Displaying publications 1961 - 1980 of 3507 in total

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  1. Fulltext Simvastatin Inhibits Endotoxin-Induced Apoptosis in Liver and Spleen Through Up-Regulation of Survivin/NF-κB/p65 Expression
    Nežić L, Amidžić L, Škrbić R, Gajanin R, Nepovimova E, Vališ M, et al.
    Front Pharmacol, 2019;10:54.
    PMID: 30828299 DOI: 10.3389/fphar.2019.00054
    Endotoxemia is associated by dysregulated apoptosis of immune and non-immune cells. We investigated whether simvastatin has anti-apoptotic effects, and induces hepatocytes and lymphocytes survival signaling in endotoxin-induced liver and spleen injuries. Wistar rats were divided into the groups pretreated with simvastatin (20 or 40 mg/kg, orally) prior to a non-lethal dose of lipopolysaccharide (LPS), the LPS group, and the control. The severity of tissue inflammatory injuries was expressed as hepatic damage scores (HDS) and spleen damage scores (SDS), respectively. The apoptotic cell was detected by TUNEL (Terminal deoxynucleotidyl transferase dUTP Nick End Labeling) and immunohistochemical staining (expression of cleaved caspase-3, and anti-apoptotic Bcl-xL, survivin and NF-κB/p65). Simvastatin dose-dependently abolished HDS and SDS induced by LPS (p < 0.01), respectively. Simvastatin 40 mg/kg significantly decreased apoptotic index and caspase-3 cleavage in hepatocytes and lymphocytes (p < 0.01 vs. LPS group, respectively), while Bcl-XL markedly increased accordingly with simvastatin doses. In the simvastatin, groups were determined markedly increased cytoplasmic expression of survivin associated with nuclear positivity of NF-κB, in both hepatocytes and lymphocytes (p < 0.01 vs. LPS group). Cell-protective effects of simvastatin against LPS seemed to be mediated by up-regulation of survivin, which leads to reduced caspase-3 activation and inhibition of hepatocytes and lymphocytes apoptosis.
    Matched MeSH terms: DNA Nucleotidylexotransferase
  2. Two reads to rule them all: Nanopore long read-guided assembly of the iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888), mitochondrial genome and the challenges of AT-rich mitogenomes
    Gan HM, Linton SM, Austin CM
    Mar Genomics, 2019 Jun;45:64-71.
    PMID: 30928201 DOI: 10.1016/j.margen.2019.02.002
    Despite recent advances in sequencing technology, a complete mitogenome assembly is still unavailable for the gecarcinid land crabs that include the iconic Christmas Island red crab (Gecarcoidea natalis) which is known for its high population density, annual mass breeding migration and ecological significance in maintaining rainforest structure. Using sequences generated from Nanopore and Illumina platforms, we assembled the complete mitogenome for G. natalis, the first for the genus and only second for the family Gecarcinidae. Nine Nanopore long reads representing 0.15% of the sequencing output from an overnight MinION Nanopore run were aligned to the mitogenome. Two of them were >10 kb and combined are sufficient to span the entire G. natalis mitogenome. The use of Illumina genome skimming data only resulted in a fragmented assembly that can be attributed to low to zero sequencing coverage in multiple high AT-regions including the mitochondrial protein-coding genes (NAD4 and NAD5), 16S ribosomal rRNA and non-coding control region. Supplementing the mitogenome assembly with previously acquired transcriptome dataset containing high abundance of mitochondrial transcripts improved mitogenome sequence coverage and assembly reliability. We then inferred the phylogeny of the Eubrachyura using Maximum Likelihood and Bayesian approaches, confirming the phylogenetic placement of G. natalis within the family Gecarcinidae based on whole mitogenome alignment. Given the substantial impact of AT-content on mitogenome assembly and the value of complete mitogenomes in phylogenetic and comparative studies, we recommend that future mitogenome sequencing projects consider generating a modest amount of Nanopore long reads to facilitate the closing of problematic and fragmented mitogenome assemblies.
    Matched MeSH terms: Sequence Analysis, DNA
  3. Fulltext Prevalence of obesity in Malaysia: perspectives in Terengganu
    Muhammad, I. N., Saifullah, K., Hassan, B., Yasrul, I., Norizan, A./G., Ahmed Zubaidi, A. L., et al.
    Asian Journal of Medicine and Biomedicine, 2018;2(1):0-0.
    MyJurnal
    A normal health status is highly depends on body weight. Many health problems may occur or impose risk for
    extremely obese individuals. Etiopathology of obesity includes interaction of several factors inclusive of
    genetic and non-genetic factors such as lifestyle changes. This study aimed to launch Malaysian Obesity
    DNA Bank and determine the prevalence of obesity along with anthropometric measurements of the subjects.
    The cross-sectional study was conducted on total of 340 subjects (obese = 95, overweight = 122 and normal =
    123), aged 19-60 years, in Terengganu. The BMI and well appropriate anthropometric measurements (waist
    circumference, hip circumference, waist to hip ratio, fat percentage and ASindex) were determined through
    standard protocols and formulae. The mean difference of anthropometrics was determined by independent ttest. Data was analysed using SPSS ver.16.0.0. The BMI was determined for all subjects and it was found that
    out of 340 subjects, a total of 95 (27.9%) subjects were obese , followed by a total of 122 (35.8%) subjects
    were overweight and normal individuals were 123 (36.1%). The mean of the BMI, WHR, Fat% and ASindex,
    in Malay obese were 32.83, 0.88, 33.5 and 13.21 respectively, while in normal healthy individuals were 22.1,
    0.78, 24.2 and 20.1 respectively. The difference of mean of BMI, WHR, Fat% and ASindex was calculated to
    be 10.73, 0.1, 9.3 and 6.89 respectively. To the best of our knowledge, this is the first report in Malaysia,
    reporting that this is very first Obesity DNA Bank in South East Asia region and prevalence of obesity in
    Terengganu, Malaysia to be 27.9%. In addition, it indicates a significant mean difference for anthropometric
    measurements among obese and normal individuals. For Asindex calculations suggest that the prevalence of
    genocide obesity is greater 89.9% of android obesity in Malay obese attributes
    .
    Matched MeSH terms: DNA
  4. Description of the female of Simulium (Gomphostilbia) aziruni (Diptera: Simuliidae) and its genetic relationships with members of the Simulium gombakense species-group
    Ya'cob Z, Takaoka H, Low VL, Tan TK, Sofian-Azirun M
    Acta Trop, 2019 May;193:66-70.
    PMID: 30807749 DOI: 10.1016/j.actatropica.2019.02.023
    Simulium (Gomphostilbia) aziruni Takaoka, Hashim & Chen was described initially based only on a pupa and a mature larva collected from Peninsular Malaysia. Herein, we describe the morphological characters of the female of S. aziruni for the first time. It resembles those of the other members of the Simulium gombakense species-group by the genital fork with a distinct projection directed medioposteriorly from each arm and claw with a large basal tooth. Cytochrome c oxidase I (COI) barcoding analysis indicates that S. aziruni is the sister species of S. maleewongae, but both are distantly separated by a genetic distance of 4.9%.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  5. Fulltext MLH1 and MSH2 gene mutations and polymorphisms in six Malay families with hereditary nonpolyposis colorectal cancer
    Wan Khairunnisa Wan Juhari, Khairul Bariah Ahmad Amin Noordin, Wan Faiziah Wan Abdul Rahman, Andee Dzulkarnaen Zakaria, Ahmad Shanwani Mohd Sidek, Muhammad Radzi Abu Hassan, et al.
    International Medical Journal Malaysia, 2018;17(1):71-78.
    MyJurnal
    Background: Hereditary nonpolyposis colorectal cancer (HNPCC) also known as Lynch syndrome is commonly caused by genetic alterations in any of the four mismatch repair (MMR) genes; MLH1, MSH2, MSH6 and PMS2. This is the first study aimed to investigate genetic variants in Malay HNPCC families. Methods: Six Malay HNPCC families who fulfilled any of the Bethesda criteria were recruited into this study. A total of 3 ml of blood was withdrawn from each patient in the families. The samples were further analyzed using polymerase chain reaction and direct sequencing of the selected exons of MLH1 and MSH2 genes. Results: Two missense mutations and four single nucleotide polymorphisms (SNPs) were identified in six patients. These variants in the MLH1 and MSH2 genes were identified in four families who met the revised Bethesda guidelines. In two families, no mutation and polymorphism was identified in both the exon and intron of the respective genes. Of the mutations and polymorphisms identified, five have never been reported in Malay HNPCC families before. A missense mutation was detected in exon 5 of the MLH1 gene, c.394G>C (p.Asp132His) and four mutations and polymorphisms were detected in the MSH2 gene; heterozygous c.211+98T>C and c.211+9C>G and homozygous c.211+98T>C and c.211+9C>G, c.367-86A>C and c.382C>G. Conclusion: The results represented a new spectrum of mutations and polymorphisms in the Malay HNPCC families. However, a larger study involving additional families and analysis is required to determine the impact and nature of the identified mutations and polymorphisms.
    Matched MeSH terms: DNA Mismatch Repair
  6. Fulltext Transcriptional alterations in Caenorhabditis elegans following exposure to an anthelmintic fraction of the plant Picria fel-terrae Lour
    Kumarasingha R, Young ND, Yeo TC, Lim DSL, Tu CL, Palombo EA, et al.
    Parasit Vectors, 2019 Apr 25;12(1):181.
    PMID: 31023350 DOI: 10.1186/s13071-019-3429-4
    BACKGROUND: Natural compounds from plants are known to provide a source of anthelmintic molecules. In previous studies, we have shown that plant extracts from the plant Picria fel-terrae Lour. and particular fractions thereof have activity against the free-living nematode Caenorhabditis elegans, causing quite pronounced stress responses in this nematode. We have also shown that a fraction, designated Pf-fraction 5, derived from this plant has a substantial adverse effect on this worm; however, nothing is known about the molecular processes affected in the worm. In the present study, we explored this aspect.

    RESULTS: Key biological processes linked to upregulated genes (n = 214) included 'response to endoplasmic reticulum stress' and 'lipid metabolism', and processes representing downregulated genes (n = 357) included 'DNA-conformation change' and 'cellular lipid metabolism'.

    CONCLUSIONS: Exposure of C. elegans to Pf-fraction 5 induces significant changes in the transcriptome. Gene ontology analysis suggests that Pf-fraction 5 induces endoplasmic reticulum and mitochondrial stress, and the changes in gene expression are either a direct or indirect consequence of this. Further work is required to assess specific responses to sub-fractions of Pf-fraction 5 in time-course experiments in C. elegans, to define the chemical(s) with potent anthelmintic properties, to attempt to unravel their mode(s) of action and to assess their selectivity against nematodes.

    Matched MeSH terms: DNA
  7. Oxidative stress-associated pathology: A review
    Sarawoot Palipoch, Phanit Koohmin
    Sains Malaysiana, 2015;44:1441-1451.
    Currently, oxidative stress (OS) has become a major interest in point of basic science and clinical research. The imbalance between generations and clearances of oxidants leads to OS. Oxidants are mainly composed of reactive oxygen species (ROS) and reactive nitrogen species (RNS) which are manifested as oxidized macromolecules causing deleterious effects in several organs. Lipid, protein and DNA oxidation products can provide extensively approach of potential oxidative stress biomarkers. OS leads to the fundamental cellular and tissue damages and consequence effect to various organs or systems. This review emphasizes the systemic pathology induced by OS that particularly affect to specialized organs or systems including the nervous system, the cardiovascular system, the lung, the liver and the kidney.
    Matched MeSH terms: DNA
  8. Phylogenetic relationships within the genus holothuria inferred from 16S mitochondiral rRNA gene sequences
    Kamarul Rahim Kamarudin, ‘Aisyah Mohamed Rehan, Ridzwan Hashim, Usup G, Maryam Mohamed Rehan
    Sains Malaysiana, 2016;45:1079-1087.
    This study aimed to resolve the taxonomic status of a morphologically undetermined sea cucumber species of order Apodida
    from Malaysia (GenBank accession no.: FJ223867) using partial 16S mitochondrial rRNA gene sequences and subsequently
    to determine the validity of morphological taxonomy of Holothuria species into its current subgenera. The undetermined
    species clustered with all taxa of Holothuria in previous study. Phylogenetic analyses using maximum parsimony and
    Bayesian methods suggest that the undetermined species was genetically closer to Holothuria (Lessonothuria) pardalis and
    Holothuria (Acanthotrapeza) coluber; and its position in both phylogenetic trees further suggests its status as a Holothuria
    taxon. Subgenera of Holothuria, Merthensiothuria and Metriatyla are monophyletic with strong bootstrap supports and
    posterior probabilities of clades, thus strengthening their morphological taxonomies. Nonetheless, the non-monophyly of
    subgenera of Halodeima, Microthele and Platyperona suggests a requirement for their taxonomic revisions using integrative
    taxonomy. The status of Holothuria (Halodeima) edulis subgroups in the maximum parsimony and Bayesian trees is
    indistinct and further taxonomic revisions are necessary. In terms of sister relationship, both phylogenetic trees suggest
    that subgenus Holothuria is a sister taxon of subgenus Roweothuria while the other sister relationships were unclear due
    to the undetermined species, paraphyly and polyphyly of a number of subgenera. Further studies with more specimens of
    genus Holothuria from broader geographical locations and various mtDNA genes along with morphological approaches
    may facilitate to provide better insights into the molecular phylogeny of subgenera of Holothuria.
    Matched MeSH terms: DNA, Mitochondrial
  9. Fulltext Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis
    Chang W, Ee-Uli J, Ng WL, Rovie-Ryan JJ, Tan SG, Yong CSY
    Sci Rep, 2019 06 11;9(1):8504.
    PMID: 31186469 DOI: 10.1038/s41598-019-44870-4
    Macaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species.
    Matched MeSH terms: DNA Primers
  10. Pencirian bakteria asid laktik dan sebatian aroma ikan pekasam
    Tan WC, Lim SJ, Wan Aida Wan Mustapha
    Sains Malaysiana, 2017;46:439-448.
    Dalam kajian ini, bakteria asid laktik (LAB) serta sebatian aroma ikan pekasam daripada spesies yang berbeza
    ditentukan. Persampelan ikan pekasam iaitu tilapia, loma, lampam, sepat dan gelama diperoleh daripada pembekal
    Perusahaan Ikan Pekasam Kiah di Kuala Kangsar, Perak. Penentuan spesies LAB dijalankan melalui kaedah pencairan
    bersiri, pengkulturan LAB, ujian katalase, ujian pewarnaan spora serta ujian pengesanan Gram bakteria dan morfologi.
    Pengesahan spesies LAB dijalankan melalui pengekstrakan asid deoksiribonukleik (DNA), amplifikasi dengan tindak
    balas rantaian polimerasi (PCR), analisis elektroforesis gel dan penjujukan DNA. Hasil jujukan DNA yang diperoleh
    dibandingkan dengan jujukan dalam pangkalan data GenBank di NCBI menggunakan BLAST. Didapati Lactobacillus
    brevis KB290 DNA dan Lactobacillus casei W56 wujud dalam pekasam tilapia, Lactobacillus plantarum 16 dalam
    pekasam lampam, Lactobacillus casei BD-II kromosom dan Lactobacillus plantarum WCFS1 dalam pekasam sepat,
    Corynebacterium vitaeruminis DSM 20294 dan Streptococcus anginosus C1051 dalam pekasam gelama. Manakala
    Staphylococcus carnosus subsp. carnosus TM300 kromosom adalah LAB dominan dalam pekasam loma. Sementara
    itu, sebatian aroma ditentukan melalui kaedah pengekstrakan cecair menggunakan pelarut metanol dan heksana.
    Pemprofilan sebatian aroma dijalankan dengan kromatografi gas-spektometer jisim (GC-MS). Sebatian aroma dalam
    ekstrak metanol dan heksana daripada lima jenis ikan pekasam dibandingkan. Bilangan sebatian aroma yang diekstrak
    menggunakan metanol adalah lebih banyak berbanding dengan yang menggunakan heksana. Sebatian aroma yang
    paling banyak dikesan adalah daripada pekasam loma. Asid karboksilik merupakan sebatian yang paling dominan
    dalam ikan pekasam dan memberi bau hamis serta tengik.
    Matched MeSH terms: DNA
  11. Phylogenetic relationships of waders (charadriiformes: scolopacidae) in Sarawak inferred from cytochrome oxidase I and recombinant activating gene 1
    Nurul Ashikeen Ab Razak, Mustafa Abdul Rahman, Tuen AA
    Sains Malaysiana, 2016;45:1089-1095.
    Family Scolopacidae includes the sandpipers, shanks, snipes, godwits and curlews. Systematic classifications of shorebirds
    at the higher level have been successfully resolved. Nevertheless, the phylogeny of shorebirds in the familial level is still
    poorly understood. Thus, this phylogenetic study on Scolopacidae was conducted upon the framework provided by the first
    sequence-based species-level phylogeny within the shorebirds to determine the phylogenetic relationships among family
    members of Scolopacidae in West Borneo, Sarawak using combined gene markers, mtDNA Cytochrome Oxidise I (COI)
    and nucDNA Recombinant Activating Gene 1 (RAG1). A total of 1,342 base pair (bp) were inferred from both COI and RAG1
    gene from 45 sequences constituted of 15 species Scolopacidae sampled from Sarawak namely Xenus cinereus, Actitis
    hypoleucos, Tringa totanus, Tringa glareola, Tringa stagnatilis, Heteroscelus brevipes, Calidris alba, Calidris ruficollis,
    Calidris ferruginea, Calidris tenuirostris, Calidris alpina, Gallinago stenura, Gallinago megala, Numenius arquata, and
    Numenius phaeopus. The phylogenetic tree was constructed with Charadrius mongulus derived as an outgroup. The
    Bayesian Inference (BI) tree constructed supported grouping of species into several lineages of Numeniinae, Calidrinae,
    Scolopacinae and Tringinae. The groupings of species into several lineages correlate with morphological features that
    contribute to their adaptation and ability of the species to fit to their ecosystems.
    Matched MeSH terms: DNA, Mitochondrial
  12. Assessing diet of the rufous-winged philentoma (philentoma pyrhoptera) in lowland tropical forest using next-generation sequencing
    Mohammad Saiful Mansor, Shukor Md. Nor, Rosli Ramli
    Sains Malaysiana, 2018;47:1045-1050.
    Dietary study provides understanding in predator-prey relationships, yet diet of tropical forest birds is poorly understood.
    In this study, a non-invasive method, next-generation sequencing (Illumina MiSeq platform) was used to identify prey in
    the faecal samples of the Rufous-winged Philentoma (Philentoma pyrhoptera). Dietary samples were collected in lowland
    tropical forest of central Peninsular Malaysia. A general invertebrate primer pair was used for the first time to assess
    diet of tropical birds. The USEARCH was used to cluster the COI mtDNA sequences into Operational Taxonomic Unit (OTU).
    OTU sequences were aligned and queried through the GenBank or Biodiversity of Life Database (BOLD). We identified
    26 distinct arthropod taxa from 31 OTUs. Of all OTUs, there was three that could be identified up to species level, 20 to
    genus level, three to family level and five could not assigned to any taxa (the BLAST hits were poor). All sequences were
    identified to class Insecta belonging to 18 families from four orders, where Lepidoptera representing major insect order
    consumed by study bird species. This non-invasive molecular approach provides a practical and rapid technique to
    understand of how energy flows across ecosystems. This technique could be very useful to screen for possible particular
    pest insects consumed by insectivores (e.g. birds and bats) in crop plantation. A comprehensive arthropod studies and
    local reference sequences need to be added to the database to improve the proportion of sequences that can be identified.
    Matched MeSH terms: DNA, Mitochondrial
  13. Rediscovery of nycticebus coucang insularis robinson, 1917 (primates: lorisidae) at tioman island and its mitochondrial genetic assessment
    Jeffrine J. Rovie-Ryan, Millawati Gani, Norsyamimi Rosli, Han Ming Gan, Gilmoore G. Bolongon, Tan Cheng Cheng, et al.
    Sains Malaysiana, 2018;47:2533-2542.
    Slow lorises (Nycticebus) consist of eight species native to Southeast Asia while three species are recognised in
    Malaysia - N. coucang, N. menagensis and N. kayan. This study reports on the rediscovery of the subspecies N. coucang
    insularis Robinson, 1917 in Tioman Island and the genetic assessment of its mitochondrial DNA variation. Morphological
    measurements conform the specimen as the putative N. coucang but with distinct colour and markings. Two mitochondrial
    DNA segments (cytochrome b and control region) were produced from the subspecies representing their first registered
    sequences in GenBank. Genetically, the subspecies showed 99% of nucleotide similarity to N. coucang species type for
    both the DNA segments and constitute its own unique haplotype. Phylogenetic trees constructed using three methods
    (neighbour joining, maximum likelihood and Bayesian inference) showed two major groups within Nycticebus; the
    basal group was formed by N. pygmaeus while the second group consisted of the remaining Nycticebus species. The
    phylogenetic position of the subspecies, however, remains unresolved due to the observed mixing between N. coucang and
    N. bengalensis. Several reasons could lead to this condition including the lack of well documented voucher specimens and
    the short DNA fragments used. In addition, the possibility of hybridisation event between N. coucang and N. bengalensis
    could not be excluded as a possible explanation since both species occur sympatrically at the Isthmus of Kra region
    until the Thailand-Malaysia border. The rediscovery of this subspecies displays the unique faunal diversity that justifies
    the importance of Tioman Island as a protected area.
    Matched MeSH terms: DNA, Mitochondrial
  14. The relationship between single nucleotide polymorphisms of the interleukin-10 gene promoter in systemic lupus erythematosus patients in Malaysia: A pilot study
    Hee CS, Gun SC, Naidu R, Somnath SD, Radhakrishnan AK
    Int J Rheum Dis, 2008;11(2):148-154.
    DOI: 10.1111/j.1756-185X.2008.00350.x
    Aim: Recent studies have shown that single nucleotide polymorphisms (SNPs) have been identified within the promoter of the human interleukin-10 (IL-10) gene may participate in the pathogenesis of systemic lupus erythematosus (SLE) and may be related to disease activity. This is a pilot study that investigated the allelic and genotype frequencies of three SNPs in the human IL-10 gene promoter [rs1800896 (position: -1082G > A), rs1800871 (position: -824C > T) and rs1800872 (position: -597C > A)]among Malaysian SLE patients and normal subjects. Methods: Blood was drawn from 44 SLE patients and 44 age- and sex-matched healthy control subjects for DNA extraction. The SNPs were identified using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Results: There was no significant difference in the genotype and allele frequencies between the SLE patients and control subjects. A statistically significant difference was detected in the haplotype frequencies between the patients and controls (P = 0.004). Conclusions: There is a significant difference in the haplotype frequencies between the SLE patients and controls; the SNPs in the human IL-10 gene promoter could play an important role in the pathogenesis of SLE. © 2008 Asia Pacific League of Associations for Rheumatology and Blackwell Publishing Asia Pty Ltd.
    Matched MeSH terms: DNA
  15. Fulltext Blau Syndrome Associated with Nucleotide-binding Oligomerization Domain Containing 2 Mutation in a Baby from Malaysia
    Leong KF, Sato R, Oh GGK, Surana U, Pramono ZAD
    Indian J Dermatol, 2019 9 24;64(5):400-403.
    PMID: 31543536 DOI: 10.4103/ijd.IJD_44_18
    Blau syndrome (BS) is a very rare autosomal dominant juvenile inflammatory disorder caused by mutation in nucleotide-binding oligomerization domain containing 2 (NOD2). Usually, dermatitis is the first symptom that appears in the 1st year of life. About 220 BS cases with confirmed NOD2 mutation have been reported. However, the rarity and lack of awareness of the disease, especially in the regions where genetic tests are very limited, often result in late diagnosis and misdiagnosis. Here, we report a de novo BS case from Malaysia, which may be the first report from southeast Asia. PCR and DNA sequencing of peripheral blood mononuclear cells were performed to screen the entire coding region of NOD2 gene. A heterozygous c.1000C>T transition in exon 4, p. R334W, of the NOD2 gene was identified in the patient. This report further reaffirms the ubiquitousness of the disease and recurrency of p. R334W mutation.
    Matched MeSH terms: Sequence Analysis, DNA
  16. Fulltext Partial mtDNA sequencing data of vulnerable Cephalopachus bancanus from the Malaysian Borneo
    Zahidin MA, Jalil NA, Naharuddin NM, Abd Rahman MR, Gani M, Abdullah MT
    Data Brief, 2019 Aug;25:104133.
    PMID: 31321260 DOI: 10.1016/j.dib.2019.104133
    Tarsier is an endangered nocturnal primate in the family Tarsiidae and is an endemic to Sundaic islands of Philippine (Carlito syrichta), Sulawesi (Tarsius tarsier-complex) and Borneo (Cephalopachus bancanus). Recent records indicated that most molecular studies were done on the Eastern Tarsier and little information for the other group of tarsiers. Here, we present a partial cytochrome b data set of C. bancanus in Sarawak, Malaysian Borneo. Standard mist nets were deployed at strategic locations in various habitat types. A total of 18 individuals were caught, measured and weighed. Approximately, 2 × 2 mm of tissue samples were taken and preserved in molecular grade alcohol. Out of 18, only 11 samples were screened with partial mtDNA (cytochrome b) and the DNA sequences were registered in the GenBank (accession numbers: KY794797-KY794807). Phylogenetic trees were constructed with 20 additional mtDNA sequences downloaded from GenBank. The data are valuable for the management authorities to regulate the type of management units for the metapopulation to sustain population genetics integrity of tarsiers in the range countries across the Sunda Shelf.
    Matched MeSH terms: DNA, Mitochondrial
  17. Fulltext The employment of q-PCR using specific primer targeting on mitochondrial cytochrome-b gene for identification of wild boar meat in meatball samples
    Aina GQ, Erwanto Y, Hossain M, Johan MR, Ali ME, Rohman A
    J Adv Vet Anim Res, 2019 Sep;6(3):300-307.
    PMID: 31583226 DOI: 10.5455/javar.2019.f348
    Objective: The objective of this study was to employ real-time or quantitative polymerase chain reaction (q-PCR) using novel species specific primer (SSP) targeting on mitochondrial cytochrome-b of wild boar species (CYTBWB2-wb) gene for the identification of non-halal meat of wild boar meat (WBM) in meatball products.

    Materials and Methods: The novel SSP of CYTBWB2-wb was designed by our group using PRIMERQUEST and NCBI software. DNA was extracted using propanol-chloroform-isoamyl alcohol method. The designed SSP was further subjected for validation protocols using DNA isolated from fresh meat and from meatball, which include specificity test, determination of efficiency, limit of detection and repeatability, and application of developed method for analysis of commercially meatball samples.

    Results: The results showed that CYTBWB2-wb was specific to wild boar species against other animal species with optimized annealing temperature of 59°C. The efficiency of q-PCR obtained was 91.9% which is acceptable according to the Codex Allimentarius Commission (2010). DNA, with as low as 5 pg/μl, could be detected using q-PCR with primer of CYTBWB2-wb. The developed method was also used for DNA analysis extracted from meatball samples commercially available.

    Conclusion: q-PCR using CYTBWB2-wb primers targeting on mitochondrial cytochrome-b gene (forward: CGG TTC CCT CTT AGG CAT TT; Reverse: GGA TGA ACA GGC AGA TGA AGA) can be fruitfully used for the analysis of WBM in commercial meatball samples.

    Matched MeSH terms: DNA
  18. Fulltext High-quality RNA isolation from pigment-rich Dendrobium flowers
    Khairul-Anuar MA, Mazumdar P, Lau SE, Tan TT, Harikrishna JA
    3 Biotech, 2019 Oct;9(10):371.
    PMID: 31588395 DOI: 10.1007/s13205-019-1898-y
    Isolation of high-quality RNA from Dendrobium flowers is challenging because of the high levels of pigment, polysaccharides, and polyphenols. In the present study, an efficient CTAB method for RNA extraction from the pigment-rich flowers of Dendrobium was optimised. The optimised method yielded high quantities of RNA (10.1-12.9 µg/g). Spectrophotometric values of A260/280 in the range of 2.2 to 2.4 and A260/230 values of 2.0 suggested that the isolated RNA was free of polyphenols, polysaccharides, and protein contaminants. RNA integrity numbers determined by microfluidics were in the range of 7.9-8.9 indicative of intact RNA. In the improved method, the addition of 3 M NaCl and 3% PVP-10 in the extraction buffer, followed by an incubation period of 45 min at 65 °C, eliminated most of the polysaccharides, polyphenolic compounds, and denatured protein. Extraction with phenol:chloroform:isoamyl alcohol (125:24:1) effectively removed pigments from the aqueous phase, while the precipitation of RNA with lithium chloride minimised the co-precipitation of protein, DNA, and polysaccharide and resulted in the extraction of high quality of RNA. The suitability of the RNA for downstream processing was confirmed via RT-PCR amplification of Chalcone synthase gene from cDNA prepared from RNA isolated from different developmental stages of the flower of a Dendrobium hybrid. The present method will be highly useful for the isolation of RNA from pigment, polyphenol, and polysaccharide-rich plant tissues.
    Matched MeSH terms: DNA, Complementary
  19. Fulltext Sequence variation data of the mitochondrial DNA D-loop region of the captive Malayan Gaur (Bos gaurus hubbacki)
    Md-Zain BM, Abdul-Aziz A, Aifat NR, Mohd-Yusof NS, Zulkifli NA, Japning JRR, et al.
    Data Brief, 2019 Jun;24:103532.
    PMID: 31193484 DOI: 10.1016/j.dib.2018.11.117
    This article contains data of the sequence variation in the mitochondrial DNA D-loop region of the Malayan gaur (Bos gaurus hubbacki), locally known as the seladang, from two captive centers. Thirty fecal samples of Malayan gaur were collected from Jenderak Selatan Wildlife Conservation Center (Pahang) and the Sungkai Wildlife Reserve (Perak) for DNA extraction and amplification with polymerase chain reactions. DNA sequences were then analyzed using neighbor joining (NJ) and maximum parsimony (MP) methods. Based on the 652 base pairs obtained, we found seven variable characters with a value of 1%. The genetic distance between the two captive centers was 0.001. Haplotype analyses detected only four haplotypes between these two captive centers. Both NJ and MP trees demonstrate that all individuals in the Jenderak and Sungkai captive centers are in the same clade. Genetic variation of the Malayan gaur in these centers is considered low, possibly because individuals share the same common parent. This sequence variation data are of paramount importance for designing a proper breeding and management program of the Malayan gaur in the future.
    Matched MeSH terms: DNA, Mitochondrial
  20. Homozygosity for a new type of G gamma (A gamma delta beta)zero-thalassemia in a Malaysian male
    George E, Faridah K, Trent RJ, Padanilam BJ, Huang HJ, Huisman TH
    Hemoglobin, 1986;10(4):353-63.
    PMID: 2427478
    Hematological and clinical data are presented for a young Malay patient with a homozygous (delta beta)zero-thalassemic condition. His red blood cells contained 100% fetal hemoglobin with alpha and G gamma chains only. Detailed gene mapping defined a large deletion with a 5' end between the Aha III and Apa I sites, some 200-400 bp 5' to the A gamma globin gene and a 3' end beyond sequences 17-18 kb 3' to the beta globin gene. This G gamma (A gamma delta beta)zero-type of thalassemia is different from all the other six types described before. Comparison of the hematological data of this patient with those of homozygotes for either the Sicilian or Spanish types of G gamma A gamma (delta beta)zero-thalassemia showed no differences; all homozygotes have a moderate anemia which is accentuated by the relatively high oxygen affinity of the Hb F containing erythrocytes.
    Matched MeSH terms: DNA Restriction Enzymes
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