Displaying publications 1541 - 1560 of 1878 in total

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  1. Nocardiopsis deserti sp. nov., isolated from a high altitude Atacama Desert soil
    Asem MD, Salam N, Idris H, Zhang XT, Bull AT, Li WJ, et al.
    Int J Syst Evol Microbiol, 2020 May;70(5):3210-3218.
    PMID: 32320378 DOI: 10.1099/ijsem.0.004158
    The taxonomic status of a Nocardiopsis strain, designated H13T, isolated from a high altitude Atacama Desert soil, was established by using a polyphasic approach. The strain was found to have chemotaxonomic, cultural and morphological characteristics consistent with its classification within the genus Nocardiopsis and formed a well-supported clade in the Nocardiopsis phylogenomic tree together with the type strains of Nocardiopsis alborubida, Nocardiopsis dassonvillei and Nocardiopsis synnematoformans. Strain H13T was distinguished from its closest relatives by low average nucleotide identity (93.2-94.9 %) and in silico DNA-DNA hybridization (52.5-62.4 %) values calculated from draft genome assemblies and by a range of phenotypic properties. On the basis of these results, it is proposed that the isolate be assigned to the genus Nocardiopsis as Nocardiopsis deserti sp. nov. with isolate H13T (=CGMCC 4.7585T=KCTC 49249T) as the type strain.
    Matched MeSH terms: Phylogeny
  2. Amycolatopsis thermophila sp. nov. and Amycolatopsis viridis sp. nov., thermophilic actinomycetes isolated from arid soil
    Zucchi TD, Tan GYA, Goodfellow M
    Int J Syst Evol Microbiol, 2012 Jan;62(Pt 1):168-172.
    PMID: 21378137 DOI: 10.1099/ijs.0.029256-0
    The taxonomic positions of two thermophilic actinomycetes isolated from an arid Australian soil sample were established based on an investigation using a polyphasic taxonomic approach. The organisms had chemical and morphological properties typical of members of the genus Amycolatopsis and formed distinct phyletic lines in the Amycolatopsis methanolica 16S rRNA subclade. The two organisms were distinguished from one another and from the type strains of related species of the genus Amycolatopsis using a range of phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the two isolates be classified in the genus Amycolatopsis as Amycolatopsis thermophila sp. nov. (type strain GY088(T)=NCIMB 14699(T)=NRRL B-24836(T)) and Amycolatopsis viridis sp. nov. (type strain GY115(T)=NCIMB 14700(T)=NRRL B-24837(T)).
    Matched MeSH terms: Phylogeny
  3. Properties of Coronavirus and SARS-CoV-2
    Malik YA
    Malays J Pathol, 2020 Apr;42(1):3-11.
    PMID: 32342926
    were identified beginning with the discovery of SARS-CoV in 2002. With the recent detection of SARS-CoV-2, there are now seven human coronaviruses. Those that cause mild diseases are the 229E, OC43, NL63 and HKU1, and the pathogenic species are SARS-CoV, MERS-CoV and SARS-CoV-2 Coronaviruses (order Nidovirales, family Coronaviridae, and subfamily Orthocoronavirinae) are spherical (125nm diameter), and enveloped with club-shaped spikes on the surface giving the appearance of a solar corona. Within the helically symmetrical nucleocapsid is the large positive sense, single stranded RNA. Of the four coronavirus genera (α,β,γ,δ), human coronaviruses (HCoVs) are classified under α-CoV (HCoV-229E and NL63) and β-CoV (MERS-CoV, SARS-CoV, HCoVOC43 and HCoV-HKU1). SARS-CoV-2 is a β-CoV and shows fairly close relatedness with two bat-derived CoV-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21. Even so, its genome is similar to that of the typical CoVs. SARS-CoV and MERS-CoV originated in bats, and it appears to be so for SARS-CoV-2 as well. The possibility of an intermediate host facilitating the emergence of the virus in humans has already been shown with civet cats acting as intermediate hosts for SARS-CoVs, and dromedary camels for MERS-CoV. Human-to-human transmission is primarily achieved through close contact of respiratory droplets, direct contact with the infected individuals, or by contact with contaminated objects and surfaces. The coronaviral genome contains four major structural proteins: the spike (S), membrane (M), envelope (E) and the nucleocapsid (N) protein, all of which are encoded within the 3' end of the genome. The S protein mediates attachment of the virus to the host cell surface receptors resulting in fusion and subsequent viral entry. The M protein is the most abundant protein and defines the shape of the viral envelope. The E protein is the smallest of the major structural proteins and participates in viral assembly and budding. The N protein is the only one that binds to the RNA genome and is also involved in viral assembly and budding. Replication of coronaviruses begin with attachment and entry. Attachment of the virus to the host cell is initiated by interactions between the S protein and its specific receptor. Following receptor binding, the virus enters host cell cytosol via cleavage of S protein by a protease enzyme, followed by fusion of the viral and cellular membranes. The next step is the translation of the replicase gene from the virion genomic RNA and then translation and assembly of the viral replicase complexes. Following replication and subgenomic RNA synthesis, encapsidation occurs resulting in the formation of the mature virus. Following assembly, virions are transported to the cell surface in vesicles and released by exocytosis.
    Matched MeSH terms: Phylogeny
  4. Detection of Bartonella sp. in ticks and their small mammal hosts in mangrove forests of Peninsular Malaysia
    Asyikha R, Sulaiman N, Mohd-Taib FS
    Trop Biomed, 2020 Dec 01;37(4):919-931.
    PMID: 33612746 DOI: 10.47665/tb.37.4.919
    Bacteria of the genus Bartonella have been known as emerging zoonotic pathogens for several human diseases including cat scratch disease, Carrion's disease and trench fever. Numerous species of small mammals have been reported to play a role as a suitable reservoir to many pathogenic Bartonella. These infections are thought to be transmitted through blood-feeding arthropod vectors such as ticks, fleas and lice. The purpose of this study is to detect the presence of Bartonella species from tick samples collected from small mammals in mangrove forests of Peninsular Malaysia. Herein, 38 individual ticks and their small mammals host were evaluated for the presence of Bartonella DNA by conventional PCR targeting the 16S rRNA intergenic spacer region (ITS) and partial sequencing of 460 bp from this locususing Bartonella genus-specific primers. Two tick individuals from Dermacentor auratus and Haemaphysalis hystricis collected from Rattus tiomanicus (host), were PCR-positive for Bartonella DNA amplification. No Bartonella amplification was possible in other tick species (Amblyomma sp.). Phylogenetic analysis of ITS fragments demonstrated that the sequences from ticks were closely related to Bartonella phoceensis, a species that has been reported from black rats (Rattus rattus) in Australia. This is the first report of a Bartonella bacteria detected in ticks from small mammals in Malaysia. Further research should be warranted to investigate the transmission of Bartonella and the potential impact of this zoonotic pathogen in animals and humans as this mangrove ecosystem is significant for local economy and tourism.
    Matched MeSH terms: Phylogeny
  5. Fulltext Psychrotolerant Mesorhizobium sp. Isolated from Temperate and Cold Desert Regions Solubilizes Potassium and Produces Multiple Plant Growth Promoting Metabolites
    Baba ZA, Hamid B, Sheikh TA, Alotaibi SH, El Enshasy HA, Ansari MJ, et al.
    Molecules, 2021 Sep 23;26(19).
    PMID: 34641302 DOI: 10.3390/molecules26195758
    Soil potassium (K) supplement depends intensively on the application of chemical fertilizers, which have substantial harmful environmental effects. However, some bacteria can act as inoculants by converting unavailable and insoluble K forms into plant-accessible forms. Such bacteria are an eco-friendly approach for enhancing plant K absorption and consequently reducing utilization of chemical fertilization. Therefore, the present research was undertaken to isolate, screen, and characterize the K solubilizing bacteria (KSB) from the rhizosphere soils of northern India. Overall, 110 strains were isolated, but only 13 isolates showed significant K solubilizing ability by forming a halo zone on solid media. They were further screened for K solubilizing activity at 0 °C, 1 °C, 3 °C, 5 °C, 7 °C, 15 °C, and 20 °C for 5, 10, and 20 days. All the bacterial isolates showed mineral K solubilization activity at these different temperatures. However, the content of K solubilization increased with the upsurge in temperature and period of incubation. The isolate KSB (Grz) showed the highest K solubilization index of 462.28% after 48 h of incubation at 20 °C. The maximum of 23.38 µg K/mL broth was solubilized by the isolate KSB (Grz) at 20 °C after 20 days of incubation. Based on morphological, biochemical, and molecular characterization (through the 16S rDNA approach), the isolate KSB (Grz) was identified as Mesorhizobium sp. The majority of the strains produced HCN and ammonia. The maximum indole acetic acid (IAA) (31.54 µM/mL) and cellulase (390 µM/mL) were produced by the isolate KSB (Grz). In contrast, the highest protease (525.12 µM/mL) and chitinase (5.20 µM/mL) activities were shown by standard strain Bacillus mucilaginosus and KSB (Gmr) isolate, respectively.
    Matched MeSH terms: Phylogeny
  6. Fulltext Emergence of Genotype I of Dengue Virus Serotype 3 during a Severe Dengue Epidemic in Sri Lanka in 2017
    Ngwe Tun MM, Muthugala R, Rajamanthri L, Nabeshima T, Buerano CC, Morita K
    Jpn J Infect Dis, 2021 Sep 22;74(5):443-449.
    PMID: 33642435 DOI: 10.7883/yoken.JJID.2020.854
    During the 2017 outbreak of severe dengue in Sri Lanka, dengue virus (DENV) serotypes 2, 3, and 4 were found to be co-circulating. Our previous study of 295 patients from the National Hospital Kandy in Sri Lanka between March 2017 and January 2018 determined that the dominant infecting serotype was DENV-2. In this study, we aimed to characterize the DENV-3 strains from non-severe and severe dengue patients from our previous study population. Patients' clinical records and previous laboratory tests, including dengue-specific nonstructural protein 1 antigen rapid test and IgM-capture and IgG enzyme-linked immunosorbent assays, were analyzed together with the present results of real-time reverse transcription polymerase chain reaction and next-generation sequencing of DENV-3. Complete genome analysis determined that DENV-3 isolates belonged to 2 different clades of genotype I and were genetically close to strains from Indonesia, China, Singapore, Malaysia, and Australia. There were 16 amino acid changes among DENV-3 isolates, and a greater number of changes were found in nonstructural proteins than in structural proteins. The emergence of DENV-3 genotype I was noted for the first time in Sri Lanka. Continuous monitoring of this newly emerged genotype and other DENV serotypes and genotypes is needed to determine their effects on future outbreaks and understand the molecular epidemiology of dengue.
    Matched MeSH terms: Phylogeny
  7. Fulltext Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice
    Abdullah-Zawawi MR, Ahmad-Nizammuddin NF, Govender N, Harun S, Mohd-Assaad N, Mohamed-Hussein ZA
    Sci Rep, 2021 10 04;11(1):19678.
    PMID: 34608238 DOI: 10.1038/s41598-021-99206-y
    Transcription factors (TFs) form the major class of regulatory genes and play key roles in multiple plant stress responses. In most eukaryotic plants, transcription factor (TF) families (WRKY, MADS-box and MYB) activate unique cellular-level abiotic and biotic stress-responsive strategies, which are considered as key determinants for defense and developmental processes. Arabidopsis and rice are two important representative model systems for dicot and monocot plants, respectively. A comprehensive comparative study on 101 OsWRKY, 34 OsMADS box and 122 OsMYB genes (rice genome) and, 71 AtWRKY, 66 AtMADS box and 144 AtMYB genes (Arabidopsis genome) showed various relationships among TFs across species. The phylogenetic analysis clustered WRKY, MADS-box and MYB TF family members into 10, 7 and 14 clades, respectively. All clades in WRKY and MYB TF families and almost half of the total number of clades in the MADS-box TF family are shared between both species. Chromosomal and gene structure analysis showed that the Arabidopsis-rice orthologous TF gene pairs were unevenly localized within their chromosomes whilst the distribution of exon-intron gene structure and motif conservation indicated plausible functional similarity in both species. The abiotic and biotic stress-responsive cis-regulatory element type and distribution patterns in the promoter regions of Arabidopsis and rice WRKY, MADS-box and MYB orthologous gene pairs provide better knowledge on their role as conserved regulators in both species. Co-expression network analysis showed the correlation between WRKY, MADs-box and MYB genes in each independent rice and Arabidopsis network indicating their role in stress responsiveness and developmental processes.
    Matched MeSH terms: Phylogeny
  8. Fulltext Exosomal miR-224 contributes to hemolymph microbiota homeostasis during bacterial infection in crustacean
    Gong Y, Wei X, Sun W, Ren X, Chen J, Aweya JJ, et al.
    PLoS Pathog, 2021 08;17(8):e1009837.
    PMID: 34379706 DOI: 10.1371/journal.ppat.1009837
    It is well known that exosomes could serve as anti-microbial immune factors in animals. However, despite growing evidences have shown that the homeostasis of the hemolymph microbiota was vital for immune regulation in crustaceans, the relationship between exosomes and hemolymph microbiota homeostasis during pathogenic bacteria infection has not been addressed. Here, we reported that exosomes released from Vibrio parahaemolyticus-infected mud crabs (Scylla paramamosain) could help to maintain the homeostasis of hemolymph microbiota and have a protective effect on the mortality of the host during the infection process. We further confirmed that miR-224 was densely packaged in these exosomes, resulting in the suppression of HSP70 and disruption of the HSP70-TRAF6 complex, then the released TRAF6 further interacted with Ecsit to regulate the production of mitochondrial ROS (mROS) and the expression of Anti-lipopolysaccharide factors (ALFs) in recipient hemocytes, which eventually affected hemolymph microbiota homeostasis in response to the pathogenic bacteria infection in mud crab. To the best of our knowledge, this is the first document that reports the role of exosome in the hemolymph microbiota homeostasis modulation during pathogen infection, which reveals the crosstalk between exosomal miRNAs and innate immune response in crustaceans.
    Matched MeSH terms: Phylogeny
  9. Fulltext Phylogeography and phylogeny of Rhinoviruses collected from Severe Acute Respiratory Infection (SARI) cases over successive epidemic periods in Tunisia
    Haddad-Boubaker S, Ben Hamda C, Ghedira K, Mefteh K, Bouafsoun A, Boutiba-Ben Boubaker I, et al.
    PLoS One, 2021;16(11):e0259859.
    PMID: 34807924 DOI: 10.1371/journal.pone.0259859
    Rhinoviruses (RV) are a major cause of Severe Acute Respiratory Infection (SARI) in children, with high genotypic diversity in different regions. However, RV type diversity remains unknown in several regions of the world. In this study, the genetic variability of the frequently circulating RV types in Northern Tunisia was investigated, using phylogenetic and phylogeographic analyses with a specific focus on the most frequent RV types: RV-A101 and RV-C45. This study concerned 13 RV types frequently circulating in Northern Tunisia. They were obtained from respiratory samples collected in 271 pediatric SARI cases, between September 2015 and November 2017. A total of 37 RV VP4-VP2 sequences, selected among a total of 49 generated sequences, was compared to 359 sequences from different regions of the world. Evolutionary analysis of RV-A101 and RV-C45 showed high genetic relationship between different Tunisian strains and Malaysian strains. RV-A101 and C45 progenitor viruses' dates were estimated in 1981 and 1995, respectively. Since the early 2000s, the two types had a wide spread throughout the world. Phylogenetic analyses of other frequently circulating strains showed significant homology of Tunisian strains from the same epidemic period, in contrast with earlier strains. The genetic relatedness of RV-A101 and RV-C45 might result from an introduction of viruses from different clades followed by local dissemination rather than a local persistence of an endemic clades along seasons. International traffic may play a key role in the spread of RV-A101, RV-C45, and other RVs.
    Matched MeSH terms: Phylogeny
  10. Complete genetic dissection and cell type-specific replication of old world alphaviruses, getah virus (GETV) and sagiyama virus (SAGV)
    Zhang Y, Yu J, Tan L, Wang X, Li R, Kim DY
    J Microbiol, 2021 Nov;59(11):1044-1055.
    PMID: 34570337 DOI: 10.1007/s12275-021-1361-8
    Getah virus (GETV), which was first isolated in Malaysia in 1955, and Sagiyama virus (SAGV), isolated in Japan in 1956, are members of the genus Alphavirus in the family Togaviridae. It is a consensus view that SAGV is a variant of GETV. In the present study, we determined the complete sequences of the prototype GETV MM2021 and SAGV M6-Mag132 genomic RNA extracted from plaque-purified viruses. The MM2021 genome was 11,692 nucleotides (nt) in length in the absence of 3' poly(A) tail, and the length of M6-Mag132 genome was 11,698 nt. Through sequence alignment of MM2021 and M6-Mag132, we located all the amino acid differences between these two strains, which were scattered in all the encoded proteins. Subsequently, we validated the close evolutionary relationship between GETV and SAGV by constructing phylogenetic trees based on either complete genomes or structural genomes. We eventually analyzed the growth kinetics of GETV and SAGV as well as other representative alphaviruses in various mammalian and insect cell lines. It was shown that human-oriented cell lines such as HEK-293T and Hela cells were relatively resistant to GETV and SAGV infection due to absence of proviral factors or species-specific barrier. On the other hand, both GETV and SAGV replicated efficiently in non-human cell lines. Our results provide essential genetic information for future epidemiological surveillance on Alphaviruses and lay the foundation for developing effective interventions against GETV and SAGV.
    Matched MeSH terms: Phylogeny
  11. Fulltext Genomic epidemiology of tuberculosis in eastern Malaysia: insights for strengthening public health responses
    Bainomugisa A, Meumann EM, Rajahram GS, Ong RT, Coin L, Paul DC, et al.
    Microb Genom, 2021 05;7(5).
    PMID: 33945455 DOI: 10.1099/mgen.0.000573
    Tuberculosis is a leading public health priority in eastern Malaysia. Knowledge of the genomic epidemiology of tuberculosis can help tailor public health interventions. Our aims were to determine tuberculosis genomic epidemiology and characterize resistance mutations in the ethnically diverse city of Kota Kinabalu, Sabah, located at the nexus of Malaysia, Indonesia, Philippines and Brunei. We used an archive of prospectively collected Mycobacterium tuberculosis samples paired with epidemiological data. We collected sputum and demographic data from consecutive consenting outpatients with pulmonary tuberculosis at the largest tuberculosis clinic from 2012 to 2014, and selected samples from tuberculosis inpatients from the tertiary referral centre during 2012-2014 and 2016-2017. Two hundred and eight M. tuberculosis sequences were available for analysis, representing 8 % of cases notified during the study periods. Whole-genome phylogenetic analysis demonstrated that most strains were lineage 1 (195/208, 93.8 %), with the remainder being lineages 2 (8/208, 3.8 %) or 4 (5/208, 2.4 %). Lineages or sub-lineages were not associated with patient ethnicity. The lineage 1 strains were diverse, with sub-lineage 1.2.1 being dominant (192, 98 %). Lineage 1.2.1.3 isolates were geographically most widely distributed. The greatest diversity occurred in a border town sub-district. The time to the most recent common ancestor for the three major lineage 1.2.1 clades was estimated to be the year 1966 (95 % HPD 1948-1976). An association was found between failure of culture conversion by week 8 of treatment and infection with lineage 2 (4/6, 67 %) compared with lineage 1 strains (4/83, 5 %) (P<0.001), supporting evidence of greater virulence of lineage 2 strains. Eleven potential transmission clusters (SNP difference ≤12) were identified; at least five included people living in different sub-districts. Some linked cases spanned the whole 4-year study period. One cluster involved a multidrug-resistant tuberculosis strain matching a drug-susceptible strain from 3 years earlier. Drug resistance mutations were uncommon, but revealed one phenotype-genotype mismatch in a genotypically multidrug-resistant isolate, and rare nonsense mutations within the katG gene in two isolates. Consistent with the regionally mobile population, M. tuberculosis strains in Kota Kinabalu were diverse, although several lineage 1 strains dominated and were locally well established. Transmission clusters - uncommonly identified, likely attributable to incomplete sampling - showed clustering occurring across the community, not confined to households or sub-districts. The findings indicate that public health priorities should include active case finding and early institution of tuberculosis management in mobile populations, while there is a need to upscale effective contact investigation beyond households to include other contacts within social networks.
    Matched MeSH terms: Phylogeny
  12. Cupriavidus malaysiensis sp. nov., a novel poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment
    Ramachandran H, Shafie NAH, Sudesh K, Azizan MN, Majid MIA, Amirul AA
    Antonie Van Leeuwenhoek, 2018 Mar;111(3):361-372.
    PMID: 29022146 DOI: 10.1007/s10482-017-0958-8
    Bacterial classification on the basis of a polyphasic approach was conducted on three poly(3 hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] accumulating bacterial strains that were isolated from samples collected from Malaysian environments; Kulim Lake, Sg. Pinang river and Sg. Manik paddy field. The Gram-negative, rod-shaped, motile, non-sporulating and non-fermenting bacteria were shown to belong to the genus Cupriavidus of the Betaproteobacteria on the basis of their 16S rRNA gene sequence analyses. The sequence similarity value with their near phylogenetic neighbour, Cupriavidus pauculus LMG3413T, was 98.5%. However, the DNA-DNA hybridization values (8-58%) and ribotyping analysis both enabled these strains to be differentiated from related Cupriavidus species with validly published names. The RiboPrint patterns of the three strains also revealed that the strains were genetically related even though they displayed a clonal diversity. The major cellular fatty acids detected in these strains included C15:0 ISO 2OH/C16:1 ω7c, hexadecanoic (16:0) and cis-11-octadecenoic (C18:1 ω7c). Their G+C contents ranged from 68.0  to 68.6 mol%, and their major isoprenoid quinone was Ubiquinone Q-8. Of these three strains, only strain USMAHM13 (= DSM 25816 = KCTC 32390) was discovered to exhibit yellow pigmentation that is characteristic of the carotenoid family. Their assembled genomes also showed that the three strains were not identical in terms of their genome sizes that were 7.82, 7.95 and 8.70 Mb for strains USMAHM13, USMAA1020 and USMAA2-4, respectively, which are slightly larger than that of Cupriavidus necator H16 (7.42 Mb). The average nucleotide identity (ANI) results indicated that the strains were genetically related and the genome pairs belong to the same species. On the basis of the results obtained in this study, the three strains are considered to represent a novel species for which the name Cupriavidus malaysiensis sp. nov. is proposed. The type strain of the species is USMAA1020T (= DSM 19416T = KCTC 32390T).
    Matched MeSH terms: Phylogeny
  13. Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species
    Nater A, Mattle-Greminger MP, Nurcahyo A, Nowak MG, de Manuel M, Desai T, et al.
    Curr Biol, 2017 Nov 20;27(22):3487-3498.e10.
    PMID: 29103940 DOI: 10.1016/j.cub.2017.09.047
    Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. VIDEO ABSTRACT.
    Matched MeSH terms: Phylogeny
  14. Next generation sequencing yields the complete mitochondrial genome of the Clarion angelfish, Holacanthus clarionensis (Perciformes: Pomacanthidae)
    Shen KN, Chang CW, Loh KH, Chen CH, Hsiao CD
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4118-4119.
    PMID: 25600747
    In this study, the complete mitogenome sequence of the Clarion angelfish, Holacanthus clarionensis (Perciformes: Pomacanthidae) has been sequenced by next-generation sequencing method. The length of the assembled mitogenome is 16,615 bp, including 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Clarion angelfish is 28.3% for A, 29.3% for C, 16.5% for G, 25.9% for T and show 85% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Clarion angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.
    Matched MeSH terms: Phylogeny
  15. Molecular evidence of Sarcocystis nesbitti in water samples of Tioman Island, Malaysia
    Shahari S, Tengku-Idris TI, Fong MY, Lau YL
    Parasit Vectors, 2016 11 23;9(1):598.
    PMID: 27881179
    BACKGROUND: Sarcocystis are intracellular protozoan parasites that are characterised by their ability to invade muscle tissue and form intramuscular sarcocysts. A muscular sarcocystosis outbreak was reported by travellers returning from Tioman Island in 2011 and 2012 where Sarcocystis nesbitti was identified as the main cause. The source of the S. nesbitti that was involved has remained elusive, although water is hypothesised to be the main cause of transmission. A surveillance study was therefore undertaken in the northern regions of Tioman Island to identify the source of S. nesbitti by screening rivers, water tanks, wells and seawater.

    METHODS: Water samples were collected from rivers, water tanks, wells and seawater on Tioman Island over the course of April to October 2015. Water samples were indirectly screened for Sarcocystis species by obtaining sediment from respective water sources. PCR amplification of the 18S rRNA gene region was conducted to identify positive samples. Microscopy was used in an attempt to reappraise PCR results, but no sporocysts were detected in any of the samples.

    RESULTS: A total of 157 water samples were obtained and 19 were positive for various Sarcocystis species. Through BLASTn and phylogenetic analysis, these species were found to be S. singaporensis, S. nesbitti, Sarcocystis sp. YLL-2013 and one unidentified Sarcocystis species.

    CONCLUSIONS: This is the first positive finding of S. nesbitti in water samples on Tioman Island, which was found in a water tank and in river water samples. This finding supports the hypothesis that water was a potential medium for the transmission of S. nesbitti during the outbreak. This will potentially identify areas in which preventive measures can be taken to prevent future outbreaks.

    Matched MeSH terms: Phylogeny
  16. More evolution underground: Accelerated mitochondrial substitution rate in Australian burrowing freshwater crayfishes (Decapoda: Parastacidae)
    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: Phylogeny
  17. Pathogens in ectoparasites from free-ranging animals: Infection with Rickettsia asembonensis in ticks, and a potentially new species of Dipylidium in fleas and lice
    Low VL, Prakash BK, Tan TK, Sofian-Azirun M, Anwar FHK, Vinnie-Siow WY, et al.
    Vet Parasitol, 2017 Oct 15;245:102-105.
    PMID: 28969827 DOI: 10.1016/j.vetpar.2017.08.015
    Vector-borne infections are persistent public health threats worldwide. In recent years, a number of mosquito-borne viruses have emerged or re-emerged to cause major disease outbreaks. Other vector-borne pathogens, however, remain understudied and much neglected especially in the developing regions of the world including Southeast Asia. In this study, the brown dog tick Rhipicephalus sanguineus sensu lato, cat louse Felicola subrostratus, and cat fleas Ctenocephalides felis and Ctenocephalides orientis collected from free-ranging cats and dogs in Malaysia were molecularly screened for the presence of Bartonella and Rickettsia bacteria, and Dipylidium tapeworm. Our results showed the presence of Bartonella clarridgeiea, Bartonella henselae (lineage Marseille and lineage Houston-1), and Rickettsia sp. in C. felis. We also detected Rickettsia asembonensis in C. orientis and R. sanguineus s.l. Additionally, this study provides the first documentation on a potentially new species of Dipylidium infecting F. subrostratus and C. felis. Our results highlight the role of ectoparasites from free-ranging animals including cats and dogs, in harboring multiple transmissible pathogens.
    Matched MeSH terms: Phylogeny
  18. Two new Bent-toed Geckos of the Cyrtodactylus pulchellus complex from Peninsular Malaysia and multiple instances of convergent adaptation to limestone forest ecosystems
    Grismer LL, Wood PL, Anuar S, Grismer MS, Quah ES, Murdoch ML, et al.
    Zootaxa, 2016 Apr 25;4105(5):401-29.
    PMID: 27394789 DOI: 10.11646/zootaxa.4105.5.1
    A new species of limestone cave-adapted gecko of the Cyrtodactylus pulchellus complex, C. hidupselamanya sp. nov., is described from an isolated karst formation at Felda Chiku 7, Kelantan, Peninsular Malaysia. This formation is scheduled to be completely quarried for its mineral content. From what we know about the life history of C. hidupselamanya sp. nov., this will result in its extinction. A new limestone forest-adapted species, C. lenggongensis sp. nov., from the Lenggong Valley, Perak was previously considered to be conspecific with C. bintangrendah but a re-evaluation of morphological, color pattern, molecular, and habitat preference indicates that it too is a unique lineage worthy of specific recognition. Fortunately C. lenggongensis sp. nov. is not facing extinction because its habitat is protected by the UNESCO Archaeological Heritage of the Lenggong Valley due to the archaeological significance of that region. Both 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. Using a time-calibrated BEAST analysis we inferred that the evolution of a limestone habitat preference and its apparently attendant morphological and color pattern adaptations evolved independently at least four times in the C. pulchellus complex between 26.1 and 0.78 mya.
    Matched MeSH terms: Phylogeny
  19. The life cycle of Thelohanellus kitauei (Myxozoa: Myxosporea) infecting common carp (Cyprinus carpio) involves aurantiactinomyxon in Branchiura sowerbyi
    Zhao D, Borkhanuddin MH, Wang W, Liu Y, Cech G, Zhai Y, et al.
    Parasitol Res, 2016 Nov;115(11):4317-4325.
    PMID: 27492197
    Thelohanellus kitauei is a freshwater myxosporean parasite causing intestinal giant cystic disease of common carp. To clarify the life cycle of T. kitauei, we investigated the oligochaete populations in China and Hungary. This study confirms two distinct aurantiactinomyxon morphotypes (Aurantiactinomyxon type 1 and Aurantiactinomyxon type 2) from Branchiura sowerbyi as developmental stages of the life cycle of T. kitauei. The morphological characteristics and DNA sequences of these two types are described here. Based on 18S rDNA sequence analysis, Aurantiactinomyxon type 1 (2048 bp) and Aurantiactinomyxon type 2 (2031 bp) share 99.2-99.4 %, 99.8-100 % similarity to the published sequences of T. kitauei, respectively. The 18S rDNA sequences of these two aurantiactinomyxon morphotypes share 99.4 % similarity, suggesting intraspecific variation within the taxon, possibly due to geographic origin. Phylogenetic analyses demonstrate the two aurantiactinomyxon types clustered with T. kitauei. Regardless, based on 18S rDNA synonymy, it is likely that Aurantiactinomyxon type 1 and 2 are conspecific with T. kitauei. This is the fourth elucidated two-host life cycle of Thelohanellus species and the first record of T. kitauei in Europe.
    Matched MeSH terms: Phylogeny
  20. Fulltext Behavioral studies and veterinary management of orangutans at Bukit Merah Orang Utan Island, Perak, Malaysia
    Hayashi M, Kawakami F, Roslan R, Hapiszudin NM, Dharmalingam S
    Primates, 2018 Mar;59(2):135-144.
    PMID: 29383576 DOI: 10.1007/s10329-018-0650-2
    The Bukit Merah Orang Utan Island (OUI) Foundation has been conducting behavioral and veterinary research on orangutans as an attempt at ex situ conservation. Since 2010, the Primate Research Institute, Kyoto University has been collaborating with OUI to promote environmental enrichment and infant rearing by biological mothers in addition to the continuous efforts of refining the veterinary management of the endangered species. In 2011, three Bornean orangutans (Pongo pygmaeus pygmaeus) were released on an island, called BJ Island, adjacent to OUI. This island is approximately 5.6 ha in size, and 635 trees belonging to 102 plant species were identified prior to their release. Behavioral monitoring of the released individuals has been conducted to evaluate their behavioral adaptation to the new environment. Two of the three released orangutans were born in the wild, whereas the youngest individual was born on OUI and expected to learn forest survival strategies from the two older individuals. One of the orangutans was pregnant at the time of release and subsequently gave birth to two male infants on BJ Island. The behavioral monitoring indicated that these orangutans traveled more and spent more time on trees following their release onto BJ Island. However, resting was longer for two females both on OUI and BJ Island when compared to other populations. The orangutans consumed some natural food resources on BJ Island. The release into a more naturalistic environment may help the orangutans to develop more naturalistic behavioral patterns that resemble their wild counterparts.
    Matched MeSH terms: Phylogeny
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