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  1. Carter BE, Larraín J, Manukjanová A, Shaw B, Shaw AJ, Heinrichs J, et al.
    Mol Phylogenet Evol, 2017 02;107:16-26.
    PMID: 27744015 DOI: 10.1016/j.ympev.2016.10.002
    Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere. A backbone phylogeny for the subgenus is proposed, providing insight into evolution of morphological patterns and establishing the basis for an improved sectional classification of species within Microfrullania. Several species complexes are identified, the presence of two undescribed but genetically and morphologically distinct species is noted, and previously neglected names are discussed.
    Matched MeSH terms: Sequence Analysis, DNA
  2. Beck SV, Carvalho GR, Barlow A, Rüber L, Hui Tan H, Nugroho E, et al.
    PLoS One, 2017;12(7):e0179557.
    PMID: 28742862 DOI: 10.1371/journal.pone.0179557
    The complex climatic and geological history of Southeast Asia has shaped this region's high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have shaped the distribution of biota within this region, and whether such patterns show evidence of isolation within palaeodrainage basins. Our analyses revealed three major mitochondrial clades within A. panchax. The basal divergence of A. panchax mitochondrial lineages was approximately 3.5 Ma, whilst the subsequent divergence timings of these clades occurred early Pleistocene (~2.6 Ma), proceeding through the Pleistocene. Continuous phylogeographic analysis showed a clear west-east dispersal followed by rapid radiation across Southeast Asia. Individuals from Krabi, just north of the Isthmus of Kra, were more closely related to the Indian lineages, providing further evidence for a freshwater faunal disjunction at the Isthmus of Kra biogeographic barrier. Our results suggest that Sulawesi, across the Wallace Line, was colonised relatively recently (~30 ka). Nuclear DNA is less geographically structured, although Mantel tests indicated that nuclear genetic distances were correlated with geographic proximity. Overall, these results imply that recent gene flow, as opposed to historical isolation, has been the key factor determining patterns of nuclear genetic variation in A. panchax, however, some evidence of historical isolation is retained within the mitochondrial genome. Our study further validates the existence of a major biogeographic boundary at the Kra Isthmus, and also demonstrates the use of widely distributed fresh/brackishwater species in phylogeographic studies, and their ability to disperse across major marine barriers in relatively recent time periods.
    Matched MeSH terms: Sequence Analysis, DNA
  3. Yahya MJ, Ismail PB, Nordin NB, Akim ABM, Binti Md Yusuf WS, Adam NLB, et al.
    J Nutr Metab, 2019;2019:8736215.
    PMID: 30719346 DOI: 10.1155/2019/8736215
    Type 2 diabetes mellitus (T2DM) is associated with a high incidence of nephropathy. The aim of this study was to investigate the association of a genetic polymorphism of carnosinase (CNDP1-D18S880 and -rs2346061), endothelial nitric oxide synthase (NOS3-rs1799983), and manganese superoxide dismutase (MnSOD-rs4880) genes with the development of diabetic nephropathy among Malaysian type 2 diabetic patients. A case-control association study was performed using 652 T2DM patients comprising 227 Malays (without nephropathy = 96 and nephropathy = 131), 203 Chinese (without nephropathy = 95 and nephropathy = 108), and 222 Indians (without nephropathy = 136 and nephropathy = 86). DNA sequencing was performed for the D18S880 of CNDP1, while the rest were tested using DNA Sequenom MassARRAY to identify the polymorphisms. DNA was extracted from the secondary blood samples taken from the T2DM patients. The alleles and genotypes were tested using four genetic models, and the best mode of inheritance was chosen based on the least p value. The rs2346061 of CNDP1 was significantly associated with diabetic nephropathy among the Indians only with OR = 1.94 and 95% CI = (1.76-3.20) and fitted best the multiplicative model, while D18S880 was associated among all the three major races with the Malays having the strongest association with OR = 2.46 and 95% CI = (1.48-4.10), Chinese with OR = 2.26 and 95% CI = (1.34-3.83), and Indians with OR = 1.77 and 95% CI = (1.18-2.65) in the genotypic multiplicative model. The best mode of inheritance for both MnSOD and NOS3 was the additive model. For MnSOD-rs4880, the Chinese had OR = 2.8 and 95% CI = (0.53-14.94), Indians had OR = 2.4 and 95% CI = (0.69-2.84), and Malays had OR = 2.16 and 95% CI = (0.54-8.65), while for NOS3-rs1799983, the Indians had the highest risk with OR = 3.16 and 95% CI = (0.52-17.56), followed by the Chinese with OR = 3.55 and 95% CI = (0.36-35.03) and the Malays with OR = 2.89 and 95% CI = (0.29-28.32). The four oxidative stress-related polymorphisms have significant effects on the development of nephropathy in type 2 diabetes patients. The genes may, therefore, be considered as risk factors for Malaysian subjects who are predisposed to T2DM nephropathy.
    Matched MeSH terms: Sequence Analysis, DNA
  4. Sarmin NIM, Tan GYA, Franco CMM, Edrada-Ebel R, Latip J, Zin NM
    Int J Syst Evol Microbiol, 2013 Oct;63(Pt 10):3733-3738.
    PMID: 23645019 DOI: 10.1099/ijs.0.047878-0
    A spore-forming streptomycete designated strain SUK12(T) was isolated from a Malaysian ethnomedicinal plant. Its taxonomic position, established using a polyphasic approach, indicates that it is a novel species of the genus Streptomyces. Morphological and chemical characteristics of the strain were consistent with those of members of the genus Streptomyces. Analysis of the almost complete 16S rRNA gene sequence placed strain SUK12(T) in the genus Streptomyces where it formed a distinct phyletic line with recognized species of this genus. The strain exhibited highest sequence similarity to Streptomyces corchorusii DSM 40340(T) (98.2 %) followed by Streptomyces chrestomyceticus NRRL B-3310(T) (98.1 %). The G+C content of the genomic DNA was 74 mol%. Chemotaxonomic data [MK-9(H8) as the major menaquinone; LL-diaminopimelic acid as a component of cell-wall peptidoglycan; C12 : 0, C14 : 0, C15 : 0 and C17 : 1 as the major fatty acids; phospholipid type II] supported the affiliation of strain SUK12(T) to the genus Streptomyces. The results of the phylogenetic analysis and phenotypic data derived from this and previous studies allowed the genotypic and phenotypic differentiation of strain SUK12(T) from the related species of the genus Streptomyces. The DNA-DNA relatedness value between strain SUK12(T) and S. corchorusii DSM 40340(T) is 18.85±4.55 %. Strain SUK12(T) produces phenazine-1-carboxylic acid, known as tubermycin B, an antibacterial agent. It is proposed, therefore, that strain SUK12(T) ( = DSM 42048(T) = NRRL B-24860(T)) be classified in the genus Streptomyces as the type strain of Streptomyces kebangsaanensis sp. nov.
    Matched MeSH terms: Sequence Analysis, DNA
  5. Sasongko TH, Gunadi, Yusoff S, Atif AB, Fatemeh H, Rani A, et al.
    Brain Dev, 2010 May;32(5):385-9.
    PMID: 19664890 DOI: 10.1016/j.braindev.2009.06.008
    The majority of spinal muscular atrophy (SMA) patients showed homozygous deletion or other mutations of SMN1. However, the genetic etiology of a significant number of SMA patients has not been clarified. Recently, mutation in the gene underlying cat SMA, limb expression 1 (LIX1), has been reported. Similarity in clinical and pathological features of cat and human SMA may give an insight into possible similarity of the genetic etiology.
    Matched MeSH terms: Sequence Analysis, DNA
  6. Peng HB, Zahary MN, Tajudin LS, Lin CL, Teck CM, Sidek MR, et al.
    Kobe J Med Sci, 2007;53(1-2):49-52.
    PMID: 17582204
    The Prostaglandin F2alpha (PGF2alpha) receptor gene has been found to play an important role in reducing the intraocular pressure of the glaucomatous patients. Variations of the PGF2alpha receptor gene may be responsible for the differences in the response to an antiglaucoma drug, Latanoprost. A combined method of denaturing High Performance Liquid Chromatography (dHPLC) and sequencing was applied to detection of the PGF2alpha receptor gene variant among the 76 Malaysian patients with glaucoma, and a novel single nucleotide polymorphism (SNP), IVS -97A>T, was identified. According to the genotyping analysis, 36.8% of the subjects were heterozygous for the variant allele T, while 9.2% homozygous. The frequency of variant allele T was 0.28. Although with a limited number of samples, our data suggested that this polymorphism is common in the Malaysian patients with glaucoma.
    Matched MeSH terms: Sequence Analysis, DNA
  7. Al-Khateeb AR, Mohd MS, Yusof Z, Zilfalil BA
    Biochem Genet, 2013 Oct;51(9-10):811-23.
    PMID: 23775634 DOI: 10.1007/s10528-013-9609-6
    Familial ligand-defective apolipoprotein B-100 is characterized by elevated plasma low-density lipoprotein levels and premature heart disease. This study aims to determine apolipoprotein B gene mutations among Malaysians with clinical diagnoses of familial hypercholesterolemia and to compare the phenotype of patients with apolipoprotein B gene mutations to those with a low-density lipoprotein receptor gene mutation. A group of 164 patients with a clinical diagnosis of familial hypercholesterolemia was analyzed. Amplicons in exon 26 and exon 29 of the apolipoprotein B gene were screened for genetic variants using denaturing gradient high-performance liquid chromatography; 10 variants were identified. Five novel mutations were detected (p.Gln2485Arg, p.Thr3526Ala, p.Glu3666Lys, p.Tyr4343CysfsX221, and p.Arg4297His). Those with familial defective apolipoprotein had a less severe phenotype than those with familial hypercholesterolemia. An apolipoprotein gene defect is present among Malaysian familial hypercholesterolemics. Those with both mutations show a more severe phenotype than those with one gene defect.
    Matched MeSH terms: Sequence Analysis, DNA
  8. Amini F, Ismail E, Zilfalil BA
    Intern Med J, 2011 Apr;41(4):351-3.
    PMID: 21507164 DOI: 10.1111/j.1445-5994.2011.02456.x
    This study aims to define the prevalence and the molecular basis of G6PD deficiency in the Negrito tribe of the Malaysian Orang Asli. Four hundred and eighty seven consenting Negrito volunteers were screened for G6PD deficiency through the use of a fluorescent spot test. DNA from deficient individuals underwent PCR-RFLP analysis using thirteen recognized G6PD mutations. In the instances when the mutation could not be identified by PCR-RFLP, the entire coding region of the G6PD gene was subjected to DNA sequencing. In total, 9% (44/486) of the sample were found to be G6PD-deficient. However, only 25 samples were subjected to PCR-RFLP and DNA sequencing. Of these, three were found to carry Viangchan, one Coimbra and 16, a combination of C1311T in exon 11 and IVS11 T93C. Mutation(s) for the five remaining samples are unknown. The mean G6PD enzyme activity ranged 5.7 IU/gHb in deficient individuals. Our results demonstrate that the frequency of G6PD deficiency is higher among the Negrito Orang Asli than other Malaysian races. The dual presence of C1311T and IVS11 T93C in 64% of the deficient individuals (16/44) could well be a result of genetic drift within this isolated group.
    Matched MeSH terms: Sequence Analysis, DNA/methods
  9. Al-Khateeb A, Zahri MK, Mohamed MS, Sasongko TH, Ibrahim S, Yusof Z, et al.
    BMC Med Genet, 2011;12:40.
    PMID: 21418584 DOI: 10.1186/1471-2350-12-40
    Familial hypercholesterolemia is a genetic disorder mainly caused by defects in the low-density lipoprotein receptor gene. Few and limited analyses of familial hypercholesterolemia have been performed in Malaysia, and the underlying mutations therefore remain largely unknown.We studied a group of 154 unrelated FH patients from a northern area of Malaysia (Kelantan). The promoter region and exons 2-15 of the LDLR gene were screened by denaturing high-performance liquid chromatography to detect short deletions and nucleotide substitutions, and by multiplex ligation-dependent probe amplification to detect large rearrangements.
    Matched MeSH terms: Sequence Analysis, DNA
  10. Yan J, Tian C, Zhou J, Bauer AM, Lee Grismer L, Zhou K
    Mitochondrial DNA, 2014 Jun;25(3):181-2.
    PMID: 23631365 DOI: 10.3109/19401736.2013.792066
    We sequenced the complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi, which is known as an endemic species to Malaysia. The complete mitogenome is 16,680 bp in size, consisting of 37 genes coding for 13 proteins, 22 transfer RNAs, two ribosomal RNAs and one control region. The A + T content of the overall base composition of H-strand is 53.09% (T: 23.20%, C: 32.48%, A: 29.89% and G: 14.43%). The major non-coding region (control region) is 1254 bp in length with the A + T content of 55.09% and four replicates of a 76-bp repeat within this region.
    Matched MeSH terms: Sequence Analysis, DNA
  11. Zhao H, Kong X, Zhou C
    Mitochondrial DNA, 2014 Oct;25(5):342-4.
    PMID: 23795847 DOI: 10.3109/19401736.2013.800492
    The Pangasius sutchi is an important ornamental and economic fish in Southeast Asia e.g. Thailand, Malaysia and China. The complete mitochondrial genome sequence of P. sutchi has been sequenced, which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and a non-coding control region with the total length of 16,522 bp. The gene order and composition are similar to most of other vertebrates. Just like most other vertebrates, the bias of G and C was found in different region/genes statistics results. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The mitogenome sequence of P. sutchi would contribute to better understand population genetics, evolution of this lineage.
    Matched MeSH terms: Sequence Analysis, DNA/methods*
  12. Sun F, Wang C, Chen H, Zheng Z
    Curr Microbiol, 2020 May;77(5):816-825.
    PMID: 31927597 DOI: 10.1007/s00284-019-01862-x
    Enteromorpha prolifera blooms considerably affected coastal environments in recent years. However, the effects of E. prolifera on microbial ecology and function remained unknown. In this study, metagenomic sequencing was used to investigate the effect of E. prolifera bloom on the microbial communities and functional genes in an aquaculture environment. Results showed that E. prolifera bloom could significantly alter the microbial composition and abundance, and heterotrophic bacteria comprised the major groups in the E. prolifera bloom pond, which was dominated by Actinomycetales and Flavobacteriales. The study indicated that viruses played an important role in shaping the microbial community and diversity during E. prolifera bloom. These viruses affected various dominant microbial taxa (such as Rhodobacteraceae, Synechococcus, and Prochlorococcus), which produced an obvious impact on potential nutrient transformation. Functional annotation analysis indicated that E. prolifera bloom would considerably shift the metabolism function by altering the structure and abundance of the microbial community. E. prolifera bloom pond had the low ability of potential metabolic capabilities of nitrogen, sulfur, and phosphate, whereas promoted gene abundance of genetic information processing. These changes in the microbial community and function could produce serious effect on aquaculture ecosystem.
    Matched MeSH terms: Sequence Analysis, DNA
  13. Nejat N, Vadamalai G, Davis RE, Harrison NA, Sijam K, Dickinson M, et al.
    Int J Syst Evol Microbiol, 2013 Feb;63(Pt 2):540-548.
    PMID: 22523165 DOI: 10.1099/ijs.0.041467-0
    This study addressed the taxonomic position and group classification of a phytoplasma responsible for virescence and phyllody symptoms in naturally diseased Madagascar periwinkle plants in western Malaysia. Unique regions in the 16S rRNA gene from the Malaysian periwinkle virescence (MaPV) phytoplasma distinguished the phytoplasma from all previously described 'Candidatus Phytoplasma' species. Pairwise sequence similarity scores, calculated through alignment of full-length 16S rRNA gene sequences, revealed that the MaPV phytoplasma 16S rRNA gene shared 96.5 % or less sequence similarity with that of previously described 'Ca. Phytoplasma' species, justifying the recognition of the MaPV phytoplasma as a reference strain of a novel taxon, 'Candidatus Phytoplasma malaysianum'. The 16S rRNA gene F2nR2 fragment from the MaPV phytoplasma exhibited a distinct restriction fragment length polymorphism (RFLP) profile and the pattern similarity coefficient values were lower than 0.85 with representative phytoplasmas classified in any of the 31 previously delineated 16Sr groups; therefore, the MaPV phytoplasma was designated a member of a new 16Sr group, 16SrXXXII. Phytoplasmas affiliated with this novel taxon and the new group included diverse strains infecting periwinkle, coconut palm and oil palm in Malaysia. Three phytoplasmas were characterized as representatives of three distinct subgroups, 16SrXXXII-A, 16SrXXXII-B and 16SrXXXII-C, respectively.
    Matched MeSH terms: Sequence Analysis, DNA
  14. Naderali N, Nejat N, Vadamalai G, Davis RE, Wei W, Harrison NA, et al.
    Int J Syst Evol Microbiol, 2017 Oct;67(10):3765-3772.
    PMID: 28905707 DOI: 10.1099/ijsem.0.002187
    Landscape-grown foxtail palm (Wodyetia bifurcata A. K. Irvine) trees displaying symptoms of severe foliar chlorosis, stunting, general decline and mortality reminiscent of coconut yellow decline disease were observed in Bangi, Malaysia, during 2012. DNA samples from foliage tissues of 15 symptomatic palms were analysed by employing a nested PCR assay primed by phytoplasma universal ribosomal RNA operon primer pairs, P1/P7 followed by R16F2n/R2. The assay yielded amplicons of a single band of 1.25 kb from DNA samples of 11 symptomatic palms. Results from cloning and sequence analysis of the PCR-amplified 16S rRNA gene segments revealed that, in three palms, three mutually distinct phytoplasmas comprising strains related to 'Candidatus Phytoplasma asteris' and 'Candidatus Phytoplasma cynodontis', as well as a novel phytoplasma, were present as triple infections. The 16S rRNA gene sequence derived from the novel phytoplasma shared less than 96 % nucleotide sequence identity with that of each previously describedspecies of the provisional genus 'Ca. Phytoplasma', justifying its recognition as the reference strain of a new taxon, 'Candidatus Phytoplasma wodyetiae'. Virtual RFLP profiles of the R16F2n/R2 portion of the 16S rRNA gene and the pattern similarity coefficient value (0.74) supported the delineation of 'Ca. Phytoplasma wodyetiae' as the sole representative subgroup A member of a new phytoplasma ribosomal group, 16SrXXXVI.
    Matched MeSH terms: Sequence Analysis, DNA
  15. Yang Q, Ge YM, Iqbal NM, Yang X, Zhang XL
    Antonie Van Leeuwenhoek, 2021 Jul;114(7):1091-1106.
    PMID: 33895907 DOI: 10.1007/s10482-021-01580-0
    Marine phycosphere harbors unique cross-kingdom associations with enormous ecological significance in aquatic ecosystems as well as relevance for algal biotechnology industry. During our investigating the microbial composition and bioactivity of marine phycosphere microbiota (PM), a novel lightly yellowish and versatile bacterium designated strain AM1-D1T was isolated from cultivable PM of marine dinoflagellate Alexandrium minutum amtk4 that produces high levels of paralytic shellfish poisoning toxins (PSTs). Strain AM1-D1T demonstrates notable bioflocculanting bioactivity with bacterial exopolysaccharides (EPS), and microalgae growth-promoting (MGP) potential toward its algal host. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AM1-D1T was affiliated to the members of genus Sulfitobacter within the family Rhodobacteraceae, showing the highest sequence similarity of 97.9% with Sulfitobacter noctilucae NB-68T, and below 97.8% with other type strains. The complete genome of strain AM1-D1T consisted of a circular 3.84-Mb chromosome and five circular plasmids (185, 95, 15, 205 and 348 Kb, respectively) with the G+C content of 64.6%. Low values obtained by phylogenomic calculations on the average nucleotide identity (ANI, 77.2%), average amino acid identity (AAI, 74.7%) and digital DNA-DNA hybridization (dDDH, 18.6%) unequivocally separated strain AM1-D1T from its closest relative. The main polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, one unidentified phospholipid and one unidentified lipid. The predominant fatty acids (> 10%) were C18:1 ω7c, C19:0 cyclo ω8c and C16:0. The respiratory quinone was Q-10. The genome of strain AM1-D1T was predicted to encode series of gene clusters responsible for sulfur oxidation (sox) and utilization of dissolved organic sulfur exometabolites from marine dinoflagellates, taurine (tau) and dimethylsulfoniopropionate (DMSP) (dmd), as well as supplementary vitamin B12 (cob), photosynthesis carotenoids (crt) which are pivotal components during algae-bacteria interactions. Based on the evidences by the polyphasic characterizations, strain AM1-D1T represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter alexandrii sp. nov. is proposed. The type strain is AM1-D1T (= CCTCC 2017277T = KCTC 62491T).
    Matched MeSH terms: Sequence Analysis, DNA
  16. Hu T, Qiu W, He B, Zhang Y, Yu J, Liang X, et al.
    BMC Microbiol, 2014;14:293.
    PMID: 25433675 DOI: 10.1186/s12866-014-0293-4
    In recent years novel human respiratory disease agents have been described for Southeast Asia and Australia. The causative pathogens were classified as pteropine orthoreoviruses with a strong phylogenetic relationship to orthoreoviruses of bat origin.
    Matched MeSH terms: Sequence Analysis, DNA/methods
  17. Hu T, Zheng Y, Zhang Y, Li G, Qiu W, Yu J, et al.
    BMC Microbiol, 2012;12:305.
    PMID: 23268691 DOI: 10.1186/1471-2180-12-305
    The identification of new virus strains is important for the study of infectious disease, but current (or existing) molecular biology methods are limited since the target sequence must be known to design genome-specific PCR primers. Thus, we developed a new method for the discovery of unknown viruses based on the cDNA--random amplified polymorphic DNA (cDNA-RAPD) technique. Getah virus, belonging to the family Togaviridae in the genus Alphavirus, is a mosquito-borne enveloped RNA virus that was identified using the Virus-Discovery-cDNA RAPD (VIDISCR) method.
    Matched MeSH terms: Sequence Analysis, DNA
  18. Hara H, Yusaimi YA, Zulkeflle SNM, Sugiura N, Iwamoto K, Goto M, et al.
    J Gen Appl Microbiol, 2019 Jan 24;64(6):284-292.
    PMID: 29877296 DOI: 10.2323/jgam.2018.02.003
    The emergence of antibiotic resistance among multidrug-resistant (MDR) microbes is of growing concern, and threatens public health globally. A total of 129 Escherichia coli isolates were recovered from lowland aqueous environments near hospitals and medical service centers in the vicinity of Kuala Lumpur, Malaysia. Among the eleven antibacterial agents tested, the isolates were highly resistant to trimethoprim-sulfamethoxazole (83.7%) and nalidixic acid (71.3%) and moderately resistant to ampicillin and chloramphenicol (66.7%), tetracycline (65.1%), fosfomycin (57.4%), cefotaxime (57.4%), and ciprofloxacin (57.4%), while low resistance levels were found with aminoglycosides (kanamycin, 22.5%; gentamicin, 21.7%). The presence of relevant resistance determinants was evaluated, and the genotypic resistance determinants were as follows: sulfonamides (sulI, sulII, and sulIII), trimethoprim (dfrA1 and dfrA5), quinolones (qnrS), β-lactams (ampC and blaCTX-M), chloramphenicol (cmlA1 and cat2), tetracycline (tetA and tetM), fosfomycin (fosA and fosA3), and aminoglycosides (aphA1 and aacC2). Our data suggest that multidrug-resistant E. coli strains are ubiquitous in the aquatic systems of tropical countries and indicate that hospital wastewater may contribute to this phenomenon.
    Matched MeSH terms: Sequence Analysis, DNA
  19. Ramaiya SD, Bujang JS, Zakaria MH
    ScientificWorldJournal, 2014;2014:598313.
    PMID: 25050402 DOI: 10.1155/2014/598313
    This study used morphological characterization and phylogenetic analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA to investigate the phylogeny of Passiflora species. The samples were collected from various regions of East Malaysia, and discriminant function analysis based on linear combinations of morphological variables was used to classify the Passiflora species. The biplots generated five distinct groups discriminated by morphological variables. The group consisted of cultivars of P. edulis with high levels of genetic similarity; in contrast, P. foetida was highly divergent from other species in the morphological biplots. The final dataset of aligned sequences from nine studied Passiflora accessions and 30 other individuals obtained from GenBank database (NCBI) yielded one most parsimonious tree with two strongly supported clades. Maximum parsimony (MP) tree showed the phylogenetic relationships within this subgenus Passiflora support the classification at the series level. The constructed phylogenic tree also confirmed the divergence of P. foetida from all other species and the closeness of wild and cultivated species. The phylogenetic relationships were consistent with results of morphological assessments. The results of this study indicate that ITS region analysis represents a useful tool for evaluating genetic diversity in Passiflora at the species level.
    Matched MeSH terms: Sequence Analysis, DNA
  20. Chehri K, Salleh B, Zakaria L
    Microb Ecol, 2015 Apr;69(3):457-71.
    PMID: 25238930 DOI: 10.1007/s00248-014-0494-2
    Members of Fusarium solani species complex (FSSC) have been known as plant, animal, and human pathogens. Nevertheless, the taxonomic status of such an important group of fungi is still very confusing and many new species as well as lineages have been elucidated recently. Unfortunately, most of the new taxa came from temperate and subtropical regions. Therefore, the objectives of the present study were to identify strains of FSSC recovered from different sources in Malaysia. In the present study, 55 strains belonging to the FSSC were examined and phylogenetically analyzed on the basis of internal transcribed spacer (ITS) regions and partial translation elongation factor-1 (TEF-1α) sequences. Based on morphological features, a total of 55 strains were selected for molecular studies. Based on morphological features, the strains were classified into four described Fusarium species, namely Fusarium keratoplasticum, Fusarium falciforme, FSSC 5, and Fusarium cf. ensiforme, and one unknown phylogenetic species was introduced. Although the data obtained from morphological and molecular studies sufficiently supported each other, the phylogenetic trees based on ITS and TEF-1α dataset clearly distinguished closely related species and distinctly separated all morphological taxa. All members of FSSC in this research were reported for the first time for Malaysian mycoflora.
    Matched MeSH terms: Sequence Analysis, DNA
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