Displaying publications 1 - 20 of 45 in total

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  1. Akter N, Hashim R, Pham HQ, Choi SD, Lee DW, Shin JH, et al.
    Front Microbiol, 2020;11:570851.
    PMID: 33162953 DOI: 10.3389/fmicb.2020.570851
    We identified an antimicrobial peptide (AMP) from Lactobacillus acidophilus that was antagonistic to Aeromonas hydrophila. In vitro studies such as well-diffusion and field trials revealed that the AMP was active against A. hydrophila. The field trials of AMP using A. hydrophila-infected Channa striatus with a mannone oligosaccharide (MOS) prebiotic, A. hydrophila antigens, A. hydrophila-infected fish serum, L. acidophilus, and Lactobacillus cell free-supernatant (LABS-CFS) on an indicator organism further revealed that the antimicrobial agent could protect C. striatus. Other than the AMP, none of the above were able to eliminate the infectious agent A. hydrophila, and were only able to delay the death rate for 3-4 days. Thus, we conclude that the AMP is antagonistic to A. hydrophila and may be used for treatment of A. hydrophila infections. Subsequent L. acidophilus whole-genome sequence analyses enabled an understanding of the (probable) gene arrangement and its location on the chromosome. This information may be useful in the generation of recombinant peptides to produce larger quantities for treatment.
    Matched MeSH terms: Gene Order
  2. Ariffin N, Abdullah R, Rashdan Muad M, Lourdes J, Emran NA, Ismail MR, et al.
    Plasmid, 2011 Sep;66(3):136-43.
    PMID: 21827784 DOI: 10.1016/j.plasmid.2011.07.002
    Polyhydroxybutyrate-co-hydroxyvalerate (PHBV) is a polyhydroxyalkanoate (PHA) bioplastic group with thermoplastic properties is thus high in quality and can be degradable. PHBV can be produced by bacteria, but the process is not economically competitive with polymers produced from petrochemicals. To overcome this problem, research on transgenic plants has been carried out as one of the solutions to produce PHBV in economically sound alternative manner. Four different genes encoded with the enzymes necessary to catalyze PHBV are bktB, phaB, phaC and tdcB. All the genes came with modified CaMV 35S promoters (except for the tdcB gene, which was promoted by the native CaMV 35S promoter), nos terminator sequences and plastid sequences in order to target the genes into the plastids. Subcloning resulted in the generation of two different orientations of the tdcB, pLMIN (left) and pRMIN (right), both 17.557 and 19.967 kb in sizes. Both plasmids were transformed in immature embryos (IE) of oil palm via Agrobacterium tumefaciens. Assays of GUS were performed on one-week-old calli and 90% of the calli turned completely blue. This preliminary test showed positive results of integration. Six-months-old calli were harvested and RNA of the calli were isolated. RT-PCR was used to confirm the transient expression of PHBV transgenes in the calli. The bands were 258, 260, 315 and 200 bp in size for bktB, phaB, phaC and tdcB transgenes respectively. The data obtained showed that the bktB, phaB, phaC and tdcB genes were successfully integrated and expressed in the oil palm genome.
    Matched MeSH terms: Gene Order
  3. Austin CM, Tan MH, Gan HY, Gan HM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4176-4177.
    PMID: 25630729
    Next-Gen sequencing was used to recover the complete mitochondrial genome of Cherax tenuimanus. The mitogenome consists of 15,797 base pairs (68.14% A + T content) containing 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs, and a 779 bp non-coding AT-rich region. Mitogenomes have now been recovered for all six species of Cherax native to Western Australia.
    Matched MeSH terms: Gene Order
  4. Balakrishnan KN, Abdullah AA, Camalxaman SN, Quah YW, Abba Y, Hani H, et al.
    Genome Announc, 2015;3(3).
    PMID: 26044413 DOI: 10.1128/genomeA.00451-15
    The complete genome sequence of the ALL-03 strain of rat cytomegalovirus (RCMV) has been determined. The RCMV genome has a length of 197,958 bp and is arranged as a single unique sequence flanked by 504-bp terminal direct repeats. This strain is closely related to the English strain of RCMV in terms of genetic arrangement but differs slightly in size.
    Matched MeSH terms: Gene Order
  5. Ee SF, Mohamed-Hussein ZA, Othman R, Shaharuddin NA, Ismail I, Zainal Z
    ScientificWorldJournal, 2014;2014:840592.
    PMID: 24678279 DOI: 10.1155/2014/840592
    Polygonum minus is an aromatic plant, which contains high abundance of terpenoids, especially the sesquiterpenes C15H24. Sesquiterpenes were believed to contribute to the many useful biological properties in plants. This study aimed to functionally characterize a full length sesquiterpene synthase gene from P. minus. P. minus sesquiterpene synthase (PmSTS) has a complete open reading frame (ORF) of 1689 base pairs encoding a 562 amino acid protein. Similar to other sesquiterpene synthases, PmSTS has two large domains: the N-terminal domain and the C-terminal metal-binding domain. It also consists of three conserved motifs: the DDXXD, NSE/DTE, and RXR. A three-dimensional protein model for PmSTS built clearly distinguished the two main domains, where conserved motifs were highlighted. We also constructed a phylogenetic tree, which showed that PmSTS belongs to the angiosperm sesquiterpene synthase subfamily Tps-a. To examine the function of PmSTS, we expressed this gene in Arabidopsis thaliana. Two transgenic lines, designated as OE3 and OE7, were further characterized, both molecularly and functionally. The transgenic plants demonstrated smaller basal rosette leaves, shorter and fewer flowering stems, and fewer seeds compared to wild type plants. Gas chromatography-mass spectrometry analysis of the transgenic plants showed that PmSTS was responsible for the production of β -sesquiphellandrene.
    Matched MeSH terms: Gene Order
  6. Forde BM, Ben Zakour NL, Stanton-Cook M, Phan MD, Totsika M, Peters KM, et al.
    PLoS One, 2014;9(8):e104400.
    PMID: 25126841 DOI: 10.1371/journal.pone.0104400
    Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.
    Matched MeSH terms: Gene Order
  7. Froufe E, Bolotov I, Aldridge DC, Bogan AE, Breton S, Gan HM, et al.
    Heredity (Edinb), 2020 Jan;124(1):182-196.
    PMID: 31201385 DOI: 10.1038/s41437-019-0242-y
    Using a new fossil-calibrated mitogenome-based approach, we identified macroevolutionary shifts in mitochondrial gene order among the freshwater mussels (Unionoidea). We show that the early Mesozoic divergence of the two Unionoidea clades, Margaritiferidae and Unionidae, was accompanied by a synchronous split in the gene arrangement in the female mitogenome (i.e., gene orders MF1 and UF1). Our results suggest that this macroevolutionary jump was completed within a relatively short time interval (95% HPD 201-226 Ma) that coincided with the Triassic-Jurassic mass extinction. Both gene orders have persisted within these clades for ~200 Ma. The monophyly of the so-called "problematic" Gonideinae taxa was supported by all the inferred phylogenies in this study using, for the first time, the M- and F-type mitogenomes either singly or combined. Within Gonideinae, two additional splits in the gene order (UF1 to UF2, UF2 to UF3) occurred in the Mesozoic and have persisted for ~150 and ~100 Ma, respectively. Finally, the mitogenomic results suggest ancient connections between freshwater basins of East Asia and Europe near the Cretaceous-Paleogene boundary, probably via a continuous paleo-river system or along the Tethys coastal line, which are well supported by at least three independent but almost synchronous divergence events.
    Matched MeSH terms: Gene Order
  8. Gan HM, Tan MH, Austin CM
    PMID: 24938115 DOI: 10.3109/19401736.2014.926490
    The mitochondrial genome sequence of the Australian crayfish, Euastacus yarraensis, is documented and compared with other Australian crayfish genera. Euastacus yarraensis has a mitogenome of 15,548 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The base composition of E. yarraensis mitogenome is 32.39% for T, 22.45% for C, 34.43% for A, and 10.73% for G, with an AT bias of 66.82%. The mitogenome gene order conforms to what is considered the primitive arrangement for parastacid crayfish.
    Matched MeSH terms: Gene Order
  9. Gan HM, Tan MH, Lee YP, Schultz MB, Austin CM
    Mitochondrial DNA, 2016;27(1):595-6.
    PMID: 24730605 DOI: 10.3109/19401736.2014.908361
    The complete mitochondrial genome of the enigmatic freshwater crayfish Engaeus lyelli was sequenced using the MiSeq Personal Sequencer (Illumina, San Diego, CA). The mitogenome has 16,027 bp consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of E. lyelli is 29.01% for T, 27.13% for C, 31.43% for A, and 12.44% for G, with an AT bias of 60.44%. The species has the distinctive gene order characteristic of parastacid crayfish with the exception of some minor rearrangements involving the tRNA genes.
    Matched MeSH terms: Gene Order
  10. Gan HM, Tan MH, Thai BT, Austin CM
    PMID: 24617474 DOI: 10.3109/19401736.2014.892104
    The complete mitochondrial genome of the commercially important snout otter clam Lutraria rhynchaena was obtained from low-coverage shotgun sequencing data on the MiSeq platform. The L. rhynchaena mitogenome has 16,927 base pairs (69% A + T content) and made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 953 bp non-coding AT-rich region. This is the first mitogenome to be sequenced from the genus Lutraria, and the seventh to be reported for the family Mactridae.
    Matched MeSH terms: Gene Order
  11. Gan HM, Tan MH, Austin CM
    PMID: 24617484 DOI: 10.3109/19401736.2014.895996
    The complete mitochondrial genome of the conservationally significant Macquarie perch (Macquaria australasica) was obtained from low-coverage shotgun sequencing using the MiSeq sequencer. The M. australasica mitogenome has 16,496 base pairs (55% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Macquaria, and the third to be reported for the family Percichthyidae.
    Matched MeSH terms: Gene Order
  12. Gan HM, Tan MH, Gan HY, Lee YP, Schultz MB, Austin CM
    PMID: 24845437 DOI: 10.3109/19401736.2014.919460
    The mitogenome of the black yabby, Geocharax gracilis, was sequenced using the MiSeq Personal Sequencer. It has 15,924 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of G. gracilis mitogenome is 32.18% for T, 22.32% for C, 34.83% for A, and 10.68% for G, with an AT bias of 67.01%. The mitogenome gene order is typical for that of parastacid crayfish with the exception of some minor rearrangements involving tRNA genes.
    Matched MeSH terms: Gene Order
  13. Gan HM, Schultz MB, Austin CM
    BMC Evol. Biol., 2014;14:19.
    PMID: 24484414 DOI: 10.1186/1471-2148-14-19
    Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline.
    Matched MeSH terms: Gene Order
  14. Gan HM, Tan MH, Lee YP, Schultz MB, Horwitz P, Burnham Q, et al.
    Mol Phylogenet Evol, 2018 01;118:88-98.
    PMID: 28966124 DOI: 10.1016/j.ympev.2017.09.022
    To further understand the evolutionary history and mitogenomic features of Australia's highly distinctive freshwater crayfish fauna, we utilized a recently described rapid mitogenome sequencing pipeline to generate 24 new crayfish mitogenomes including a diversity of burrowing crayfish species and the first for Astacopsis gouldi, the world's largest freshwater invertebrate. Whole mitogenome-based phylogeny estimates using both Bayesian and Maximum Likelihood methods substantially strengthen existing hypotheses for systematic relationships among Australian freshwater crayfish with evidence of pervasive diversifying selection and accelerated mitochondrial substitution rate among the members of the clade representing strongly burrowing crayfish that may reflect selection pressures for increased energy requirement for adaptation to terrestrial environment and a burrowing lifestyle. Further, gene rearrangements are prevalent in the burrowing crayfish mitogenomes involving both tRNA and protein coding genes. In addition, duplicated control regions were observed in two closely related Engaeus species, together with evidence for concerted evolution. This study significantly adds to the understanding of Australian freshwater crayfish evolutionary relationships and suggests a link between mitogenome evolution and adaptation to terrestrial environments and a burrowing lifestyle in freshwater crayfish.
    Matched MeSH terms: Gene Order
  15. Gan HY, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):3985-3986.
    PMID: 25543913
    The complete mitochondrial genome of the Bass yabby Trypaea australiensis was obtained from a partial genome scan using the MiSeq sequencing system. The T. australiensis mitogenome is 16,821 bp in length (70.25% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1977 bp non-coding AT-rich region. This Trypaea mitogenome sequence is the 5th for the family Callianassidae and represents a new gene order for the Decapoda involving protein-coding, rRNA and tRNA genes and the control region.
    Matched MeSH terms: Gene Order*
  16. Gan HY, Gan HM, Lee YP, Austin CM
    PMID: 25693708 DOI: 10.3109/19401736.2015.1007311
    The mitochondrial genome of the rock pool prawn (Palaemon serenus), is sequenced, making it the third for genera of the family Palaemonidae and the first for the genus Palaemon. The mitogenome is 15,967 base pairs in length and comprises 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The P. serenus mitogenome has an AT bias of 58.97% and a base composition of 29.79% for T, 24.14% for C, 29.18% for A, and 16.89% for G. The mitogenome gene order of P. serenus is identical to Exopalaemon carinicauda.
    Matched MeSH terms: Gene Order
  17. Gan HY, Gan HM, Tan MH, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4099-4100.
    PMID: 25629489
    The complete mitochondrial genome of the hermit crab Clibanarius infraspinatus was recovered by genome skimming using Next-Gen sequencing. The Clibanarius infraspinatus mitogenome has 16,504 base pairs (67.94% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1500 bp non-coding AT-rich region. The Clibanarius infraspinatus mitogenome sequence is the first for the family Diogenidae and the second for the superfamily Paguroidea and exhibits a translocation of the ND3 gene not previously reported for the Decapoda.
    Matched MeSH terms: Gene Order/genetics*
  18. Grandjean F, Tan MH, Gan HY, Gan HM, Austin CM
    PMID: 25738217 DOI: 10.3109/19401736.2015.1018207
    The Austropotamobius pallipes complete mitogenome has been recovered using Next-Gen sequencing. Our sample of A. pallipes has a mitogenome of 15,679 base pairs (68.44% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 877 bp non-coding AT-rich region. This is the first mitogenome sequenced for a crayfish from the family Astacidae and the 4(th) for northern hemisphere genera.
    Matched MeSH terms: Gene Order
  19. Guan M, Liu X, Lin F, Xie Z, Fazhan H, Ikhwanuddin M, et al.
    Mitochondrial DNA B Resour, 2018 Mar 14;3(1):368-369.
    PMID: 33490509 DOI: 10.1080/23802359.2018.1450685
    In this study, we sequenced and analyzed the whole mitochondrial genome of Metopograpsus frontalis Miers, 1880 (Decapoda, Grapsidae). The circular genome is 15,587 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, as well as a control region. Both atp8/atp6 and nad4L/nad4 share 7 nucleotides in their adjacent overlapping region, which is identical to those observed in other Grapsidae crabs. The genome composition and gene order follow a classic crab-type arrangement regulation. The phylogenetic analysis suggested that Grapsidae crabs formed a solid monophyletic group. The newly described mitochondrial genome may provide genetic marker for studies on phylogeny of the grapsid crabs.
    Matched MeSH terms: Gene Order
  20. Hoe LN, Wan KL, Nathan S
    Parasitology, 2005 Dec;131(Pt 6):759-68.
    PMID: 16336729
    The protozoan parasite Toxoplasma gondii produces a family of microneme proteins that are thought to play diverse roles in aiding the parasite's intracellular existence. Among these, TgMIC2 has a putative function in parasite adhesion to the host cell to initiate the invasion process. The invasion process may be localized and inhibited by monoclonal antibodies against the protein(s) involved. Here we report on the construction of a phage-displayed single-chain variable fragment (scFv) library from mice immunized with whole T. gondii parasites. The library was subsequently panned against recombinant TgMIC2 (rpTgMIC2) and 2 different groups of antibody clones were obtained, based on fingerprinting and sequencing data. The expressed recombinant scFv antibody was able to recognize rpTgMIC2 in a Western blot detection experiment. These results show that the phage display technology allows quick and effective production of monoclonal antibodies against parasite antigens. By panning the scFv-displayed library, we should be able to obtain a plethora of multi-functional scFv antibodies towards T. gondii proteins.
    Matched MeSH terms: Gene Order/genetics
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