Displaying publications 1 - 20 of 855 in total

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  1. Naher L, Tan SG, Ho CL, Yusuf UK, Ahmad SH, Abdullah F
    ScientificWorldJournal, 2012;2012:647504.
    PMID: 22919345 DOI: 10.1100/2012/647504
    Basal stem rot (BSR) disease caused by the fungus Ganoderma boninense is the most serious disease affecting the oil palm; this is because the disease escapes the early disease detection. The biocontrol agent Trichoderma harzianum can protect the disease only at the early stage of the disease. In the present study, the expression levels of three oil palm (Elaeis guineensis Jacq.) chitinases encoding EgCHI1, EgCHI2, and EgCHI3 at 2, 5, and 8 weeks inoculation were measured in oil palm leaves from plants treated with G. boninense or T. harzianum alone or both.
    Matched MeSH terms: Base Sequence
  2. He C, Ding N, Li J, Li Y
    Wei Sheng Wu Xue Bao, 2002 Aug;42(4):436-41.
    PMID: 12557549
    A Chicken anemia virus has been isolated from a chicken flock in Harbin of China. The genome of the ivrus was cloned through polymerase chain reaction(PCR) and sequence of the genome was analyzed. The cycle genome is made of 2298 base pairs including three overlapping open reading frames(vp1, vp2, vp3) and a regulative region. Comparing sequence of the genome through BLAST in GenBank, this sequence exhibits 96.9% identity with other genome of CA Vs and least. Multiple alignment of this genome of this virus, 26p4, strain isolated in Germany, strain isolated in Malaysia and Cux-1 found that this sequence exhibits 98.2% (42/2298), 98.2% (42/2298), 96.9% (72/2298) and 97.5% (60/2319) identify with them, respectively. A new CAV strain was isolated and it has better identify with CAV isolated in Europe countries than is Asia country Malaysia. Multiple alignment of VP1, VP2, VP3 of 26p4, strain isolated in Germany, strain isolated in Malaysia, Cux-1 and strain isolated in Harbin of China found the VP2 the most conservative.
    Matched MeSH terms: Base Sequence
  3. Liu Z, Gopinath SCB, Wang Z, Li Y, Anbu P, Zhang W
    Mikrochim Acta, 2021 05 15;188(6):187.
    PMID: 33990848 DOI: 10.1007/s00604-021-04834-w
    A new zeolite-iron oxide nanocomposite (ZEO-IO) was extracted from waste fly ash of a thermal power plant and utilized for capturing aptamers used to quantify the myocardial infarction (MI) biomarker N-terminal prohormone B-type natriuretic peptide (NT-ProBNP); this was used in a probe with an integrated microelectrode sensor. High-resolution microscopy revealed that ZEO-IO displayed a clubbell structure and a particle size range of 100-200 nm. Energy-dispersive X-ray spectroscopy and X-ray photoelectron spectroscopy confirmed the presence of Si, Al, Fe, and O in the synthesized ZEO-IO. The limit of detection for NT-ProBNP was 1-2 pg/mL (0.1-0.2 pM) when the aptamer was sandwiched with antibody and showed the doubled current response even at a low NT-ProBNP abundance. A dose-dependent interaction was identified for this sandwich with a linear plot in the concentration range 1 to 32 pg/mL (0.1-3.2 pM) with a determination coefficient R2 = 0.9884; y = 0.8425x-0.5771. Without  sandwich, the detection limit was 2-4 pg/mL (0.2-0.4 pM) and the determination coefficient was R2 = 0.9854; y = 1.0996x-1.4729. Stability and nonfouling assays in the presence of bovine serum albumin, cardiac troponin I, and myoglobin revealed that the aptamer-modified surface is stable and specific for NT-Pro-BNP. Moreover, NT-ProBNP-spiked human serum exhibited selective detection. This new nanocomposite-modified surface helps in detecting NT-Pro-BNP and diagnosing MI at stages of low expression.
    Matched MeSH terms: Base Sequence
  4. Issa R, Seradja VH, Abdullah MK, Abdul H
    Genome Announc, 2016;4(3).
    PMID: 27340053 DOI: 10.1128/genomeA.00513-16
    This is a report of an annotated genome sequence of Mycobacterium tuberculosis MTBR1/09. The organism was isolated from a sputum sample from a male patient in Malaysia.
    Matched MeSH terms: Base Sequence
  5. Issa R, Seradja VH, Abdullah MK
    Genome Announc, 2016;4(3).
    PMID: 27365342 DOI: 10.1128/genomeA.00376-16
    Here, we report of the annotated genome sequence of Mycobacterium tuberculosis MTB221/11. The organism was isolated from the cerebrospinal fluid of a patient in Malaysia.
    Matched MeSH terms: Base Sequence
  6. Bashir A, Zunita Z, Jesse FFA, Ramanoon SZ
    Microbiol Resour Announc, 2019 Feb;8(6).
    PMID: 30746526 DOI: 10.1128/MRA.01618-18
    Streptococcus agalactiae, commonly known as group B streptococcus (GBS), is among the most implicated pathogens in bovine mastitis worldwide. Proper control measures can curb both economic and public health effects it may cause. Here, we report the sequenced genome of S. agalactiae sequence type 167 (ST167) strain 3966RFQB obtained from a bovine mastitis case at a dairy herd in Banting, Selangor, Malaysia (longitude 2.8121°N, latitude 101.5026°E).
    Matched MeSH terms: Base Sequence
  7. Chan KG, Yunos NY
    Genome Announc, 2016;4(2).
    PMID: 26941152 DOI: 10.1128/genomeA.00081-16
    Here, we report the draft genome sequence of Chromobacterium piscinae strain ND17. This bacterium was isolated from a fresh water sample in Malaysia and exhibits quorum-sensing activity. This first draft genome of C. piscinae strain ND17 will pave the way to future studies of the quorum-sensing properties of this isolate.
    Matched MeSH terms: Base Sequence
  8. Gan HM, Eng WWH, Barton MK, Adams LE, Samsudin NA, Bartl AJ, et al.
    Genome Announc, 2017 Aug 24;5(34).
    PMID: 28839032 DOI: 10.1128/genomeA.00857-17
    We report here the genome sequences of Salmonella enterica subsp. enterica serovar Typhimurium strains TT6675 and TT9097, which we utilize for genetic analyses of giant bacterial viruses. Our analyses identified several genetic variations between the two strains, most significantly confirming strain TT6675 as a serine suppressor and TT9097 as a nonsuppressor.
    Matched MeSH terms: Base Sequence
  9. Chan KG, Chong TM, Adrian TG, Kher HL, Hong KW, Grandclément C, et al.
    Genome Announc, 2015;3(6).
    PMID: 26659682 DOI: 10.1128/genomeA.01442-15
    Stenotrophomonas maltophilia ZBG7B was isolated from vineyard soil of Zellenberg, France. Here, we present the draft genome sequence of this bacterial strain, which has facilitated the prediction of function for several genes encoding biotechnologically important enzymes, such as xylosidase, xylanase, laccase, and chitinase.
    Matched MeSH terms: Base Sequence
  10. Chan XY, Chen JW, Adrian TG, Hong KW, Chang CY, Yin WF, et al.
    Genome Announc, 2017 Mar 30;5(13).
    PMID: 28360153 DOI: 10.1128/genomeA.00067-17
    Bacillus sp. is a Gram-positive bacterium that is commonly found in seawater. In this study, the genome of marine Bacillus sp. strain G3(2015) was sequenced using MiSeq. The fosfomycin resistant gene fosB was identified upon bacterial genome annotation.
    Matched MeSH terms: Base Sequence
  11. Zakaria Z, Othman N, Ismail A, Kamaluddin NR, Esa E, Abdul Rahman EJ, et al.
    Asian Pac J Cancer Prev, 2017 04 01;18(4):1169-1175.
    PMID: 28548470
    Background: ETV6/RUNX1 gene fusion is the most frequently seen chromosomal abnormality in childhood acute
    lymphobastic leukamia (ALL). However, additional genetic changes are known to be required for the development of
    this type of leukaemia. Therefore, we here aimed to assess the somatic mutational profile of four ALL cases carrying the
    ETV6/RUNX1 fusion gene using whole-exome sequencing. Methods: DNA was isolated from bone marrow samples
    using a QIAmp DNA Blood Mini kit and subsequently sequenced using the Illumina MiSeq system. Results: We
    identified 12,960 to17,601 mutations in each sample, with a total of 16,466 somatic mutations in total. Some 15,533
    variants were single nucleotide polymorphisms (SNPs), 129 were substitutions, 415 were insertions and 389 were
    deletions. When taking into account the coding region and protein impact, 1,875 variants were synonymous and 1,956
    were non-synonymous SNPs. Among non-synonymous SNPs, 1,862 were missense, 13 nonsense, 35 frameshifts, 11
    nonstop, 3 misstart, 15 splices disrupt and 17 in-frame indels. A total of 86 variants were located in leukaemia-related
    genes of which 32 variants were located in the coding regions of GLI2, SP140, GATA2, SMAD5, KMT2C, CDH17,
    CDX2, FLT3, PML and MOV10L1. Conclusions: Detection and identification of secondary genetic alterations are
    important in identifying new therapeutic targets and developing rationally designed treatment regimens with less
    toxicity in ALL patients.
    Matched MeSH terms: Base Sequence
  12. Mastor NN, Subbiah VK, Bakar WNWA, Begum K, Alam MJ, Hoque MZ
    Data Brief, 2020 Dec;33:106370.
    PMID: 33102652 DOI: 10.1016/j.dib.2020.106370
    Enterococcus gallinarum is a gram positive facultatively anaerobic bacteria that is typically found in mammalian intestinal tracts. It is generally not considered pathogenic to humans and is rarely reported. Here, we present the draft genome sequence data of Enterococcus gallinarum strain EGR748 isolated from a human clinical sample, and sequenced using the Illumina HiSeq 4000 system. The estimated whole genome size of the strain was 3,730,000 bp with a G + C content of 40.43%. The de novo assembly of the genome generated 55 contigs with an N50 of 208,509 bp. In addition, the Maximum Likelihood phylogenetic analysis based on the 16S rRNA sequence data accurately clustered EGR748 with other E. gallinarum strains. The data may be useful to demonstrate the capacity of this enterococcal species becoming the causal agents of nosocomial blood-stream infections. The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number JAABOR000000000.
    Matched MeSH terms: Base Sequence
  13. McInerney-Leo AM, Harris JE, Leo PJ, Marshall MS, Gardiner B, Kinning E, et al.
    Clin Genet, 2015 Dec;88(6):550-7.
    PMID: 25492405 DOI: 10.1111/cge.12550
    Short-rib thoracic dystrophies (SRTDs) are congenital disorders due to defects in primary cilium function. SRTDs are recessively inherited with mutations identified in 14 genes to date (comprising 398 exons). Conventional mutation detection (usually by iterative Sanger sequencing) is inefficient and expensive, and often not undertaken. Whole exome massive parallel sequencing has been used to identify new genes for SRTD (WDR34, WDR60 and IFT172); however, the clinical utility of whole exome sequencing (WES) has not been established. WES was performed in 11 individuals with SRTDs. Compound heterozygous or homozygous mutations were identified in six confirmed SRTD genes in 10 individuals (IFT172, DYNC2H1, TTC21B, WDR60, WDR34 and NEK1), giving overall sensitivity of 90.9%. WES data from 993 unaffected individuals sequenced using similar technology showed two individuals with rare (minor allele frequency <0.005) compound heterozygous variants of unknown significance in SRTD genes (specificity >99%). Costs for consumables, laboratory processing and bioinformatic analysis were
    Matched MeSH terms: Base Sequence
  14. Mishra SS, Shekhar MS
    Indian J Exp Biol, 2005 Jul;43(7):654-61.
    PMID: 16053274
    Microbiological analysis of samples collected from cases of white spot disease outbreaks in cultured shrimp in different farms located in three regions along East Coast of India viz. Chidambram (Tamil Nadu), Nellore (Andhra Pradesh) and Balasore (Orissa), revealed presence of Vibrio alginolyticus, Vibrio parahaemolyticus, and Aeromonas spp. but experimental infection trials in Penaeus monodon with these isolates did not induce any acute mortality or formation of white spots on carapace. Infection trials using filtered tissue extracts by oral and injection method induced mortality in healthy P. monodon with all samples and 100% mortality was noted by the end of 7 day post-inoculation. Histopathological analysis demonstrated degenerated cells characterized by hypertrophied nuclei in gills, hepatopancreas and lymphoid organ with presence of intranuclear basophilic or eosino-basophilic bodies in tubular cells and intercellular spaces. Analysis of samples using 3 different primer sets as used by other for detection of white spot syndrome virus (WSSV) generated 643, 1447 and 520bp amplified DNA products in all samples except in one instance. Variable size virions with mean size in the range of 110 x 320 +/- 20 nm were observed under electron microscope. It could be concluded that the viral isolates in India involved with white spot syndrome in cultured shrimp are similar to RV-PJ and SEMBV in Japan, WSBV in Taiwan and WSSV in Malaysia, Indonesia, Thailand, China and Japan.
    Matched MeSH terms: Base Sequence
  15. Teoh PG, Ooi AS, AbuBakar S, Othman RY
    J Biomed Biotechnol, 2009;2009:781712.
    PMID: 19325913 DOI: 10.1155/2009/781712
    A Cucumber green mottle mosaic virus (CGMMV) was used to present a truncated dengue virus type 2 envelope (E) protein binding region from amino acids 379 to 423 (EB4). The EB4 gene was inserted at the terminal end of the CGMMV coat protein (CP) open reading frame (ORF). Read-through sequences of TMV or CGMMV, CAA-UAG-CAA-UUA, or AAA-UAG-CAA-UUA were, respectively, inserted in between the CP and the EB4 genes. The chimeric clones, pRT, pRG, and pCG+FSRTRE, were transcribed into full-length capped recombinant CGMMV transcripts. Only constructs with the wild-type CGMMV read-through sequence yielded infectious viruses following infection of host plant, muskmelon (Cucumis melo) leaves. The ratio of modified to unmodified CP for the read-through expression clone developed was also found to be approximately 1:1, higher than what has been previously reported. It was also observed that infectivity was not affected by differences in pI between the chimera and its wild counterpart. Analysis of recombinant viruses after 21-days-postinculation (dpi) revealed that deletions occurred resulting in partial reversions of the viral population to near wild type and suggesting that this would be the limiting harvest period for obtaining true to type recombinants with this construct.
    Matched MeSH terms: Base Sequence
  16. Sudthongkong C, Miyata M, Miyazaki T
    Arch Virol, 2002 Nov;147(11):2089-109.
    PMID: 12417946
    Tropical iridovirus infection causes severe epizootic resulting in mass mortalities and large economic losses in freshwater ornamental fishes cultured in Southeast Asian countries, in wild fish seedlings captured in South China Sea, and in marine fishes farmed in Japan, Singapore, and Thailand. All of tropical iridovirus-infected fishes histopathologically showed the systemic formation of inclusion body-bearing cells and necrosis of virus-infected splenocytes and hematopoietic cells. We designed primer sets for the ATPase gene and the major capsid protein (MCP) gene and sequenced the PCR products derived from 5 iridovirus isolates from sea bass in South China Sea, red sea bream in Japan, brown-spotted grouper with a grouper sleepy disease in Thailand, dwarf gourami from Malaysia and African lampeye from Sumatra Island, Indonesia. The ATPase gene and the MCP gene of these 5 viral isolates were highly homologous (> 95.8%, > 94.9% identity, respectively) and the deduced amino acid sequences of the ATPase and the MCP were also highly identical (> 98.1%, > 97.2% identity, respectively). Based on the high homology, these 5 isolates of tropical iridovirus from various fishes in geographically different regions were determined to have a single origin and to be native to Southeast Asian regions. However, these sequences were far different from those of members of the genera Ranavirus, Lymphocystivirus and Iridovirus in the Family Iridoviridae. We propose a new genus "Tropivirus" for tropical iridovirus in the Family Iridoviridae.
    Matched MeSH terms: Base Sequence
  17. Anderson DL, Trueman JW
    Exp Appl Acarol, 2000 Mar;24(3):165-89.
    PMID: 11108385
    Varroa jacobsoni was first described as a natural ectoparasitic mite of the Eastern honeybee (Apis cerana) throughout Asia. It later switched host to the Western honeybee (A. mellifera) and has now become a serious pest of that bee worldwide. The studies reported here on genotypic, phenotypic and reproductive variation among V. jacobsoni infesting A. cerana throughout Asia demonstrate that V. jacobsoni is a complex of at least two different species. In a new classification V. jacobsoni is here redefined as encompassing nine haplotypes (mites with distinct mtDNA CO-I gene sequences) that infest A. cerana in the Malaysia Indonesia region. Included is a Java haplotype, specimens of which were used to first describe V. jacobsoni at the beginning of this century. A new name, V. destructor n. sp., is given to six haplotypes that infest A. cerana on mainland Asia. Adult females of V. destructor are significantly larger and less spherical in shape than females of V. jacobsoni and they are also reproductively isolated from females of V. jacobsoni. The taxonomic positions of a further three unique haplotypes that infest A. cerana in the Philippines is uncertain and requires further study. Other studies reported here also show that only two of the 18 different haplotypes concealed within the complex of mites infesting A. cerana have become pests of A. mellifera worldwide. Both belong to V. destructor, and they are not V. jacobsoni. The most common is a Korea haplotype, so-called because it was also found parasitizing A. cerana in South Korea. It was identified on A. mellifera in Europe, the Middle East, Africa, Asia, and the Americas. Less common is a Japan/Thailand haplotype, so-called because it was also found parasitizing A. cerana in Japan and Thailand. It was identified on A. mellifera in Japan, Thailand and the Americas. Our results imply that the findings of past research on V. jacobsoni are applicable mostly to V. destructor. Our results will also influence quarantine protocols for bee mites, and may present new strategies for mite control.
    Matched MeSH terms: Base Sequence
  18. Rao ES, Kadirvel P, Symonds RC, Geethanjali S, Thontadarya RN, Ebert AW
    PLoS One, 2015;10(7):e0132535.
    PMID: 26161546 DOI: 10.1371/journal.pone.0132535
    Association analysis was conducted in a core collection of 94 genotypes of Solanum pimpinellifolium to identify variations linked to salt tolerance traits (physiological and yield traits under salt stress) in four candidate genes viz., DREB1A, VP1.1, NHX1, and TIP. The candidate gene analysis covered a concatenated length of 4594 bp per individual and identified five SNP/Indels in DREB1A and VP1.1 genes explaining 17.0% to 25.8% phenotypic variation for various salt tolerance traits. Out of these five alleles, one at 297 bp in DREB1A had in-frame deletion of 6 bp (CTGCAT) or 12 bp (CTGCATCTGCAT), resulting in two alleles, viz., SpDREB1A_297_6 and SpDREB1A_297_12. These alleles individually or as haplotypes accounted for maximum phenotypic variance of about 25% for various salt tolerance traits. Design of markers for selection of the favorable alleles/haplotypes will hasten marker-assisted introgression of salt tolerance from S. pimpinellifolium into cultivated tomato.
    Matched MeSH terms: Base Sequence
  19. Fan Z, Dahal G, Dasgupta I, Hay J, Hull R
    J Gen Virol, 1996 May;77 ( Pt 5):847-54.
    PMID: 8609480
    The DNA genomes of isolates of rice tungro bacilliform virus from Bangladesh, India, Indonesia, Malaysia and Thailand were cloned and compared with that of the type isolate from the Philippines. Restriction endonuclease maps revealed differences between the isolates and cross-hybridization showed that they fell into two groups, those from the Indian subcontinent and those from south-east Asian countries. The genomes of isolates from the Indian subcontinent contained a deletion of 64 bp when compared with those from south-east Asia. The implications of this variation are discussed.
    Matched MeSH terms: Base Sequence
  20. Zhang S, Lee G, Davies JW, Hull R
    Arch Virol, 1997;142(9):1873-9.
    PMID: 9672645
    The variation in the sequence of the coat protein genes of four isolates of rice tungro spherical virus from different countries, Malaysia, Thailand, India and Bangladesh, was compared with an isolate from the Philippines. The evidence from RT-PCR, Southern blot hybridization and sequences of the coat protein genes indicated that the isolates appeared to fall into two groups. One comprised the Philippine and Malaysian isolates (about 95% sequence similarity) and the other the Bangladeshi and Indian isolates, the sequences of which differed by about 15% from that of the Philippine isolate. The Thai isolate seemed to be a mixture of these two subgroups.
    Matched MeSH terms: Base Sequence
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