Displaying publications 381 - 400 of 3507 in total

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  1. Fulltext Potential lethal damage repair in glioblastoma cells irradiated with ion beams of various types and levels of linear energy transfer
    Chew MT, Nisbet A, Suzuki M, Matsufuji N, Murakami T, Jones B, et al.
    J Radiat Res, 2019 Jan 01;60(1):59-68.
    PMID: 30452663 DOI: 10.1093/jrr/rry081
    Glioblastoma (GBM), a Grade IV brain tumour, is a well-known radioresistant cancer. To investigate one of the causes of radioresistance, we studied the capacity for potential lethal damage repair (PLDR) of three altered strains of GBM: T98G, U87 and LN18, irradiated with various ions and various levels of linear energy transfer (LET). The GBM cells were exposed to 12C and 28Si ion beams with LETs of 55, 100 and 200 keV/μm, and with X-ray beams of 1.7 keV/μm. Mono-energetic 12C ions and 28Si ions were generated by the Heavy Ion Medical Accelerator at the National Institute of Radiological Science, Chiba, Japan. Clonogenic assays were used to determine cell inactivation. The ability of the cells to repair potential lethal damage was demonstrated by allowing one identical set of irradiated cells to repair for 24 h before subplating. The results show there is definite PLDR with X-rays, some evidence of PLDR at 55 keV/μm, and minimal PLDR at 100 keV/μm. There is no observable PLDR at 200 keV/μm. This is the first study, to the authors' knowledge, demonstrating the capability of GBM cells to repair potential lethal damage following charged ion irradiations. It is concluded that a GBM's PLDR is dependent on LET, dose and GBM strain; and the more radioresistant the cell strain, the greater the PLDR.
    Matched MeSH terms: DNA Damage*; DNA Repair*
  2. MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements
    Rey-Iglesia A, Gopalakrishan S, Carøe C, Alquezar-Planas DE, Ahlmann Nielsen A, Röder T, et al.
    Mol Ecol Resour, 2019 Mar;19(2):512-525.
    PMID: 30575257 DOI: 10.1111/1755-0998.12984
    In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome-scale studies to characterize both model and non-model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome-wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site-associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms-enabling the exploration of diverse evolutionary and conservation questions.
    Matched MeSH terms: DNA Transposable Elements*; Sequence Analysis, DNA/methods*
  3. Fulltext Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders
    Pinotti T, Bergström A, Geppert M, Bawn M, Ohasi D, Shi W, et al.
    Curr Biol, 2019 01 07;29(1):149-157.e3.
    PMID: 30581024 DOI: 10.1016/j.cub.2018.11.029
    The Americas were the last inhabitable continents to be occupied by humans, with a growing multidisciplinary consensus for entry 15-25 thousand years ago (kya) from northeast Asia via the former Beringia land bridge [1-4]. Autosomal DNA analyses have dated the separation of Native American ancestors from the Asian gene pool to 23 kya or later [5, 6] and mtDNA analyses to ∼25 kya [7], followed by isolation ("Beringian Standstill" [8, 9]) for 2.4-9 ky and then a rapid expansion throughout the Americas. Here, we present a calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C [10], with four major conclusions. First, we identify three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C3-P39/Z30536 in North America. Second, from the divergence times and Eurasian/American distribution of lineages, we estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky, according to alternative models, and entry south of the ice sheet after 19.5 kya. Third, we describe the star-like expansion of Q-M848 (within Q-M3) starting at 15 kya [11] in the Americas, followed by establishment of substantial spatial structure in South America by 12 kya. Fourth, the deep branches of the Q-CTS1780 lineage present at low frequencies throughout the Americas today [12] may reflect a separate out-of-Beringia dispersal after the melting of the glaciers at the end of the Pleistocene.
    Matched MeSH terms: DNA, Mitochondrial/genetics; DNA, Ancient/analysis*
  4. DNA barcoding of shrimps from a mangrove biodiversity hotspot
    Jamaluddin JAF, Mohammed Akib NA, Ahmad SZ, Abdul Halim SAA, Abdul Hamid NK, Mohd Nor SA
    Mitochondrial DNA A DNA Mapp Seq Anal, 2019 05;30(4):618-625.
    PMID: 31012766 DOI: 10.1080/24701394.2019.1597073
    A total of 74 shrimp specimens were sequenced at a 584 bp segment of the cytochrome oxidase subunit I (COI) gene to examine patterns of DNA barcode variation in a mangrove biodiversity hotspot. The Maximum Likelihood tree, barcode gap analysis, Automatic Barcode Gap Discovery analysis and sequence comparisons with data available from Barcode of Life Data System and GenBank recovered 18 taxa of which 15 were identified to species level, 2 at genus level and a single taxon at order level. Two deep mitochondrial DNA lineage divergences were found in the giant tiger prawn, Penaeus monodon. It is suggested that one of the lineages is a consequence of an introduction from aquaculture activity. These results have provided a reliable barcode library for cataloguing shrimps in this area.
    Matched MeSH terms: DNA, Mitochondrial/genetics; DNA Barcoding, Taxonomic*
  5. Sistem minigenom virus Penyakit Newcastle (NDV) AF2240 sebagai sistem pengekspresan gen sel mamalia
    SHAHRUL HISHAM ZAINAL ARIFFIN, ROSLINA SHAMSUDIN, NURUL ATIKAH AHMAD, ZULKIFLIE ZAMROD
    Sains Malaysiana, 2012;41:423-430.
    Sistem minigenom telah digunakan untuk mengkaji replikasi dan transkripsi virus RNA tidak bersegmen. Objektif kajian ini adalah untuk membina sistem minigenom bagi virus NDV strain tempatan, AF2240 serta bagi mengkaji mekanisme transkripsi dan replikasi virus ini. Bagi tujuan ini lima plasmid digunakan iaitu pMGNDV, pCITENP, pCITEP, pTriEX-T7, dan pGEML. Kesemua plasmid diekstrak secara berskala besar dan dimendakkan menggunakan polietilina glikol. Hasil ekstrak ini digunakan untuk transfeksi ke dalam sel. Translasi in vitro dilakukan dengan menggunakan pCITENP, pCITEP, dan pTriEX-T7 untuk memastikan kesemua konstruk ini berfungsi. Hasil pemblotan western menunjukkan protein bersaiz ~100 kDa (T7), ~53 kDa (NP), ~53 dan 55 kDa (P) berjaya diekspreskan. Protein CAT diperoleh apabila plasmid yang mengekodkan minigenom NDV ditransfeksi bersama plasmid yang mengekodkan protein nukleokapsid (NP), fosfoprotein (P) dan subunit besar polimerase (L) ke dalam sel BHK-21. Dianggarkan 55 pg protein CAT berjaya diperoleh menggunakan kit CAT ELISA. Hasil pemblotan western turut menunjukkan protein CAT bersaiz 25 kDa dihasilkan. Kesimpulannnya, system minigenom ini berupaya untuk berfungsi dan mampu mengekspreskan gen asing di dalam sel mamalia BHK-21.
    Matched MeSH terms: DNA Viruses
  6. Infeksi Entamoeba histolytica dan/atau Entamoeba dispar dalam kalangan kanak-kanak Orang Asli di Pos Sungai Rual, Jeli, Kelantan
    Mariam Ahmad Zawawi, Mohamed Kamel Abd Ghani, Gopal G, Hidayatulfathi Othman, Hartini Yusof, Norhisham Haron
    Sains Malaysiana, 2012;41:1095-1098.
    entamoeba histolytica dan/atau entamoeba dispar merupakan protozoa usus yang mempunyai prevalens infeksi yang tinggi dalam kalangan masyarakat pedalaman terutamanya masyarakat Orang Asli. Ia tersebar secara meluas di kawasan tropika dan subtropika serta di negara membangun berbanding negara maju. Sebanyak 111 sampel feses kanak-kanak Orang Asli daripada suku kaum Jahai telah diterima dan disaring untuk entamoeba histolytica dan/atau entamoeba dispar menggunakan kaedah apusan langsung yang memberi hasil positif terhadap 43 sampel atau 38.7%. Oleh sebab amaun sampel yang diterima adalah sedikit, hanya 66 sampel feses sahaja yang dapat diperiksa menggunakan tiga jenis teknik diagnostik berbeza iaitu apusan langsung, kepekatan formalin-eter dan pewarnaan trikrom. Hasil kajian mendapati, prevalens yang tinggi bagi infeksi entamoeba histolytica dan/atau entamoeba dispar iaitu 50% menggunakan
    ketiga-tiga teknik diagnosis. Prevalens infeksi yang tinggi juga turut ditunjukkan pada kanak-kanak perempuan iaitu 62.5% berbanding kanak-kanak lelaki 30.8% (p<0.05). Selain itu, daripada segi umur, kanak-kanak yang berumur 7-9 tahun adalah lebih terdedah kepada infeksi entamoeba histolytica dan/atau entamoeba dispar dengan prevalens 60.7% (p>0.05). Teknik pewarnaan trikrom menunjukkan pengesanan 100% ke atas infeksi entamoeba histolytica dan/atau entamoeba dispar, diikuti teknik kepekatan formalin-eter 78.8% dan apusan langsung 72.7%. Prevalens infeksi entamoeba histolytica dan/atau entamoeba dispar yang tinggi dalam kalangan kanak-kanak Orang Asli di Pos Sungai Rual ini berhubungkait dengan pelbagai faktor iaitu status sosioekonomi yang rendah, kekurangan pengetahuan tentang penjagaan kesihatan serta kebersihan diri yang rendah. Peningkatan prevalens infeksi dalam kajian ini juga menunjukkan pentingnya penggunaan teknik diagnostik yang lebih berkesan dalam pemeriksaan rutin bagi mendapatkan hasil diagnosis yang lebih tepat.
    Matched MeSH terms: DNA, Protozoan
  7. Synthesis of γ-N-modified 8-oxo-2'-deoxyguanosine triphosphate and its characterization
    Thavoncharoensub N, Maruyama K, Heh CH, Hoong Leong K, Shi H, Shigematsu Y, et al.
    Nucleosides Nucleotides Nucleic Acids, 2019;38(8):578-589.
    PMID: 30929604 DOI: 10.1080/15257770.2019.1586919
    8-OxodGTP is generated by the reaction between dGTP and reactive oxygen species and a considered mutagenic nucleotide. It can be incorporated into the duplex DNA during replication processes by the DNA polymerase, and thus the repair enzyme removes oxodGTP from the nucleotide pools in living cells. On the other hand, the γ-modified triphosphates show interesting properties for use as biological tools. Therefore, the γ-N-pyrenylalkyl-oxodGTP derivatives were synthesized and their effect on the enzymatic reactions were evaluated. The γ-N-pyrenylmethyl-oxodGTP was found to be accepted by the DNA polymerase just like oxodGTP, but showed a competitive inhibition property for the human oxodGTPase.
    Matched MeSH terms: DNA-Directed DNA Polymerase/chemistry
  8. Construction of molecule markers for prolific oil palm tissue culture
    Siti Khadijah A. Karim, Nik Marzuki Sidik
    Sains Malaysiana, 2018;47:1701-1708.
    Penggunaan penanda DNA boleh mengurangkan masalah dalam kultur tisu khususnya apabila diaplikasikan semasa
    pemilihan pokok untuk kultur tisu. Oleh itu, penyelidikan ini dijalankan bertujuan untuk membina penanda molekul
    bagi kultur tisu kelapa sawit prolifik dengan menggunakan teknik polimorfisme panjang cebisan teramplifikasi (AFLP).
    Analisis AFLP dijalankan ke atas 20 klon kelapa sawit yang terbahagi kepada tiga kelas iaitu klon tidak prolifik (10
    jenis klon), klon normal (6 jenis klon) dan klon prolifik (4 jenis klon). Kesemua klon yang digunakan adalah daripada
    titisan sel yang berbeza. Sebanyak 25 kombinasi pencetus telah digunakan dalam analisis AFLP dan 13 daripada mereka
    memberikan corak amplifikasi polimorfisme. Daripada hasil ini, sebanyak 44 cebisan polimorfik telah dipencilkan dengan
    33 cebisan adalah bagi klon tidak prolifik, 1 cebisan bagi normal dan 10 cebisan bagi klon prolifik. Cebisan ini telah
    diklon ke dalam plasmid, berjujukan dan seterusnya, analisis jujukan dijalankan. Sebanyak 36 cebisan polimorfik telah
    digunakan bagi kajian seterusnya. Berdasarkan kepada jujukan yang diperoleh, sepasang pencetus yang khusus kepada
    setiap cebisan telah dijana. Jangkaan julat saiz jalur DNA yang diamplifikasi bagi setiap pencetus adalah antara 70
    hingga 500 bp. Pasangan pencetus yang optimum diuji ke atas 20 jenis klon kelapa sawit untuk mengesahkan penanda
    yang telah dibina. Daripada 36 pasangan pencetus yang dibina, 2 pasang pencetus telah menunjukkan potensi untuk
    digunakan sebagai penanda kepada kultur tisu kelapa sawit prolifik.
    Matched MeSH terms: DNA
  9. Fulltext Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns
    Czamara D, Eraslan G, Page CM, Lahti J, Lahti-Pulkkinen M, Hämäläinen E, et al.
    Nat Commun, 2019 06 11;10(1):2548.
    PMID: 31186427 DOI: 10.1038/s41467-019-10461-0
    Epigenetic processes, including DNA methylation (DNAm), are among the mechanisms allowing integration of genetic and environmental factors to shape cellular function. While many studies have investigated either environmental or genetic contributions to DNAm, few have assessed their integrated effects. Here we examine the relative contributions of prenatal environmental factors and genotype on DNA methylation in neonatal blood at variably methylated regions (VMRs) in 4 independent cohorts (overall n = 2365). We use Akaike's information criterion to test which factors best explain variability of methylation in the cohort-specific VMRs: several prenatal environmental factors (E), genotypes in cis (G), or their additive (G + E) or interaction (GxE) effects. Genetic and environmental factors in combination best explain DNAm at the majority of VMRs. The CpGs best explained by either G, G + E or GxE are functionally distinct. The enrichment of genetic variants from GxE models in GWAS for complex disorders supports their importance for disease risk.
    Matched MeSH terms: DNA/blood*; DNA Methylation/genetics*
  10. Phage N15 protelomerase resolves its tos recognition site into hairpin telomeres within mammalian cells
    Liew PS, Chen Q, Ng AWR, Chew YC, Ravin NV, Sim EUH, et al.
    Anal Biochem, 2019 10 15;583:113361.
    PMID: 31306622 DOI: 10.1016/j.ab.2019.113361
    Phage N15 protelomerase (TelN) cleaves double-stranded circular DNA containing a telomerase-occupancy-site (tos) and rejoins the resulting linear-ends to form closed-hairpin-telomeres in Escherichia coli (E. coli). Continued TelN expression is essential to support resolution of the linear structure. In mammalian cells, no enzyme with TelN-like activities has been found. In this work, we show that phage TelN, expressed transiently and stably in human and mouse cells, recapitulates its native activities in these exogenous environments. We found TelN to accurately resolve tos-DNA in vitro and in vivo within human and mouse cells into linear DNA-containing terminal telomeres that are resistant to RecBCD degradation, a hallmark of protelomerase processing. In stable cells, TelN activity was detectable for at least 60 days, which suggests the possibility of limited silencing of its expression. Correspondingly, linear plasmid containing a 100 kb human β-globin gene expressed for at least 120 h in non-β-globin-expressing mouse cells with TelN presence. Our results demonstrate TelN is able to cut and heal DNA as hairpin-telomeres within mammalian cells, providing a tool for creating novel structures by DNA resolution in these hosts. The TelN protelomerase may be useful for exploring novel technologies for genome interrogation and chromosome engineering.
    Matched MeSH terms: DNA/metabolism*; DNA Replication/physiology*
  11. A new Cosmocercoides species (Ascaridida: Cosmocercidae), C. wuyiensis n. sp., from the Asiatic frog Amolops wuyiensis (Amphibia: Anura)
    Liu Y, Yu Q, Shu YL, Zhao JH, Fang JY, Wu HL
    J Helminthol, 2019 Jul 12;94:e59.
    PMID: 31296272 DOI: 10.1017/S0022149X19000518
    We identified and characterized a new cosmocercid nematode species, Cosmocercoides wuyiensis n. sp., through microscopic examination and sequencing of the partial small ribosomal RNA gene (18S rDNA), internal transcribed spacer (ITS) and mitochondrial cytochrome c oxidase subunit 1 (COI) genes. The new species was isolated from the intestine of the Asiatic frog Amolops wuyiensis Liu and Hu, 1975 captured from four localities of the Anhui province in south-east China. Among the 25 recorded species of the Cosmocercoides genus, the morphology of C. wuyiensis n. sp. is closest to that of C. kiliwai and C. malayensis, which were isolated from various Mexican frog and Malaysian lizard species, respectively. However, C. wuyiensis n. sp. displayed several distinguishing features, such as small size of the male body, two spicules of unequal lengths in the male, small gubernaculum, pre-, ad- and post-cloacal caudal rosette papillae in the ratio of 18-24:2:6 and simple papillae in the ratio of 14:multiple:4, circle and number of punctation in each rosette at 1:11-16, sharply conical tail-end and the presence of lateral alae and somatic papillae in both sexes. BLAST and the phylogenetic analyses of the 18S rDNA and ITS sequences indicated that C. wuyiensis n. sp. belonged to the genus Cosmocercoides, while that of the COI gene sequence of C. wuyiensis n. sp. showed 16.36% nucleotide divergence with C. pulcher and 47.99% nucleotide divergence with C. qingtianensis. The morphological and molecular characterization of C. wuyiensis n. sp. provides new taxonomic data for this genus.
    Matched MeSH terms: DNA, Ribosomal/genetics; DNA, Intergenic/genetics
  12. Fulltext Assessment of autosomal and male DNA extracted from casework samples using Casework Direct Kit, Custom and Maxwell 16 System DNA IQ Casework Pro Kit for autosomal-STR and Y-STR profiling
    Hakim HM, Khan HO, Ismail SA, Ayob S, Lalung J, Kofi EA, et al.
    Sci Rep, 2019 10 10;9(1):14558.
    PMID: 31601905 DOI: 10.1038/s41598-019-51154-4
    Short repetitive regions in autosomal and Y chromosomes known as short tandem repeats (STRs) are currently used for DNA profiling in crime investigations. However, DNA profiling requires a sufficient quality and quantity of DNA template, which is often not obtained from trace evidence or degraded biological samples collected at the scene of a crime. Here, we assessed autosomal and male DNA components extracted from crime scene and mock casework samples using the Casework Direct Kit, Custom and compared the results against those obtained by extraction of matching samples using well-established Maxwell 16 System DNA IQ Casework Pro Kit. The quantity and quality of extracted DNA obtained using both Casework Direct Kit, Custom and Maxwell 16 System DNA IQ Casework Pro Kit were analyzed using PowerQuant Systems followed by autosomal and Y-chromosome STR profiling using GlobalFiler Express PCR Amplification Kit and PowerPlex Y23 System, respectively. Our results showed that the Casework Direct Kit and Maxwell 16 DNA IQ Casework Pro Kit have more or less equal capacity to extract inhibitor free DNA, but that the latter produces slightly better quality and more DNA template and subsequently higher numbers of STR allele calls for autosomal and Y-STR analyses. Nonetheless, the Casework Direct Kit, Custom is the quicker and cheaper option for extraction of good, clean DNA from high content material and might best be used for extraction of reference samples. Such reference DNA samples typically come from buccal swabs or freshly drawn blood. So, in general, they can confidently be expected to have a high nucleic acid content and to be inhibitor-free.
    Matched MeSH terms: DNA/analysis*; DNA Fingerprinting*
  13. Indel-informed Bayesian analysis suggests cryptic population structure between Plasmodium knowlesi of humans and long-tailed macaques (Macaca fascicularis) in Malaysian Borneo
    Wilcox JS, Kerschner A, Hollocher H
    Infect Genet Evol, 2019 11;75:103994.
    PMID: 31421245 DOI: 10.1016/j.meegid.2019.103994
    Plasmodium knowlesi is an important causative agent of malaria in humans of Southeast Asia. Macaques are natural hosts for this parasite, but little is conclusively known about its patterns of transmission within and between these hosts. Here, we apply a comprehensive phylogenetic approach to test for patterns of cryptic population genetic structure between P. knowlesi isolated from humans and long-tailed macaques from the state of Sarawak in Malaysian Borneo. Our approach differs from previous investigations through our exhaustive use of archival 18S Small Subunit rRNA (18S) gene sequences from Plasmodium and Hepatocystis species, our inclusion of insertion and deletion information during phylogenetic inference, and our application of Bayesian phylogenetic inference to this problem. We report distinct clades of P. knowlesi that predominantly contained sequences from either human or macaque hosts for paralogous A-type and S-type 18S gene loci. We report significant partitioning of sequence distances between host species across both types of loci, and confirmed that sequences of the same locus type showed significantly biased assortment into different clades depending on their host species. Our results support the zoonotic potential of Plasmodium knowlesi, but also suggest that humans may be preferentially infected with certain strains of this parasite. Broadly, such patterns could arise through preferential zoonotic transmission of some parasite lineages or a disposition of parasites to transmit within, rather than between, human and macaque hosts. Available data are insufficient to address these hypotheses. Our results suggest that the epidemiology of P. knowlesi may be more complicated than previously assumed, and highlight the need for renewed and more vigorous explorations of transmission patterns in the fifth human malarial parasite.
    Matched MeSH terms: DNA, Protozoan/genetics; Sequence Analysis, DNA/methods*
  14. Evidence for a general-purpose genotype in Candida albicans, highly prevalent in multiple geographical regions, patient types and types of infection
    Schmid J, Herd S, Hunter PR, Cannon RD, Yasin MSM, Samad S, et al.
    Microbiology (Reading), 1999 Sep;145 ( Pt 9):2405-2413.
    PMID: 10517593 DOI: 10.1099/00221287-145-9-2405
    Epidemiological studies, using the probe Ca3, have shown that in a given patient population a single cluster of genetically related Candida albicans isolates usually predominates. The authors have investigated whether these local clusters are part of a single group, geographically widespread and highly prevalent as an aetiological agent of various types of candidiasis. An unrooted neighbour-joining tree of 266 infection-causing C. albicans isolates (each from a different individual) from 12 geographical regions in 6 countries was created, based on genetic distances generated by Ca3 fingerprinting. Thirty-seven per cent of all isolates formed a single genetically homogeneous cluster (cluster A). The remainder of isolates were genetically diverse. Using the maximum branch length within cluster A as a cut-off, they could be divided into 37 groups, whose prevalence ranged between 0.3% and 9%. Strains from cluster A were highly prevalent in all but one geographical region, with a mean prevalence across all regions of 41%. When isolates were separated into groups based on patient characteristics or type of infection, strains from cluster A had a prevalence exceeding 27% in each group, and their mean prevalence was 43% across all patient characteristics. These data provide evidence that cluster A constitutes a general-purpose genotype, which is geographically widespread and acts as a predominant aetiological agent of all forms of candidiasis in all categories of patients surveyed.
    Matched MeSH terms: DNA, Fungal/analysis; DNA, Fungal/genetics; DNA Fingerprinting
  15. Variations in mitochondrial DNA control region among Malay and Chinese subpopulations (sequence 16000-16200)
    Ishar SM, Parameswaran K, Masduki NS, Rus Din RD
    Mitochondrial DNA A DNA Mapp Seq Anal, 2019 12;30(8):843-847.
    PMID: 31709874 DOI: 10.1080/24701394.2019.1687693
    DNA variations are alterations found in DNA sequence, occurring in both nuclear DNA and mitochondrial DNA. Variations might differ in individual following population, respectively. The aim of this study was to find variations in target sequence of mtDNA (16000-16200) to be used as marker in Malay and Chinese population. A total of 30 buccal swab samples from 20 Malay and 10 Chinese subjects were collected and preserved on FTA card. The FTA card that contained DNA sample was punched to be included into polymerase chain reaction mixture. Amplification was carried out and the products were sequenced. Sequence variations were found in both Malay and Chinese populations. A total of nine variations (16129, 16108, 16162, 16172, 16148, 16127, 16173, 16099 and 16100) were found in Malay population while a total of seven variations (16129, 16104, 16111, 16109, 16164, 16170 and 16136) were found in Chinese population. Nucleotide position 16129 was found as variation in both Malay and Chinese populations. This study implies that np 16129 can be used as a marker for Malaysian population. For further investigation, the length of the target sequence may be increased to obtain more variations that can be used as markers. This will increase the discrimination power of Malaysian population.
    Matched MeSH terms: DNA, Mitochondrial/genetics*; Sequence Analysis, DNA*
  16. Molecular Prevalence and Epidemiology of Trypanosoma evansi Among Cattle in Peninsular Malaysia
    Ola-Fadunsin SD, Gimba FI, Abdullah DA, Abdullah FJF, Sani RA
    Acta Parasitol, 2020 Mar;65(1):165-173.
    PMID: 31797192 DOI: 10.2478/s11686-019-00150-9
    BACKGROUND: Animal trypanosomiasis (Surra) caused by Trypanosoma evansi (T. evansi) is known to be one of the important haemoprotozoan parasites that causes great economical loss on animal production due to mortality and loss of condition.

    METHODS: A cross-sectional study was designed to evaluate the prevalence and risk factors associated with T. evansi infection among cattle in Peninsular Malaysia. Polymerase chain reaction (PCR) was employed on 1045 blood samples collected from 43 farms. A well-structured questionnaire was used to collect data on risk factors associated with T. evansi prevalence. The RoTat 1.2 set of primers was used to amplify products of 205 base pair.

    RESULTS: The overall prevalence was found to be 17.9% (187/1045; 95% CI = 15.66-20.31). Trypanosoma evansi was detected among cattle in all the States of Peninsular Malaysia. Breeds of cattle and closeness to waste area, where the risk factors significantly (p 

    Matched MeSH terms: DNA, Protozoan/genetics; DNA Primers/genetics
  17. Fulltext Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages
    Ramos-Madrigal J, Sinding MS, Carøe C, Mak SST, Niemann J, Samaniego Castruita JA, et al.
    Curr Biol, 2021 01 11;31(1):198-206.e8.
    PMID: 33125870 DOI: 10.1016/j.cub.2020.10.002
    Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1-3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.
    Matched MeSH terms: DNA, Mitochondrial/genetics; DNA, Ancient*
  18. Amycolatopsis nigrescens sp. nov., an actinomycete isolated from a Roman catacomb
    Groth I, Tan GYA, González JM, Laiz L, Carlsohn MR, Schütze B, et al.
    Int J Syst Evol Microbiol, 2007 Mar;57(Pt 3):513-519.
    PMID: 17329776 DOI: 10.1099/ijs.0.64602-0
    The taxonomic status of two actinomycetes isolated from the wall of a hypogean Roman catacomb was established based on a polyphasic investigation. The organisms were found to have chemical and morphological markers typical of members of the genus Amycolatopsis. They also shared a range of chemical, molecular and phenotypic markers which served to separate them from representatives of recognized Amycolatopsis species. The new isolates formed a branch in the Amycolatopsis 16S rRNA gene sequence tree with Amycolatopsis minnesotensis NRRL B-24435(T), but this association was not supported by a particularly high bootstrap value or by the product of the maximum-parsimony tree-making algorithm. The organisms were distinguished readily from closely related Amycolatopsis species based on a combination of phenotypic properties and from all Amycolatopsis strains by their characteristic menaquinone profiles, in which tetra-hydrogenated menaquinones with 11 isoprene units predominated. The combined genotypic and phenotypic data indicate that the isolates merit recognition as representing a novel species of the genus Amycolatopsis. The name proposed for this novel species is Amycolatopsis nigrescens sp. nov., with type strain CSC17Ta-90(T) (=HKI 0330(T)=DSM 44992(T)=NRRL B-24473(T)).
    Matched MeSH terms: DNA, Bacterial/genetics; DNA, Ribosomal/genetics
  19. Comparative analysis of tests used to assess sperm chromatin integrity and DNA fragmentation
    Dutta S, Henkel R, Agarwal A
    Andrologia, 2021 Mar;53(2):e13718.
    PMID: 32628294 DOI: 10.1111/and.13718
    Male infertility has a complex etiology, and many times, the cause is unknown. While routine semen analysis provides an overview of basic semen parameters, such as sperm concentration, motility, viability and morphology, a significant overlap of these parameters has been reported in fertile and infertile men. Moreover, conventional semen parameters do not reveal the cellular or molecular mechanisms of sperm dysfunctions leading to infertility. Therefore, sperm functional parameters, including sperm chromatin integrity, are evaluated to provide information on subtle sperm defects that are not routinely identified. Incomplete or defective sperm chromatin condensation increases the susceptibility of the sperm DNA to oxidative damage or other factors. To evaluate sperm chromatin integrity, different methods with varying degrees of diagnostic and prognostic capabilities are available. Among these assays, SCSA, TUNEL and SCD assays are most commonly used. While these assays rather evaluate the DNA directly for damages, the aniline blue and chromomycin A3 stains test for the quality of chromatin condensation. Thus, this review discusses and compares different methods used to evaluate sperm chromatin integrity and condensation, and their inclusion in the routine evaluation of the male infertility.
    Matched MeSH terms: DNA Fragmentation
  20. Fulltext Genetic diversity of Pantoea stewartii subspecies stewartii causing jackfruit-bronzing disease in Malaysia
    Abidin N, Ismail SI, Vadamalai G, Yusof MT, Hakiman M, Karam DS, et al.
    PLoS One, 2020;15(6):e0234350.
    PMID: 32530926 DOI: 10.1371/journal.pone.0234350
    Jackfruit-bronzing is caused by bacteria Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii), showing symptoms of yellowish-orange to reddish discolouration and rusty specks on pulps and rags of jackfruit. Twenty-eight pure bacterial strains were collected from four different jackfruit outbreak collection areas in Peninsular Malaysia (Jenderam, Maran, Muadzam Shah and Ipoh). Positive P. stewartii subsp. stewartii verification obtained in the study was based on the phenotypic, hypersensitivity, pathogenicity and molecular tests. Multilocus sequence analysis (MLSA) was performed using four housekeeping genes (gyrB, rpoB, atpD and infB) on all 28 bacterial strains. Single gyrB, rpoB, atpD and infB phylogenetic trees analyses revealed the bootstrap value of 99-100% between our bacterial strains with P. stewartii subsp. stewartii reference strains and P. stewartii subsp. indologenes reference strains. On the other hand, phylogenetic tree of the concatenated sequences of the four housekeeping genes revealed that our 28 bacterial strains were more closely related to P. stewartii subsp. stewartii (99% similarities) compared to its close relative P. stewartii subsp. indologenes, although sequence similarity between these two subspecies were up to 100%. All the strains collected from the four collection areas clustered together, pointing to no variation among the bacterial strains. This study improves our understanding and provided new insight on the genetic diversity of P. stewartii subsp. stewartii associated with jackfruit-bronzing in Malaysia.
    Matched MeSH terms: DNA, Bacterial/genetics; DNA, Intergenic/genetics
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