Displaying publications 321 - 340 of 1902 in total

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  1. Fulltext Complete mitochondrial genome of six Cheilinus undulatus (Napoleon Wrasse): an endangered marine fish species from Sabah, Malaysia
    Matthew P, Manjaji-Matsumoto BM, Rodrigues KF
    Mitochondrial DNA B Resour, 2018 Oct 12;3(2):943-944.
    PMID: 33474374 DOI: 10.1080/23802359.2018.1473725
    We report here the complete mitochondrial (mt) genomes of six individuals of Cheilinus undulatus (Napoleon Wrasse), an endangered marine fish species. The six mt DNA sequences had an average size of 17,000 kb and encoded 22 tRNA, two sRNA, 13 highly conserved protein coding genes and a control region. The polymorphic variation (control region) in these six individuals suggests their potential use as a specific marker for phylogeographic conservation. Moreover, the sequence polymorphism within the control region (D-loop) suggests that this locus can be applied for phylogenetic studies.
    Matched MeSH terms: Phylogeny
  2. Fulltext Markers for genetic change
    Forcina G, Camacho-Sanchez M, Tuh FYY, Moreno S, Leonard JA
    Heliyon, 2021 Jan;7(1):e05583.
    PMID: 33437884 DOI: 10.1016/j.heliyon.2020.e05583
    Background and aims: Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question.

    Methods: We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined.

    Results: The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders.

    Conclusions: Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here.

    Matched MeSH terms: Phylogeny
  3. Fulltext Phylogeny of Algal Sequences Encoding Carbohydrate Sulfotransferases, Formylglycine-Dependent Sulfatases, and Putative Sulfatase Modifying Factors
    Ho CL
    Front Plant Sci, 2015;6:1057.
    PMID: 26635861 DOI: 10.3389/fpls.2015.01057
    Many algae are rich sources of sulfated polysaccharides with biological activities. The physicochemical/rheological properties and biological activities of sulfated polysaccharides are affected by the pattern and number of sulfate moieties. Sulfation of carbohydrates is catalyzed by carbohydrate sulfotransferases (CHSTs) while modification of sulfate moieties on sulfated polysaccharides was presumably catalyzed by sulfatases including formylglycine-dependent sulfatases (FGly-SULFs). Post-translationally modification of Cys to FGly in FGly-SULFs by sulfatase modifiying factors (SUMFs) is necessary for the activity of this enzyme. The aims of this study are to mine for sequences encoding algal CHSTs, FGly-SULFs and putative SUMFs from the fully sequenced algal genomes and to infer their phylogenetic relationships to their well characterized counterparts from other organisms. Algal sequences encoding CHSTs, FGly-SULFs, SUMFs, and SUMF-like proteins were successfully identified from green and brown algae. However, red algal FGly-SULFs and SUMFs were not identified. In addition, a group of SUMF-like sequences with different gene structure and possibly different functions were identified for green, brown and red algae. The phylogeny of these putative genes contributes to the corpus of knowledge of an unexplored area. The analyses of these putative genes contribute toward future production of existing and new sulfated carbohydrate polymers through enzymatic synthesis and metabolic engineering.
    Matched MeSH terms: Phylogeny
  4. Fulltext The complete chloroplast genome of tropical and sub-tropical fruit tree Lucuma nervosa (Sapotaceae)
    Niu YF, Ni SB, Liu ZY, Zheng C, Mao CL, Shi C, et al.
    Mitochondrial DNA B Resour, 2018 Apr 03;3(1):440-441.
    PMID: 33490512 DOI: 10.1080/23802359.2018.1457995
    The Lucuma nervosa, native to Western Ghats of India, Malaysia and south-eastern Asia, is a tree member of the mulberry family (Sapotaceae). Chloroplast genome sequences play an significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of L. nervosa for the first time. The chloroplast genome is 157,920 bp long and includes 113 genes. Its LSC, SSC, and IR regions are 88,123, 18,861, and 25,468 bp long, respectively. Phylogenetic tree analysis exhibited that L. nervosa was clustered with other Sapotaceae species with high bootstrap values.
    Matched MeSH terms: Phylogeny
  5. Fulltext The whole mitochondrial genome of the mangrove crab, Metopograpsus frontalis (Miers, 1880) (Decapoda, Grapsidae) and its phylogenetic relationship
    Guan M, Liu X, Lin F, Xie Z, Fazhan H, Ikhwanuddin M, et al.
    Mitochondrial DNA B Resour, 2018 Mar 14;3(1):368-369.
    PMID: 33490509 DOI: 10.1080/23802359.2018.1450685
    In this study, we sequenced and analyzed the whole mitochondrial genome of Metopograpsus frontalis Miers, 1880 (Decapoda, Grapsidae). The circular genome is 15,587 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, as well as a control region. Both atp8/atp6 and nad4L/nad4 share 7 nucleotides in their adjacent overlapping region, which is identical to those observed in other Grapsidae crabs. The genome composition and gene order follow a classic crab-type arrangement regulation. The phylogenetic analysis suggested that Grapsidae crabs formed a solid monophyletic group. The newly described mitochondrial genome may provide genetic marker for studies on phylogeny of the grapsid crabs.
    Matched MeSH terms: Phylogeny
  6. Fulltext Molecular identification and phylogenetic analysis of a Callosciurus notatus complete mitogenome from Peninsular Malaysia
    Jahari PNS, Mohd Azman S, Munian K, Ahmad Ruzman NH, Shamsir MS, Richter SR, et al.
    Mitochondrial DNA B Resour, 2020 Aug 26;5(3):3004-3006.
    PMID: 33458034 DOI: 10.1080/23802359.2020.1797583
    The mitogenome of a plantain squirrel, Callosciurus notatus, collected from Bukit Tarek Forest Reserve (Extension), Selangor, Malaysia was sequenced using BGISEQ-500RS technology. The 16,582 bp mitogenome consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. A phylogenetic and BLASTn analysis against other available datasets showed that the mitogenome matched with 99.49% similarity to a previously published C. notatus mitogenome from Peninsular Malaysia. However, it also diverged by nearly 8% (92.24% match) from a second previously published mitogenome for the same species, sampled in East Kalimantan, Indonesia. This suggests a difference in landscape features between both localities might affect its genetic connectivity.
    Matched MeSH terms: Phylogeny
  7. Deep-time convergent evolution in animal communication presented by shared adaptations for coping with noise in lizards and other animals
    Ord TJ, Klomp DA, Summers TC, Diesmos A, Ahmad N, Das I
    Ecol Lett, 2021 Sep;24(9):1750-1761.
    PMID: 34196091 DOI: 10.1111/ele.13773
    Convergence in communication appears rare compared with other forms of adaptation. This is puzzling, given communication is acutely dependent on the environment and expected to converge in form when animals communicate in similar habitats. We uncover deep-time convergence in territorial communication between two groups of tropical lizards separated by over 140 million years of evolution: the Southeast Asian Draco and Caribbean Anolis. These groups have repeatedly converged in multiple aspects of display along common environmental gradients. Robot playbacks to free-ranging lizards confirmed that the most prominent convergence in display is adaptive, as it improves signal detection. We then provide evidence from a sample of the literature to further show that convergent adaptation among highly divergent animal groups is almost certainly widespread in nature. Signal evolution is therefore curbed towards the same set of adaptive solutions, especially when animals are challenged with the problem of communicating effectively in noisy environments.
    Matched MeSH terms: Phylogeny
  8. Fulltext Molecular Phylogenesis and Spatiotemporal Spread of SARS-CoV-2 in Southeast Asia
    Zhu M, Shen J, Zeng Q, Tan JW, Kleepbua J, Chew I, et al.
    Front Public Health, 2021 07 30;9:685315.
    PMID: 34395364 DOI: 10.3389/fpubh.2021.685315
    Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the region. Materials and Methods: A total of 1491 complete SARS-CoV-2 genome sequences from 10 Southeast Asian countries were downloaded from the Global Initiative on Sharing Avian Influenza Data (GISAID) database on November 17, 2020. The evolutionary relationships were assessed using maximum likelihood (ML) and time-scaled Bayesian phylogenetic analyses, and the phylogenetic clustering was tested using principal component analysis (PCA). The spatial patterns of SARS-CoV-2 spread within Southeast Asia were inferred using the Bayesian stochastic search variable selection (BSSVS) model. The effective population size (Ne) trajectory was inferred using the Bayesian Skygrid model. Results: Four major clades (including one potentially endemic) were identified based on the maximum clade credibility (MCC) tree. Similar clustering was yielded by PCA; the first three PCs explained 46.9% of the total genomic variations among the samples. The time to the most recent common ancestor (tMRCA) and the evolutionary rate of SARS-CoV-2 circulating in Southeast Asia were estimated to be November 28, 2019 (September 7, 2019 to January 4, 2020) and 1.446 × 10-3 (1.292 × 10-3 to 1.613 × 10-3) substitutions per site per year, respectively. Singapore and Thailand were the two most probable root positions, with posterior probabilities of 0.549 and 0.413, respectively. There were high-support transmission links (Bayes factors exceeding 1,000) in Singapore, Malaysia, and Indonesia; Malaysia involved the highest number (7) of inferred transmission links within the region. A twice-accelerated viral population expansion, followed by a temporary setback, was inferred during the early stages of the pandemic in Southeast Asia. Conclusions: With available genomic data, we illustrate the phylogeography and phylodynamics of SARS-CoV-2 circulating in Southeast Asia. Continuous genomic surveillance and enhanced strategic collaboration should be listed as priorities to curb the pandemic, especially for regional communities dominated by developing countries.
    Matched MeSH terms: Phylogeny
  9. Quaternary land bridges have not been universal conduits of gene flow
    Cros E, Chattopadhyay B, Garg KM, Ng NSR, Tomassi S, Benedick S, et al.
    Mol Ecol, 2020 07;29(14):2692-2706.
    PMID: 32542783 DOI: 10.1111/mec.15509
    Quaternary climate oscillations are a well-known driver of animal diversification, but their effects are most well studied in areas where glaciations lead to habitat fragmentation. In large areas of the planet, however, glaciations have had the opposite effect, but here their impacts are much less well understood. This is especially true in Southeast Asia, where cyclical changes in land distribution have generated enormous land expansions during glacial periods. In this study, we selected a panel of five songbird species complexes covering a range of ecological specificities to investigate the effects Quaternary land bridges have had on the connectivity of Southeast Asian forest biota. Specifically, we combined morphological and bioacoustic analysis with an arsenal of population genomic and modelling approaches applied to thousands of genome-wide DNA markers across a total of more than 100 individuals. Our analyses show that species dependent on forest understorey exhibit deep differentiation between Borneo and western Sundaland, with no evidence of gene flow during the land bridges accompanying the last 1-2 ice ages. In contrast, dispersive canopy species and habitat generalists have experienced more recent gene flow. Our results argue that there remains much cryptic species-level diversity to be discovered in Southeast Asia even in well-known animal groups such as birds, especially in nondispersive forest understorey inhabitants. We also demonstrate that Quaternary land bridges have not been equally suitable conduits of gene flow for all species complexes and that life history is a major factor in predicting relative population divergence time across Quaternary climate fluctuations.
    Matched MeSH terms: Phylogeny
  10. Molecular characterization of non-polio enteroviruses isolated from children with acute flaccid paralysis in IRAN, 2015-2018
    Nejati A, Zahraei SM, Mahmoudi S, Yousefi M, Mollaei-Kandelous Y, Tabatabaie H, et al.
    Virus Genes, 2020 Oct;56(5):531-536.
    PMID: 32451907 DOI: 10.1007/s11262-020-01768-y
    In addition to polioviruses, non-polio enteroviruses (NPEVs) are frequently isolated from patients with acute flaccid paralysis (AFP) worldwide. In polio-free countries, there have been expectations that with disappearing wild poliovirus from the community, the rate of AFP would decrease, but the increasing number of AFP cases proved this notion to be wrong. There are speculations that NPEVs might be the cause of increasing AFP rate. The aim of this study was to investigate frequency, genetic diversity, circulation patterns of NPEVs isolated from AFP cases in Iran from 2015 to 2018. Fifty-three NPEVs were isolated from stool specimens of AFP cases during four years of AFP surveillance. Nested PCR and VP1 sequencing revealed 20 NPEV types in which Echovirus 3 (13.2%), Echovirus 6 (13.2%), Echovirus 7 (7.5%), Echovirus 13 (7.5%) and Echovirus 21 (7.5%) were the most frequent. Coxsackie B viruses were isolated for the first time in AFP cases in Iran. The phylogenetic analysis of Echovirus 3 and Echovirus 6 revealed that Iranian echovirus strains belonged to the same cluster, indicating these viruses have been circulating in Iran for a long time. Compared to global Echovirus 3 and Echovirus 6 references, Echovirus 3 and Echovirus 6 strains detected in this study were closely related to Indian and Malaysia strains, respectively. The results of this study demonstrated a wide variety of NPEV types in Iranian patients, some of which had not been reported in previous studies. Moreover, this study highlights the need for NPEV surveillance in AFP cases.
    Matched MeSH terms: Phylogeny
  11. Fulltext Phylogenetic Relatedness of Several Agarwood-Producing Taxa (Thymelaeaceae) from Indonesia
    Lee SY, Turjaman M, Mohamed R
    Trop Life Sci Res, 2018 Jul;29(2):13-28.
    PMID: 30112138 MyJurnal DOI: 10.21315/tlsr2018.29.2.2
    Indonesia is home to several tree taxa that are harvested for agarwood. This highly valuable oleoresin ironically was the cause for some species to become vulnerable due to gluttonous human activity. However, information on the genetic diversity of these endangered trees is limited. In this study, 28 specimens representing eight species from two genera, Aquilaria and Gyrinops, were collected from ex-situ and in-situ populations in Indonesia. Phylogenetic analysis conducted on DNA sequences of the nuclear ribosomal internal transcribed spacer (ITS) and the trnL-trnF intergenic spacer regions, revealed that Aquilaria and Gyrinops are paraphyletic when Aquilaria cumingiana is excluded. The phylogenetic analysis for ITS and trnL-trnF showed capability to categorise agarwood-producing species based on their regions: East Indonesia and West Indonesia, using Wallace's Line as the divider. In addition, we discuss challenges in species identification and taxonomy of agarwood-producing genera, and their conservation efforts in Indonesia.
    Matched MeSH terms: Phylogeny
  12. Comparative Genome Analysis of Fusobacterium nucleatum
    Ang MY, Dutta A, Wee WY, Dymock D, Paterson IC, Choo SW
    Genome Biol Evol, 2016 10 05;8(9):2928-2938.
    PMID: 27540086
    Fusobacterium nucleatum is considered to be a key oral bacterium in recruiting periodontal pathogens into subgingival dental plaque. Currently F. nucleatum can be subdivided into five subspecies. Our previous genome analysis of F. nucleatum W1481 (referred to hereafter as W1481), isolated from an 8-mm periodontal pocket in a patient with chronic periodontitis, suggested the possibility of a new subspecies. To further investigate the biology and relationships of this possible subspecies with other known subspecies, we performed comparative analysis between W1481 and 35 genome sequences represented by the five known Fusobacterium subspecies. Our analyses suggest that W1481 is most likely a new F. nucleatum subspecies, supported by evidence from phylogenetic analyses and maximal unique match indices (MUMi). Interestingly, we found a horizontally transferred W1481-specific genomic island harboring the tripartite ATP-independent (TRAP)-like transporter genes, suggesting this bacterium might have a high-affinity transport system for the C4-dicarboxylates malate, succinate, and fumarate. Moreover, we found virulence genes in the W1481 genome that may provide a strong defense mechanism which might enable it to colonize and survive within the host by evading immune surveillance. This comparative study provides better understanding of F. nucleatum and the basis for future functional work on this important pathogen.
    Matched MeSH terms: Phylogeny
  13. Fulltext Random amplified polymorphic DNA-PCR and ERIC PCR analysis on Vibrio parahaemolyticus isolated from cockles in Padang, Indonesia
    Zulkifli, Y., Alitheen, N.B., Son, R., Raha, A.R., Samuel, L., Yeap, S.K., et al.
    International Food Research Journal, 2009;16(2):141-150.
    MyJurnal
    In this study, RAPD-PCR and ERIC-PCR were used to study the epidemiology of V. parahaemolyticus isolated from cockles in Padang, Indonesia. The Gold Oligo OPAR3 primer produced bands ranged from 1-8 with sizes from 0.2 – 5.0 kb and the Gold Oligo OPAR8 primer produced 1-7 bands with sizes 0.7 – 1.5 kb. Both primers produced twenty five RAPD patterns with a few isolates failed to produce any products. Based on phylogenetic dendrogram, all the isolates can be divided into 6 major clusters with similarity between 0 to 52%. For the ERIC primer, it produced bands ranged from 3-15 with sizes from 0.1 – 5.0 kb and twenty seven different ERIC patterns. Construction of the phylogenetic dendogram showed the isolates can be divided into 4 major clusters with similarity between 56 to 86%. The high diversity of both processes may be due to the multiple contamination sources of V. parahaemolyticus.
    Matched MeSH terms: Phylogeny
  14. Fulltext Genetic diversity of Elaeis oleifera (HBK) Cortes populations using cross species SSRs: implication's for germplasm utilization and conservation
    Ithnin M, Teh CK, Ratnam W
    BMC Genet, 2017 04 19;18(1):37.
    PMID: 28420332 DOI: 10.1186/s12863-017-0505-7
    BACKGROUND: The Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining such collections is expensive and requires sizable land. Information on the genetic diversity of these collections can help achieve efficient conservation via maintenance of core collection. For this purpose, we have applied fourteen unlinked microsatellite markers to evaluate 532 E. oleifera palms representing 19 populations distributed across Honduras, Costa Rica, Panama and Colombia.

    RESULTS: In general, the genetic diversity decreased from Costa Rica towards the north (Honduras) and south-east (Colombia). Principle coordinate analysis (PCoA) showed a single cluster indicating low divergence among palms. The phylogenetic tree and STRUCTURE analysis revealed clusters based on country of origin, indicating considerable gene flow among populations within countries. Based on the values of the genetic diversity parameters, some genetically diverse populations could be identified. Further, a total of 34 individual palms that collectively captured maximum allelic diversity with reduced redundancy were also identified. High pairwise genetic differentiation (Fst > 0.250) among populations was evident, particularly between the Colombian populations and those from Honduras, Panama and Costa Rica. Crossing selected palms from highly differentiated populations could generate off-springs that retain more genetic diversity.

    CONCLUSION: The results attained are useful for selecting palms and populations for core collection. The selected materials can also be included into crossing scheme to generate offsprings that capture greater genetic diversity for selection gain in the future.

    Matched MeSH terms: Phylogeny
  15. Fulltext Oil palm microsatellites: implications and potentials
    Chua, B. H., Rajinder, S., Tan, S. G., Faridah, Q. Z., Cheah, S. C.
    Buletin Persatuan Genetik Malaysia, 2006;12(1):1-5.
    MyJurnal
    Microsatellites or simple sequence repeats (SSRs) are tandem repeats of DNA of 1-6 bp long. They ubiquitously occur in both eukaryotic and prokaryotic genomes. Because of their abundance,
    they have widespread applications in both animal and plant sciences; such as varietal identification, genetic mapping, QTL mapping, phylogenetic and diversity studies. Thus, SSRs have become valuable DNA markers for molecular biologists and geneticists. Microsatellites are markers
    of choice for many molecular geneticists because of their hypervariability, codominant
    inheritance, multi-allelism and PCR-based assaying of variations that are amenable to automation and high throughput assay. However, the utilization of microsatellite markers in the past was
    hampered by its laborious de novo isolations and species-specific nature.
    Matched MeSH terms: Phylogeny
  16. Fulltext Isolation and rapid identification of streptomonospora, a strictly halophilic filamentous actinomycetes from antarctic soil (Barrientos Island, Antarctic)
    Cheah Y.K., Lee, L.H., Radu, S., Wong, M.C.V.L., Andrade, H.M.
    ASM Science Journal, 2009;3(2):113-120.
    MyJurnal
    The genus Streptomonospora is a group of extremely halophilic filamentous actinomycetes that form a distinct branch in the 16S rRNA gene phylogenetic tree adjacent to the genera Nocardiopsis and Thermobifida, family Norcadiopsaceae. To date, genus Streptomonospora only contain two validly described species which are Streptomonospora salina and Streptomonospora alba. During a biodiversity study on halophilic filamentous actinomycetes from 18 co-ordinates in Barrientos Island, Antarctic, numerous actinomycetes strains were isolated. To identify whether these isolates were members of the genus Streptomonospora, a genus specific primer that allow the rapid detection of the genus Streptomonospora by means of PCR amplification was used. Furthermore molecular cloning was performed to make identical and multiple copies of the target gene. In addition, morphological characteristic identification was performed to validate isolates with positive amplification during PCR.
    Matched MeSH terms: Phylogeny
  17. Phylogenetic position of Aerumnosa Mohrig (Diptera, Sciaridae) as revealed by multigene analysis, with the description of four new Oriental species
    Vilkamaa P, Rudzinski HG, BurdÍkovÁ N, ŠevČÍk J
    Zootaxa, 2018 Mar 21;4399(2):248-260.
    PMID: 29690308 DOI: 10.11646/zootaxa.4399.2.8
    Four Oriental species of Aerumnosa Mohrig, 1999 (Diptera: Sciaridae), a genus previously known only from Papua New Guinea, are newly described and illustrated: Aerumnosa bituberculata sp. n. (India), A. gemmifera sp. n. (Malaysia: Sabah), A. horrifica sp. n. (Brunei, Thailand) and A. impar sp. n. (Malaysia: Sabah). On the basis of the new material, the genus is redefined. A key to the known species of Aerumnosa is presented, including four new species. An updated molecular phylogenetic analysis based on four gene markers (18S, 28S, 16S and COI) shows Aerumnosa to be a member of the subfamily Cratyninae. The monophyly of Cratyninae is well supported, which clade also includes the genera Hyperlasion Schmitz, 1919, Pnyxiopalpus Vilkamaa Hippa, 1999 and Pseudoaerumnosa Rudzinski, 2006. According to the present phylogenetic hypothesis, the monophyly of Cratyna Winnertz, 1967 s. l. needs to be revisited. The clade including Cratyna (s. str.) ambigua (Lengersdorf, 1934) appears as the sister group of Aerumnosa.
    Matched MeSH terms: Phylogeny
  18. Low-dissolved-oxygen nitrification in tropical sewage: an investigation on potential, performance and functional microbial community
    How SW, Lim SY, Lim PB, Aris AM, Ngoh GC, Curtis TP, et al.
    Water Sci Technol, 2018 May;77(9-10):2274-2283.
    PMID: 29757179 DOI: 10.2166/wst.2018.143
    Intensive aeration for nitrification is a major energy consumer in sewage treatment plants (STPs). Low-dissolved-oxygen (low-DO) nitrification has the potential to lower the aeration demand. However, the applicability of low-DO nitrification in the tropical climate is not well-understood. In this study, the potential of low-DO nitrification in tropical setting was first examined using batch kinetic experiments. Subsequently, the performance of low-DO nitrification was investigated in a laboratory-scale sequential batch reactor (SBR) for 42 days using real tropical sewage. The batch kinetic experiments showed that the seed sludge has a relatively high oxygen affinity. Thus, the rate of nitrification was not significantly reduced at low DO concentrations (0.5 mg/L). During the operation of the low-DO nitrification SBR, 90% of NH4-N was removed. The active low-DO nitrification was mainly attributed to the limited biodegradable organics in the sewage. Fluorescence in-situ hybridisation and 16S rRNA amplicon sequencing revealed the nitrifiers were related to Nitrospira genus and Nitrosomonadaceae family. Phylogenetic analysis suggests 47% of the operational taxonomic units in Nitrospira genus are closely related to a comammox bacteria. This study has demonstrated active low-DO nitrification in tropical setting, which is a more sustainable process that could significantly reduce the energy footprint of STPs.
    Matched MeSH terms: Phylogeny
  19. Systematics of the combtooth blenny clade Omobranchus (Blenniidae: Omobranchini), with notes on early life history stages
    Gibbs S, Hundt PJ, Nelson A, Egan JP, Tongnunui P, Simons AM
    Zootaxa, 2018 Jan 03;4369(2):270-280.
    PMID: 29689891 DOI: 10.11646/zootaxa.4369.2.7
    The combtooth blenny (Blenniidae) genus Omobranchus contains small, cryptobenthic fishes common to nearshore habitats throughout the Indo-West Pacific. Recent molecular systematic studies have resolved Omobranchus as monophyletic but little research has been done to resolve species-level relationships. Herein, phylogenetic analyses of one mitochondrial (CO1) and four nuclear (ENC1, myh6, sreb2, and tbr1) genes provide evidence for the monophyly of Omobranchus and support for the elongatus and banditus species group. Sampling of multiple individuals from widespread species (O. ferox, O. punctatus, and O. elongatus) suggested that the Thai-Malay Peninsula is a phylogeographic break that may be a historic barrier to gene flow. Additionally, common meristics and other morphological characters are used to describe an early life history stage of O. ferox and O. punctatus.
    Matched MeSH terms: Phylogeny
  20. Fulltext Draft Genome Sequence of Candida pseudohaemulonii Isolated from the Blood of a Neutropenic Patient
    Mohd Tap R, Kamarudin NA, Ginsapu SJ, Ahmed Bakri AR, Ahmad N, Amran F, et al.
    Genome Announc, 2018 Apr 05;6(14).
    PMID: 29622608 DOI: 10.1128/genomeA.00166-18
    Candida pseudohaemulonii is phylogenetically close to the C. haemulonii complex and exhibits resistance to amphotericin B and azole agents. We report here the draft genome sequence of C. pseudohaemulonii UZ153_17 isolated from the blood culture of a neutropenic patient. The draft genome is 3,532,003,666 bp in length, with 579,838 reads, 130 contigs, and a G+C content of 47.15%.
    Matched MeSH terms: Phylogeny
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