MyMedR

Displaying publications 1501 - 1520 of 3446 in total

Abstract:

Sort:

STR Data for the AmpFlSTR Identifiler loci in three ethnic groups (Malay, Chinese, Indian) of the Malaysian population

Seah LH, Jeevan NH, Othman MI, Jaya P, Ooi YS, Wong PC, et al.

Forensic Sci Int, 2003 Dec 17;138(1-3):134-7.
PMID: 14642733

Allele frequencies for the 15 STR loci in the AmpFlSTR Identifiler kit were determined and compared for the three main ethnic groups of the Malaysian population comprising 210 Malays, 219 Chinese and 209 Indians. Blood was placed on FTA paper and DNA was purified in-situ.

Matched MeSH terms: DNA Fingerprinting/methods
Fulltext Identification of diagnostic markers in colorectal cancer via integrative epigenomics and genomics data

Kok-Sin T, Mokhtar NM, Ali Hassan NZ, Sagap I, Mohamed Rose I, Harun R, et al.

Oncol Rep, 2015 Jul;34(1):22-32.
PMID: 25997610 DOI: 10.3892/or.2015.3993

Apart from genetic mutations, epigenetic alteration is a common phenomenon that contributes to neoplastic transformation in colorectal cancer. Transcriptional silencing of tumor-suppressor genes without changes in the DNA sequence is explained by the existence of promoter hypermethylation. To test this hypothesis, we integrated the epigenome and transcriptome data from a similar set of colorectal tissue samples. Methylation profiling was performed using the Illumina InfiniumHumanMethylation27 BeadChip on 55 paired cancer and adjacent normal epithelial cells. Fifteen of the 55 paired tissues were used for gene expression profiling using the Affymetrix GeneChip Human Gene 1.0 ST array. Validation was carried out on 150 colorectal tissues using the methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) technique. PCA and supervised hierarchical clustering in the two microarray datasets showed good separation between cancer and normal samples. Significant genes from the two analyses were obtained based on a ≥2-fold change and a false discovery rate (FDR) p-value of <0.05. We identified 1,081 differentially hypermethylated CpG sites and 36 hypomethylated CpG sites. We also found 709 upregulated and 699 downregulated genes from the gene expression profiling. A comparison of the two datasets revealed 32 overlapping genes with 27 being hypermethylated with downregulated expression and 4 hypermethylated with upregulated expression. One gene was found to be hypomethylated and downregulated. The most enriched molecular pathway identified was cell adhesion molecules that involved 4 overlapped genes, JAM2, NCAM1, ITGA8 and CNTN1. In the present study, we successfully identified a group of genes that showed methylation and gene expression changes in well-defined colorectal cancer tissues with high purity. The integrated analysis gives additional insight regarding the regulation of colorectal cancer-associated genes and their underlying mechanisms that contribute to colorectal carcinogenesis.

Matched MeSH terms: DNA Methylation/genetics
Fulltext Buccal swab as a suitable source of genomic DNA for screening of selected human leukocyte antigen (HLA) alleles

Vivek Prasad, Lam Yan Shim, Sethu Thakachy Subha, Fazlina Nordin, Maha Abdullah

Malaysian Journal of Medicine and Health Sciences, 2019;15(108):46-46.
MyJurnal

Introduction: Human leukocyte antigens (HLA) are a group of unique transmembrane glycoproteins that are ex-pressed on the surface of virtually all types of cells within the human body. These molecules are encoded by a set of highly polymorphic gene sequences known also as the major histocompatibility complex (MHC) and play an essential role in the presentation of antigenic peptides to immune cells for recognition and response. In recent years, various HLA alleles have been found to be associated with different autoimmune and inflammatory diseases such as rheumatoid arthritis, systemic lupus erythematosus (SLE) and allergic rhinitis. Identification of these alleles via HLA typing is necessary for initial screening and diagnosis purposes. Besides that, HLA typing is also used to determine compatibility matching between a donor and a recipient for tissue/organ transplantations in order to prevent graft rejection. Therefore, good quality and quantity of genomic DNA is required. In most scenarios, peripheral blood is chosen as the most reliable source of DNA for analysis, however this approach is seen as invasive and may cause pain and anxiety among the patients, particularly young children and weak subjects. Hence, derivation of genomic DNA from buccal cells as an alternative source material is becoming increasingly popular, especially in PCR-based genetic assays. Some of the most commonly described methods to collect buccal cells include using oral swabs, cytological brushes, mouthwashes and treated cards. Each technique yields varying quantities of DNA with diverse purity levels. In this study, we aim to evaluate the amount and purity of genomic DNA extracted from buccal swabs and brushes as well as blood for screening of selected HLA class II alleles. Methods: Cheek cell samples were col-lected using sterile foam tipped buccal swabs (Whatman) and buccal collection brushes (Gentra Puregene) whereas peripheral blood samples were withdrawn following routine venipuncture techniques. All samples were subjected to DNA extraction according to modified commercial kit protocols. Screening of selected HLA-DRB1 alleles was con-ducted via PCR with sequence-specific primers as established by Bunce et al. 1995. Results: There was no significant difference (p > 0.05) in the total DNA yield obtained from blood and buccal swab samples, which were 17.57μg (± 8.66) and 13.28μg (± 4.81), respectively. All samples exhibited similar 260/280 ratios of about ~1.80 (p > 0.05). However, buccal brush samples contributed the least amount of DNA (0.29μg, ± 0.12) compared to other sources (p < 0.05). The pure genomic DNA isolated from both blood and buccal swab samples were successfully typed for low resolution HLA-DRB1 alleles. Conclusion: Buccal swabs provide good quantity and quality of DNA for screening of HLA alleles with high accuracy and thus can be utilized as a non-invasive substitute for venipuncture.

Matched MeSH terms: DNA; DNA Primers
The biology and the importance of Photobacterium species

Moi IM, Roslan NN, Leow ATC, Ali MSM, Rahman RNZRA, Rahimpour A, et al.

Appl Microbiol Biotechnol, 2017 Jun;101(11):4371-4385.
PMID: 28497204 DOI: 10.1007/s00253-017-8300-y

Photobacterium species are Gram-negative coccobacilli which are distributed in marine habitats worldwide. Some species are unique because of their capability to produce luminescence. Taxonomically, about 23 species and 2 subspecies are validated to date. Genomes from a few Photobacterium spp. have been sequenced and studied. They are considered a special group of bacteria because some species are capable of producing essential polyunsaturated fatty acids, antibacterial compounds, lipases, esterases and asparaginases. They are also used as biosensors in food and environmental monitoring and detectors of drown victim, as well as an important symbiont.

Matched MeSH terms: DNA, Bacterial; Sequence Analysis, DNA
Plasmodium inui is not closely related to other quartan Plasmodium species

Kissinger JC, Collins WE, Li J, McCutchan TF

J Parasitol, 1998 Apr;84(2):278-82.
PMID: 9576499

Plasmodium inui (Halberstaedter and von Prowazek, 1907), a malarial parasite of Old World monkeys that occurs in isolated pockets throughout the Celebes, Indonesia, Malaysia, and the Philippines, has traditionally been considered to be related more closely to Plasmodium malariae of humans (and its primate counterpart Plasmodium brasilianum), than to other primate Plasmodium species. This inference was made in part because of the similarities in the periodicities or duration of the asexual cycle in the blood, the extended sporogonic cycle, and the longer period of time for development of the pre-erythrocytic stages in the liver. Both P. inui and P. malariae have quartan (72 hr) periodicities associated with their asexual cycle, whereas other primate malarias, such as Plasmodium fragile and Plasmodium cynomolgi, are associated with tertian periodicities (48 hr), and Plasmodiumn knowlesi, with a quotidian (24 hr) periodicity. Phylogenetic analyses of portions of orthologous small subunit ribosomal genes reveal that P. inui is actually more closely related to the Plasmodium species of the "vivax-type" lineage than to P. malariae. Ribosomal sequence analysis of many different, geographically isolated, antigenically distinct P. inui isolates reveals that the isolates are nearly identical in sequence and thus members of the same species.

Matched MeSH terms: DNA, Protozoan/chemistry
Loxodonta Localizer: A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA

Zhao K, Ishida Y, Green CE, Davidson AG, Sitam FAT, Donnelly CL, et al.

J Hered, 2019 12 17;110(7):761-768.
PMID: 31674643 DOI: 10.1093/jhered/esz058

Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poachers than die from natural causes. DNA from tusks has been used to infer the source populations for confiscated ivory, relying on nuclear genetic markers. However, mitochondrial DNA (mtDNA) sequences can also provide information on the geographic origins of elephants due to female elephant philopatry. Here, we introduce the Loxodonta Localizer (LL; www.loxodontalocalizer.org), an interactive software tool that uses a database of mtDNA sequences compiled from previously published studies to provide information on the potential provenance of confiscated ivory. A 316 bp control region sequence, which can be readily generated from DNA extracted from ivory, is used as a query. The software generates a listing of haplotypes reported among 1917 African elephants in 24 range countries, sorted in order of similarity to the query sequence. The African locations from which haplotype sequences have been previously reported are shown on a map. We demonstrate examples of haplotypes reported from only a single locality or country, examine the utility of the program in identifying elephants from countries with varying degrees of sampling, and analyze batches of confiscated ivory. The LL allows for the source of confiscated ivory to be assessed within days, using widely available molecular methods that do not depend on a particular platform or laboratory. The program enables identification of potential regions or localities from which elephants are being poached, with capacity for rapid identification of populations newly or consistently targeted by poachers.

Matched MeSH terms: DNA, Mitochondrial*
Fulltext Genetic diversity of Nile tilapia (Oreochromis niloticus) throughout West Africa

Lind CE, Agyakwah SK, Attipoe FY, Nugent C, Crooijmans RPMA, Toguyeni A

Sci Rep, 2019 11 14;9(1):16767.
PMID: 31727970 DOI: 10.1038/s41598-019-53295-y

Nile tilapia (Oreochromis niloticus) is a globally significant aquaculture species rapidly gaining status as a farmed commodity. In West Africa, wild Nile tilapia genetic resources are abundant yet knowledge of fine-scale population structure and patterns of natural genetic variation are limited. Coinciding with this is a burgeoning growth in tilapia aquaculture in Ghana and other countries within the region underpinned by locally available genetic resources. Using 192 single nucleotide polymorphism (SNP) markers this study conducted a genetic survey of Nile tilapia throughout West Africa, sampling 23 wild populations across eight countries (Benin, Burkina Faso, Côte d'Ivoire, Ghana, Togo, Mali, Gambia and Senegal), representing the major catchments of the Volta, Niger, Senegal and Gambia River basins. A pattern of isolation-by-distance and significant spatial genetic structure was identified throughout West Africa (Global FST = 0.144), which largely corresponds to major river basins and, to a lesser extent, sub-basins. Two populations from the Gambia River (Kudang and Walekounda), one from the western Niger River (Lake Sélingué) and one from the upper Red Volta River (Kongoussi) showed markedly lower levels of diversity and high genetic differentiation compared to all other populations, suggesting genetically isolated populations occurring across the region. Genetic structure within the Volta Basin did not always follow the pattern expected for sub-river basins. This study identifies clear genetic structuring and differentiation amongst West African Nile tilapia populations, which concur with broad patterns found in previous studies. In addition, we provide new evidence for fine-scale genetic structuring within the Volta Basin and previously unidentified genetic differences of populations in Gambia. The 192 SNP marker suite used in this study is a useful tool for differentiating tilapia populations and we recommend incorporating this marker suite into future population screening of O. niloticus. Our results form the basis of a solid platform for future research on wild tilapia genetic resources in West Africa, and the identification of potentially valuable germplasm for use in ongoing breeding programs for aquaculture.

Matched MeSH terms: Sequence Analysis, DNA/methods*
Fulltext Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations

Benavente ED, Gomes AR, De Silva JR, Grigg M, Walker H, Barber BE, et al.

Sci Rep, 2019 07 08;9(1):9873.
PMID: 31285495 DOI: 10.1038/s41598-019-46398-z

The zoonotic Plasmodium knowlesi parasite is the most common cause of human malaria in Malaysia. Genetic analysis has shown that the parasites are divided into three subpopulations according to their geographic origin (Peninsular or Borneo) and, in Borneo, their macaque host (Macaca fascicularis or M. nemestrina). Whilst evidence suggests that genetic exchange events have occurred between the two Borneo subpopulations, the picture is unclear in less studied Peninsular strains. One difficulty is that P. knowlesi infected individuals tend to present with low parasitaemia leading to samples with insufficient DNA for whole genome sequencing. Here, using a parasite selective whole genome amplification approach on unprocessed blood samples, we were able to analyse recent genomes sourced from both Peninsular Malaysia and Borneo. The analysis provides evidence that recombination events are present in the Peninsular Malaysia parasite subpopulation, which have acquired fragments of the M. nemestrina associated subpopulation genotype, including the DBPβ and NBPXa erythrocyte invasion genes. The NBPXb invasion gene has also been exchanged within the macaque host-associated subpopulations of Malaysian Borneo. Our work provides strong evidence that exchange events are far more ubiquitous than expected and should be taken into consideration when studying the highly complex P. knowlesi population structure.

Matched MeSH terms: DNA, Protozoan/genetics*
Genetic characterization of Theileria species infecting bovines in India

Kundave VR, Ram H, Shahzad M, Garg R, Banerjee PS, Nehra AK, et al.

Infect Genet Evol, 2019 11;75:103962.
PMID: 31302242 DOI: 10.1016/j.meegid.2019.103962

Genetic characterization of Theileria species infecting bovines in India was attempted targeting the 18S ribosomal RNA region of the parasite. Blood samples of bovines (n = 452), suspected for haemoprotozoan infections, from 9 different states of the country were microscopically examined for Theileria species infection. Four Theileria spp. positive blood samples from each state were randomly utilized for PCR amplification of the 18S rRNA gene (approx. 1529 bp) followed by cloning and sequencing. The sequence data analysis of all the 36 isolates revealed that 33 isolates had high sequence similarity with published sequences of T. annulata, whereas 3 isolates (MF287917, MF287924 and MF287928) showed close similarity with published sequences of T. orientalis. Sequence homology within the isolates ranged between 95.8 and 100% and variation in the length of targeted region was also noticed in different isolates (1527-1538 nt). Phylogenetic tree created for T. annulata sequences revealed that a total of 24 Indian isolates formed a major clade and grouped together with isolates originating from countries like China, Spain, Turkey and USA. Remaining 09 isolates clustered in a separate group and were closely related to the TA5 isolate of T. annulata (a new genotype) originating from India and also with the isolates from East Asian countries like Japan and Malaysia. All the three T. orientalis isolates had minimal intraspecific variation (99-100% homology) amongst themselves. Further, in the phylogenetic analysis T. orientalis Indian isolates were found to cluster away from other 14 isolates of T. buffeli/sergenti/orientalis originating from different countries (Australia, China, Indonesia and Spain). However, these 3 isolates clustered together with the T. buffeli Indian isolate (EF126184). Present study confirmed the circulation of different genotypes of T. annulata in India, along with T. orientalis isolates.

Matched MeSH terms: DNA, Protozoan/genetics
The Morphological and Molecular Description of Acanthogyrus (Acanthosentis) fusiformis n. sp. (Acanthocephala: Quadrigyridae) from the Catfish Arius sp. (Ariidae) in the Pacific Ocean off Vietnam, with Notes on Zoogeography

Amin OM, Chaudhary A, Heckmann RA, Ha NV, Singh HS

Acta Parasitol, 2019 Dec;64(4):779-796.
PMID: 31332657 DOI: 10.2478/s11686-019-00102-3

BACKGROUND: Most (82%) of the 46 recognized species of Acanthogyrus (Acanthosentis) Verma and Datta, 1929 are known from Asian freshwater fishes. Only three species of Acanthosentis are known from marine or brackish water fishes from India and Pakistan. We have discovered another marine species of Acanthosentis in the Pacific Ocean, off Vietnam.
PURPOSE: The purpose is to describe the new species morphologically and molecularly and provide new information of its evolutionally relationships with other species of the subgenus.
METHODS: Standard methods of collection and examination of marine hosts, processing and illustrating of specimens, and taxonomic identification of parasites using the extensive collection of the lead author were used. Specimens were further studied using energy-dispersive X-ray analysis and ion sectioning of hooks, SEM analysis, and molecular sequencing. Type specimens were deposited at the Harold W. Manter Lab. collection, Lincoln, Nebraska.
RESULTS: Acanthogyrus (Acanthosentis) fusiformis n. sp. is described from the catfish, Arius sp. (Ariidae: Siluriformes) off the Pacific Coast of Vietnam at Bac Lieu in the Gulf of Thailand. The three other marine Indian species include A. (A.) arii Bilqees, 1971 which is also described from a similar catfish, Arius serratus Day off the Karachi coast in the Arabian Sea, Indian Ocean. Our new species from Vietnam is distinguished from the other 46 species by a combination of characters including a small fusiform trunk, complete circles of small hollow spines covering the entire trunk, prominent double apical organs often extending posteriorly past posterior hooks, middle and posterior hooks of equal size slightly smaller than anterior hooks, large neck continuous with the outline of the proboscis without distinct separation, big drop-shaped cephalic ganglion, extension of the proboscis receptacle anteriorly past the base of the proboscis up to the insertion point of the posterior hooks, presence of two para-receptacle structures (PRSs), free unattached thick lemnisci, short female reproductive system with filamentous attachment of the distal end of the uterine bell to the ventral body wall, and small narrowly ellipsoid eggs with thickened polar ends. Partial sequences of the 18S and internal transcribed spacers (ITS1-5.8S-ITS2) of ribosomal RNA were generated and used for phylogenetic analyses to confirm the taxonomic identity of Acanthogyrus (Acanthosentis) fusiformis n. sp.
CONCLUSIONS: We describe unique morphological features of A. fusiformis never before known in the subgenus Acanthosentis. The uniqueness of A. fusiformis is further demonstrated by its EDXA fingerprint characterized by high levels of calcium and phosphorous in hooks. The zoogeography of species of Acanthosentis is elucidated in the Indian subcontinent, the Caribbean, China, and Africa. Molecular data have been available only in few species of Acanthogyrus (Acanthosentis) to date on GenBank database. For 18S, only two sequences from unknown Acanthosentis sp. from India are available, while for the ITS1-5.8S-ITS2 region, only sequences of A. cheni from China and of two unidentified species from Malaysia are available. Additional studies of species of Acanthosentis based on morphological and molecular genetic data will be needed to reconstruct the evolutionary history and phylogenetic affinities of this group of acanthocephalans.

Matched MeSH terms: DNA, Helminth/genetics
Target DNA detection of human papilloma virus-16 E7 gene by capture-target-reporter sandwich on interdigitated electrode sensor

Lin J, Gopinath SCB, Lakshmipriya T, Chen Y, Yuan WR, Yang M

Int J Biol Macromol, 2019 Dec 01;141:564-569.
PMID: 31493451 DOI: 10.1016/j.ijbiomac.2019.09.012

Human papilloma virus (HPV) affects predominantly the genital area, which includes vagina, cervix, penis, vulva scrotum, rectum and anus. Among 100 types of HPV, 14 types are considered to cause the risky cancer. The gene HPV-16 E7 is responsible for the development of cancer with the infected women. Earlier identification of this gene sequence avoids the cancer progression. The targeted HPV-16 E7 sequence was sandwiched by capture and reporter sequences on the carbodiimidazole-modified interdigitated electrode (IDE) surface. Target sequence at 100 f. was paired to the capture sequence immobilized on IDE sensing surface. To this surface, different concentrations of reporter sequence with and without gold rod (GNR) were evaluated. In both cases the detections were attained 1 aM by the reporter sequence pairing and with GNR increments in current were found. This enhancement was found to be 1000 folds, considering the condition was revealed in the absence of reporter. This sandwich detection strategy of capture-target-reporter sequences for HPV-16 detection on the IDE sensing surface helps to diagnose the association of cervical cancer.

Matched MeSH terms: DNA, Viral/analysis*
Fulltext Pertussis clinical case definition: Time for change in developing countries?

Gopal Krishnan S, Fun WH, Ramadras MD, Yunus R, Lye YF, Sararaks S

PLoS One, 2019;14(7):e0219534.
PMID: 31291359 DOI: 10.1371/journal.pone.0219534

BACKGROUND: Developing countries still struggle with late detection and mortality from pertussis. A review of clinical case definitions is necessary for early disease detection. This paper aimed to study possible clinical characteristics for earlier pertussis detection in a sporadic setting.
METHODS: We conducted a retrospective review of medical and laboratory records in a general paediatric ward of a district hospital in a developing country. Inclusion criteria were all children hospitalised with nasopharyngeal swab taken for Bordetella pertussis. We compared sensitivity and specificity of World Health Organization diagnostic criteria with other clinical characteristics. Polymerase chain reaction Bordetella pertussis was the gold standard used.
RESULTS: Out of 207 eligible admissions, the study retrieved 128 complete records. Approximately half of the children were less than 3 months old. The World Health Organization diagnostic criteria had a low sensitivity (15%), but high specificity (92%). In comparison, combinations that included paroxysmal cough, ill contact and facial congestion had higher sensitivity. Increasing cough duration improved specificity while compromising sensitivity.
CONCLUSION: Several clinical characteristics such as paroxysmal cough, facial congestion and a history of ill contact have potential for early clinical detection. Conventional emphasis on cough duration may hamper early detection.

Matched MeSH terms: DNA, Bacterial/isolation & purification
A DNA based visual and colorimetric aggregation assay for the early growth factor receptor (EGFR) mutation by using unmodified gold nanoparticles

Ramanathan S, Gopinath SCB, Arshad MKM, Poopalan P, Anbu P

Mikrochim Acta, 2019 07 18;186(8):546.
PMID: 31321546 DOI: 10.1007/s00604-019-3696-y

A genomic DNA-based colorimetric assay is described for the detection of the early growth factor receptor (EGFR) mutation, which is the protruding reason for non-small cell lung cancer. A DNA sequence was designed and immobilized on unmodified gold nanoparticles (GNPs). The formation of the respective duplex indicates the presence of an EGFR mutation. It is accompanied by the aggregation of the GNPs in the presence of monovalent ions, and it indicates the presence of an EGFR mutation. This is accompanied by a color change from red (520 nm) to purple (620 nm). Aggregation was evidenced by transmission electron microscopy, scanning electron microscopy and atomic force microscopy. The limit of detection is 313 nM of the mutant target strand. A similar peak shift was observed for 2.5 μM concentrations of wild type target. No significant peak shift was observed with probe and non-complementary DNA. Graphical abstract Schematic representation of high-specific genomic DNA sequence on gold nanoparticle (GNP) aggregation with sodium chloride (NaCl). It illustrates the detection method for EGFR mutation on lung cancer detection. Red and purple colors of tubes represent dispersed and aggregated GNP, respectively.

Matched MeSH terms: DNA, Single-Stranded/chemistry*
Fulltext Transposable Elements Adaptive Role in Genome Plasticity, Pathogenicity and Evolution in Fungal Phytopathogens

Mat Razali N, Cheah BH, Nadarajah K

Int J Mol Sci, 2019 Jul 23;20(14).
PMID: 31340492 DOI: 10.3390/ijms20143597

Transposable elements (TEs) are agents of genetic variability in phytopathogens as they are a source of adaptive evolution through genome diversification. Although many studies have uncovered information on TEs, the exact mechanism behind TE-induced changes within the genome remains poorly understood. Furthermore, convergent trends towards bigger genomes, emergence of novel genes and gain or loss of genes implicate a TE-regulated genome plasticity of fungal phytopathogens. TEs are able to alter gene expression by revamping the cis-regulatory elements or recruiting epigenetic control. Recent findings show that TEs recruit epigenetic control on the expression of effector genes as part of the coordinated infection strategy. In addition to genome plasticity and diversity, fungal pathogenicity is an area of economic concern. A survey of TE distribution suggests that their proximity to pathogenicity genes TEs may act as sites for emergence of novel pathogenicity factors via nucleotide changes and expansion or reduction of the gene family. Through a systematic survey of literature, we were able to conclude that the role of TEs in fungi is wide: ranging from genome plasticity, pathogenicity to adaptive behavior in evolution. This review also identifies the gaps in knowledge that requires further elucidation for a better understanding of TEs' contribution to genome architecture and versatility.

Matched MeSH terms: DNA Transposable Elements*
Amplification-free and direct fluorometric determination of telomerase activity in cell lysates using chimeric DNA-templated silver nanoclusters

Lee ST, Rahman R, Muthoosamy K, Mohamed NAH, Su X, Tayyab S, et al.

Mikrochim Acta, 2019 01 09;186(2):81.
PMID: 30627857 DOI: 10.1007/s00604-018-3194-7

A fluorogenic probe has been developed for determination of telomerase activity using chimeric DNA-templated silver nanoclusters (AgNCs). The formation of AgNCs was investigated before (route A) and after (route B) telomerase elongation reaction. Both routes caused selective quenching of the yellow emission of the AgNCs (best measured at excitation/emission wavelength of 470/557 nm) in telomerase-positive samples. The quenching mechanism was studied using synthetically elongated DNA to mimic the telomerase-catalyzed elongation. The findings show that quenching is due to the formation of parallel G-quadruplexes with a -TTA- loop in the telomerase elongated products. The assay was validated using different cancer cell extracts, with intra- and interassay coefficients of variations of <9.8%. The limits of detection for MCF7, RPMI 2650 and HT29 cell lines are 15, 22 and 39 cells/μL. This represents a distinct improvement over the existing telomeric repeat amplification protocol (TRAP) assay in terms of time, sensitivity and cost. Graphical Abstract A method was developed using chimeric DNA-templated silver nanoclusters to detect telomerase activity directly in cell extracts. The sensitivity of this new method outperforms the traditional TRAP assay, and without the need for amplification.

Matched MeSH terms: DNA/chemistry
Species Identification and Unlocking Hidden Genetic Diversity of Confiscated Slow Lorises (Nycticebus spp.) Based on Mitochondrial DNA Markers

Kongrit C, Markviriya D, Laithong P, Khudamrongsawat J

Folia Primatol., 2020;91(1):1-14.
PMID: 31593962 DOI: 10.1159/000500007

Confiscated slow lorises (Nycticebus spp.) at Bangpra Water-Bird Breeding Center (BWBC) in Thailand provided an opportunity to demonstrate the application of noninvasive genetic approaches for species identification when morphology of the animals was ambiguous. The slow lorises at BWBC had been assigned to either N. bengalensis or N. pygmaeus, based on body size. However, the morphology of N. bengalensis is highly variable and overlaps with that of N. coucang (sensu stricto). Phylogenetic analysis of cytochrome b and d-loop mitochondrial regions placed all confiscated N. pygmaeus with the published sequences of N. pygmaeus and distinguished them from other Nycticebus. All other confiscated individuals formed a monophyletic clade, most individuals grouping with published N. bengalensis sequences from wild populations in Vietnam and distinct from Peninsular Malaysian and Sumatran N. coucang, Javan N. javanicus and Bornean N. menagensis. Six individuals within the N. bengalensis clade formed a separate subgroup that did not group with any reference material as indicated by phylogenetic and haplotype network analyses. Whether these trafficked individuals are undiscovered wild populations will require further investigation. Additional genetic studies of wild slow loris populations in different regions are therefore urgently required for reference to aid the protection and conservation of these threatened species.

Matched MeSH terms: DNA, Mitochondrial/analysis
An infectious full-length cDNA clone of duck Tembusu virus, a newly emerging flavivirus causing duck egg drop syndrome in China

Li S, Zhang L, Wang Y, Wang S, Sun H, Su W, et al.

Virus Res, 2013 Jan;171(1):238-41.
PMID: 23116594 DOI: 10.1016/j.virusres.2012.10.019

Duck Tembusu virus (TMUV) is a recently identified pathogenic flavivirus that causes severe egg drop and encephalitis in Chinese ducks and geese. It has been found to be most closely related to the mosquito-origin Tembusu virus and chicken Sitiawan virus reported in Malaysia. However, the ecological characteristics and the pathogenesis of duck TMUV are largely unknown. We report the construction of full-length cDNA clone of duck TMUV strain JXSP. The virus genome was reverse transcribed, amplified as seven overlapping fragments and successively ligated into the low copy number vector pWSK29 under the control of a T7 promoter. Transfection of BHK-21 cells with the transcribed RNA from the full-length cDNA clone resulted in production of highly infectious progeny virus. In vitro growth characteristics in BHK-21 cells and virulence in ducklings and BALB/c mice were similar for the rescued and parental viruses. This stable infectious cDNA clone will be a valuable tool for studying the genetic determinants of duck TMUV.

Matched MeSH terms: DNA, Complementary*
Detection and molecular identification of Leucocytozoon and Plasmodium species from village chickens in different areas of Myanmar

Win SY, Chel HM, Hmoon MM, Htun LL, Bawm S, Win MM, et al.

Acta Trop, 2020 Dec;212:105719.
PMID: 32976841 DOI: 10.1016/j.actatropica.2020.105719

Village chicken production, a traditional, small-scale, and extensive backyard poultry industry, has been profitable for local farmers in Myanmar. However, there is scanty information available concerning the infection of these chickens with avian pathogens, including haemoprotozoan parasites. In the present study, we provide the first report of microscopic detection and molecular identification of Leucocytozoon and Plasmodium parasites from seven different areas of Myanmar. Leucocytozoon gametocytes were detected in 17.6% (81/461) of the blood smears from village chickens. The nested polymerase chain reaction (PCR) for targeting Leucocytozoon mitochondrial cytochrome b (cyt b) genes had a 17.6% positive rate. Although the positive rate of nested PCR targeting Plasmodium/Haemoproteus cyt b was 34.3%, the PCR protocol was observed to possibly amplify DNA of a certain species of Leucocytozoon. There were no obvious clinical signs in the infected birds. Statistical analysis of the microscopic detection and PCR detection rates using the age and sex of birds as internal factors revealed that the statistical significances differed according to the study area. The sequencing of 32 PCR products obtained from each study area revealed infection by Leucocytozoon caulleryi in three birds, Leucocytozoon sabrazesi in two birds, Leucocytozoon schoutedeni in two birds, Leucocytozoon sp. in eighteen birds, and Plasmodium juxtanucleare in seven birds; however, Haemoproteus infection was not detected. While L. sabrazesi was detected in chickens from the central region of Myanmar, the other haemosporidians were detected in those from different areas. In the haplotype analysis, we detected 17 haemosporidian cyt b haplotypes, including two for L. caulleryi, one for L. sabrazesi, two for L. schoutedeni, nine for Leucocytozoon sp., and three for P. juxtanucleare. Phylogenetic analysis of the cyt b haplotypes revealed a considerably close genetic relationship among chicken haemosporidians detected in Myanmar, Thailand, and Malaysia. These results indicate that well-recognized widespread species of chicken Leucocytozoon and Plasmodium are distributed nationwide in Myanmar, providing new insights into the ecosystem and control strategies of haemosporidian parasites in domesticated chickens in Myanmar.

Matched MeSH terms: DNA, Protozoan/genetics*
Polymerase chain reaction assay targeting cytochrome b gene for the detection of dog meat adulteration in meatball formulation

Rahman MM, Ali ME, Hamid SB, Mustafa S, Hashim U, Hanapi UK

Meat Sci, 2014 Aug;97(4):404-9.
PMID: 24769096 DOI: 10.1016/j.meatsci.2014.03.011

A polymerase chain reaction (PCR) assay for the assessment of dog meat adulteration in meatballs was developed. The assay selectively amplified a 100-bp region of canine mitochondrial cytochrome b gene from pure, raw, processed and mixed backgrounds. The specificity of the assay was tested against 11 animals and 3 plants species, commonly available for meatball formulation. The stability of the assay was proven under extensively autoclaving conditions that breakdown target DNA. A blind test from ready to eat chicken and beef meatballs showed that the assay can repeatedly detect 0.2% canine meat tissues under complex matrices using 0.04 ng of dog DNA extracted from differentially treated meatballs. The simplicity, stability and sensitivity of the assay suggested that it could be used in halal food industry for the authentication of canine derivatives in processed foods.

Matched MeSH terms: DNA/analysis*
Hb Bart's level in cord blood and deletions of alpha-globin genes

Lie-Injo LE, Solai A, Herrera AR, Nicolaisen L, Kan YW, Wan WP, et al.

Blood, 1982 Feb;59(2):370-6.
PMID: 6895707

The white blood cell DNA of 36 cord blood samples with Hb Bart's in the red blood cells was studied for alpha-globin gene deletions by hybridization of DNA fragments digested by the restriction endonucleases Eco RI, Hpa I, Bam HI, and Bgl II. All 16 DNA samples from cord blood with Hb Bart's below 3% and no other abnormal hemoglobin had one alpha-globin gene deletion (alpha thal2), except one which had two alpha-globin gene deletions (alpha thal1). Most of the alpha thal2 were of the rightward deletion alpha thal2 genotype. Two new types of alpha thal2 variation was found, probably due to a polymorphism somewhere in an area outside the alpha-globin gene. All 14 cases with Hb Bart's between 3.5% and 8.5% and no other abnormal hemoglobin had two alpha-globin gene deletions (alpha thal1), except one that did not have any alpha-globin gene deletion and one that had one alpha-globin gene deletion. Three DNA samples of cord blood with Hb Bart's accompanied by Hb CoSp did not have any alpha-globin gene deletion. Sixty-five DNA samples from cord blood without Hb Bart's or other abnormal hemoglobin had no alpha-globin gene deletions, except one that had one alpha-globin gene deletion (alpha thal2). Two of the 65 DNA samples were found to have triplicated alpha-globin gene loci.

Matched MeSH terms: DNA/blood

Filters

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links