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  1. Systematic placement of an enigmatic Southeast Asian taxon Eupetes macrocerus and implications for the biogeography of a main songbird radiation, the Passerida
    Jønsson KA, Fjeldså J, Ericson PG, Irestedt M
    Biol Lett, 2007 Jun 22;3(3):323-6.
    PMID: 17347105
    Biogeographic connections between Australia and other continents are still poorly understood although the plate tectonics of the Indo-Pacific region is now well described. Eupetes macrocerus is an enigmatic taxon distributed in a small area on the Malay Peninsula and on Sumatra and Borneo. It has generally been associated with Ptilorrhoa in New Guinea on the other side of Wallace's Line, but a relationship with the West African Picathartes has also been suggested. Using three nuclear markers, we demonstrate that Eupetes is the sister taxon of the South African genus Chaetops, and their sister taxon in turn being Picathartes, with a divergence in the Eocene. Thus, this clade is distributed in remote corners of Africa and Asia, which makes the biogeographic history of these birds very intriguing. The most parsimonious explanation would be that they represent a relictual basal group in the Passerida clade established after a long-distance dispersal from the Australo-Papuan region to Africa. Many earlier taxonomic arrangements may have been based on assumptions about relationships with similar-looking forms in the same, or adjacent, biogeographic regions, and revisions with molecular data may uncover such cases of neglect of ancient relictual patterns reflecting past connections between the continents.
    Matched MeSH terms: Sequence Analysis, DNA
  2. Fulltext Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent
    Baker RJ, Dickins B, Wickliffe JK, Khan FAA, Gaschak S, Makova KD, et al.
    Evol Appl, 2017 09;10(8):784-791.
    PMID: 29151870 DOI: 10.1111/eva.12475
    Currently, the effects of chronic, continuous low dose environmental irradiation on the mitochondrial genome of resident small mammals are unknown. Using the bank vole (Myodes glareolus) as a model system, we tested the hypothesis that approximately 50 generations of exposure to the Chernobyl environment has significantly altered genetic diversity of the mitochondrial genome. Using deep sequencing, we compared mitochondrial genomes from 131 individuals from reference sites with radioactive contamination comparable to that present in northern Ukraine before the 26 April 1986 meltdown, to populations where substantial fallout was deposited following the nuclear accident. Population genetic variables revealed significant differences among populations from contaminated and uncontaminated localities. Therefore, we rejected the null hypothesis of no significant genetic effect from 50 generations of exposure to the environment created by the Chernobyl meltdown. Samples from contaminated localities exhibited significantly higher numbers of haplotypes and polymorphic loci, elevated genetic diversity, and a significantly higher average number of substitutions per site across mitochondrial gene regions. Observed genetic variation was dominated by synonymous mutations, which may indicate a history of purify selection against nonsynonymous or insertion/deletion mutations. These significant differences were not attributable to sample size artifacts. The observed increase in mitochondrial genomic diversity in voles from radioactive sites is consistent with the possibility that chronic, continuous irradiation resulting from the Chernobyl disaster has produced an accelerated mutation rate in this species over the last 25 years. Our results, being the first to demonstrate this phenomenon in a wild mammalian species, are important for understanding genetic consequences of exposure to low-dose radiation sources.
    Matched MeSH terms: DNA Mutational Analysis
  3. Epigenetic Changes and Its Intervention in Age-Related Neurodegenerative Diseases
    Mohd Murshid N, Aminullah Lubis F, Makpol S
    Cell Mol Neurobiol, 2020 Oct 19.
    PMID: 33074454 DOI: 10.1007/s10571-020-00979-z
    Epigenetic mechanisms involving the modulation of gene activity without modifying the DNA bases are reported to have lifelong effects on mature neurons in addition to their impact on synaptic plasticity and cognition. Histone methylation and acetylation are involved in synchronizing gene expression and protein function in neuronal cells. Studies have demonstrated in experimental models of neurodegenerative disorders that manipulations of these two mechanisms influence the susceptibility of neurons to degeneration and apoptosis. In Alzheimer's disease (AD), the expression of presenilin 1 (PSEN1) is markedly increased due to decreased methylation at CpG sites, thus promoting the accumulation of toxic amyloid-β (Aβ) peptide. In Parkinson's disease (PD), dysregulation of α-synuclein (SNCA) expression is presumed to occur via aberrant methylation at CpG sites, which controls the activation or suppression of protein expression. Mutant Huntingtin (mtHTT) alters the activity of histone acetyltransferases (HATs), causing the dysregulation of transcription observed in most Huntington's disease (HD) cases. Folate, vitamin B6, vitamin B12, and S-adenosylmethionine (SAM) are vital cofactors involved in DNA methylation modification; 5-azacytidine (AZA) is the most widely studied DNA methyltransferase (DNMT) inhibitor, and dietary polyphenols are DNMT inhibitors in vitro. Drug intervention is believed to reverse the epigenetic mechanisms to serve as a regulator in neuronal diseases. Nevertheless, the biochemical effect of the drugs on brain function and the underlying mechanisms are not well understood. This review focuses on further discussion of therapeutic targets, emphasizing the potential role of epigenetic factors including histone and DNA modifications in the diseases.
    Matched MeSH terms: DNA Methylation
  4. Fulltext The epigenetics changes in childhood solid cancer: a review
    Wan Faiziah Wan Abdul Rahman
    Malaysian Journal of Paediatrics and Child Health, 2019;23(2):1-15.
    MyJurnal
    Epigenetics is the study of heritable changes in gene expression that do not involve changes to the underlying DNA sequence. It is a change in phenotype without changing in genotype which in turn affects how cellsread the genes. The epigenetic change is a regular occurrence but can also be influenced by several factors including age, environment, lifestyle, and disease state. It may have damaging effects that result in diseases like cancer. At least three systems including DNA methylation, histone modification and RNA-associated gene silencing are currently considered to initiate and sustain epigenetic change. New and ongoing research is continuously uncovering the role of epigenetics in a variety of diseases including in childhood solid cancer such as Ewing sarcoma, neuroblastoma, Wilms tumours, brain tumours and rhabdomyosarcoma. A better understanding of epigenetic changes in childhood cancers can guide towards future therapy and diagnosis.
    Matched MeSH terms: DNA Methylation
  5. Fulltext Genotypic to Phenotypic Resistance Discrepancies Identified Involving β-Lactamase Genes, blaKPC, blaIMP, blaNDM-1, and blaVIM in Uropathogenic Klebsiella pneumoniae
    Urmi UL, Nahar S, Rana M, Sultana F, Jahan N, Hossain B, et al.
    Infect Drug Resist, 2020;13:2863-2875.
    PMID: 32903880 DOI: 10.2147/IDR.S262493
    Introduction: Klebsiella pneumoniae carbapenemase (KPC) belongs to the Group-A β-lactamases that incorporate serine at their active site and hydrolyze various penicillins, cephalosporins, and carbapenems. Metallo-beta-lactamases (MBLs) are group-B enzymes that contain one or two essential zinc ions in the active sites and hydrolyze almost all clinically available β-lactam antibiotics. Klebsiella pneumoniae remains the pathogen with the most antimicrobial resistance to KPC and MBLs.

    Methods: This research investigated the blaKPC, and MBL genes, namely, blaIMP, blaVIM, and blaNDM-1 and their phenotypic resistance to K. pneumoniae isolated from urinary tract infections (UTI) in Bangladesh. Isolated UTI K. pneumoniae were identified by API-20E and 16s rDNA gene analysis. Their phenotypic antimicrobial resistance was examined by the Kirby-Bauer disc diffusion method, followed by minimal inhibitory concentration (MIC) determination. blaKPC, blaIMP, blaNDM-1, and blaVIM genes were evaluated by polymerase chain reactions (PCR) and confirmed by sequencing.

    Results: Fifty-eight K. pneumoniae were identified from 142 acute UTI cases. Their phenotypic resistance to amoxycillin-clavulanic acid, cephalexin, cefuroxime, ceftriaxone, and imipenem were 98.3%, 100%, 96.5%, 91.4%, 75.1%, respectively. Over half (31/58) of the isolates contained either blaKPC or one of the MBL genes. Individual prevalence of blaKPC, blaIMP, blaNDM-1, and blaVIM were 15.5% (9), 10.3% (6), 22.4% (13), and 19% (11), respectively. Of these, eight isolates (25.8%, 8/31) were found to have two genes in four different combinations. The co-existence of the ESBL genes generated more resistance than each one individually. Some isolates appeared phenotypically susceptible to imipenem in the presence of blaKPC, blaIMP, blaVIM, and blaNDM-1 genes, singly or in combination.

    Conclusion: The discrepancy of genotype and phenotype resistance has significant consequences for clinical bacteriology, precision in diagnosis, the prudent selection of antimicrobials, and rational prescribing. Heterogeneous phenotypes of antimicrobial susceptibility testing should be taken seriously to avoid inappropriate diagnostic and therapeutic decisions.

    Matched MeSH terms: DNA, Ribosomal
  6. Fulltext Detection of anti-cell membrane DNA antibodies by indirect immunoflouresencence technique in systemic lupus erythematosus
    Faten Nurul Amira Awing Kechik, Maha Abdullah, Masriana Hassan, Masita Arip, Hasni Mahayidin
    Malaysian Journal of Medicine and Health Sciences, 2019;15(108):28-28.
    MyJurnal
    Introduction: Systemic lupus erythematosus (SLE) has a broad spectrum of clinical presentations. The diagnosis of SLE remains a challenge and largely depends on the presence of several serum autoantibodies including anti-nuclear antibody (ANA), anti-double-stranded DNA antibody (anti-dsDNA) and anti-Smith antibody (anti-Sm). ANA, a highly sensitive but not specific marker is used for SLE screening Anti-dsDNA and anti-Sm are SLE-specific biomarkers but has lower sensitivity of 80% and 30% for SLE, respectively. However, it is noted that there are SLE patients who are persistently negative for SLE-specific autoantibodies. Anti-dsDNA and anti-Sm were reported to be negative in up to 51.2% and 62.4% of SLE, respectively. This limitation can lead to misdiagnosis and halter proper treatment to SLE patients. Previous studies have suggested that cell membrane DNA (cmDNA) can act as a specific target for the autoantibodies in SLE patients. Autoantibodies towards cmDNA (anti-cmDNA) were reported to have promis-ing value as a reliable biomarker for SLE. In this study, we would like to determine the usefulness of anti-cmDNA in diagnosing SLE as compared to the standard SLE-specific autoantibodies. Methods: Serum samples from 83 SLE patients, 86 other connective tissue diseases and 61 healthy subjects were included in this study. The other connec-tive tissue diseases include samples from 10 Sjogren’s syndrome, 56 rheumatoid arthritis, 12 scleroderma and eight mixed connected tissues disease (MCTD) patients. All samples were analysed by indirect immunofluorescence (IIF) technique using Raji cells as substrate to detect the presence of anti-cmDNA. Anti-cmDNA was reported as positive if there was presence of a fluorescent ring, either continuous or punctate. Sera from SLE patients were also tested for anti-dsDNA and anti-Sm antibodies by using enzyme-immunoassays. Results: Anti-cmDNA positivity was highest in SLE (55.4%) than in other connective tissue diseases (9.3%) and healthy subjects (0%). Anti-cmDNA was 100% spe-cific at differentiating SLE from healthy subjects and 90.7% specific at differentiating SLE from other connective tissue diseases. There was no difference in the sensitivity (55.4%) of anti-cmDNA at differentiating SLE from both groups. Anti-cmDNA were present in 46 SLE samples negative for standard SLE-specific autoantibodies. It was detected in 11 (42.3%) of anti-dsDNA, 23 (63.9%) of anti-Sm and 8 (12.9%) of both anti-Sm and anti-dsDNA negative samples. Conclusion: The high specificity of anti-cmDNA detection using IIF method makes it an excellent diagnostic tool for SLE. Anti-cmDNA is potentially a very useful biomarker for SLE with negative anti-dsDNA or/and anti-Sm antibodies.
    Matched MeSH terms: DNA
  7. Fulltext Prostaglandin-endoperoxide synthase (PTGS2) and defensin beta 1 (DEFB1) gene polymorphism in Malaysian Malay chronic periodontitis subjects
    Jasmin Kaur Jagender Singh, Ching Ching Ng, Nor Adinar Baharuddin, Syarida Hasnur Safii, Rathna Devi Vaithilingam
    Malaysian Journal of Medicine and Health Sciences, 2019;15(108):31-31.
    MyJurnal
    Introduction:PTGS2 and DEFB1 single nucleotide polymorphisms (SNP) have been validated to be associated with chronic periodontitis (CP) in European, Japanese and Chinese populations. Polymorphisms of these genes play a role in the pathogenesis of CP. Thus far, no study has been done on the Malay ethnic group. Hence, this study assessed the allele and genotype frequencies of PTGS2 and DEFB1 variants in subjects with chronic periodontitis and healthy individuals in Malaysian Malays. Methods: Malay CP subjects and periodontally-healthy controls were obtained from Malaysian Periodontal Database and Biobanking system (MPDBS) for this case-control study. Diagnosis for cas-es was based on case definition by Eke et al (2012). DNA samples were genotyped for 4 candidate SNPs, rs689466, rs5275, rs20417 (PTGS2) and rs1047031 (DEFB1). Genotyping was carried out using Taqman genotyping method. The association between SNPs and study groups were assessed using logistic regression analysis. Results: DNA sam-ples from 140 individuals, 76 CP cases and 64 healthy controls were genotyped. Logistic regression results demon-strated that rs689466 for PTGS2 gene was associated with CP susceptibility in the Malay study group (p=0.03; OR: 1.80; 95% CI=1.05-3.07). The dominant and additive model test showed significant association with rs689466 (C/T) (pdominant-adjusted=0.02; OR: 2.22; 95% CI=1.11-4.43;padditive-adjusted=0.03; OR:1.85; 95% CI=1.07-3.19) after controlling for age and smoking. However, no significant association with CP was observed with other SNPs. Conclusion: The results suggest that rs689466 of PTGS2 gene may contribute to CP susceptibility in Malaysian Malay population in our preliminary study.
    Matched MeSH terms: DNA
  8. Fulltext Role of Traditional Chinese Medicine in the Management of Viral Pneumonia
    Xi S, Li Y, Yue L, Gong Y, Qian L, Liang T, et al.
    Front Pharmacol, 2020;11:582322.
    PMID: 33192523 DOI: 10.3389/fphar.2020.582322
    Viral pneumonia is one kind of acute respiratory tract infection caused by the virus. There have been many outbreaks of viral pneumonia with high contagiousness and mortality both in China and abroad, such as the great influenza in 1918, the severe acute respiratory syndrome (SARS) coronavirus in 2003, the Influenza A (H1N1) virus in 2009, and the Middle East Respiratory Syndrome coronavirus (MERS-CoV) in 2012 and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019. These outbreaks and/or pandemic have significant impact on human life, social behaviors, and economic development. Moreover, no specific drug has been developed for these viruses. Traditional Chinese medicine (TCM) plays an important role in the treatment of viral pneumonia during these outbreaks especially in SARS and SARS-CoV-2 because studies suggest that TCM formulations may target several aspects of the disease and may have lesser side effects than manufactured pharmaceuticals. In recent years, a lot of clinicians and researchers have made a series of in-depth explorations and investigations on the treatment of viral pneumonia with TCM, which have understood TCM therapeutic mechanisms more specifically and clearly. But critical analysis of this research in addition to further studies are needed to assess the potential of TCM in the treatment of viral pneumonia.
    Matched MeSH terms: DNA Viruses
  9. Fulltext Arctic-adapted dogs emerged at the Pleistocene-Holocene transition
    Sinding MS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, et al.
    Science, 2020 06 26;368(6498):1495-1499.
    PMID: 32587022 DOI: 10.1126/science.aaz8599
    Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.
    Matched MeSH terms: Sequence Analysis, DNA
  10. Fulltext Induction of cytotoxicity by Bruguiera gymnorrhiza in human breast carcinoma (MCF-7) cell line via activation of the intrinsic pathway
    Chaudhry GE, Rahman NH, Sevakumaran V, Ahmad A, Mohamad H, Zafar MN, et al.
    J Adv Pharm Technol Res, 2020 10 10;11(4):233-237.
    PMID: 33425710 DOI: 10.4103/japtr.JAPTR_81_20
    Breast cancer is among the frequently occurring cancer worldwide. The foremost underline aim of this study was to determine the growth inhibitory effect along with mechanistic study of a Bruguiera gymnorrhiza extract on MCF-7. The cytotoxicity activity was determined by using the MTS assay. Butanol extract exhibited the maximum cytotoxicity activity against the MCF-7 cells with IC50 of 3.39 μg/mL, followed by diethyl ether and methanol extract (IC50 at 16.22 μg/mL and 37.15 μg/mL, respectively) at 72 h. The DeadEndTM Colorimetric Apoptosis Detection System confirmed the induction of apoptosis (via DNA fragmentation) in MCF-7 cells. Both butanol and diethyl ether extracts of B. gymnorrhiza significantly increase the caspase-3 level. However, the diethyl ether extract induced higher caspase-9 levels compared to caspase-8, suggesting that the intrinsic pathway was the major route in the process of apoptosis. Thin-layer chromatography profiling demonstrated the presence of phenolic, terpene, and alkaloid compounds in crude methanol, diethyl ether, and butanol extracts. The phytochemicals present in the extracts of B. gymnorrhiza might have the potential to be a future therapeutic agent against breast cancer.
    Matched MeSH terms: DNA Fragmentation
  11. Genetic Structure and Diversity Among Historic and Modern Populations of the Sumatran Rhinoceros (Dicerorhinus sumatrensis)
    Brandt JR, van Coeverden de Groot PJ, Witt KE, Engelbrektsson PK, Helgen KM, Malhi RS, et al.
    J Hered, 2018 06 27;109(5):553-565.
    PMID: 29684146 DOI: 10.1093/jhered/esy019
    The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean rhinos were highly diverse, but dissimilar from those of other regions, supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent with their traditional placement into a single subspecies D. s sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18 microsatellite loci. Rhinos within Sumatra formed 2 sub-populations, likely separated by the Barisan Mountains, though with only modest genetic differentiation between them. There are so few remaining Sumatran rhinoceros that separate management strategies for subspecies or subpopulations may not be viable, while each surviving rhino pedigree is likely to retain alleles found in no other individuals. Given the low population size and low reproductive potential of Sumatran rhinos, rapid genetic erosion is inevitable, though an under-appreciated concern is the potential for fixation of harmful genetic variants. Both concerns underscore 2 overriding priorities for the species: 1) translocation of wild rhinos to ex situ facilities, and 2) collection and storage of gametes and cell lines from every surviving captive and wild individual.
    Matched MeSH terms: DNA, Mitochondrial
  12. Genetic Diversity and Demographic History of an Upper Hill Dipterocarp (Shorea platyclados): Implications for Conservation
    Ng CH, Lee SL, Tnah LH, Ng KKS, Lee CT, Diway B, et al.
    J Hered, 2019 12 17;110(7):844-856.
    PMID: 31554011 DOI: 10.1093/jhered/esz052
    Southeast Asian rainforests at upper hill elevations are increasingly vulnerable to degradation because most lowland forest areas have been converted to different land uses. As such, understanding the genetics of upper hill species is becoming more crucial for their future management and conservation. Shorea platyclados is an important, widespread upper hill dipterocarp in Malaysia. To elucidate the genetic structure of S. platyclados and ultimately provide guidelines for a conservation strategy for this species, we carried out a comprehensive study of the genetic diversity and demographic history of S. platyclados. Twenty-seven populations of S. platyclados across its range in Malaysia were genotyped at 15 polymorphic microsatellite loci and sequenced at seven noncoding chloroplast DNA (cpDNA) regions. A total of 303 alleles were derived from the microsatellite loci, and 29 haplotypes were identified based on 2892 bp of concatenated cpDNA sequences. The populations showed moderately high genetic diversity (mean HE = 0.680 for microsatellite gene diversity and HT = 0.650 for total haplotype diversity) and low genetic differentiation (FST = 0.060). Bayesian clustering divided the studied populations into two groups corresponding to western and eastern Malaysia. Bottleneck analysis did not detect any recent bottleneck events. Extended Bayesian skyline analyses showed a model of constant size for the past population history of this species. Based on our findings, priority areas for in situ and ex situ conservation and a minimum population size are recommended for the sustainable utilization of S. platyclados.
    Matched MeSH terms: DNA, Chloroplast
  13. De-novo mutations and genetic variation in the SCN1A gene in Malaysian patients with generalized epilepsy with febrile seizures plus (GEFS+)
    Tan EH, Razak SA, Abdullah JM, Mohamed Yusoff AA
    Epilepsy Res, 2012 Dec;102(3):210-5.
    PMID: 22944210 DOI: 10.1016/j.eplepsyres.2012.08.004
    Generalized epilepsy with febrile seizures plus (GEFS+) comprises a group of clinically and genetically heterogeneous epilepsy syndrome. Here, we provide the first report of clinical presentation and mutational analysis of SCN1A gene in 36 Malaysian GEFS+ patients. Mutational analysis of SCN1A gene revealed twenty seven sequence variants (missense mutation and silent polymorphism also intronic polymorphism), as well as 2 novel de-novo mutations were found in our patients at coding regions, c.5197A>G (N1733D) and c.4748A>G (H1583R). Our findings provide potential genetic insights into the pathogenesis of GEFS+ in Malaysian populations concerning the SCN1A gene mutations.
    Matched MeSH terms: DNA Mutational Analysis
  14. Paternal lineage affinity of the Malay subethnic and Orang Asli populations in Peninsular Malaysia
    SharifahNany RahayuKarmilla S, Aedrianee AR, Nur Haslindawaty AR, Nur Azeelah A, Panneerchelvam S, Norazmi MN, et al.
    Int J Legal Med, 2018 Jul;132(4):1087-1090.
    PMID: 29052042 DOI: 10.1007/s00414-017-1697-0
    Peninsular Malaysia is populated by the Malays, Chinese, Indians, and Orang Asli. We have analyzed 17 Y-STRs loci for 243 randomly unrelated individuals, which include 153 Malays (7 Acheh, 13 Champa, 11 Rawa, 9 Kedah, 23 Minang, 15 Bugis, 43 Kelantan, 14 Jawa, and 18 Bugis) and 90 Orang Asli [54 Semang (16 Kensiu, 13 Lanoh, 25 Bateq); 30 Senoi (21 Semai, 9 Che Wong); and 6 Proto-Malay (6 Orang Kanaq)] from selected settlements in Peninsular Malaysia using the AmpFlSTR Yfiler™ kit (Applied Biosystems™). The overall haplotype diversity is 0.9966, i.e., 0.9984 for the Malays and 0.9793 for the Orang Asli. A total of 158 haplotypes (65.02%) were individually unique. The p value and pairwise Rst analysis was calculated to show the genetic structure of the samples with other world populations (from YHRD website). Based on the Y-STR data, Champa, Acheh, Kedah, Minang, and Kelantan are clustered together. Lanoh and Kensiu (Semang) are very closely related, suggesting similar paternal ancestry. Jawa Malays and Indonesian Java, plus the Bugis Malays and Australian Aborigines shared high degree of paternal lineage affinity. This study presents data for very precious relict groups, who are the earliest inhabitants of Peninsular Malaysia.
    Matched MeSH terms: DNA Fingerprinting
  15. Fulltext An expanded mammal mitogenome dataset from Southeast Asia
    Mohd Salleh F, Ramos-Madrigal J, Peñaloza F, Liu S, Mikkel-Holger SS, Riddhi PP, et al.
    Gigascience, 2017 08 01;6(8):1-8.
    PMID: 28873965 DOI: 10.1093/gigascience/gix053
    Southeast (SE) Asia is 1 of the most biodiverse regions in the world, and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic diversity is still poorly characterized. The growing interest in using environmental DNA to assess and monitor SE Asian species, in particular threatened mammals-has created the urgent need to expand the available reference database of mitochondrial barcode and complete mitogenome sequences. We have partially addressed this need by generating 72 new mitogenome sequences reconstructed from DNA isolated from a range of historical and modern tissue samples. Approximately 55 gigabases of raw sequence were generated. From this data, we assembled 72 complete mitogenome sequences, with an average depth of coverage of ×102.9 and ×55.2 for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Our new database of 52 taxa will strongly enhance the utility of environmental DNA approaches for monitoring mammals in SE Asia as it greatly increases the likelihoods that identification of metabarcoding sequencing reads can be assigned to reference sequences. This magnifies the confidence in species detections and thus allows more robust surveys and monitoring programmes of SE Asia's threatened mammal biodiversity. The extensive collections of historical samples from SE Asia in western and SE Asian museums should serve as additional valuable material to further enrich this reference database.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  16. A New Black Fly Species of the Simulium (Gomphostilbia) duolongum Subgroup (Diptera: Simuliidae) From Vietnam, and Molecular Comparisons With Related Species Using the COI Barcoding Gene
    Takaoka H, Low VL, Tan TK, Ya'cob Z, Sofian-Azirun M, Dhang Chen C, et al.
    J Med Entomol, 2019 02 25;56(2):432-440.
    PMID: 30597034 DOI: 10.1093/jme/tjy222
    Simulium (Gomphostilbia) yvonneae sp. nov. is described based on adults, pupae, and mature larvae from Vietnam. This new species belongs to the Simulium duolongum subgroup in the S. batoense species-group of the subgenus Gomphostilbia Enderlein. It is distinguished by having a relatively larger number of male upper-eye facets in 16 vertical columns and 16 horizontal rows and a pupal gill with eight filaments arranged as 3+(1+2)+2 from dorsal to ventral, of which two filaments of the ventral pair are 1.8 times as long as the longest filament of the middle and dorsal triplets. Morphological comparisons are made to distinguish this new species from all 22 related species. The genetic distinctiveness of this new species in the S. duolongum subgroup is also presented based on the DNA barcoding COI gene.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  17. 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
  18. STK15 Phe31Ile and Val57Ile polymorphisms increase the risk of gastrointestinal cancer
    TianXin Lai, Eric Tzyy Jiann Chong, Ping-Chin Lee, Jitt Aun Chuah, Kek Heng Chua
    Sains Malaysiana, 2018;47:141-148.
    STK15 is a serine/threonine kinase that regulates chromosomal segregation during mitosis. Single nucleotide polymorphisms (SNPs) in this gene, Phe31Ile (rs2273535) and Val57Ile (rs1047972), are inconsistently associated with gastrointestinal cancer (GIC) across different populations. However, this association is unclear in Malaysian population. Therefore, this study investigated the association of STK15 Phe31Ile and Val57Ile polymorphisms to GIC risk in Malaysia. Genomic DNA was extracted from 185 GIC patients and 1110 healthy controls and was subjected to polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. SNPs were further confirmed using sequencing. We found that the 31Phe allele and 31Phe/Phe genotype in the Phe31Ile SNP significantly increased GIC risk in Malaysian population, particularly in gastric cancer (p<0.017). The combined analysis for both SNPs also increased the risk of GIC in this study. Etiological factors such as age, gender and ethnicity were not associated with GIC in the population. This is the first study to report the association of STK15 Phe31Ile and Val57Ile SNPs with an increased risk of GIC in Malaysians; the 31Phe allele is exclusively associated with the risk of gastric cancer. In addition, GIC incidences among Malaysians have significantly shifted to a younger age (<50 years).
    Matched MeSH terms: DNA
  19. Comparison of DNA profiling between fishes and pork meat using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) analysis
    Safiyyah Shahimi, Wan Sakeenah Wan Nazri, Aminah Abdullah, Norrakiah Abdullah Sani, Sahilah Abd. Mutalib
    Sains Malaysiana, 2018;47:1535-1540.
    Genomic DNA of 13 fish (n=13) species consist of four freshwater which were catfish (Clarias gariepinus), shark catfish (Pangasius larnaudii), tilapia (Oreochromis mossambicus), perch (Lates calcarifer) and nine marine species which were black pomfret (Parastromateus niger), anchovy (Stolephorus commersonii), mabong (Rastrelliger kanagurta), red snapper (Lutjanus erythropterus), herring (Chirocentrus dorab), ray fish (Himantura gerrardii), sardine (Decapterus macrosoma), mackerel (Euthynnus affinis) and tuna (Thunnus tuna) were differentiated using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Seven endonucleases of AluI, BsaJI, HaeIII, HindIII, HinfI, MboI and MboII were examined for the ability to digest cyt b amplicon from each species. Genomic DNA of pork (Sus scrofa domestica) were differentiated from fishes by comparing the digestion patterns produced by similar amplified region and enzymes used. In the present study, it was demonstrated that fishes and pork DNA genome were successfully differentiated using all endonucleases except for HindIII. Thus, PCR-RFLP analysis was found useful for future pork DNA detection in fish products.
    Matched MeSH terms: DNA
  20. Eristalinus arvorum (Fabricius, 1787) (Diptera: Syrphidae) in Human Skull: A New Fly Species of Forensic Importance
    Heo CC, Rahimi R, Mengual X, M Isa MS, Zainal S, Khofar PN, et al.
    J Forensic Sci, 2020 Jan;65(1):276-282.
    PMID: 31305956 DOI: 10.1111/1556-4029.14128
    A body of an unknown adult female was found within a shallow burial ground in Malaysia whereas the skull was exposed and visible on the ground. During autopsy examination, nine insect larvae were recovered from the interior of the human skull and subsequently preserved in 70% ethanol. The larvae were greyish in appearance, each with a posterior elongated breathing tube. A week after the autopsy, more larvae were collected at the burial site, and some of them were reared into adults. Adult specimens and larvae from the skull and from the burial site were sequenced to obtain DNA barcodes. Results showed all adult flies reared from the burial site, as well as the larvae collected from the skull were identified as Eristalinus arvorum (Fabricius, 1787) (Diptera: Syrphidae). Here, we report the colonization of E. arvorum larvae on a human corpse for the first time.
    Matched MeSH terms: DNA Barcoding, Taxonomic
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