Displaying publications 781 - 800 of 1878 in total

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  1. Fulltext A genetic comparison of two alleged subspecies of Philippine cynomolgus macaques
    Smith DG, Ng J, George D, Trask JS, Houghton P, Singh B, et al.
    Am J Phys Anthropol, 2014 Sep;155(1):136-48.
    PMID: 24979664 DOI: 10.1002/ajpa.22564
    Two subspecies of cynomolgus macaques (Macaca fascicularis) are alleged to co-exist in the Philippines, M. f. philippensis in the north and M. f. fascicularis in the south. However, genetic differences between the cynomolgus macaques in the two regions have never been studied to document the propriety of their subspecies status. We genotyped samples of cynomolgus macaques from Batangas in southwestern Luzon and Zamboanga in southwestern Mindanao for 15 short tandem repeat (STR) loci and sequenced an 835 bp fragment of the mtDNA of these animals. The STR genotypes were compared with those of cynomolgus macaques from southern Sumatra, Singapore, Mauritius and Cambodia, and the mtDNA sequences of both Philippine populations were compared with those of cynomolgus macaques from southern Sumatra, Indonesia and Sarawak, Malaysia. We conducted STRUCTURE and PCA analyses based on the STRs and constructed a median joining network based on the mtDNA sequences. The Philippine population from Batangas exhibited much less genetic diversity and greater genetic divergence from all other populations, including the Philippine population from Zamboanga. Sequences from both Batangas and Zamboanga were most closely related to two different mtDNA haplotypes from Sarawak from which they are apparently derived. Those from Zamboanga were more recently derived than those from Batangas, consistent with their later arrival in the Philippines. However, clustering analyses do not support a sufficient genetic distinction of cynomolgus macaques from Batangas from other regional populations assigned to subspecies M. f. fascicularis to warrant the subspecies distinction M. f. philippensis.
    Matched MeSH terms: Phylogeny
  2. Fulltext Multilocus sequence typing of clinical Burkholderia pseudomallei isolates from Cambodia
    Gyamfi E, Delvallez G, Cheng S, Meng S, Oeurn K, Sam C, et al.
    PLoS Negl Trop Dis, 2024 Nov;18(11):e0012652.
    PMID: 39541393 DOI: 10.1371/journal.pntd.0012652
    Melioidosis is a neglected tropical disease caused by Burkholderia pseudomallei, endemic to Southeast Asia and Northern Australia. Despite its increasing global public health and clinical significance, the molecular epidemiology of melioidosis and genetic diversity of B. pseudomallei in Cambodia remains poorly understood. This study aims to elucidate the genetic diversity and antibiotic susceptibility profiles of B. pseudomallei isolates responsible for melioidosis in humans. For this purpose, 14 clinical isolates cryopreserved at the Medical Biology Laboratory at Institut Pasteur du Cambodge from 2016 to 2020 were subjected to antimicrobial susceptibility testing and Multilocus Sequence Typing (MLST). Phenotypic testing revealed that 92.86% (13/14) of the isolates were sensitive to all tested antibiotics, while one isolate exhibited resistance to trimethoprim-sulfamethoxazole. MLST analysis resolved our isolates into 14 unique Sequence Types (STs), including 10 previously documented in Southeast Asia. Notably, ST1858, ST2064, ST2065, and ST2066 were identified as novel STs, while ST54, ST99, ST211, and ST1359 were reported in Cambodia for the first time in this study. Comparing our MLST data with available sequences on PubMLST (n = 165), our study unveiled a high genetic diversity of B. pseudomallei in Cambodia. The identified STs were closely associated with isolates from other Southeast Asian countries, particularly Thailand, Vietnam, and Malaysia. In conclusion, this study provided insight into the genetic diversity among B. pseudomallei clinical isolates in Cambodia and their close genetic association with Southeast Asian isolates. To further our understanding, a One Health approach, incorporating human, environmental (mainly soil), and animal compartments, is essential to decipher the epidemiology of B. pseudomallei in Cambodia.
    Matched MeSH terms: Phylogeny
  3. Novel black yeast-like species in chaetothyriales with ant-associated life styles
    Quan Y, Ahmed SA, Menezes da Silva N, Al-Hatmi AMS, Mayer VE, Deng S, et al.
    Fungal Biol, 2021 Apr;125(4):276-284.
    PMID: 33766306 DOI: 10.1016/j.funbio.2020.11.006
    Among ancestral fungi in Chaetothyriales, several groups have a life style in association with tropical ants, either in domatia or in carton-nests. In the present study, two strains collected from ant carton in Thailand and Malaysia were found to represent hitherto undescribed species. Morphological, physiological, phylogenetic data and basic genome information are provided for their classification. Because of the relatively large phylogenetic distances with known species confirmed by overall genome data, large subunit (LSU) and Internal Transcribed Spacer (ITS) ribosomal DNA sequences were sufficient for taxonomic circumscription of the species. The analyzed strains clustered with high statistical support as a clade in the family Trichomeriaceae. Morphologically they were rather similar, lacking sporulation in vitro. In conclusion, Incumbomyces delicatus and Incumbomyces lentus were described as new species based on morphological, physiological and phylogenetic analysis.
    Matched MeSH terms: Phylogeny
  4. Time and place in the prehistory of the Aslian languages
    Dunn M, Kruspe N, Burenhult N
    Hum Biol, 2013 Feb-Jun;85(1-3):383-400.
    PMID: 24297234
    The Aslian language family, located in the Malay Peninsula and southern Thai Isthmus, consists of four distinct branches comprising some 18 languages. These languages predate the now dominant Malay and Thai. The speakers of Aslian languages exhibit some of the highest degree of phylogenetic and societal diversity present in Mainland Southeast Asia today, among them a foraging tradition particularly associated with locally ancient, Pleistocene genetic lineages. Little advance has been made in our understanding of the linguistic prehistory of this region or how such complexity arose. In this article we present a Bayesian phylogeographic analysis of a large sample of Aslian languages. An explicit geographic model of diffusion is combined with a cognate birth-word death model of lexical evolution to infer the location of the major events of Aslian cladogenesis. The resultant phylogenetic trees are calibrated against dates in the historical and archaeological record to infer a detailed picture of Aslian language history, addressing a number of outstanding questions, including (1) whether the root ancestor of Aslian was spoken in the Malay Peninsula, or whether the family had already divided before entry, and (2) the dynamics of the movement of Aslian languages across the peninsula, with a particular focus on its spread to the indigenous foragers.
    Matched MeSH terms: Phylogeny
  5. Surveillance, isolation and genomic characterization of Pteropine orthoreovirus of probable bat origin among patients with acute respiratory infection in Malaysia
    Tee KK, Chan PQ, Loh AM, Singh S, Teo CH, Iyadorai T, et al.
    J Med Virol, 2023 Feb;95(2):e28520.
    PMID: 36691929 DOI: 10.1002/jmv.28520
    Pteropine orthoreovirus (PRV), an emerging bat-borne virus, has been linked to cases of acute respiratory infections (ARI) in humans. The prevalence, epidemiology and genomic diversity of PRV among ARI of unknown origin were studied. Among 632 urban outpatients tested negative for all known respiratory viruses, 2.2% were PRV-positive. Patients mainly presented with moderate to severe forms of cough, sore throat and muscle ache, but rarely with fever. Phylogenetic analysis revealed that over 90% of patients infected with the Melaka virus (MelV)-like PRV, while one patient infected with the Pulau virus previously found only in fruit bats. Human oral keratinocytes and nasopharyngeal epithelial cells were susceptible to clinical isolates of PRV, including the newly isolated MelV-like 12MYKLU1034. Whole genome sequence of 12MYKLU1034 using Nanopore technique revealed a novel reassortant strain. Evolutionary analysis of the global PRV strains suggests the continuous evolution of PRV through genetic reassortment among PRV strains circulating in human, bats and non-human primate hosts, creating a spectrum of reassortant lineages with complex evolutionary characteristics. In summary, the role of PRV as a common etiologic agent of ARI is evident. Continuous monitoring of PRV prevalence, pathogenicity and diversity among human and animal hosts is important to trace the emergence of novel reassortants.
    Matched MeSH terms: Phylogeny
  6. Comparison of common human respiratory pathogens among hospitalized children aged ≤ 6 years in Hainan Island, China, during spring and early summer in 2019-2021
    Mai W, Ren Y, Tian X, Al-Mahdi AY, Peng R, An J, et al.
    J Med Virol, 2023 Apr;95(4):e28692.
    PMID: 36946502 DOI: 10.1002/jmv.28692
    The coronavirus disease 2019 (COVID-19) pandemic and related public health intervention measures have been reported to have resulted in the reduction of infections caused by influenza viruses and other common respiratory viruses. However, the influence may be varied in areas that have different ecological, economic, and social conditions. This study investigated the changing epidemiology of 8 common respiratory pathogens, including Influenza A (IFVA), Influenza B (IFVB), Respiratory syncytial virus (HRSV), rhinovirus (RV), Human metapneumovirus Adenovirus, Human bocavirus, and Mycoplasma pneumoniae, among hospitalized children during spring and early summer in 2019-2021 in two hospitals in Hainan Island, China, in the COVID-19 pandemic era. The results revealed a significant reduction in the prevalence of IFVA and IFVB in 2020 and 2021 than in 2019, whereas the prevalence of HRSV increased, and it became the dominant viral pathogen in 2021. RV was one of the leading pathogens in the 3 year period, where no significant difference was observed. Phylogenetic analysis revealed close relationships among the circulating respiratory viruses. Large scale studies are needed to study the changing epidemiology of seasonal respiratory viruses to inform responses to future respiratory virus pandemics.
    Matched MeSH terms: Phylogeny
  7. High Prevalence of Rodent-Borne Bartonella spp. in Urbanizing Environments in Sarawak, Malaysian Borneo
    Blasdell KR, Perera D, Firth C
    Am J Trop Med Hyg, 2019 03;100(3):506-509.
    PMID: 30526734 DOI: 10.4269/ajtmh.18-0616
    Rodents are the most prominent animal host of Bartonella spp., which are associated with an increasing number of human diseases worldwide. Many rodent species thrive in urban environments and live in close contact with people, which can lead to an increased human risk of infection from rodent-borne pathogens. In this study, we explored the prevalence and distribution of Bartonella spp. in rodents in urban, developing, and rural environments surrounding a growing city in Sarawak, Malaysian Borneo. We found that although Bartonella spp. infection was pervasive in most rodent species sampled, prevalence was highest in urban areas and infection was most commonly detected in the predominant indigenous rodent species sampled (Sundamys muelleri). Within the urban environment, parks and remnant green patches were significantly associated with the presence of both S. muelleri and Bartonella spp., indicating higher localized risk of infection for people using these environments for farming, foraging, or recreation.
    Matched MeSH terms: Phylogeny
  8. Isolation of Coronavirus NL63 from Blood from Children in Rural Haiti: Phylogenetic Similarities with Recent Isolates from Malaysia
    Beau De Rochars VM, Lednicky J, White S, Loeb J, Elbadry MA, Telisma T, et al.
    Am J Trop Med Hyg, 2017 Jan 11;96(1):144-147.
    PMID: 27799635 DOI: 10.4269/ajtmh.16-0585
    Human coronavirus (HCoV) NL63 is recognized as a common cause of upper respiratory infections and influenza-like illness. In screening children with acute undifferentiated febrile illness in a school cohort in rural Haiti, we identified HCoV-NL63 in blood samples from four children. Cases clustered over an 11-day period; children did not have respiratory symptoms, but two had gastrointestinal complaints. On phylogenetic analysis, the Haitian HCoV-NL63 strains cluster together in a highly supported monophyletic clade linked most closely with recently reported strains from Malaysia; two respiratory HCoV-NL63 strains identified in north Florida in the same general period form a separate clade, albeit again with close linkages with the Malaysian strains. Our data highlight the variety of presentations that may be seen with HCoV-NL63, and underscore the apparent ease with which CoV strains move among countries, with our data consistent with recurrent introduction of strains into the Caribbean (Haiti and Florida) from Asia.
    Matched MeSH terms: Phylogeny
  9. Fulltext Detection of Wolbachia in Aedes albopictus and Their Effects on Chikungunya Virus
    Ahmad NA, Vythilingam I, Lim YAL, Zabari NZAM, Lee HL
    Am J Trop Med Hyg, 2017 Jan 11;96(1):148-156.
    PMID: 27920393 DOI: 10.4269/ajtmh.16-0516
    Wolbachia-based vector control strategies have been proposed as a means to augment the currently existing measures for controlling dengue and chikungunya vectors. Prior to utilizing Wolbachia as a novel vector control strategy, it is crucial to understand the Wolbachia-mosquito interactions. In this study, field surveys were conducted to screen for the infection status of Wolbachia in field-collected Aedes albopictus The effects of Wolbachia in its native host toward the replication and dissemination of chikungunya virus (CHIKV) was also studied. The prevalence of Wolbachia-infected field-collected Ae. albopictus was estimated to be 98.6% (N = 142) for females and 95.1% (N = 102) for males in the population studied. The Ae. albopictus were naturally infected with both wAlbA and wAlbB strains. We also found that the native Wolbachia has no impact on CHIKV infection and minimal effect on CHIKV dissemination to secondary organs.
    Matched MeSH terms: Phylogeny
  10. Fulltext 2013 dengue outbreaks in Singapore and Malaysia caused by different viral strains
    Ng LC, Chem YK, Koo C, Mudin RNB, Amin FM, Lee KS, et al.
    Am J Trop Med Hyg, 2015 Jun;92(6):1150-1155.
    PMID: 25846296 DOI: 10.4269/ajtmh.14-0588
    Characterization of 14,079 circulating dengue viruses in a cross-border surveillance program, UNITEDengue, revealed that the 2013 outbreaks in Singapore and Malaysia were associated with replacement of predominant serotype. While the predominant virus in Singapore switched from DENV2 to DENV1, DENV2 became predominant in neighboring Malaysia. Dominance of DENV2 was most evident on the southern states where higher fatality rates were observed.
    Matched MeSH terms: Phylogeny
  11. Short report: a major genotype of Japanese encephalitis virus currently circulating in Japan
    Ma SP, Yoshida Y, Makino Y, Tadano M, Ono T, Ogawa M
    Am J Trop Med Hyg, 2003 Aug;69(2):151-4.
    PMID: 13677370
    A 240-nucleotide sequence of the capsid/premembrane gene region of 23 Japanese encephalitis virus (JEV) strains isolated in Tokyo and Oita, Japan was determined and phylogenetic analyses were performed. All the strains clustered into two distinct genotypes (III and I). All strains isolated before 1991 belonged to genotype III, while those isolated after 1994 belonged to genotype I. In addition, the strains of the genotype I isolated in Japan showed a close genetic relationship with those from Korea and Malaysia.
    Matched MeSH terms: Phylogeny
  12. Fulltext Seasonal variation in the stomach microbiota of two sympatrically breeding Pygoscelis penguin species at Signy Island, South Orkney Islands
    Yew WC, Adlard S, Dunn MJ, Alias SA, Pearce DA, Abu Samah A, et al.
    Microbiology (Reading), 2024 Sep;170(9).
    PMID: 39324257 DOI: 10.1099/mic.0.001503
    The gut microbiomes of Antarctic penguins are important for the fitness of the host birds and their chicks. The compositions of microbial communities in Antarctic penguin guts are strongly associated with the birds' diet, physiological adaptation and phylogeny. Whilst seasonal changes in food resources, distribution and population parameters of Antarctic penguins have been well addressed, little research is available on the stability or variability of penguin stomach microbiomes over time. Here, we focused on two Pygoscelis penguin species breeding sympatrically in the maritime Antarctic and analysed their stomach contents to assess whether penguin gut microbiota differed over three austral summer breeding seasons. We used a high-throughput DNA sequencing approach to study bacterial diversity in stomach regurgitates of Adélie (Pygoscelis adeliae) and chinstrap (Pygoscelis antarctica) penguins that have a similar foraging regime on Signy Island (South Orkney Islands). Our data revealed significant differences in bacterial alpha and beta diversity between the study seasons. We also identified bacterial genera that were significantly associated with specific breeding seasons, diet compositions, chick-rearing stages and sampling events. This study provides a baseline for establishing future monitoring of penguin gut microbiomes in a rapidly changing environment.
    Matched MeSH terms: Phylogeny
  13. Identification of polyunsaturated fatty acid and diterpenoid biosynthesis pathways from draft genome of Aureispira sp. CCB-QB1
    Furusawa G, Lau NS, Shu-Chien AC, Jaya-Ram A, Amirul AA
    Mar Genomics, 2015 Feb;19:39-44.
    PMID: 25468060 DOI: 10.1016/j.margen.2014.10.006
    The genus Aureispira consisting of two species, Aureispira marina and Aureispira maritima is an arachidonic acid-producing bacterium and produces secondary metabolites. In this study, we isolated a new Aureispira strain, Aureispira sp. CCB-QB1 from coastal area of Penang, Malaysia and the genome sequence of this strain was determined. The draft genome of this strain is composed of 185 contigs for 7,370,077 bases with 35.6% G+C content and contains 5911 protein-coding genes and 76 RNA genes. Linoleoyl-CoA desaturase, the key gene in arachidonic acid biosynthesis, is present in the genome. It was found that this strain uses mevalonate pathway for the synthesis of geranylgeranyl diphosphate (GGPP), which is precursor of diterpenoid, and novel pathway via futalosine for the synthesis of menaquinones. This is the first draft genome sequence of a member of the genus Aureispira.
    Matched MeSH terms: Phylogeny*
  14. Fulltext Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase
    Hossain MA, Roslan HA
    ScientificWorldJournal, 2014;2014:186029.
    PMID: 25165734 DOI: 10.1155/2014/186029
    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom.
    Matched MeSH terms: Phylogeny*
  15. Fulltext Mitochondrial DNA markers reveal high genetic diversity but low genetic differentiation in the black fly Simulium tani Takaoka & Davies along an elevational gradient in Malaysia
    Low VL, Adler PH, Takaoka H, Ya'cob Z, Lim PE, Tan TK, et al.
    PLoS One, 2014;9(6):e100512.
    PMID: 24941043 DOI: 10.1371/journal.pone.0100512
    The population genetic structure of Simulium tani was inferred from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI) and II (COII) along an elevational gradient in Cameron Highlands, Malaysia. A statistical parsimony network of 71 individuals revealed 71 haplotypes in the COI gene and 43 haplotypes in the COII gene; the concatenated sequences of the COI and COII genes revealed 71 haplotypes. High levels of genetic diversity but low levels of genetic differentiation were observed among populations of S. tani at five elevations. The degree of genetic diversity, however, was not in accordance with an altitudinal gradient, and a Mantel test indicated that elevation did not have a limiting effect on gene flow. No ancestral haplotype of S. tani was found among the populations. Pupae with unique structural characters at the highest elevation showed a tendency to form their own haplotype cluster, as revealed by the COII gene. Tajima's D, Fu's Fs, and mismatch distribution tests revealed population expansion of S. tani in Cameron Highlands. A strong correlation was found between nucleotide diversity and the levels of dissolved oxygen in the streams where S. tani was collected.
    Matched MeSH terms: Phylogeny*
  16. Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system
    Zarkasi KZ, Abell GC, Taylor RS, Neuman C, Hatje E, Tamplin ML, et al.
    J Appl Microbiol, 2014 Jul;117(1):18-27.
    PMID: 24698479 DOI: 10.1111/jam.12514
    The relationship of Atlantic salmon gastrointestinal (GI) tract bacteria to environmental factors, in particular water temperature within a commercial mariculture system, was investigated.
    Matched MeSH terms: Phylogeny*
  17. Fulltext A phylogeny of the family Poritidae (Cnidaria, Scleractinia) based on molecular and morphological analyses
    Kitano YF, Benzoni F, Arrigoni R, Shirayama Y, Wallace CC, Fukami H
    PLoS One, 2014;9(5):e98406.
    PMID: 24871224 DOI: 10.1371/journal.pone.0098406
    The family Poritidae formerly included 6 genera: Alveopora, Goniopora, Machadoporites, Porites, Poritipora, and Stylaraea. Morphologically, the genera can be differentiated based on the number of tentacles, the number of septa and their arrangement, the length of the polyp column, and the diameter of the corallites. However, the phylogenetic relationships within and between the genera are unknown or contentious. On the one hand, Alveopora has been transferred to the Acroporidae recently because it was shown to be more closely related to this family than to the Poritidae by previous molecular studies. On the other hand, Goniopora is morphologically similar to 2 recently described genera, Machadoporites and Poritipora, particularly with regard to the number of septa (approximately 24), but they have not yet been investigated at the molecular level. In this study, we analyzed 93 samples from all 5 poritid genera and Alveopora using 2 genetic markers (the barcoding region of the mitochondrial COI and the ITS region of the nuclear rDNA) to investigate their phylogenetic relationships and to revise their taxonomy. The reconstructed molecular trees confirmed that Alveopora is genetically distant from all poritid genera but closely related to the family Acroporidae, whereas the other genera are genetically closely related. The molecular trees also revealed that Machadoporites and Poritipora were indistinguishable from Goniopora. However, Goniopora stutchburyi was genetically isolated from the other congeneric species and formed a sister group to Goniopora together with Porites and Stylaraea, thus suggesting that 24 septa could be an ancestral feature in the Poritidae. Based on these data, we move G. stutchburyi into a new genus, Bernardpora gen. nov., whereas Machadoporites and Poritipora are merged with Goniopora.
    Matched MeSH terms: Phylogeny*
  18. Novosphingobium malaysiense sp. nov. isolated from mangrove sediment
    Lee LH, Azman AS, Zainal N, Eng SK, Fang CM, Hong K, et al.
    Int J Syst Evol Microbiol, 2014 Apr;64(Pt 4):1194-201.
    PMID: 24408529 DOI: 10.1099/ijs.0.059014-0
    A novel bacterium, strain MUSC 273(T), was isolated from mangrove sediments of the Tanjung Lumpur river in the state of Pahang in peninsular Malaysia. The bacterium was yellow-pigmented, Gram-negative, rod-shaped and non-spore-forming. The taxonomy of strain MUSC 273(T) was studied by a polyphasic approach and the organism showed a range of phenotypic and chemotaxonomic properties consistent with those of the genus Novosphingobium. The 16S rRNA gene sequence of strain MUSC 273(T) showed the highest sequence similarity to those of Novosphingobium indicum H25(T) (96.8 %), N. naphthalenivorans TUT562(T) (96.4 %) and N. soli CC-TPE-1(T) (95.9 %) and lower sequence similarity to members of all other species of the genus Novosphingobium. Furthermore, in phylogenetic analyses based on the 16S rRNA gene sequence, strain MUSC 273(T) formed a distinct cluster with members of the genus Novosphingobium. DNA-DNA relatedness of strain MUSC 273(T) to the type strains of the most closely related species, N. indicum MCCC 1A01080(T) and N. naphthalenivorans DSM 18518(T), was 29.2 % (reciprocal 31.0 %) and 17 % (reciprocal 18 %), respectively. The major respiratory quinone was ubiquinone Q-10, the major polyamine was spermidine and the DNA G+C content was 63.3±0.1 mol%. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine and sphingoglycolipid. The major fatty acids were C18 : 1ω7c, C17 : 1ω6c, C16 : 0, C15 : 0 2-OH and C16 : 1ω7c. Comparison of BOX-PCR fingerprints indicated that strain MUSC 273(T) represented a unique DNA profile. The combined genotypic and phenotypic data showed that strain MUSC 273(T) represents a novel species of the genus Novosphingobium, for which the name Novosphingobium malaysiense sp. nov. is proposed. The type strain is MUSC 273(T) ( = DSM 27798(T) = MCCC 1A00645(T) = NBRC 109947(T)).
    Matched MeSH terms: Phylogeny*
  19. [Molecular-genetic analysis of the genomes of porcine reproductive and respiratory syndrome virus and porcine circovirus type 2 circulating in the area of Russian Federation]
    Bulgakov AD, Grebennikova TV, Iuzhakov AG, Aliper TI, Nepoklonov EA
    Mol. Gen. Mikrobiol. Virusol., 2014.
    PMID: 25845139
    The molecular genetic analysis of the genomes of the virus of porcine reproductive respiratory syndrome (VPRRS) and porcine circovirus type 2 (PCV-2) circulating in the area of the Russian Federation was discussed. The results of this work showed the circulation of the strains of the European genotype VPRRS similar to those found in France and Denmark from 1998 to 2001. The homology of the fragment of one of the genes between the Russian isolates and the vaccine strain Porcilis PRRS (Intervet) was found. It requires further study. The strains representing the North American genotype VPRRS were not found. The PCV-2 genomes fall into three separate goups. One (genotype 2b) is formed by isolates in Malaysia, Brazil, Switzerland, China, Slovakia, UK, USA, isolated during the period from 2004 to the present time. The second group consists of sequences of the viruses isolated in 2000-2012 in Canada, the U.S., China, and South Korea (genotype 2a). The third group is formed by highly pathogenic isolates in 2013 from China (highly pathogenic genotype 2c). The circulation of all three known genotypes of PCV-2: 2a, 2b, and 2c in Russian Federation was demonstrated.
    Matched MeSH terms: Phylogeny*
  20. Fulltext Subtype distribution of Blastocystis isolates in Sebha, Libya
    Abdulsalam AM, Ithoi I, Al-Mekhlafi HM, Al-Mekhlafi AM, Ahmed A, Surin J
    PLoS One, 2013;8(12):e84372.
    PMID: 24376805 DOI: 10.1371/journal.pone.0084372
    BACKGROUND: Blastocystis is a genetically diverse and a common intestinal parasite of humans with a controversial pathogenic potential. This study was carried out to identify the Blastocystis subtypes and their association with demographic and socioeconomic factors among outpatients living in Sebha city, Libya.

    METHODS/FINDINGS: Blastocystis in stool samples were cultured followed by isolation, PCR amplification of a partial SSU rDNA gene, cloning, and sequencing. The DNA sequences of isolated clones showed 98.3% to 100% identity with the reference Blastocystis isolates from the Genbank. Multiple sequence alignment showed polymorphism from one to seven base substitution and/or insertion/deletion in several groups of non-identical nucleotides clones. Phylogenetic analysis revealed three assemblage subtypes (ST) with ST1 as the most prevalent (51.1%) followed by ST2 (24.4%), ST3 (17.8%) and mixed infections of two concurrent subtypes (6.7%).

    BLASTOCYSTIS: ST1 infection was significantly associated with female (P = 0.009) and low educational level (P = 0.034). ST2 was also significantly associated with low educational level (P= 0.008) and ST3 with diarrhoea (P = 0.008).

    CONCLUSION: Phylogenetic analysis of Libyan Blastocystis isolates identified three different subtypes; with ST1 being the predominant subtype and its infection was significantly associated with female gender and low educational level. More extensive studies are needed in order to relate each Blastocystis subtype with clinical symptoms and potential transmission sources in this community.

    Matched MeSH terms: Phylogeny*
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