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  1. First Report of Plumeria spp. Rust Caused by Coleosporium plumeriae in Louisiana and Malaysia and Catheranthus roseus, a New Host of this Rust
    Holcomb GE, Aime MC
    Plant Dis, 2010 Feb;94(2):272.
    PMID: 30754293 DOI: 10.1094/PDIS-94-2-0272C
    Plumeria spp., native to tropical America, are popular small trees grown widely in tropical areas of the world and as potted plants elsewhere. P. rubra and P. obtusa cultivars and hybrids are most common. A rust disease of a Plumeria sp. (likely P. rubra based on pointed leaf tips, leaves more than 18 cm (7 inches) long, and high rust susceptibility) was observed in November 2008 and again in June 2009 on homeowner plants in Baton Rouge, LA. A survey of five Baton Rouge retail nurseries in September 2009 revealed that 87% (90 of 103) of the plumeria plants were heavily infected with rust. Early symptoms included numerous 1-mm chlorotic spots on adaxial leaf surfaces followed by leaf chlorosis, necrosis, and abscission. Uredinia were numerous, mostly hypophyllous and yellowish orange. Urediniospores were catenulate, orange en masse, verrucose, globose, ovoid, ellipsoidal or angular, and measured 21.8 to 41.9 × 16.4 to 32.8 μm (average 29.4 × 22.6 μm). The rust was identified as Coleosporium plumeriae Pat. (= C. plumierae) (3). Teliospores were not found during this study. Pathogenicity tests were performed by spraying urediniospores (20,000/ml of deionized water) on three healthy Thai hybrid plumeria plants. Five leaves of each plant were misted with water and covered with plastic bags and three to five leaves were inoculated. Plants were held at 27°C for 27 h in a dew chamber and then moved outdoors. Typical rust symptoms and uredinia with urediniospores developed in 10 days on all inoculated leaves while noninoculated leaves remained healthy. Characteristics and spore measurements matched those of the rust from original infected plants. Additional plumeria rust inoculations were made to other Apocynaceae family members that included Allamanda cathartica, Catheranthus roseus (Madagascar periwinkle), Mandevilla splendens, Nerium oleander, and Vinca major. Catheranthus roseus was very susceptible to C. plumeriae with chlorotic leaf spots developing on the six inoculated plants after 8 days and uredinia with urediniospores appearing after 11 days. None of the other plant genera were susceptible to the rust. Plumeria rust was also observed on plumeria trees in urban landscapes in peninsular (Penang) and Bornean (Kota Kinabalu, Sabah) Malaysia in December 2007. To confirm identity, ~1,000 bp of nuclear rDNA 28S subunit from each (Lousiana, Penang, and Kota Kinabalu) was sequenced with rust-specific primers (1) and shared 100% identity (GenBank No. GU145555-6). Plumeria rust was first found on the island of Guadeloupe (3) and then spread to Central and South America. It has been known from Florida since 1960 under the synonym C. domingense (2), but has not been reported elsewhere in the continental United States. In more recent years, plumeria rust has spread to Hawaii, many Pacific islands, India, China, Taiwan, Thailand, Australia, and Nigeria (4). To our knowledge, this is the first report of plumeria rust from Louisiana and Malaysia and of susceptibility of another member of the Apocynaceae, Madagascar periwinkle, to C. plumeriae. Voucher material from Louisiana and Malaysia has been deposited in the Mycology Herbarium of Louisiana State University (LSUM). References: (1) M. C. Aime. Mycoscience 47:112, 2006. (2) Anonymous. Index of Plant Diseases in the United States. U.S. Dept. Agric. Handb. No. 165. Washington, D.C., 1960. (3) N. Patouillard. Bull. Soc. Mycol. Fr. 18:171, 1902. (4) C. To-Anun et al. Nat. Hist. J. Chulalongkorn Univ. 4:41, 2004.
    Matched MeSH terms: DNA, Ribosomal
  2. Fulltext Sequence-Specific Detection of Aristolochia DNA - A Simple Test for Contamination of Herbal Products
    Sgamma T, Masiero E, Mali P, Mahat M, Slater A
    Front Plant Sci, 2018;9:1828.
    PMID: 30619401 DOI: 10.3389/fpls.2018.01828
    Herbal medicines are used globally for their health benefits as an alternative therapy method to modern medicines. The market for herbal products has increased rapidly over the last few decades, but this has in turn increased the opportunities for malpractices such as contamination or substitution of products with alternative plant species. In the 1990s, a series of severe renal disease cases were reported in Belgium associated with weight loss treatment, in which the active species Stephania tetrandra was found to be substituted with Aristolochia fangchi. A. fangchi contains toxic aristolochic acids, which have been linked to kidney failure, as well as cancers of the urinary tract. Because of these known toxicities, herbal medicines containing these compounds, or potentially contaminated by these plants, have been restricted or banned in some countries, but they are still available via the internet and in alternate formulations. In this study, a DNA based method based on quantitative real-time PCR (qPCR) was tested to detect and distinguish Aristolochia subg. Siphisia (Duch.) O.C.Schmidt species from a range of medicinal plants that could potentially be contaminated with Aristolochia material. Specific primers were designed to confirm that Aristolochia subg. Siphisia can be detected, even in small amounts, if it is present in the products, fulfilling the aim of offering a simple, cheaper and faster solution than the chemical methods. A synthetic gBlock template containing the primer sequences was used as a reference standard to calibrate the qPCR assay and to estimate the copy number of a target gene per sample. Generic primers covering the conserved 5.8S rRNA coding region were used as internal control to verify DNA quality and also as a reference gene for relative quantitation. To cope with potentially degraded DNA, all qPCR primer sets were designed to generate PCR products of under 100 bp allowing detection and quantification of A. fangchi gBlock even when mixed with S. tetrandra gBlock in different ratios. All proportions of Aristolochia, from 100 to 2%, were detected. Using standards, associating the copy number to each start quantity, the detection limit was calculated and set to about 50 copies.
    Matched MeSH terms: DNA
  3. Fulltext Different Concentrations of Doxycycline in Swine Manure Affect the Microbiome and Degradation of Doxycycline Residue in Soil
    Yan Q, Li X, Ma B, Zou Y, Wang Y, Liao X, et al.
    Front Microbiol, 2018;9:3129.
    PMID: 30619199 DOI: 10.3389/fmicb.2018.03129
    Antibiotic residues that enter the soil through swine manure could disturb the number, community structure and functions of microbiota which could also degrade antibiotics in soil. Five different concentrations of doxycycline (DOX) incorporated into swine manure were added to soil to explore the effects of DOX on microbiota in soil and degradation itself. The results showed that the soil microbiome evolved an adaptation to the soil containing DOX by generating resistance genes. Moreover, some of the organisms within the soil microbiome played crucial roles in the degradation of DOX. The average degradation half-life of DOX in non-sterile groups was 13.85 ± 0.45 days, which was significantly shorter than the 29.26 ± 0.98 days in the group with sterilized soil (P < 0.01), indicating that the soil microbiome promoted DOX degradation. DOX addition affected the number of tetracycline resistance genes, depending on the type of gene and the DOX concentration. Among these genes, tetA, tetM, tetW, and tetX had significantly higher copy numbers when the concentration of DOX was higher. In contrast, a lower concentration of DOX had an inhibitory effect on tetG. At the same time, the microbial compositions were affected by the initial concentration of DOX and the different experimental periods. The soil chemical indicators also affected the microbial diversity changes, mainly because some microorganisms could survive in adversity and become dominant bacterial groups, such as the genera Vagococcus and Enterococcus (which were associated with electrical conductivity) and Caldicoprobacter spp. (which were positively correlated with pH). Our study mainly revealed soil microbiota and DOX degradation answered differently under variable concentrations of DOX mixed with swine manure in soil.
    Matched MeSH terms: DNA Copy Number Variations
  4. Fulltext Within-population genetic diversity and population structure of Plasmodium knowlesi merozoite surface protein 1 gene from geographically distinct regions of Malaysia and Thailand
    Ahmed MA, Chu KB, Vythilingam I, Quan FS
    Malar J, 2018 Nov 29;17(1):442.
    PMID: 30497496 DOI: 10.1186/s12936-018-2583-z
    BACKGROUND: The C-terminal 42 kDa domain of Plasmodium knowlesi merozoite surface protein 1 (PkMSP1) is a potential asexual blood-stage vaccine candidate, however, only a limited number of clinical isolates have been analysed from Malaysia and no inter-country comparative diversity study has been conducted. In the present study, nucleotide diversity, haplotypes and natural selection levels of pkmsp1 in clinical samples from geographically distinct regions of Malaysia and Thailand were investigated. The overall population structure of the parasite from the region was determined.

    METHODS: Eleven full-length pkmsp1 sequences obtained from clinical isolates of Malaysia along with the H-strain were downloaded from the database for domain wise characterization of pkmsp1 gene. Additionally, 76 pkmsp-142 sequences from Thailand and Malaysia were downloaded from the database for intra and inter-population analysis. DnaSP 5.10 and MEGA 5.0 software were used to determine genetic diversity, polymorphism, haplotypes and natural selection. Genealogical relationships were determined using haplotype network tree in NETWORK software v5.0. Population genetic differentiation index (FST) of parasites were analysed using Arlequin v3.5.

    RESULTS: Sequence analysis of 11 full-length pkmsp1 sequences along with the H-strain identified 477 (8.4%) polymorphic sites, of which 107 were singleton sites. The overall diversity observed in the full-length genes were high in comparison to its ortholog pvmsp1 and the 4 variable domains showed extensive size variations. The nucleotide diversity was low towards the pkmsp1-42 compared to the conserved domains. The 19 kDa domain was less diverse and completely conserved among isolates from Malaysian Borneo. The nucleotide diversity of isolates from Peninsular Malaysia and Thailand were higher than Malaysian Borneo. Network analysis of pkmsp1-42 haplotypes showed geographical clustering of the isolates from Malaysian Borneo and grouping of isolates from Peninsular Malaysia and Thailand. Population differentiation analysis indicated high FST values between parasite populations originating from Malaysian Borneo, Peninsular Malaysia and Thailand attributing to geographical distance. Moderate genetic differentiation was observed for parasite populations from Thailand and Peninsular Malaysia. Evidence of population expansion and purifying selection were observed in all conserved domains with strongest selection within the pkmsp1-42 domain.

    CONCLUSIONS: This study is the first to report on inter country genetic diversity and population structure of P. knowlesi based on msp1. Strong evidence of negative selection was observed in the 42 kDa domain, indicating functional constrains. Geographical clustering of P. knowlesi and moderate to high genetic differentiation values between populations identified in this study highlights the importance of further evaluation using larger number of clinical samples from Southeast Asian countries.

    Matched MeSH terms: Sequence Analysis, DNA
  5. First Report of Ralstonia solanacearum Race 2 Biovar 1 Causing Moko Disease of Banana in Malaysia
    Zulperi D, Sijam K
    Plant Dis, 2014 Feb;98(2):275.
    PMID: 30708756 DOI: 10.1094/PDIS-03-13-0321-PDN
    During March 2011 to June 2012, 50 banana plants of cultivar Musa × paradisiaca 'Horn' with Moko disease symptoms were randomly sampled in 12 different locations of 5 outbreak states in Peninsular Malaysia comprising Kedah, Selangor, Pahang, Negeri Sembilan, and Johor, with disease incidence exceeding 90% in some severely affected plantations. The disease symptoms observed in the infected plants included yellowing and wilting of the oldest leaves, which became necrotic, and eventually led to their dieback or collapse. The pulp of banana fruits also became discolored and exuded bacterial ooze. Vascular tissues in pseudostems were discolored. Fragments from symptomatic plant samples were excised and cultured on Kelman's-tetrazolium salt (TZC) medium. Twenty positive samples produced fluidal colonies that were either entirely white or white with pink centers after incubation for 24 to 48 h at 28°C on Kelman's-TZC medium and appeared as gram-negative rods after Gram staining. They were also positive for potassium hydroxide (KOH), Kovacs oxidase, and catalase tests, but negative for utilization of disaccharides and hexose alcohols, which are characteristics of biovar 1 Ralstonia solanacearum. For the pathogenicity test, 30 μl of 108 CFU/ml bacterial suspension of three selected virulent strains were injected into banana (Musa × paradisiaca 'Horn') leaves explants grown in plastic pots of 1,440 cm3 volume in a greenhouse, with temperature range from 26 to 35°C. Leaves that were infiltrated with sterile distilled water served as a negative control. Inoculations with all isolates were performed in three replications, as well as the uninoculated control leaves explants. The inoculated plants produced the same symptoms as observed on naturally diseased samples, whereas control plants remained asymptomatic. Strain cultures were re-isolated and possessed the morphological and biochemical characteristics as previously described. PCR amplification using race 2 R. solanacearum primers ISRso19-F (5'-TGGGAGAGGATGGCGGCTTT-3') and ISRso19-R (5'-TGACCCGCCTTTCGGTGTTT-3') (3) produced a 1,900-bp product from DNA of all bacterial strains. BLAST searches resulted that the sequences were 95 to 98% identical to published R. solanacearum strain race 2 insertion sequence ISRso19 (GenBank Accession No. AF450275). These genes were later deposited in GenBank (KC812051, KC812052, and KC812053). Phylotype-specific multiplex PCR (Pmx-PCR) and Musa-specific multiplex PCR (Mmx-PCR) were performed to identify the phylotype and sequevar of all isolates (4). Pmx-PCR showed that all isolates belonged to phylotype II, whereas Mmx-PCR showed that they belonged to phylotype II sequevar 4 displaying 351-bp amplicon. Although there were previously extensive studies on R. solanacearum associated with bacterial wilt disease of banana crops in Malaysia, none related to Moko disease has been reported (1,2). The result has a great importance to better understand and document R. solanacearum race 2 biovar 1, since banana has been identified as the second most important commercial fruit crop with a high economic value in Malaysia. References: (1) R. Khakvar et al. Plant Pathol. J. 7:162, 2008. (2) R. Khakvar et al. Am. J. Agri. Biol. Sci. 3:490, 2008. (3) Y. A. Lee and C. N. Khor. Plant Pathol. Bull. 12:57, 2003. (4) P. Prior et al. Pages 405-414 in: Bacterial Wilt Disease and the Ralstonia solanacearum Species Complex. The American Phytopathological Society, St. Paul, MN, 2005.
    Matched MeSH terms: DNA Transposable Elements
  6. Fulltext Hepatitis C infection and detection of antibodies, RNA and genotypes among female healthcare workers in Baghdad
    Waqar, A.K., Nik Shamsidah N.I., Nor Aini M.N., Waqar, Abd Alqahar Al –Kubaisy
    JUMMEC, 2018;21(1):14-20.
    MyJurnal
    Background: Hepatitis C Virus (HCV) is a major public health problem worldwide. About 130- 200 million people
    are infected with HCV worldwide leading to 500,000 deaths annually (WHO 2014). Healthcare workers (HCWs)
    have played an important role in the transmission of HCV infection, either as victims or as sources of infection.
    Objectives: To determine the prevalence of HCV, antibodies (Abs) RNA and genotypes among the female HCWs
    in Baghdad and to identify whether HCWs were infective or only infected.
    Subjects and Methods: A cross-sectional study involving 1001 women attending 17 health care centres in
    Baghdad, Iraq, was carried out. Information on type and duration of their occupation was obtained. HCV Abs
    (anti-HCV) were tested using a third generation enzyme immunoassay (EIA-3) and immunoblot assay (Lia
    Tek-111). Molecular analysis using RT-PCR and DNA enzyme immunoassay (DEIA) for HCV-RNA and genotype
    detections were carried out for 63 serum samples.
    Results: Only 160/1001 (15.98%) were HCWs. Anti-HCV and HCV- RNA seroprevalence were significantly higher
    (6.37%, p=0.0057, 88.83%, p= 0.011 respectively) among HCWs than non HCWs. HCWs were at a significantly
    higher risk of exposure to HCV infection (OR=2.75, 95% C.I. =1.31-5.79). There was no significant association
    between HCV genotypes and the HCWs. HCV-4 showed higher expression (62.5%) among HCWs.
    Conclusion: Female HCWs were infective and infected with HCV, thus there is a need for medical equipment
    to be sterilized and cleaned thoroughly.
    Matched MeSH terms: DNA
  7. Is Malaysia's banded langur, Presbytis femoralis femoralis, actually Presbytis neglectus neglectus? Taxonomic revision with new insights on the radiation history of the Presbytis species group in Southeast Asia
    Abdul-Latiff MAB, Baharuddin H, Abdul-Patah P, Md-Zain BM
    Primates, 2019 Jan;60(1):63-79.
    PMID: 30471014 DOI: 10.1007/s10329-018-0699-y
    The disjunct distribution of Presbytis femoralis subspecies across Sumatra (P. f. percura), southern (P. f. femoralis) and northern (P. f. robinsoni) Peninsular Malaysia marks the unique vicariance events in the Sunda Shelf. However, the taxonomic positions and evolutionary history of P. f. femoralis are unresolved after decades of research. To elucidate this evolutionary history, we analyzed 501 base pairs of the mitochondrial HVSI gene from 25 individuals representing Malaysia's banded langur, with the addition of 29 sequences of Asian Presbytis from Genbank. Our results revealed closer affinity of P. f. femoralis to P. m. mitrata and P. m. sumatrana while maintaining the monophyletic state of P. f. femoralis as compared to P. f. robinsoni. Two central theses were inferred from the results; (1) P. f. femoralis does not belong in the same species classification as P. f. robinsoni, and (2) P. f. femoralis is the basal lineage of the Presbytis in Peninsular Malaysia. Proving the first hypothesis through genetic analysis, we reassigned P. f. femoralis of Malaysia to Presbytis neglectus (Schlegel's banded langur) (Schlegel in Revue Methodique, Museum d'Histoire Naturelle des Pays-Bas 7:1, 1876) following the International Code of Zoological Nomenclature (article 23.3). The ancestors of P. neglectus are hypothesized to have reached southern Peninsular Malaysia during the Pleistocene and survived in refugium along the western coast. Consequently, they radiated upward, forming P. f. robinsoni and P. siamensis resulting in the highly allopatric distribution in Peninsular Malaysia. This study has successfully resolved the taxonomic position of P. neglectus in Peninsular Malaysia while providing an alternative biogeographic theory for the Asian Presbytis.
    Matched MeSH terms: Sequence Analysis, DNA
  8. Fulltext Determination of genetic aberrations and novel transcripts involved in the pathogenesis of oligodendroglioma using array comparative genomic hybridization and next generation sequencing
    Hassanudin SA, Ponnampalam SN, Amini MN
    Oncol Lett, 2019 Feb;17(2):1675-1687.
    PMID: 30675227 DOI: 10.3892/ol.2018.9811
    The aim of the present study was to determine the genetic aberrations and novel transcripts, particularly the fusion transcripts, involved in the pathogenesis of low-grade and anaplastic oligodendroglioma. In the present study, tissue samples were obtained from patients with oligodendroglioma and additionally from archived tissue samples from the Brain Tumor Tissue Bank of the Brain Tumor Foundation of Canada. Six samples were obtained, three of which were low-grade oligodendroglioma and the other three anaplastic oligodendroglioma. DNA and RNA were extracted from each tissue sample. The resulting genomic DNA was then hybridized using the Agilent CytoSure 4×180K oligonucleotide array. Human reference DNA and samples were labeled using Cy3 cytidine 5'-triphosphate (CTP) and Cy5 CTP, respectively, while human Cot-1 DNA was used to reduce non-specific binding. Microarray-based comparative genomic hybridization data was then analyzed for genetic aberrations using the Agilent Cytosure Interpret software v3.4.2. The total RNA isolated from each sample was mixed with oligo dT magnetic beads to enrich for poly(A) mRNA. cDNAs were then synthesized and subjected to end-repair, poly(A) addition and connected using sequencing adapters using the Illumina TruSeq RNA Sample Preparation kit. The fragments were then purified and selected as templates for polymerase chain reaction amplification. The final library was constructed with fragments between 350-450 base pairs and sequenced using deep transcriptome sequencing on an Illumina HiSeq 2500 sequencer. The array comparative genomic hybridization revealed numerous amplifications and deletions on several chromosomes in all samples. However, the most interesting result was from the next generation sequencing, where one anaplastic oligodendroglioma sample was demonstrated to have five novel fusion genes that may potentially serve a critical role in tumor pathogenesis and progression.
    Matched MeSH terms: DNA, Complementary
  9. Phylogenetic analysis of respiratory syncytial virus identified at Universiti Kebangsaan Malaysia Medical Centre
    Rahman M, Wong K, Ishak I, Rashid Z, Alfizah H
    Sains Malaysiana, 2014;43:739-744.
    Human respiratory syncytial virus (RSV) is an important cause of acute respiratory tract infection in infants and young children. Phylogenetic analysis for RSV in Malaysia has not been reported before. We investigated the genetic features of RSV in respiratory specimens from March to August 2011 with molecular methods. From a total of 130 throat swab and nasopharyngeal aspirate specimens, 54 (41.5%) were positive with RSV, identified by in-house real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay. Thirty-four out of 54 (63.0%) RSV positive patients were children below two years old and two (1.4%) were adults. Phylogenetic analysis showed 39 isolates were genotype GA5, 13 genotypes GA2, one genotype GA1 and one genotype GA7. The findings indicated four genotypes of RSV circulating in the country and the predominant genotype is GA5.
    Matched MeSH terms: RNA-Directed DNA Polymerase
  10. Fulltext Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis
    Xia W, Luo T, Zhang W, Mason AS, Huang D, Huang X, et al.
    Front Plant Sci, 2019;10:130.
    PMID: 30809240 DOI: 10.3389/fpls.2019.00130
    High-density single nucleotide polymorphisms (SNPs) are used as highly favored makers to analyze genetic diversity and population structure, to construct high-density genetic maps and provide genotypes for genome-wide association analysis. In order to develop genome-wide SNP markers in oil palm (Elaeis guineensis), single locus amplified fragment sequencing (SLAF-seq) technology was performed in a diversity panel of 200 oil palm individuals and 1,261,501 SNPs were identified with minor allele frequency > 0.05 and integrity > 1. Among them, only 17.81% can be mapped within the genic region and the remaining was located into the intergenic region. A positive correlation was detected between the distribution of SNP markers and retrotransposons [transposable elements (TEs)]. Population structure analysis showed that the 200 individuals of oil palm can be divided into five subgroups based on cross-validation errors. However, the subpopulations divided for the 200 oil palm individuals based on the SNP markers were not accurately related to their geographical origins and 80 oil palm individuals from Malaysia showed highest genetic diversity. In addition, the physical distance of linkage disequilibrium (LD) decay in the analyzed oil palm population was 14.516 kb when r2 = 0.1. The LD decay distances for different chromosomes varied from 3.324 (chromosome 15) to 19.983 kb (chromosome 7). Our research provides genome-wide SNPs for future targeted breeding in palm oil.
    Matched MeSH terms: DNA, Intergenic
  11. Identification of male-specific SNP markers and development of PCR-based genetic sex identification technique in crucifix crab (Charybdis feriatus) with implication of an XX/XY sex determination system
    Fang S, Zhang Y, Shi X, Zheng H, Li S, Zhang Y, et al.
    Genomics, 2020 01;112(1):404-411.
    PMID: 30851358 DOI: 10.1016/j.ygeno.2019.03.003
    In this study, we first identified male-specific SNP markers using restriction site-associated DNA sequencing, and further developed a PCR-based sex identification technique for Charybdis feriatus. A total of 296.96 million clean reads were obtained, with 114.95 and 182.01 million from females and males. After assembly and alignment, 10 SNP markers were identified being heterozygous in males but homozygous in females. Five markers were further confirmed to be male-specific in a large number of individuals. Moreover, two male-specific sense primers and a common antisense primer were designed, using which, a PCR-based genetic sex identification method was successfully developed and used to identify the sex of 103 individuals, with a result of 49 females and 54 males. The presence of male-specific SNP markers suggests an XX/XY sex determination system for C. feriatus. These findings should be helpful for better understanding sex determination mechanism, and drafting artificial breeding program in crustaceans.
    Matched MeSH terms: Sequence Analysis, DNA
  12. Two Groups of Phytoplasmas from Japan Distinguished on the Basis of Amplification and Restriction Analysis of 16S rDNA
    Okuda S, Prince JP, Davis RE, Dally EL, Lee IM, Mogen B, et al.
    Plant Dis, 1997 Mar;81(3):301-305.
    PMID: 30861775 DOI: 10.1094/PDIS.1997.81.3.301
    Phytoplasmas (mycoplasmalike organisms, MLOs) associated with mitsuba (Japanese hone-wort) witches'-broom (JHW), garland chrysanthemum witches'-broom (GCW), eggplant dwarf (ED), tomato yellows (TY), marguerite yellows (MY), gentian witches'-broom (GW), and tsu-wabuki witches'-broom (TW) in Japan were investigated by polymerase chain reaction (PCR) amplification of DNA and restriction enzyme analysis of PCR products. The phytoplasmas could be separated into two groups, one containing strains JHW, GCW, ED, TY, and MY, and the other containing strains GW and TW, corresponding to two groups previously recognized on the basis of transmission by Macrosteles striifrons and Scleroracus flavopictus, respectively. The strains transmitted by M. striifrons were classified in 16S rRNA gene group 16SrI, which contains aster yellows and related phytoplasma strains. Strains GW and TW were classified in group 16SrIII, which contains phytoplasmas associated with peach X-disease, clover yellow edge, and related phytoplasmas. Digestion of amplified 16S rDNA with HpaII indicated that strains GW and TW were affiliated with subgroup 16SrIII-B, which contains clover yellow edge phytoplasma. All seven strains were distinguished from other phytoplasmas, including those associated with clover proliferation, ash yellows, elm yellows, and beet leafhopper-transmitted virescence in North America, and Malaysian periwinkle yellows and sweet potato witches'-broom in Asia.
    Matched MeSH terms: DNA, Ribosomal
  13. QTL Mapping for Red Blotches in Malaysia Red Tilapia (Oreochromis spp.)
    Li BJ, Zhu ZX, Gu XH, Lin HR, Xia JH
    Mar Biotechnol (NY), 2019 Jun;21(3):384-395.
    PMID: 30863905 DOI: 10.1007/s10126-019-09888-9
    Body color is an interesting economic trait in fish. Red tilapia with red blotches may decrease its commercial values. Conventional selection of pure red color lines is a time-consuming and labor-intensive process. To accelerate selection of pure lines through marker-assisted selection, in this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) technology was applied to genotype a full-sib mapping family of Malaysia red tilapia (Oreochromis spp.) (N = 192). Genome-wide significant quantitative trait locus (QTL)-controlling red blotches were mapped onto two chromosomes (chrLG5 and chrLG15) explaining 9.7% and 8.2% of phenotypic variances by a genome-wide association study (GWAS) and linkage-based QTL mapping. Six SNPs from the chromosome chrLG5 (four), chrLG15 (one), and unplaced supercontig GL831288-1 (one) were significantly associated to the red blotch trait in GWAS analysis. We developed nine microsatellite markers and validated significant correlations between genotypes and blotch data (p 
    Matched MeSH terms: Sequence Analysis, DNA
  14. The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses
    Mohd-Assaad N, McDonald BA, Croll D
    Environ Microbiol, 2019 08;21(8):2677-2695.
    PMID: 30838748 DOI: 10.1111/1462-2920.14583
    Plant pathogens secrete effector proteins to manipulate the host and facilitate infection. Cognate hosts trigger strong defence responses upon detection of these effectors. Consequently, pathogens and hosts undergo rapid coevolutionary arms races driven by adaptive evolution of effectors and receptors. Because of their high rate of turnover, most effectors are thought to be species-specific and the evolutionary trajectories are poorly understood. Here, we investigate the necrosis-inducing protein 1 (NIP1) effector in the multihost pathogen genus Rhynchosporium. We retraced the evolutionary history of the NIP1 locus using whole-genome assemblies of 146 strains covering four closely related species. NIP1 orthologues were present in all species but the locus consistently segregated presence-absence polymorphisms suggesting long-term balancing selection. We also identified previously unknown paralogues of NIP1 that were shared among multiple species and showed substantial copy-number variation within R. commune. The NIP1A paralogue was under significant positive selection suggesting that NIP1A is the dominant effector variant coevolving with host immune receptors. Consistent with this prediction, we found that copy number variation at NIP1A had a stronger effect on virulence than NIP1B. Our analyses unravelled the origins and diversification mechanisms of a pathogen effector family shedding light on how pathogens gain adaptive genetic variation.
    Matched MeSH terms: DNA Copy Number Variations
  15. Annatto ( Bixa orellana ) δ-TCT supplementation protected against embryonic DNA damages through alterations in PI3K/ Akt-Cyclin D1 pathway
    Mutalip SSM, Rajikin MH, Rahim SA, Khan NMN
    Int J Vitam Nutr Res, 2018 Feb;88(1-2):16-26.
    PMID: 30907699 DOI: 10.1024/0300-9831/a000492
    Protective action by annatto-derived delta-tocotrienol (δ-TCT) and soy-derived alpha-tocopherol (α-TOC) through the regulation of PI3K/Akt-Cyclin D1 pathway against the nicotine-induced DNA damages is the focus of the present study. Nicotine, which has been widely reported to have numerous adverse effects on the reproductive system, was used as reproductive toxicant. 48 female balb/c mice (6-8 weeks) (23-25 g) were randomly divided into 8 groups (G1-G8; n = 6) and treated with either nicotine or/and annatto δ-TCT/soy α-TOC for 7 consecutive days. On Day 8, the females were superovulated and mated before euthanized for embryo collection (46 hours post-coitum). Fifty 2-cell embryos from each group were used in gene expression analysis using Affymetrix QuantiGene Plex2.0 assay. Findings indicated that nicotine (G2) significantly decreased (p < 0.05) the number of produced 2-cell embryos compared to control (G1). Intervention with mixed annatto δ-TCT (G3) and pure annatto δ-TCT (G4) significantly increased the number of produced 2-cell embryos by 127 % and 79 % respectively compared to G2, but these were lower than G1. Concurrent treatment with soy α-TOC (G5) decreased embryo production by 7 %. Supplementations with δ-TCT and α-TOC alone (G6-G8) significantly increased (p < 0.05) the number of produced 2-cell embryos by 50 %, 36 % and 41 % respectively, compared to control (G1). These results were found to be associated with the alterations in the PI3K/Akt-Cyclin D1 gene expressions, indicating the inhibitory effects of annatto δ-TCT and soy α-TOC against the nicotinic embryonic damages. To our knowledge, this is the first attempt on studying the benefits of annatto δ-TCT on murine preimplantation 2-cell embryos.
    Matched MeSH terms: DNA Damage
  16. Protective Role of Natural Products in Cisplatin-Induced Nephrotoxicity
    Ridzuan NRA, Rashid NA, Othman F, Budin SB, Hussan F, Teoh SL
    Mini Rev Med Chem, 2019;19(14):1134-1143.
    PMID: 30894108 DOI: 10.2174/1389557519666190320124438
    Cisplatin is a widely used antineoplastic agent for the treatment of metastatic tumors, advanced bladder cancer and many other solid tumors. However, at higher doses, toxicities such as nephrotoxicity may appear. Cisplatin leads to DNA damage and subsequently renal cell death. Besides that, oxidative stress is also implicated as one of the main causes of nephrotoxicity. Several studies showed that numerous natural products: ginseng, curcumin, licorice, honey and pomegranate were able to reduce the oxidative stress by restoring the levels of antioxidant enzymes and also at the same time act as an anti-inflammatory agent. Furthermore, pre-treatment with vitamin supplementation, such as vitamin C, E and riboflavin markedly decreased serum urea and increased the levels of antioxidant enzymes in the kidney even after cisplatin induction in cancer patients. These natural products possess potent antioxidant and anti-inflammatory medicinal properties, and they can be safely used as a supplementary regime or combination therapy against cisplatin-induced nephrotoxicity. The present review focused on the protective role of a few natural products which is widely used in folk medicines in cisplatin-induced nephrotoxicity.
    Matched MeSH terms: DNA Damage
  17. Fulltext Plasmodium knowlesi clinical isolates from Malaysia show extensive diversity and strong differential selection pressure at the merozoite surface protein 7D (MSP7D)
    Ahmed MA, Quan FS
    Malar J, 2019 Apr 29;18(1):150.
    PMID: 31035999 DOI: 10.1186/s12936-019-2782-2
    BACKGROUND: The high proportion of human cases due to the simian malaria parasite Plasmodium knowlesi in Malaysia is a cause of concern, as they can be severe and even fatal. Merozoite surface protein 7 (MSP7) is a multigene family which forms a non-covalent complex with MSP-1 prior to receptor-ligand recognition in Plasmodium falciparum and thus an important antigen for vaccine development. However, no study has been done in any of the ortholog family members in P. knowlesi from clinical samples. This study investigates the level of polymorphism, haplotypes, and natural selection acting at the pkmsp-7D gene in clinical samples from Malaysia.

    METHODS: Thirty-six full-length pkmsp7D gene sequences (along with the reference H-strain: PKNH_1266000) obtained from clinical isolates of Malaysia, which were orthologous to pvmsp7H (PVX_082680) were downloaded from public databases. Population genetic, evolutionary and phylogenetic analyses were performed to determine the level of genetic diversity, polymorphism, recombination and natural selection.

    RESULTS: Analysis of 36 full-length pkmsp7D sequences identified 147 SNPs (91 non-synonymous and 56 synonymous substitutions). Nucleotide diversity across the full-length gene was higher than its ortholog in Plasmodium vivax (msp7H). Region-wise analysis of the gene indicated that the nucleotide diversity at the central region was very high (π = 0.14) compared to the 5' and 3' regions. Most hyper-variable SNPs were detected at the central domain. Multiple test for natural selection indicated the central region was under strong positive natural selection however, the 5' and 3' regions were under negative/purifying selection. Evidence of intragenic recombination were detected at the central region of the gene. Phylogenetic analysis using full-length msp7D genes indicated there was no geographical clustering of parasite population.

    CONCLUSIONS: High genetic diversity with hyper-variable SNPs and strong evidence of positive natural selection at the central region of MSP7D indicated exposure of the region to host immune pressure. Negative selection at the 5' and the 3' regions of MSP7D might be because of functional constraints at the unexposed regions during the merozoite invasion process of P. knowlesi. No evidence of geographical clustering among the clinical isolates from Malaysia indicated uniform selection pressure in all populations. These findings highlight the further evaluation of the regions and functional characterization of the protein as a potential blood stage vaccine candidate for P. knowlesi.

    Matched MeSH terms: Sequence Analysis, DNA
  18. Two types of triplicated alpha-globin loci in humans
    Lie-Injo LE, Herrera AR, Kan YW
    Nucleic Acids Res, 1981 Aug 11;9(15):3707-17.
    PMID: 6269090
    DNA from healthy Malaysian newborns was studied on gene maps after digestion with different restriction endonucleases. Of 65 newborns, two were found to be carriers of two different variants of triplicated alpha-globin loci. In variant no. 1, found in an Malay, the three alpha-globin genes are in an elongated DNA fragment on digestion with Eco RI and Bam HI. The third alpha-globin gene was found in a additional 3.7-kb fragment on digestion with Hpa I, Bgl II and Hind III. In variant no. 2, a new type of triplicated alpha-globin loci, found in a Chinese, the three alpha-globin genes reside in an elongated DNA fragment longer than that of variant no. 1 on digestion with Eco RI and Bam HI. The third alpha-globin gene was found in an additional 4.2-kb fragment on digestion with Hpa I and Hind III. Digestion of this variant DNA with Bg1 II produced an abnormal 16.7-kb fragment in addition to the normal 7.0-kb Bgl-II fragment. The locations of the restriction sites in the two types of triplicated alpha-globin loci are compatible with a mechanism of unequal crossing over following two different modes of misalignment.
    Matched MeSH terms: DNA Restriction Enzymes
  19. Fulltext Cytostatic and Antiproliferative Activities of F5 Fraction of Crinum amabile Leaf Chloroform Extract Showed Its Potential as Cancer Chemotherapeutic Agent
    Lim CP, Yam MF, Asmawi MZ, Chin VK, Khairuddin NH, Yong YK, et al.
    Evid Based Complement Alternat Med, 2019;2019:7521504.
    PMID: 31097973 DOI: 10.1155/2019/7521504
    Medicinal plants have been considered as promising sources of drugs in treating various cancers. Crinum amabile (C. amabile), a plant species from the Amaryllidaceae family, is claimed to be a potential source for cancer chemotherapeutic compounds. Here, we aimed to investigate the potential of C. amabile as an anticancer agent. Dried leaves of C. amabile were serially extracted and our findings showed that chloroform extract (CE) was shown to exhibit cytotoxic effect against all cancer cell lines used. This active extract was further fractionated in which F5 fraction was shown to possess the highest cytotoxicity among all fractions. F5 fraction was then tested in-depth through Annexin V/FITC apoptosis and DNA fragmentation assays to determine its apoptotic effect on MCF-7 cells. Results revealed that F5 fraction only showed induction of cell apoptosis starting at 72-hour treatment while DNA fragmentation was not detected at any of the concentrations and treatment periods tested. Meanwhile, cell proliferation assay revealed that F5 fraction was able to inhibit normal cell proliferation as well as VEGF-induced cell proliferation of normal endothelial cell (HUVECs). In conclusion, F5 fraction from C. amabile leaf CE was able to exhibit cytostatic effect through antiproliferation activity rather than induction of cell apoptosis and therefore has the potential to be further investigated as an anticancer agent.
    Matched MeSH terms: DNA Fragmentation
  20. Fulltext Cytogenetic analysis of buccal cells from farmers in Tanjung Karang and Kelantan who were exposed to pesticides
    Ahmad Rohi Ghazali, Maziani Abdullah, Asmah Hamid, Asmariah Ahmad, Tava Shelan Nagapan, Ismarulyusda Ishak, et al.
    Jurnal Sains Kesihatan Malaysia, 2018;16(101):1-8.
    MyJurnal
    Pesticides and chemical fertilizers are widely used in agriculture to increase crop productivity among farmers. However, exposure to pesticides will give potential risk to human health. The aim of this study was to analyze the frequency of micronucleus (MN) and binucleus (BNu) formation in buccal cells from farmers who were exposed to pesticides using the MN assay. Buccal swabs were collected from the farmers in Tanjung Karang (n = 32) and Kelantan (n = 43) using wooden tongue depressor. A structured questionnaire was used to obtain demographic data of the farmers. Cytogenetic analysis was carried out by Acridin Orange (AO) staining 0.0025% (w/v). The frequency of MN and BNu as the biomarkers for cytogenetic damage was observed by using a fluorescence microscope. Comparison of frequency of MN and BNu is conducted in two areas namely Tanjung Karang, Selangor and Kelantan because of the agricultural activity and the type of pesticides used are different. Results showed that the frequencies of both MN and BNu among farmers in Tanjung Karang were significantly higher (p < 0.05) compared to farmers in Kelantan. Meanwhile, for the socio-demographic factors (age, smoking status, working period), MN and BNu frequencies among farmers in Tanjung Karang were also significantly higher (p < 0.05) as compared to farmers in Kelantan. While in the aspect of pesticide exposure, the frequencies of MN and BNu showed no significant difference between the frequency of pesticide spraying (p > 0.05) and the practices of PPE (Personal Protective Equipment) (p > 0.05). This may suggests that cytogenetic changes were not influenced by these factors. In addition, correlation study shows positive correlation between the frequency of MN with the pesticide exposure of farmers in Tanjung Karang (p > 0.05, r = 0.015) and Kelantan (p > 0.05, r = 0.0158). Besides, the frequency of BNu also has a positive correlation with the pesticide exposure among farmers in Tanjung Karang (p > 0.05, r = 0.036) and farmers in Kelantan (p > 0.05, r = 0.013). Hence, this present study demonstrated that exposure to pesticides increased the formation of MN and BNu among farmers and the prolonged use of pesticides may induce genotoxicity and DNA damage to human
    Matched MeSH terms: DNA Damage
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