Displaying publications 61 - 80 of 1877 in total

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  1. Matinja AI, Kamarudin NHA, Leow ATC, Oslan SN, Ali MSM
    J Mol Evol, 2024 Dec;92(6):944-963.
    PMID: 39549052 DOI: 10.1007/s00239-024-10219-3
    Cold-active enzymes have recently gained popularity because of their high activity at lower temperatures than their mesophilic and thermophilic counterparts, enabling them to withstand harsh reaction conditions and enhance industrial processes. Cold-active lipases are enzymes produced by psychrophiles that live and thrive in extremely cold conditions. Cold-active lipase applications are now growing in the detergency, synthesis of fine chemicals, food processing, bioremediation, and pharmaceutical industries. The cold adaptation mechanisms exhibited by these enzymes are yet to be fully understood. Using phylogenetic analysis, and advanced deep learning-based protein structure prediction tool Alphafold2, we identified an evolutionary processes in which a conserved cold-active-like motif is presence in a distinct subclade of the tree and further predicted and simulated the three-dimensional structure of a putative cold-active lipase with the cold active motif, Glalip03, from Glaciozyma antarctica PI12. Molecular dynamics at low temperatures have revealed global stability over a wide range of temperatures, flexibility, and the ability to cope with changes in water and solvent entropy. Therefore, the knowledge we uncover here will be crucial for future research into how these low-temperature-adapted enzymes maintain their overall flexibility and function at lower temperatures.
    Matched MeSH terms: Phylogeny*
  2. Ng KT, Lee YM, Al-Darraji HA, Xia X, Takebe Y, Chan KG, et al.
    Genome Announc, 2013 Jan;1(1).
    PMID: 23409272 DOI: 10.1128/genomeA.00168-12
    We report the full genome sequence of hepatitis C virus (HCV) subtype 6n from Kuala Lumpur, Malaysia. Phylogenetic analysis of the isolate 10MYKJ032 suggests that Southeast Asia might be the origin for the HCV subtype 6n and highlights the possible spread of this lineage from Southeast Asia to other regions.
    Matched MeSH terms: Phylogeny
  3. Mita T, Shaw SR
    Zookeys, 2012.
    PMID: 23378818 DOI: 10.3897/zookeys.254.4182
    Three new species of Ettchellsia Cameron, namely, Ettchellsia ignitasp. n. from Peninsular Malaysia and Borneo, Ettchellsia nigripessp. n. from Sulawesi and Ettchellsia reidisp. n. from Borneo are described and illustrated. A key to the species of Ettchellsia is provided based on females.
    Matched MeSH terms: Phylogeny
  4. Nabilah Mohamad Khairi, Wilson Thau Lym Yong, Julius Kulip, Kenneth Francis Rodrigues
    MyJurnal
    Conservation of plant species plays a vital role in preventing the loss of valuable plant resources. The success of conservation depends on the correct identification and characterization of plant species. Bamboo is one of the most important plants with multiple uses that have contributed to the economy and socio-economy of many people in rural areas. It is under the subfamily of Bambusoideae that includes both woody and herbaceous bamboo. Conventionally, like other plants, bamboo has been classified dependently based on morphological characteristics. However, morphological identification leads to difficulties and misclassification of bamboo species due to their infrequent flowering behaviour and peculiar reproductive biology. Since then, molecular markers have been introduced to overcome the problems associated with bamboo taxonomy and phylogeny. This paper provides an overview of the diverse, predominantly molecular techniques used to assess and determine the genetic diversity of bamboo species.
    Matched MeSH terms: Phylogeny
  5. Quah ESH, Lim KKP, Grismer LL
    Zootaxa, 2021 Mar 24;4949(1):zootaxa.4949.1.2.
    PMID: 33756993 DOI: 10.11646/zootaxa.4949.1.2
    The taxonomic status of Asthenodipsas vertebralis in Borneo has been plagued with uncertainty over the last eighty years. An examination of museum collections resulted in the discovery of a voucher specimen of A. vertebralis from Sarawak, East Malaysia that confirms the presence of the species in Borneo and a previously unrecognised species, Asthenodipsas ingeri sp. nov. from Mount Kinabalu, Sabah. Asthenodipsas ingeri sp. nov. can be differentiated from its congeners by the combination of an absence of preoculars and suboculars, 1st and 3rd pair of infralabials in contact, two pairs of posterior inframaxillaries, supralabials 3-5 (sometimes 3 4) in contact with orbit, 15/15/15 rows of dorsal scales, presence of sharp vertebral keel, and divided subcaudals. This study highlights the importance of careful re-examination of museum collections that could potentially harbour new species hiding in plain sight. These discoveries also add to the growing number of reptile and amphibian species being described from Borneo that shows no signs of abating but are already potentially threatened by the continued deforestation and developments on the island.
    Matched MeSH terms: Phylogeny
  6. Matsui M, Nishikawa K, Eto K, Hamidy A, Hossman Y, Fukuyama I
    Zootaxa, 2021 Feb 10;4926(4):zootaxa.4926.4.4.
    PMID: 33756730 DOI: 10.11646/zootaxa.4926.4.4
    We found a uniquely colored dicroglossid frog of the genus Occidozyga from western Sarawak, East Malaysia. It is divergent from other congeners in morphology and mtDNA sequences. In a molecular phylogeny, this species is the sister lineage to the continental species O. lima and O. martensii with weak support. The species is small with SVL 16-18 mm in males and 18-19 mm in females, without dorsolateral fold but with transverse wrinkles on dorsum, tips of fingers lacking disks but of toes with disks, only first and second toes webbed to disks, and orange-brown dorsum with dark brown band. We thus describe it as a new species.
    Matched MeSH terms: Phylogeny
  7. Satyaveanthan MV, Suhaimi SA, Ng CL, Muhd-Noor ND, Awang A, Lam KW, et al.
    Plant Physiol Biochem, 2021 Apr;161:143-155.
    PMID: 33588320 DOI: 10.1016/j.plaphy.2021.01.050
    The juvenile hormones (JH) in plants are suggested to act as a form of plant defensive strategy especially against insect herbivory. The oxidation of farnesol to farnesoic acid is a key step in the juvenile hormone biosynthesis pathway. We herein present the purification and characterisation of the recombinant Theobroma cacao farnesol dehydrogenase enzyme that catalyses oxidation of farnesol to farnesal. The recombinant enzyme was purified to apparent homogeneity by affinity chromatography. The purified enzyme was characterised in terms of its deduced amino acid sequences, phylogeny, substrate specificity, kinetic parameters, structural modeling, and docking simulation. The phylogenetic analysis indicated that the T. cacao farnesol dehydrogenase (TcFolDH) showed a close relationship with A. thaliana farnesol dehydrogenase gene. The TcFolDH monomer had a large N-terminal domain which adopted a typical Rossmann-fold, harboring the GxxGxG motif (NADP(H)-binding domain) and a small C-terminal domain. The enzyme was a homotrimer comprised of subunits with molecular masses of 36 kDa. The TcFolDH was highly specific to NADP+ as coenzyme. The substrate specificity studies showed trans, trans-farnesol was the most preferred substrate for the TcFolDH, suggesting that the purified enzyme was a NADP+-dependent farnesol dehydrogenase. The docking of trans, trans-farnesol and NADP+ into the active site of the enzyme showed the important residues, and their interactions involved in the substrate and coenzyme binding of TcFolDH. Considering the extensive involvement of JH in both insects and plants, an in-depth knowledge on the recombinant production of intermediate enzymes of the JH biosynthesis pathway could help provide a potential method for insect control.
    Matched MeSH terms: Phylogeny
  8. Yap PSX, Tan TS, Chan YF, Tee KK, Kamarulzaman A, Teh CSJ
    J Microbiol Biotechnol, 2020 Jul 28;30(7):962-966.
    PMID: 32627759 DOI: 10.4014/jmb.2006.06009
    Monitoring the mutation dynamics of human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical in understanding its infectivity, virulence and pathogenicity for development of a vaccine. In an "age of mobility," the pandemic highlights the importance and vulnerability of regionalization and labor market interdependence in Southeast Asia. We intend to characterize the genetic variability of viral populations within the region to provide preliminary information for regional surveillance in the future. By analyzing 142 complete genomes from South East Asian (SEA) countries, we identified three central variants distinguished by nucleotide and amino acid changes.
    Matched MeSH terms: Phylogeny
  9. Rosli H, Batzer JC, Hernández E, Beruski G, Dixon PM, Gleason ML
    Plant Dis, 2020 Sep;104(9):2398-2405.
    PMID: 32689919 DOI: 10.1094/PDIS-11-19-2340-RE
    The spatial dissemination of three prevalent taxa of sooty blotch and flyspeck (SBFS) fungi under several levels of precipitation was compared during 2015 and 2016 in an Iowa apple orchard. Overhead irrigation was used to supplement ambient precipitation in order to insure SBFS spore dissemination and colony development. There were five irrigation levels, involving 1-min-long periods of irrigation that were imposed either once or twice per hour at intervals of 3, 6, or 12 h, as well as a nonirrigated control. Preselected apple fruit were inoculated with one of the three SBFS taxa to serve as sources of inoculum. Dissemination from these inoculated apple fruit was assessed at harvest by counting SBFS colonies on water-sprayed and nontreated fruit. As a further control, additional fruit were enclosed in fruit bags throughout the fruit development period. In both 2015 and 2016, the number of colonies of the SBFS fungus Peltaster gemmifer per apple increased sharply as the duration of irrigation increased, whereas the number of colonies of Microcyclosporella mali increased to a lesser extent and Stomiopeltis sp. RS1 showed no increase. In 2015, the linear relationship between the duration of irrigation-imposed precipitation levels and the number of colonies on the water-sprayed apple fruit was similar for P. gemmifer (slope = 0.09), Stomiopeltis sp. RS1 (slope = 0.07), and Microcyclosporella mali (slope = 0.13); whereas, in 2016, the slope was higher for P. gemmifer (0.28) than for Stomiopeltis sp. RS1 (-0.09) or M. mali (0.06). The results indicated that dissemination of P. gemmifer increased sharply in response to increased irrigation-imposed precipitation, and that dissemination patterns differed considerably among the three SBFS taxa. The apparent advantage of P. gemmifer in precipitation-triggered dissemination may stem from its ability to produce spores rapidly by budding. To our knowledge, this is the first article to assess splash dispersal by SBFS fungi in the field and the first to document taxon-specific patterns of dissemination in this pathogen complex.
    Matched MeSH terms: Phylogeny
  10. Gan HM, Takahashi H, Hammer MP, Tan MH, Lee YP, Voss JM, et al.
    Mitochondrial DNA B Resour, 2017 Feb 06;2(1):73-75.
    PMID: 33473721 DOI: 10.1080/23802359.2017.1285206
    The complete mitochondrial genomes of four fish species of the commercially important family Latidae were sequenced using the Illumina MiSeq, thereby significantly increasing the mitogenomic resources for the family. Whole mitogenome-based phylogenetic analysis supports the monophyly of the genus Lates and more generally the family Latidae. The mitogenome sequences from this study will be useful for future assessments of the diversity within and between Lates species and studies of phylogenetic relationships within the diverse and taxonomically challenging perciform fishes.
    Matched MeSH terms: Phylogeny
  11. González-Gómez JP, Soto-Rodriguez S, López-Cuevas O, Castro-Del Campo N, Chaidez C, Gomez-Gil B
    Curr Microbiol, 2020 Dec;77(12):3851-3860.
    PMID: 32959087 DOI: 10.1007/s00284-020-02214-w
    Acute hepatopancreatic necrosis disease (AHPND) is a severe disease affecting recently stocked cultured shrimps. The disease is mainly caused by V. parahaemolyticus that harbors the pVA1 plasmid; this plasmid contains the pirA and pirB genes, which encode a delta-endotoxin. AHPND originated in China in 2009 and has since spread to several other Asian countries and recently to Latin America (2013). Many Asian strains have been sequenced, and their sequences are publicly accessible in scientific databases, but only four strains from Latin America have been reported. In this study, we analyzed nine pVA1-harboring V. parahaemolyticus sequences from strains isolated in Mexico along with the 38 previously available pVA1-harboring V. parahaemolyticus sequences and the reference strain RIMD 2210633. The studied sequences were clustered into three phylogenetic clades (Latin American, Malaysian, and Cosmopolitan) through pangenomic and phylogenomic analysis. The nucleotide sequence alignment of the pVA1 plasmids harbored by the Asian and Latin American strains confirmed that the main structural difference in the plasmid between the Asian and Latin American strains is the absence of the Tn3 transposon in the Asian strains; in addition, some deletions in the pirAB region were found in two of the Latin American strains. Our study represents the most robust and inclusive phylogenomic analysis of pVA1-harboring V. parahaemolyticus conducted to date and provides insight into the epidemiology of AHPND. In addition, this study highlights that disease diagnosis through the detection of the pirA and pirB genes is an inadequate approach due to the instability of these genes.
    Matched MeSH terms: Phylogeny
  12. Yap PSX, Ahmad Kamar A, Chong CW, Yap IKS, Teh CSJ
    J Glob Antimicrob Resist, 2020 06;21:246-251.
    PMID: 32304769 DOI: 10.1016/j.jgar.2020.03.024
    BACKGROUND: Resistance to colistin, the last line therapy for infections caused by multidrug-resistant Gram-negative bacteria, represents a major public health threat. Citrobacter freundii B9-C2 which was isolated from the stool of preterm neonate on the first week of life, displayed resistance to almost all major antibiotics, including colistin. Through whole genome sequencing (WGS), we characterised the genome features that underline the antibiotic-resistance phenotype of this isolate.

    METHODS: Genome of C. freundii B9-C2 was sequenced on an Illumina MiSeq platform. The assembled genome was annotated and deposited into GenBank under the accession number CP027849.

    RESULTS: Multiple antimicrobial resistance genes including blaCMY-66 were identified. Further, the presence of 15 antibiotic efflux pump-encoding resistance genes, including crp, baeR, hns, patA, emrB, msbA, acrA, acrB, emrR, mdtC, mdtB, mdtG, kdpE, mdfA and msrB, were detected and likely to account for the observed cephalosporins, carbapenems, aminoglycosides and monobactams resistance in C. freundii B9-C2. The isolate also presented unique virulence genes related to biofilm formation, motility and iron uptake. The genome was compared to publicly available genomes and it was closely related to strains with environmental origins.

    CONCLUSION: To the best of our knowledge, this is the first report of intestinal carriage of colistin-resistant C. freundii from the stool of a neonate in Malaysia. Using genomic analysis, we have contributed to the understanding of the potential mechanism of resistance and the phylogenetic relationship of the isolates with draft genomes available in the public domain.

    Matched MeSH terms: Phylogeny
  13. Sulaiman B, Boyce PC
    Trop Life Sci Res, 2010 Dec;21(2):1-6.
    PMID: 24575195
    Rhaphidophora megasperma Engl., a species hitherto regarded as endemic to Sarawak, East Malaysia, is published as a new record for Peninsular Malaysia. It is the first species in the Rhaphidophora Spathacea group recorded for western Sunda. The species is illustrated and a key to the perforate-laminated Rhaphidophora in Peninsular Malaysia is presented.
    Matched MeSH terms: Phylogeny
  14. Sam IC, Kamarulzaman A, Ong GS, Veriah RS, Ponnampalavanar S, Chan YF, et al.
    Trop Biomed, 2010 Aug;27(2):343-7.
    PMID: 20962735
    Chikungunya virus (CHIKV) is a mosquito-borne alphavirus which causes fever, rash, and arthralgia. In the past, life-threatening complications were very rarely reported. However, during the recent worldwide outbreaks, there have been several reports of unusually severe complications and deaths. Malaysia is experiencing a nationwide outbreak of CHIKV, with over 10 000 patients affected since April 2008. We report the first case of culture-confirmed CHIKV-associated death in Malaysia, in a patient with fever, rash, acute exacerbation of pre-existing heart failure, rhabdomyolysis, and multiple organ failure. CHIKV infections may cause atypical, severe or fatal presentations.
    Matched MeSH terms: Phylogeny
  15. Zhang W, Liang Y, Zheng K, Gu C, Liu Y, Wang Z, et al.
    BMC Genomics, 2021 Sep 20;22(1):675.
    PMID: 34544379 DOI: 10.1186/s12864-021-07978-4
    BACKGROUND: Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions. However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown.

    RESULTS: Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. The recombinant module was highly adapted to the host, according to the tetranucleotides correlations. Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans.

    CONCLUSIONS: These results describe the first Oceanospirillum phage, vB_OliS_GJ44, that represents a novel viral cluster and exhibits interesting genetic features related to phage-host interactions and evolution. Thus, we propose a new viral genus Oceanospirivirus within the Siphoviridae family to reconcile this cluster, with vB_OliS_GJ44 as a representative member.

    Matched MeSH terms: Phylogeny
  16. Karin BR, Freitas ES, Shonleben S, Grismer LL, Bauer AM, Das I
    Zootaxa, 2018 Jan 12;4370(4):345-362.
    PMID: 29689833 DOI: 10.11646/zootaxa.4370.4.2
    We collected two specimens of an undescribed species of Lygosoma from pitfall traps in an urban rainforest in Kuching and from the base of a forested hill in western Sarawak, East Malaysia. The new species is diagnosable from all south-east Asian congeners by morphological characters, and most closely resembles Lygosoma herberti from the Thai-Malay Peninsula. The new species shows substantial molecular divergence from its closest relatives in two protein-coding genes, one mitochondrial (ND1) and one nuclear (R35) that we sequenced for several south-east Asian congeners. We describe the new species on the basis of this distinct morphology and genetic divergence. It is the third species of Lygosoma known from Borneo, and highlights the continuing rise in lizard species diversity on the island. In addition, the discovery of this species from a small urban rainforest underscores the importance of preserving intact rainforest areas of any size in maintaining species diversity.
    Matched MeSH terms: Phylogeny
  17. Kurita T, Nishikawa K, Matsui M, Hikida T
    Zootaxa, 2017 05 03;4258(6):525-538.
    PMID: 28609895 DOI: 10.11646/zootaxa.4258.6.2
    A new species of Asian rock gecko, genus Cnemaspis, is described from Padawan, western Sarawak, Malaysian Borneo. The new species forms a clade with C. paripari and C. nigridia of the C. nigridia group in a mitochondrial DNA phylogeny and is similar to them morphologically in some characters such as caudal scalation. It differs from the other Asian Cnemaspis species in its unique combination of snout-vent length (up to 62.7 mm), 4-9 precloacal pores in males, keeled subcaudals with an enlarged, smooth, median row, presence of ventrolateral caudal tubercles, and coloration (head and upper flanks dark-yellow; anterior portion of tail black; posterior portion of tail white with black, paravertebral blob). Phylogenetic relationships within the C. nigridia group and the distributional ranges of species within the group suggest allopatric speciation by geographic isolation.
    Matched MeSH terms: Phylogeny
  18. Berčič RL, Bányai K, Růžek D, Fehér E, Domán M, Danielová V, et al.
    Microorganisms, 2019 Oct 13;7(10).
    PMID: 31614950 DOI: 10.3390/microorganisms7100447
    Lednice virus (LEDV) has been detected in Culex modestus mosquitoes in several European countries within the last six decades. In this study, phylogenetic analyses of the complete genome segments confirm that LEDV belongs to the Turlock orthobunyavirus (Orthobunyavirus, Peribunyaviridae) species and is closely related to Umbre, Turlock, and Kedah viruses.
    Matched MeSH terms: Phylogeny
  19. Quah ESH, Grismer LL, Wood PLJ, Mohd Sah SA
    Zootaxa, 2019 Sep 09;4668(1):zootaxa.4668.1.3.
    PMID: 31716638 DOI: 10.11646/zootaxa.4668.1.3
    A new species of limestone karst-adapted gecko of the Cyrtodactylus pulchellus complex, C. dayangbuntingensis sp. nov., is described from Dayang Bunting Island of the Langkawi Archipelago off the northwest coast of Peninsular Malaysia. It is the third species of the group to be described from the archipelago after C. langkawiensis and C. macrotuberculatus. The new species can be distinguished from all other species of Cyrtodactylus based on molecular evidence from the mitochondrial gene ND2 and its flanking tRNAs as well as having unique combinations of morphological and color pattern characteristics. This discovery underscores the need for continued surveys of the many islands in the archipelago to properly ascertain its true herpetological diversity.
    Matched MeSH terms: Phylogeny
  20. Grismer LL, Wood PLJ, Quah ESH, Anuar S, Poyarkov NA, Thy N, et al.
    Zootaxa, 2019 Oct 09;4683(3):zootaxa.4683.3.4.
    PMID: 31715918 DOI: 10.11646/zootaxa.4683.3.4
    Molecular phylogenetic analyses of the sister species Sphenomorphus stellatus and S. praesignis based on the mitochondrial genes 12S and 16S rRNA recover the former as paraphyletic with respect to the latter in that a specimen of S. stellatus from the type locality in Peninsular Malaysia is more closely related to S. praesignis than to Indochinese populations of S. stellatus. Furthermore, the phylogeny indicates that the Indochinese populations represent two species, thus resulting in four major lineages within this clade. These relationships are consistent with multivariate and univariate analyses of morphological and discrete color pattern data which statistically define and diagnose the four lineages and together with the molecular data, provide the foundation for robust, testable, species-level hypotheses. As such, S. stellatus is herein restricted to Peninsular Malaysia; S. annamiticus is resurrected for the circum-continental populations ranging through southeastern Thailand, southern Cambodia, and southern Vietnam; a new species-S. preylangensis sp. nov.-is described from an isolated mountain, Phnom Chi, from the Prey Lang Wildlife Sanctuary in central Cambodia; and the taxonomy of S. praesignis remains unchanged. The description of S. preylangensis sp. nov. underscores the necessity to conserve this remnant of lowland evergreen rainforest in the Prey Lang Wildlife Sanctuary.
    Matched MeSH terms: Phylogeny
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