matched MeSH terms: Recombination, Genetic
  20. 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
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