Displaying publications 141 - 160 of 1821 in total

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  1. Antibiograms and molecular subtypes of methicillin-resistant Staphylococcus aureus in local teaching hospital, Malaysia
    Thong KL, Junnie J, Liew FY, Yusof MY, Hanifah YA
    J Microbiol Biotechnol, 2009 Oct;19(10):1265-70.
    PMID: 19884790
    The objectives of this study were to determine the antibiotypes, SCCmec subtypes, PVL carriage, and genetic diversity of MRSA strains from a tertiary hospital. Sixtysix MRSA strains were selected randomly (2003, 2004, and 2007) and tested for the Panton-Valentine leukocidin gene, mecA gene, and SCCmec type via a PCR. The antibiograms were determined using a standard disc diffusion method, and the genetic diversity of the isolates was determined by PFGE. Thirty-four antibiograms were obtained, with 55% of the 66 strains exhibiting resistance to more than 4 antimicrobials. All the isolates remained susceptible to vancomycin, and low resistance rates were noted for fusidic acid (11%), rifampicin (11%), and clindamycin acid (19%). The MRSA isolates that were multisensitive (n=12) were SCCmec type IV, whereas the rest (multiresistant) were SCCmec type III. Only two isolates (SCCmec type IV) tested positive for PVL, whereas all the isolates were mecA-positive. The PFGE was very discriminative and subtyped the 66 isolates into 55 pulsotypes (F=0.31-1.0). The multisensitive isolates were distinctly different from the multidrug-resistant MRSA. In conclusion, no vancomycin-resistant isolate was observed. The Malaysian MDR MRSA isolates were mostly SCCmec type III and negative for PVL. These strains were genetically distinct from the SCCmec type IV strains, which were sensitive to SXT, tetracycline, and erythromycin. Only two strains were SCCmec IV and PVL-positive. The infections in the hospital concerned were probably caused by multiple subtypes of MRSA.
    Matched MeSH terms: Phylogeny
  2. Fulltext Antibodies to Intercellular Adhesion Molecule 1-Binding Plasmodium falciparum Erythrocyte Membrane Protein 1-DBLβ Are Biomarkers of Protective Immunity to Malaria in a Cohort of Young Children from Papua New Guinea
    Tessema SK, Utama D, Chesnokov O, Hodder AN, Lin CS, Harrison GLA, et al.
    Infect Immun, 2018 08;86(8).
    PMID: 29784862 DOI: 10.1128/IAI.00485-17
    Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) mediates parasite sequestration to the cerebral microvasculature via binding of DBLβ domains to intercellular adhesion molecule 1 (ICAM1) and is associated with severe cerebral malaria. In a cohort of 187 young children from Papua New Guinea (PNG), we examined baseline levels of antibody to the ICAM1-binding PfEMP1 domain, DBLβ3PF11_0521, in comparison to four control antigens, including NTS-DBLα and CIDR1 domains from another group A variant and a group B/C variant. Antibody levels for the group A antigens were strongly associated with age and exposure. Antibody responses to DBLβ3PF11_0521 were associated with a 37% reduced risk of high-density clinical malaria in the follow-up period (adjusted incidence risk ratio [aIRR] = 0.63 [95% confidence interval {CI}, 0.45 to 0.88; P = 0.007]) and a 25% reduction in risk of low-density clinical malaria (aIRR = 0.75 [95% CI, 0.55 to 1.01; P = 0.06]), while there was no such association for other variants. Children who experienced severe malaria also had significantly lower levels of antibody to DBLβ3PF11_0521 and the other group A domains than those that experienced nonsevere malaria. Furthermore, a subset of PNG DBLβ sequences had ICAM1-binding motifs, formed a distinct phylogenetic cluster, and were similar to sequences from other areas of endemicity. PfEMP1 variants associated with these DBLβ domains were enriched for DC4 and DC13 head structures implicated in endothelial protein C receptor (EPCR) binding and severe malaria, suggesting conservation of dual binding specificities. These results provide further support for the development of specific classes of PfEMP1 as vaccine candidates and as biomarkers for protective immunity against clinical P. falciparum malaria.
    Matched MeSH terms: Phylogeny
  3. Antifungal Mechanism of Rhodotorula mucilaginosa and Aureobasidium sp. nov. Isolated from Cerbera manghas L. against the Growth of Destructive Molds in Post Harvested Apples
    Sukmawati D, Shabrina A, Indrayanti R, Kurniati TH, Nurjayadi M, Hidayat I, et al.
    Recent Pat Food Nutr Agric, 2020;11(3):219-228.
    PMID: 32324527 DOI: 10.2174/2212798411666200423101159
    BACKGROUND: Apples often experience postharvest damage due to being attacked by mold organisms. Several groups of molds such as Aspergillus sp., Penicilium expansum, Botrytis cinerea, and Venturia sp. can cause a serious postharvest disease exhibited as watery regions where areas of blue-green tufts of spores develop. Current methods using fungicides to control pathogenic fungi can cause resistance if applied in the long term. An alternative procedure using yeast as a biological agent has been found.

    OBJECTIVE: The aim of this study is to screen potential yeast, which has the ability to inhibit the growth of Aspergillus brasielensis (isolate A1) and Aspergillus flavus section flavi (isolate A17) isolated from apple fruits.

    METHODS: Antagonism test using YMA dual culture medium using in vitro assays and ITS rDNA identification were performed.

    RESULTS: The result showed that 3 out of 19 yeast isolated from Cerbera manghas L, T1, T3 and T4, demonstrated the potential ability as a biocontrol agent. ITS rDNA identification demonstrated that T1 has a similarity to Rhodotorula mucilaginosa while T3 and T4 were identified as Aureobasidium sp. nov. The 3 isolates exhibited the ability to reduce the growth of A. brasiliensis sensu lato better than dithane 0.3% with a Disease Incidence (DI) of 100% and a Disease Severity (DS) value of 45%. Only isolate T1 and T3 were able to reduce decay symptoms in apples inoculated with A. flavus sensu lato (with DO and DS were 100% and 25%, respectively) compared to dithane pesticides 0.3%.

    CONCLUSION: This study indicated that competition between nutrients occurs between pathogenic molds and under-yeast in vitro and in vivo conditions. However, further studies in the future might be able to elucidate the 'killer' activity and interaction with the pathogen cells and the bio-product production using Rhodotorula mucilaginosa and Aureoubasidium namibiae strains to control postharvest diseases.

    Matched MeSH terms: Phylogeny
  4. Fulltext Antigenic Variation of East/Central/South African and Asian Chikungunya Virus Genotypes in Neutralization by Immune Sera
    Chua CL, Sam IC, Merits A, Chan YF
    PLoS Negl Trop Dis, 2016 08;10(8):e0004960.
    PMID: 27571254 DOI: 10.1371/journal.pntd.0004960
    BACKGROUND: Chikungunya virus (CHIKV) is a re-emerging mosquito-borne virus which causes epidemics of fever, severe joint pain and rash. Between 2005 and 2010, the East/Central/South African (ECSA) genotype was responsible for global explosive outbreaks across India, the Indian Ocean and Southeast Asia. From late 2013, Asian genotype CHIKV has caused outbreaks in the Americas. The characteristics of cross-antibody efficacy and epitopes are poorly understood.

    METHODOLOGY/PRINCIPAL FINDINGS: We characterized human immune sera collected during two independent outbreaks in Malaysia of the Asian genotype in 2006 and the ECSA genotype in 2008-2010. Neutralizing capacity was analyzed against representative clinical isolates as well as viruses rescued from infectious clones of ECSA and Asian CHIKV. Using whole virus antigen and recombinant E1 and E2 envelope glycoproteins, we further investigated antibody binding sites, epitopes, and antibody titers. Both ECSA and Asian sera demonstrated stronger neutralizing capacity against the ECSA genotype, which corresponded to strong epitope-antibody interaction. ECSA serum targeted conformational epitope sites in the E1-E2 glycoprotein, and E1-E211K, E2-I2T, E2-H5N, E2-G118S and E2-S194G are key amino acids that enhance cross-neutralizing efficacy. As for Asian serum, the antibodies targeting E2 glycoprotein correlated with neutralizing efficacy, and I2T, H5N, G118S and S194G altered and improved the neutralization profile. Rabbit polyclonal antibody against the N-terminal linear neutralizing epitope from the ECSA sequence has reduced binding capacity and neutralization efficacy against Asian CHIKV. These findings imply that the choice of vaccine strain may impact cross-protection against different genotypes.

    CONCLUSION/SIGNIFICANCE: Immune serum from humans infected with CHIKV of either ECSA or Asian genotypes showed differences in binding and neutralization characteristics. These findings have implications for the continued outbreaks of co-circulating CHIKV genotypes and effective design of vaccines and diagnostic serological assays.

    Matched MeSH terms: Phylogeny
  5. Fulltext Antimicrobial activities of Bacillus velezensis strains isolated from stingless bee products against methicillin-resistant Staphylococcus aureus
    Baharudin MMA, Ngalimat MS, Mohd Shariff F, Balia Yusof ZN, Karim M, Baharum SN, et al.
    PLoS One, 2021;16(5):e0251514.
    PMID: 33974665 DOI: 10.1371/journal.pone.0251514
    Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) have reached epidemic proportions globally. Therefore, there is an urgent need for a continuous supply of antibiotics to combat the problem. In this study, bacteria initially identified as species belonging to the Bacillus amyloliquefaciens operational group were re-identified based on the housekeeping gene, gyrB. Cell-free supernatants (CFS) from the strains were used for antimicrobial tests using the agar well diffusion assay against MRSA and various types of pathogenic bacteria. The minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and physicochemical characteristics of the CFS were determined. Based on gyrB sequence analysis, five strains (PD9, B7, PU1, BP1 and L9) were identified as Bacillus velezensis. The CFS of all B. velezensis strains showed broad inhibitory activities against Gram-negative and -positive as well as MRSA strains. Strain PD9 against MRSA ATCC 33742 was chosen for further analysis as it showed the biggest zone of inhibition (21.0 ± 0.4 mm). The MIC and MBC values obtained were 125 μl/ml. The crude antimicrobial extract showed bactericidal activity and was stable at various temperatures (40-80°C), pH (4-12), surfactants (Tween 20, Tween 80, SDS and Triton X-100) and metal ions (MgCI2, NaCI2, ZnNO3 and CuSO4) when tested. However, the crude extract was not stable when treated with proteinase K. All these properties resembled the characteristics of peptides. The antimicrobial compound from the selected strain was purified by using solvent extraction method and silica gel column chromatography. The purified compound was subjected to High Performance Liquid Chromatography which resulted in a single peak of the anti-MRSA compound being detected. The molecular weight of the anti-MRSA compound was determined by using SDS-PAGE and zymogram. The size of the purified antimicrobial peptide was approximately ~ 5 kDa. The antimicrobial peptide produced from B. velezensis strain PD9 is a promising alternative to combat the spread of MRSA infections in the future.
    Matched MeSH terms: Phylogeny
  6. Antimicrobial susceptibility and pulsed-field gel electrophoresis of Shigella sonnei strains in Malaysia (1997-2000)
    Hoe CH, Yasin RM, Koh YT, Thong KL
    J Appl Microbiol, 2005;99(1):133-40.
    PMID: 15960673
    Antimicrobial resistance of Shigella sonnei from Malaysia was determined and subtyping was carried by pulsed-field gel electrophoresis (PFGE) to assess the extent of genetic diversity of these strains.
    Matched MeSH terms: Phylogeny
  7. Fulltext Antimicrobial susceptibility, serotype distribution, virulence profile and molecular typing of piliated clinical isolates of pneumococci from east coast, Peninsular Malaysia
    Dzaraly ND, Mohd Desa MN, Muthanna A, Masri SN, Taib NM, Suhaili Z, et al.
    Sci Rep, 2021 Apr 15;11(1):8220.
    PMID: 33859249 DOI: 10.1038/s41598-021-87428-z
    Pilus has been recently associated with pneumococcal pathogenesis in humans. The information regarding piliated isolates in Malaysia is scarce, especially in the less developed states on the east coast of Peninsular Malaysia. Therefore, we studied the characteristics of pneumococci, including the piliated isolates, in relation to antimicrobial susceptibility, serotypes, and genotypes at a major tertiary hospital on the east coast of Peninsular Malaysia. A total of 100 clinical isolates collected between September 2017 and December 2019 were subjected to serotyping, antimicrobial susceptibility test, and detection of pneumococcal virulence and pilus genes. Multilocus sequence typing (MLST) and phylogenetic analysis were performed only for piliated strains. The most frequent serotypes were 14 (17%), 6A/B (16%), 23F (12%), 19A (11%), and 19F (11%). The majority of isolates were resistant to erythromycin (42%), tetracycline (37%), and trimethoprim-sulfamethoxazole (24%). Piliated isolates occurred in a proportion of 19%; 47.3% of them were multidrug-resistant (MDR) and a majority had serotype 19F. This study showed ST236 was the most predominant sequence type (ST) among piliated isolates, which was related to PMEN clone Taiwan19F-14 (CC271). In the phylogenetic analysis, the piliated isolates were grouped into three major clades supported with 100% bootstrap values. Most piliated isolates belonged to internationally disseminated clones of S. pneumoniae, but pneumococcal conjugate vaccines (PCVs) have the potential to control them.
    Matched MeSH terms: Phylogeny
  8. Fulltext Antioxidative Potential of a Streptomyces sp. MUM292 Isolated from Mangrove Soil
    Tan LT, Chan KG, Chan CK, Khan TM, Lee LH, Goh BH
    Biomed Res Int, 2018;2018:4823126.
    PMID: 29805975 DOI: 10.1155/2018/4823126
    Mangrove derived microorganisms constitute a rich bioresource for bioprospecting of bioactive natural products. This study explored the antioxidant potentials of Streptomyces bacteria derived from mangrove soil. Based on 16S rRNA phylogenetic analysis, strain MUM292 was identified as the genus Streptomyces. Strain MUM292 showed the highest 16S rRNA gene sequence similarity of 99.54% with S. griseoruber NBRC12873T. Furthermore, strain MUM292 was also characterized and showed phenotypic characteristics consistent with Streptomyces bacteria. Fermentation and extraction were performed to obtain the MUM292 extract containing the secondary metabolites of strain MUM292. The extract displayed promising antioxidant activities, including DPPH, ABTS, and superoxide radical scavenging and also metal-chelating activities. The process of lipid peroxidation in lipid-rich product was also retarded by MUM292 extract and resulted in reduced MDA production. The potential bioactive constituents of MUM292 extract were investigated using GC-MS and preliminary detection showed the presence of pyrazine, pyrrole, cyclic dipeptides, and phenolic compound in MUM292 extract. This work demonstrates that Streptomyces MUM292 can be a potential antioxidant resource for food and pharmaceutical industries.
    Matched MeSH terms: Phylogeny
  9. Fulltext Antiretroviral drug resistance and HIV-1 subtypes among treatment-naive prisoners in Kelantan, Malaysia
    Ariffin TA, Mohamad S, Yusuf WN, Shueb RH
    J Infect Dev Ctries, 2014 Aug;8(8):1063-7.
    PMID: 25116676 DOI: 10.3855/jidc.4095
    INTRODUCTION: The widespread use of highly active antiretroviral therapy (HAART) and continuous reports of HIV-1 strains developing resistance to these drugs is rather alarming, as transmission of resistant viruses to newly infected persons is possible. This study aimed to determine HIV-1 subtypes and the prevalence of primary mutations associated with antiretroviral (ARV) resistance among treatment-naive prisoners on the east coast of Malaysia.
    METHODOLOGY: Viral RNA was extracted from plasma samples of 21 treatment-naive prisoners. Protease (PR) and reverse transcriptase (RT) regions were amplified and sequenced. Stanford HIV database algorithms were used for interpretation of resistance, and phylogenetic analysis was performed for subtype assignment.
    RESULTS: In the PR gene, no antiviral resistance-associated mutation was detected. For RT-associated mutations, K103N was the most prevalent in sequenced samples (14.3%). Genetic subtyping on the pol gene revealed that the majority of the prisoners were infected with subtype CRF33_01B (52.4%).
    CONCLUSION: Continuous surveillance of newly infected individuals is required to help strategize the best antiviral treatment for these patients.
    Matched MeSH terms: Phylogeny
  10. Fulltext Ants are the major agents of resource removal from tropical rainforests
    Griffiths HM, Ashton LA, Walker AE, Hasan F, Evans TA, Eggleton P, et al.
    J Anim Ecol, 2018 Jan;87(1):293-300.
    PMID: 28791685 DOI: 10.1111/1365-2656.12728
    Ants are diverse and abundant, especially in tropical ecosystems. They are often cited as the agents of key ecological processes, but their precise contributions compared with other organisms have rarely been quantified. Through the removal of food resources from the forest floor and subsequent transport to nests, ants play an important role in the redistribution of nutrients in rainforests. This is an essential ecosystem process and a key energetic link between higher trophic levels, decomposers and primary producers. We used the removal of carbohydrate, protein and seed baits as a proxy to quantify the contribution that ants, other invertebrates and vertebrates make to the redistribution of nutrients around the forest floor, and determined to what extent there is functional redundancy across ants, other invertebrate and vertebrate groups. Using a large-scale, field-based manipulation experiment, we suppressed ants from c. 1 ha plots in a lowland tropical rainforest in Sabah, Malaysia. Using a combination of treatment and control plots, and cages to exclude vertebrates, we made food resources available to: (i) the whole foraging community, (ii) only invertebrates and (iii) only non-ant invertebrates. This allowed us to partition bait removal into that taken by vertebrates, non-ant invertebrates and ants. Additionally, we examined how the non-ant invertebrate community responded to ant exclusion. When the whole foraging community had access to food resources, we found that ants were responsible for 52% of total bait removal whilst vertebrates and non-ant invertebrates removed the remaining 48%. Where vertebrates were excluded, ants carried out 61% of invertebrate-mediated bait removal, with all other invertebrates removing the remaining 39%. Vertebrates were responsible for just 24% of bait removal and invertebrates (including ants) collectively removed the remaining 76%. There was no compensation in bait removal rate when ants and vertebrates were excluded, indicating low functional redundancy between these groups. This study is the first to quantify the contribution of ants to the removal of food resources from rainforest floors and thus nutrient redistribution. We demonstrate that ants are functionally unique in this role because no other organisms compensated to maintain bait removal rate in their absence. As such, we strengthen a growing body of evidence establishing ants as ecosystem engineers, and provide new insights into the role of ants in maintaining key ecosystem processes. In this way, we further our basic understanding of the functioning of tropical rainforest ecosystems.
    Matched MeSH terms: Phylogeny
  11. Fulltext Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees
    Kwong WK, Moran NA
    Int J Syst Evol Microbiol, 2016 Mar;66(3):1323-1329.
    PMID: 26743158 DOI: 10.1099/ijsem.0.000882
    Honey bees and bumble bees harbour a small, defined set of gut bacterial associates. Strains matching sequences from 16S rRNA gene surveys of bee gut microbiotas were isolated from two honey bee species from East Asia. These isolates were mesophlic, non-pigmented, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and C16 : 0 3-OH. The DNA G+C content was 29-31 mol%. They had ∼87 % 16S rRNA gene sequence identity to the closest relatives described. Phylogenetic reconstruction using 20 protein-coding genes showed that these bee-derived strains formed a highly supported monophyletic clade, sister to the clade containing species of the genera Chryseobacterium and Elizabethkingia within the family Flavobacteriaceae of the phylum Bacteroidetes. On the basis of phenotypic and genotypic characteristics, we propose placing these strains in a novel genus and species: Apibacter adventoris gen. nov., sp. nov. The type strain of Apibacter adventoris is wkB301T ( = NRRL B-65307T = NCIMB 14986T).
    Matched MeSH terms: Phylogeny*
  12. Application of 16s rDNA and cytochrome b ribosomal markers in studies of lineage and fish populations structure of aquatic species
    Baharum SN, Nurdalila AA
    Mol Biol Rep, 2012 May;39(5):5225-32.
    PMID: 22167328 DOI: 10.1007/s11033-011-1320-2
    The most economically important form of aquaculture is fish farming, which is an industry that accounts for an ever increasing share of world fishery production. Molecular markers can be used to enhance the productivity of the aquaculture and fish industries to meet the increasing demand. Molecular markers can be identified via a DNA test regardless of the developmental stage, age or environmental challenges experienced by the organism. The application of 16s and cytochrome b markers has enabled rapid progress in investigations of genetic variability and inbreeding, parentage assignments, species and strain identification and the construction of high resolution genetic linkage maps for aquaculture fisheries. In this review, the advantages of principles and potential power tools of 16s and cytochrome b markers are discussed. Main findings in term of trend, aspects and debates on the reviewed issue made from the model of aquatic species for the benefit of aquaculture genomics and aquaculture genetics research are discussed. The concepts in this review are illustrated with various research examples and results that relate theory to reality and provide a strong review of the current status of these biotechnology topics.
    Matched MeSH terms: Phylogeny*
  13. Application of rDNA-PCR amplification and DGGE fingerprinting for detection of microbial diversity in a Malaysian crude oil
    Liew PW, Jong BC
    J Microbiol Biotechnol, 2008 May;18(5):815-20.
    PMID: 18633276
    Two culture-independent methods, namely ribosomal DNA libraries and denaturing gradient gel electrophoresis (DGGE), were adopted to examine the microbial community of a Malaysian light crude oil. In this study, both 16S and 18S rDNAs were PCR-amplified from bulk DNA of crude oil samples, cloned, and sequenced. Analyses of restriction fragment length polymorphism (RFLP) and phylogenetics clustered the 16S and 18S rDNA sequences into seven and six groups, respectively. The ribosomal DNA sequences obtained showed sequence similarity between 90 to 100% to those available in the GenBank database. The closest relatives documented for the 16S rDNAs include member species of Thermoincola and Rhodopseudomonas, whereas the closest fungal relatives include Acremonium, Ceriporiopsis, Xeromyces, Lecythophora, and Candida. Others were affiliated to uncultured bacteria and uncultured ascomycete. The 16S rDNA library demonstrated predomination by a single uncultured bacterial type by >80% relative abundance. The predomination was confirmed by DGGE analysis.
    Matched MeSH terms: Phylogeny
  14. Arcobacter haliotis sp. nov., isolated from abalone species Haliotis gigantea
    Tanaka R, Cleenwerck I, Mizutani Y, Iehata S, Bossier P, Vandamme P
    Int J Syst Evol Microbiol, 2017 Aug;67(8):3050-3056.
    PMID: 28820118 DOI: 10.1099/ijsem.0.002080
    A Gram-negative, aerobic, polar-flagellated and rod-shaped, sometimes slightly curved bacterium, designated MA5T, was isolated from the gut of an abalone of the species Haliotis gigantea collected in Japan. Phylogenetic analyses based on 16S rRNA, gyrB, hsp60 and rpoB gene sequences placed strain MA5T in the genus Arcobacter in an independent phylogenetic line. Comparison of the 16S rRNA gene sequence of this strain with those of the type strains of the established Arcobacter species revealed A. nitrofigilis (95.1 %) as nearest neighbour. Strain MA5T grew optimally at 25 °C, pH 6.0 to 9.0 and in the presence of 2 to 5 % (w/v) NaCl under both aerobic and microaerobic conditions. The predominant fatty acids found were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c), C12 : 0 3-OH and C18 : 1 ω7c. Menaquinone-6 (MK-6) and menaquinone-7 (MK-7) were found as the major respiratory quinones. The major polar lipids detected were phosphatidylethanolamine and phosphatidylglycerol. Strain MA5T could be differentiated phenotypically from the phylogenetic closest Arcobacter species by its ability to grow on 0.05 % safranin and 0.01 % 2,3,5-triphenyl tetrazolium chloride (TTC), but not on 0.5 % NaCl. The obtained DNA G+C content of strain MA5T was 27.9 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic distinctiveness of MA5T, this strain is considered to represent a novel species of the genus Arcobacter, for which the name Arcobacter haliotis sp. nov. is proposed. The type strain is MA5T (=LMG 28652T=JCM 31147T).
    Matched MeSH terms: Phylogeny*
  15. Argiope hoiseni, a new species of the spider genus Argiope (Araneae, Araneidae) from Peninsular Malaysia based on morphology and molecular analyses
    Tan J
    Zootaxa, 2018 Aug 07;4457(1):129-142.
    PMID: 30314183 DOI: 10.11646/zootaxa.4457.1.6
    A new species of Argiope Audouin 1826, A. hoiseni new species is described from Perak and Selangor, Peninsular Malaysia based on morphology and DNA information of the mitochondrial (16S rRNA, COI and COII) and nuclear-encoded (H3A, 18S rRNA) molecular markers. Epigynal structure suggested Argiope hoiseni to be similar to A. jinghongensis Yin, Peng Wang 1994, A. luzona (Walckenaer 1841), A. pulchella Thorell 1881 and A. taprobanica Thorell 1887. Molecular sequence data including the new species inferred that it is monophyletic with an intraspecific variation of 0.87-3.59 % based on the 16S+COI+COII+H3A dataset. Phylogenetic analyses also revealed insights into the evolutionary lineages of Argiope species in Southeast Asia as well as corroborated recent taxonomic changes and species synonymies associated with Argiope. Two new distribution records were also reported for A. chloreis Thorell,1877 and A. doleschalli Thorell, 1873 in Peninsular Malaysia.
    Matched MeSH terms: Phylogeny*
  16. Fulltext Arthropod Ectoparasites Have Potential to Bind SARS-CoV-2 via ACE
    Lam SD, Ashford P, Díaz-Sánchez S, Villar M, Gortázar C, de la Fuente J, et al.
    Viruses, 2021 04 19;13(4).
    PMID: 33921873 DOI: 10.3390/v13040708
    Coronavirus-like organisms have been previously identified in Arthropod ectoparasites (such as ticks and unfed cat flea). Yet, the question regarding the possible role of these arthropods as SARS-CoV-2 passive/biological transmission vectors is still poorly explored. In this study, we performed in silico structural and binding energy calculations to assess the risks associated with possible ectoparasite transmission. We found sufficient similarity between ectoparasite ACE and human ACE2 protein sequences to build good quality 3D-models of the SARS-CoV-2 Spike:ACE complex to assess the impacts of ectoparasite mutations on complex stability. For several species (e.g., water flea, deer tick, body louse), our analyses showed no significant destabilisation of the SARS-CoV-2 Spike:ACE complex, suggesting these species would bind the viral Spike protein. Our structural analyses also provide structural rationale for interactions between the viral Spike and the ectoparasite ACE proteins. Although we do not have experimental evidence of infection in these ectoparasites, the predicted stability of the complex suggests this is possible, raising concerns of a possible role in passive transmission of the virus to their human hosts.
    Matched MeSH terms: Phylogeny
  17. Fulltext Artificial Neural Networks (ANNs) and Response Surface Methodology (RSM) Approach for Modelling the Optimization of Chromium (VI) Reduction by Newly Isolated Acinetobacter radioresistens Strain NS-MIE from Agricultural Soil
    Ram Talib NS, Halmi MIE, Abd Ghani SS, Zaidan UH, Shukor MYA
    Biomed Res Int, 2019;2019:5785387.
    PMID: 31240217 DOI: 10.1155/2019/5785387
    Numerous technologies and approaches have been used in the past few decades to remove hexavalent chromium (Cr[VI]) in wastewater and the environment. However, these conventional technologies are not economical and efficient in removing Cr(VI) at a very low concentration (1-100 ppm). As an alternative, the utilization of bioremediation techniques which uses the potential of microorganisms could represent an effective technique for the detoxification of Cr(VI). In this study, we reported a newly isolated bacterium identified as Acinetobacter radioresistens sp. NS-MIE from Malaysian agricultural soil. The chromate reduction potential of strain NS-MIE was optimized using RSM and ANN techniques. The optimum condition predicted by RSM for the bacterium to reduce hexavalent chromium occurred at pH 6, 10 g/L ppm of nutrient broth (NB) concentration and 100 ppm of chromate concentration while the optimum condition predicted by ANN is at pH 6 and 10 g/L of NB concentration and of 60 ppm of chromate concentration with chromate reduction (%) of 75.13 % and 96.27 %, respectively. The analysis by the ANN model shows better prediction data with a higher R2 value of 0.9991 and smaller average absolute deviation (AAD) and root mean square error (RMSE) of 0.33 % and 0.302 %, respectively. Validation analysis showed the predicted values by RSM and ANN were close to the validation values, whereas the ANN showed the lowest deviation, 2.57%, compared to the RSM. This finding suggests that the ANN showed a better prediction and fitting ability compared to the RSM for the nonlinear regression analysis. Based on this study, A. radioresistens sp. NS-MIE exhibits strong potential characteristics as a candidate for the bioremediation of hexavalent chromium in the environment.
    Matched MeSH terms: Phylogeny
  18. Fulltext Assessing the genetic relationships of Curcuma alismatifolia varieties using simple sequence repeat markers
    Taheri S, Abdullah TL, Abdullah NA, Ahmad Z, Karimi E, Shabanimofrad MR
    Genet. Mol. Res., 2014;13(3):7339-46.
    PMID: 25222232 DOI: 10.4238/2014.September.5.12
    The genus Curcuma is a member of the ginger family (Zingiberaceae) that has recently become popular for use as flowering pot plants, both indoors and as patio and landscape plants. We used PCR-based molecular markers (SSRs) to elucidate genetic variation and relationships between five varieties of Curcuma (Curcuma alismatifolia) cultivated in Malaysia. Of the primers tested, 8 (of 17) SSR primers were selected for their reproducibility and high rates of polymorphism. The number of presumed alleles revealed by the SSR analysis ranged from two to six alleles, with a mean value of 3.25 alleles per locus. The values of HO and HE ranged from 0 to 0.8 (mean value of 0.2) and 0.1837 to 0.7755 (mean value of 0.5102), respectively. Eight SSR primers yielded 26 total amplified fragments and revealed high rates of polymorphism among the varieties studied. The polymorphic information content varied from 0.26 to 0.73. Dice's similarity coefficient was calculated for all pairwise comparisons and used to construct an unweighted pair group method with arithmetic average (UPGMA) dendrogram. Similarity coefficient values from 0.2105 to 0.6667 (with an average of 0.4386) were found among the five varieties examined. A cluster analysis of data using a UPGMA algorithm divided the five varieties/hybrids into 2 groups.
    Matched MeSH terms: Phylogeny*
  19. Assessing ureolytic bacteria with calcifying abilities isolated from limestone caves for biocalcification
    Omoregie AI, Ong DEL, Nissom PM
    Lett Appl Microbiol, 2019 Feb;68(2):173-181.
    PMID: 30537001 DOI: 10.1111/lam.13103
    Biocalcification through the use of ureolytic bacteria and biochemical activities has evolved in recent decades into a fervent resourceful effective technology suitable for soil stabilization, crack repair and bioremediation. Extensive studies have been carried out on numerous ureolytic bacterial species isolated from soils and sewage samples. However, very limited attention has been given to limestone caves with natural calcite formations as a possible source for isolation of ureolytic bacteria. In this study, bacterial isolates were recovered from limestone cave samples to determine their suitability for biocalcification. Twenty-seven morphologically distinct bacterial isolates were identified by partial 16S rRNA gene sequencing and their various genetic diversity was characterized according to their phylogenetic affiliations. Based on the molecular identification, Sporosarcina was the most abundant genus among all the ureolytic isolates, while the rest belonged to Pseudogracilibacillus and Bacillus genera. Analytical analysis on urease measurement showed that urease activities for the isolates ranged from 1·130 to 21·513 mol urea hydrolysed per minute, with isolate NB33 achieving the highest value and TSB4 achieving the lowest value. The estimated CaCO3 precipitates for the isolates ranged from 4·04 to 17·26 mg ml-1 , with isolate NB30 achieving the highest value and TSB20 achieving the lowest value. The findings in this study demonstrated that the ureolytic bacteria from limestone caves are promising bio-calcifying agents. SIGNIFICANCE AND IMPACT OF THE STUDY: Ureolytic bacteria continues to play an important role as microbial tools used in geotechnical engineering for soil biocalcification. Microbial strains with the ability to produce urease enzyme and induce calcium carbonate mineral are often isolated from soil, water and sludge samples. However, screening for these essential microbes from extreme regions such as caves are rarely investigated. In this study, native bacteria which were isolated from limestone cave samples are identified and characterized. The findings suggested that these ureolytic bacterial isolates have the potential to serve as suitable alternative microbial agents for soil strengthening and stabilization.
    Matched MeSH terms: Phylogeny
  20. Fulltext Assessment of four molecular markers as potential DNA barcodes for red algae Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta)
    Tan J, Lim PE, Phang SM, Hong DD, Sunarpi H, Hurtado AQ
    PLoS One, 2012;7(12):e52905.
    PMID: 23285223 DOI: 10.1371/journal.pone.0052905
    DNA barcoding has been a major advancement in the field of taxonomy, seeing much effort put into the barcoding of wide taxa of organisms, macro and microalgae included. The mitochondrial-encoded cox1 and plastid-encoded rbcL has been proposed as potential DNA barcodes for rhodophytes, but are yet to be tested on the commercially important carrageenophytes Kappaphycus and Eucheuma. This study gauges the effectiveness of four markers, namely the mitochondrial cox1, cox2, cox2-3 spacer and the plastid rbcL in DNA barcoding on selected Kappaphycus and Eucheuma from Southeast Asia. Marker assessments were performed using established distance and tree-based identification criteria from earlier studies. Barcoding patterns on a larger scale were simulated by empirically testing on the commonly used cox2-3 spacer. The phylogeny of these rhodophytes was also briefly described. In this study, the cox2 marker which satisfies the prerequisites of DNA barcodes was found to exhibit moderately high interspecific divergences with no intraspecific variations, thus a promising marker for the DNA barcoding of Kappaphycus and Eucheuma. However, the already extensively used cox2-3 spacer was deemed to be in overall more appropriate as a DNA barcode for these two genera. On a wider scale, cox1 and rbcL were still better DNA barcodes across the rhodophyte taxa when practicality and cost-efficiency were taken into account. The phylogeny of Kappaphycus and Eucheuma were generally similar to those earlier reported. Still, the application of DNA barcoding has demonstrated our relatively poor taxonomic comprehension of these seaweeds, thus suggesting more in-depth efforts in taxonomic restructuring as well as establishment.
    Matched MeSH terms: Phylogeny
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