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  1. 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*
  2. 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*
  3. 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*
  4. DNA fragmentation, an indicator of apoptosis, in cultured black tiger shrimp Penaeus monodon infected with white spot syndrome virus (WSSV)
    Sahtout AH, Hassan MD, Shariff M
    Dis Aquat Organ, 2001 Mar 9;44(2):155-9.
    PMID: 11324818
    Fifty black tiger shrimp Penaeus monodon from commercial cultivation ponds in Malaysia were examined by Tdt-mediated dUTP nick-end labeling (TUNEL) fluorescence assay and agarose gel electrophoresis of DNA extracts for evidence of DNA fragmentation as an indicator of apoptosis. From these specimens, 30 were grossly normal and 20 showed gross signs of white spot syndrome virus (WSSV) infection. Of the 30 grossly normal shrimp, 5 specimens were found to be positive for WSSV infection by normal histology and by nested polymerase chain reaction (PCR) analysis. All of the specimens showing gross signs of WSSV infection were positive for WSSV by normal histology, while 5 were positive by nested PCR only (indicating light infections) and 15 were positive by 1-step PCR (indicating heavy infections). Typical histological signs of WSSV infection included nuclear hypertrophy, chromatin condensation and margination. None of the 25 grossly normal shrimp negative for WSSV by 1-step PCR showed any signs of DNA fragmentation by TUNEL assay or agarose gel electrophoresis of DNA extracts. The 10 specimens that gave PCR-positive results for WSSV by nested PCR only (i.e., 5 grossly normal shrimp and 5 grossly positive for WSSV) gave mean counts of 16 +/- 8% TUNEL-positive cells, while the 25 specimens PCR positive by 1-step PCR gave mean counts of 40 +/- 7% TUNEL-positive cells. Thus, the number of TUNEL positive cells present in tissues increased with increasing severity of infection, as determined by gross signs of white spots on the cuticle, the number of intranuclear inclusions in histological sections, and results from single and nested PCR assays. DNA extracts of PCR-positive specimens tested by agarose gel electrophoresis showed indications of DNA fragmentation either as smears or as 200 bp ladders. Given that DNA fragmentation is generally considered to be a hallmark of apoptosis, the results suggested that apoptosis might be implicated in shrimp death caused by WSSV.
    Matched MeSH terms: DNA Viruses/physiology*; DNA Fragmentation*
  5. 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*
  6. Fulltext Development of species-specific SCAR markers for identification and authentication of three rare Peninsular Malaysian endemic Coelogyne (Orchidaceae) orchids
    Kok Hon Y, Yong CS, Abdullah JO, Go R
    F1000Res, 2020;9:1161.
    PMID: 33299554 DOI: 10.12688/f1000research.26170.2
    Background:Coelogyne kaliana, Coelogyne stenochila and Coelogyne tiomanensis are three valuable rare orchid species endemic to Peninsular Malaysia, currently rampantly traded illegally via the internet and through local nurseries, which label them as hybrids to avoid enforcement detection. Drastic measures to ensure the continued existence of their populations in the wild should be introduced as they are rapidly diminishing into extinction, including the development of rapid and accurate species-specific identification tools. These three orchid species are highly similar morphologically and currently it is impossible to distinguish among them without their reproductive structures. Methods:  RAPD-based species-specific SCAR markers were developed to distinguish and authenticate the identity of these three endemic Peninsular Malaysian Coelogyne species. Results: Three SCAR markers were successfully developed in this study. SCAR marker primer pair , CKL_f / CKL_r was specific to C. kaliana as it produced a unique single band of 271 bp but not in C. stenochila and C. tiomanensis.  SCAR marker primer pair CST_f / CST_r amplified a single band of 854 bp in C. stenochila and two bands of different sizes (372 bp and 858 bp) in C. tiomanensis, but no amplification in C. kaliana. The third SCAR marker primer pair, CTI_f / CTI_r produced a single band (about 500 bp) for both C. stenochila and C. tiomanensis, but showed no amplification in C. kaliana. Conclusions: Although not all these SCAR markers were species amplification specific, they could be used to discriminate among the three Coelogyne species effectively.  Accurate species identification is one of the most important steps to allow a proper management plan to be established in the effort to conserve these three endangered orchid species of Peninsular Malaysia. Besides, it could effectively put a stop to the illegal trading of these rare endangered orchid species worldwide.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  7. Static watson-crick linear grammars and its computational power
    Aqilahfarhana Abdul Rahman, Wan Heng Fong, Nor Haniza Sarmin, Sherzod Turaev, Nurul Liyana Mohamad Zulkufli
    MATEMATIKA, 2019;35(3):283-296.
    MyJurnal
    DNA computing, or more generally, molecular computing, is a recent development on computations using biological molecules, instead of the traditional silicon-chips. Some computational models which are based on different operations of DNA molecules have been developed by using the concept of formal language theory. The operations of DNA molecules inspire various types of formal language tools which include sticker systems, grammars and automata. Recently, the grammar counterparts of Watson-Crick automata known as Watson-Crick grammars which consist of regular, linear and context-free grammars, are defined as grammar models that generate double-stranded strings using the important feature of Watson-Crick complementarity rule. In this research, a new variant of static Watson-Crick linear grammar is introduced as an extension of static Watson-Crick regular grammar. A static Watson-Crick linear grammar is a grammar counterpart of sticker system that generates the double-stranded strings and uses rule as in linear grammar. The main result of the paper is to determine some computational properties of static Watson-Crick linear grammars. Next, the hierarchy between static Watson-Crick languages, Watson-Crick languages, Chomsky languages and families of languages generated by sticker systems are presented.
    Matched MeSH terms: DNA
  8. Isolation, identification, characterization, and evaluation of cadmium removal capacity of Enterobacter species
    Abbas SZ, Rafatullah M, Ismail N, Lalung J
    J Basic Microbiol, 2014 Dec;54(12):1279-87.
    PMID: 24852724 DOI: 10.1002/jobm.201400157
    This study focused on the isolation and characterization of high cadmium-resistant bacterial strains, possible exploitation of its cadmium-accumulation and cadmium-induced proteins. Cadmium-resistant bacterial strains designated as RZ1 and RZ2 were isolated from industrial wastewater of Penang, Malaysia. These isolates were identified as Enterobacter mori and Enterobacter sp. WS12 on the basis of phenotypic, biochemical and 16S rDNA sequence based molecular phylogenetic characteristics. Both isolates were Gram negative, cocci, and growing well in Lauria-Bertani broth medium at 35 °C temperature and pH 7.0. Results also indicated that Enterobacter mori and Enterobacter sp. WS12are capable to remove 87.75 and 85.11% of the cadmium from 100 µg ml(-1) concentration, respectively. This study indicates that these strains can be useful as an inexpensive and efficient bioremediation technology to remove and recover the cadmium from wastewater.
    Matched MeSH terms: DNA, Bacterial/genetics; DNA, Ribosomal/genetics
  9. Dysplasia and DNA ploidy to prognosticate clinical outcome in oral potentially malignant disorders
    Sathasivam HP, Nayar D, Sloan P, Thomson PJ, Odell EW, Robinson M
    J Oral Pathol Med, 2021 Feb;50(2):200-209.
    PMID: 33151583 DOI: 10.1111/jop.13121
    BACKGROUND: Oral potentially malignant disorders are a clinical conundrum as there are no reliable methods to predict their behaviour. We combine conventional oral epithelial dysplasia grading with DNA ploidy analysis to examine the validity of this approach to risk assessment in a cohort of patients with known clinical outcomes.

    METHODS: Sections from diagnostic biopsies were assessed for oral epithelial dysplasia using the WHO grading system, and DNA ploidy analysis was performed using established methods. Patients reviewed for a minimum of 5 years who did not develop oral squamous cell carcinoma were classified as "non-transforming" cases. Patients that developed oral squamous cell carcinoma ≥ 6 months after the initial diagnostic biopsy were classified as having "malignant transformation."

    RESULTS: Ninety cases were included in the study. Seventy cases yielded informative DNA ploidy results. Of these 70 cases, 31 progressed to cancer. Oral epithelial dysplasia grading and DNA ploidy status were both significantly associated with clinical outcome (P DNA ploidy status and 0.688 when DNA ploidy status was combined with dysplasia grading.

    CONCLUSION: Our findings suggest that combining dysplasia grading with DNA ploidy status has clinical utility which could be used to develop novel management algorithms.

    Matched MeSH terms: DNA
  10. The genetic structure of Oreochromis spp. (Tilapia) populations in Malaysia as revealed by microsatellite DNA analysis
    Bhassu S, Yusoff K, Panandam JM, Embong WK, Oyyan S, Tan SG
    Biochem Genet, 2004 Aug;42(7-8):217-29.
    PMID: 15487586
    The genetic make-up of five populations of Oreochromis spp. was examined by microsatellite analysis. Eleven polymorphic microsatellite loci showed significant departures from the Hardy-Weinberg equilibrium. The mean heterozygosity ranged from 0.6280 to 0.7040 for each population. The genetic distance values showed a clear separation between O. niloticus and O. mossambicus. The differentiation of the O. niloticus populations was then tested with various genetic measures, which are based on both the Infinite Allele and the Stepwise Mutation models. All these measures grouped the populations similarly.
    Matched MeSH terms: DNA/genetics; DNA/metabolism; DNA Primers
  11. Identification and characterization of Malaysian river catfish, Mystus nemurus (C&V): RAPD and AFLP analysis
    Chong LK, Tan SG, Yusoff K, Siraj SS
    Biochem Genet, 2000 Apr;38(3-4):63-76.
    PMID: 11100266
    This work represents the first application of the amplified fragment length polymorphism (AFLP) technique and the random amplified polymorphic DNA (RAPD) technique in the study of genetic variation within and among five geographical populations of M. nemurus. Four AFLP primer combinations and nine RAPD primers detected a total of 158 and 42 polymorphic markers, respectively. The results of AFLP and RAPD analysis provide similar conclusions as far as the population clustering analysis is concerned. The Sarawak population, which is located on Borneo Island, clustered by itself and was thus isolated from the rest of the populations located in Peninsular Malaysia. Both marker systems revealed high genetic variability within the Universiti Putra Malaysia (UPM) and Sarawak populations. Three subgroups each from the Kedah, Perak, and Sarawak populations were detected by AFLP but not by RAPD. Unique AFLP fingerprints were also observed in some unusual genotypes sampled in Sarawak. This indicates that AFLP may be a more efficient marker system than RAPD for identifying genotypes within populations.
    Matched MeSH terms: DNA Fingerprinting; DNA Primers; Random Amplified Polymorphic DNA Technique*
  12. Hebeloma in the Malay Peninsula: Masquerading within Psathyrella
    Eberhardt U, Schütz N, Beker HJ, Lee SS, Horak E
    MycoKeys, 2021;77:117-141.
    PMID: 33551660 DOI: 10.3897/mycokeys.77.57394
    In 1994 Corner published five new species within the genus Psathyrella, all having been collected on the Malay Peninsula between 1929 and 1930. Three of these species belong to the genus Hebeloma and with their vinaceous colored lamellae and spore print, when fresh, they belong to H. sect. Porphyrospora. Of these three species, only one, P. flavidifolia, was validly published and thus we herewith recombine it as H. flavidifolium. The other two species, P. splendens and P. verrucispora, are synonyms of H. parvisporum and H. lactariolens, respectively. We also describe a new Malayan species, H. radicans, which also belongs to H. sect. Porphyrospora. These findings confirm the western Pacific Rim as a diversity hotspot for H. sect. Porphyrospora. The records described within this paper, represent the first recognition that the genus Hebeloma, and indeed that members of the ectomycorrhizal Hymenogastraceae, are present on the Malay Peninsula.
    Matched MeSH terms: DNA, Ribosomal Spacer
  13. Fulltext The complete mitochondrial genome of the cavity-nesting honeybee, Apis koschevnikovi (Insecta: Hymenoptera: Apidae)
    Wakamiya T, Tingek S, Okuyama H, Kiyoshi T, Takahashi JI
    Mitochondrial DNA B Resour, 2017 Jan 17;2(1):24-25.
    PMID: 33490434 DOI: 10.1080/23802359.2016.1275847
    In this study, we analyzed the complete mitochondrial genome of the cavity-nesting honeybee, A. koschevnikovi. The mitochondrial genome of A. koschevnikovi was observed to be a circular molecule of 15,278 bp and was similar to that of the other cavity-nesting honeybee species. The average AT content in the A. koschevnikovi mitochondrial genome was 84%. It was predicted to contain 13 protein-coding, 24 tRNA and two rRNA genes, along with one A + T-rich control region, besides three tRNA-Met repeats.
    Matched MeSH terms: DNA, Mitochondrial
  14. Fulltext Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes
    Takeuchi Y, Chaffron S, Salcher MM, Shimizu-Inatsugi R, Kobayashi MJ, Diway B, et al.
    Syst Appl Microbiol, 2015 Jul;38(5):330-9.
    PMID: 26138047 DOI: 10.1016/j.syapm.2015.05.006
    Pitchers are modified leaves used by carnivorous plants for trapping prey. Their fluids contain digestive enzymes from the plant and they harbor abundant microbes. In this study, the diversity of bacterial communities was assessed in Nepenthes pitcher fluids and the composition of the bacterial community was compared to that in other environments, including the phyllosphere of Arabidopsis, animal guts and another pitcher plant, Sarracenia. Diversity was measured by 454 pyrosequencing of 16S rRNA gene amplicons. A total of 232,823 sequences were obtained after chimera and singleton removal that clustered into 3260 distinct operational taxonomic units (OTUs) (3% dissimilarity), which were taxonomically distributed over 17 phyla, 25 classes, 45 orders, 100 families, and 195 genera. Pyrosequencing and fluorescence in situ hybridization yielded similar estimates of community composition. Most pitchers contained high proportions of unique OTUs, and only 22 OTUs (<0.6%) were shared by ≥14/16 samples, suggesting a unique bacterial assemblage in each pitcher at the OTU level. Diversity analysis at the class level revealed that the bacterial communities of both opened and unopened pitchers were most similar to that of Sarracenia and to that in the phyllosphere. Therefore, the bacterial community in pitchers may be formed by environmental filtering and/or by phyllosphere bacteria.
    Matched MeSH terms: DNA, Ribosomal/genetics; DNA, Ribosomal/chemistry; Sequence Analysis, DNA
  15. 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
  16. An electrochemical DNA biosensor fabricated from graphene decorated with graphitic nanospheres
    Raja Jamaluddin RZA, Tan LL, Chong KF, Heng LY
    Nanotechnology, 2020 Nov 27;31(48):485501.
    PMID: 32748805 DOI: 10.1088/1361-6528/abab2e
    Graphene decorated with graphitic nanospheres functionalized with pyrene butyric acid (PBA) is used for the first time to fabricate a DNA biosensor. The electrode was formed by attaching a DNA probe onto PBA, which had been stacked onto a graphene material decorated with graphene nanospheres (GNSs). The nanomaterial was drop-coated onto a carbon screen-printed electrode (SPE) to create the GNS-PBA modified electrode (GNS-PBA/SPE). A simple method was used to produce GNS by annealing graphene oxide (GO) solution at high temperature. Field emission scanning electron micrographs confirmed the presence of a spherical shape of GNS with a diameter range of 40-80 nm. A stable and uniform PBA-modified GNS (GNS-PBA) was obtained with a facile ultrasonication step. Thus allowing aminated DNA probes of genetically modified (GM) soybean to be attached to the nanomaterials to form the DNA biosensor. The GNS-PBA/SPE exhibited excellent electrical conductivity via cyclic voltammetry (CV) and differential pulse voltammetry (DPV) tests using potassium ferricyanide (K3[Fe(CN)6]) as the electroactive probe. By employing an anthraquinone monosulfonic acid (AQMS) redox intercalator as the DNA hybridization indicator, the biosensor response was evaluated using the DPV electrochemical method. A good linear relationship between AQMS oxidation peak current and target DNA concentrations from 1.0 × 10-16 to 1.0 × 10-8 M with a limit of detection (LOD) of less than 1.0 × 10-16 M was obtained. Selectivity experiments revealed that the voltammetric GM DNA biosensor could discriminate complementary sequences of GM soybean from non-complementary sequences and hence good recoveries were obtained for real GM soybean sample analysis. The main advantage of using GNS is an improvement of the DNA biosensor analytical performance.
    Matched MeSH terms: DNA/analysis*; DNA Probes/chemistry*
  17. Two microsatellite loci from Brugia malayi show polymorphisms among isolates from Indonesia and Malaysia
    Underwood AP, Supali T, Wu Y, Bianco AE
    Mol Biochem Parasitol, 2000 Mar 05;106(2):299-302.
    PMID: 10699259
    Matched MeSH terms: DNA Primers/genetics; DNA, Helminth/genetics
  18. Enhanced DNA double-strand break repair of microbeam targeted A549 lung carcinoma cells by adjacent WI38 normal lung fibroblast cells via bi-directional signaling
    Kobayashi A, Tengku Ahmad TAF, Autsavapromporn N, Oikawa M, Homma-Takeda S, Furusawa Y, et al.
    Mutat Res, 2017 10;803-805:1-8.
    PMID: 28689138 DOI: 10.1016/j.mrfmmm.2017.06.006
    Understanding the mechanisms underlying the radiation-induced bystander effect (RIBE) and bi-directional signaling between irradiated carcinoma cells and their surrounding non-irradiated normal cells is relevant to cancer radiotherapy. The present study investigated propagation of RIBE signals between human lung carcinoma A549 cells and normal lung fibroblast WI38 cells in bystander cells, either directly or indirectly contacting irradiated A549 cells. We prepared A549-GFP/WI38 co-cultures and A549-GFP/A549 co-cultures, in which A549-GFP cells stably expressing H2BGFP were co-cultured with either A549 cells or WI38 cells, respectively. Using the SPICE-NIRS microbeam, only the A549-GFP cells were irradiated with 500 protons per cell. The level of γ-H2AX, a marker for DNA double-strand breaks (DSB), was subsequently measured for up to 24h post-irradiation in three categories of cells: (1) "targeted"/irradiated A549-GFP cells; (2) "neighboring"/non-irradiated cells directly contacting the "targeted" cells; and (3) "distant"/non-irradiated cells, which were not in direct contact with the "targeted" cells. We found that DSB repair in targeted A549-GFP cells was enhanced by co-cultured WI38 cells. The bystander response in A549-GFP/A549 cell co-cultures, as marked by γ-H2AX levels at 8h post-irradiation, showed a decrease to non-irradiated control level when approaching 24h, while the neighboring/distant bystander WI38 cells in A549-GFP/WI38 co-cultures was maintained at a similar level until 24h post-irradiation. Surprisingly, distant A549-GFP cells in A549-GFP/WI38 co-cultures showed time dependency similar to bystander WI38 cells, but not to distant cells in A549-GFP/A549 co-cultures. These observations indicate that γ-H2AX was induced in WI38 cells as a result of RIBE. WI38 cells were not only involved in rescue of targeted A549, but also in the modification of RIBE against distant A549-GFP cells. The present results demonstrate that radiation-induced bi-directional signaling had extended a profound influence on cellular sensitivity to radiation as well as the sensitivity to RIBE.
    Matched MeSH terms: DNA Repair*; DNA Breaks, Double-Stranded*
  19. 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
  20. 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
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