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  1. Du J, Loh KH, Then AY, Zheng X, Teguh Peristiwady, Rizman-Idid M, et al.
    Zookeys, 2019;861:107-118.
    PMID: 31333328 DOI: 10.3897/zookeys.861.34043
    Five specimens of Epinephelusepistictus (Temminck & Schlegel, 1843) were collected from a major landing site located on the west coast of Peninsula Malaysia during a fish faunal survey on 23 August 2017. The present study extends the distribution range of E.epistictus southwards from Andaman Sea to the Strait of Malacca. Species identification was confirmed by colour pattern and DNA barcoding (567 bp of cytochrome C oxidase I) of all E.epistictus specimens and nine closely related Epinephelus species. The interspecies genetic distance ranged from 0.002-0.245. This study also presents, for the first time for Malaysia, data on length-weight relationships and otolith measurements. It contributes to a better understanding of taxonomy, and phylogenetic and genetic diversity of E.epistictus.
    Matched MeSH terms: DNA; DNA Barcoding, Taxonomic
  2. Mohd Ali MR, Lih Huey L, Foo PC, Goay YX, Ismail AS, Mustaffa KMF, et al.
    Biomed Res Int, 2019;2019:9451791.
    PMID: 31355287 DOI: 10.1155/2019/9451791
    Melioidosis and leptospirosis, caused by two different bacteria, Burkholderia pseudomallei and Leptospira spp., are potentially fatal infections that share a very similar spectrum of clinical features and cause significant mortality and morbidity in humans and livestock. Early detection is important for better clinical consequences. To our knowledge, there is no diagnostic tool available to simultaneously detect and differentiate melioidosis and leptospirosis in humans and animals. In this study, we described a duplex TaqMan probe-based qPCR for the detection of B. pseudomallei and Leptospira spp. DNA. The performance of the assay was evaluated on 20 B. pseudomallei isolates, 23 Leptospira strains, and 39 other microorganisms, as well as two sets of serially diluted reference strains. The duplex qPCR assay was able to detect 0.02 pg (~ 4 copies) Leptospira spp. DNA and 0.2 pg (~ 25.6 copies) B. pseudomallei DNA. No undesired amplification was observed in other microorganisms. In conclusion, the duplex qPCR assay was sensitive and specific for the detection of B. pseudomallei & Leptospira spp. DNA and is suitable for further analytical and clinical evaluation.
    Matched MeSH terms: DNA, Bacterial/genetics*
  3. Kang TL, Chelliah S, Velappan RD, Kabir N, Mohamad J, Nor Rashid N, et al.
    Lett Appl Microbiol, 2019 Nov;69(5):366-372.
    PMID: 31508837 DOI: 10.1111/lam.13215
    We evaluate the efficacy of recombinant DNA vaccine ABA392 against haemorrhagic septicaemia infection through intranasal administration route by targeting the mucosal immunity. The DNA vaccine was constructed and subjected to animal study using the Sprague Dawley (SD) rat. The study was divided into two major parts: (i) active and (ii) passive immunization studies, involving 30 animals for each part. Each group was then divided into five test groups: two test samples G1 and G2 with 50 and 100 µg ml-1 purified DNA vaccine; one positive control G5 with 106  CFU per ml formalin-killed PMB2; and two negative controls, G3 and G4 with normal saline and pVAX1 vector. Both studies were conducted for the determination of immunogenicity by total white blood cell count (TWBC), indirect ELISA and histopathological changes for the presence of the bronchus-associated lymphoid tissue (BALT). Our findings demonstrate that TWBC, IgA and IgG increased after each of the three vaccination regimes: groups G1, G2 and G5. Test samples G1 and G2 showed significant differences (P DNA vaccine ABA392 can provoke mucosal immunity which makes it a potential prophylactic against HS. SIGNIFICANCE AND IMPACT OF THE STUDY: New approach of combating haemorrhagic septicaemia disease among bovines by recombinant DNA vaccine is crucial to overcome the loss of edible products from the infected bovines. DNA vaccine can potentially serve as a better immunogen which would elicit both cellular and humoral immunity, and it is also stable for its molecular reproduction. This research report demonstrates an effective yet simple way of administering the DNA vaccine via the intranasal route in rats, to provoke the mucosal immunity through the development of immunoglobulins IgA, IgG and bronchus-associated lymphoid tissue which guard as the first-line defence at the host's mucosal lining.
    Matched MeSH terms: DNA, Recombinant/administration & dosage; DNA, Recombinant/genetics; DNA, Recombinant/immunology; Vaccines, DNA/administration & dosage*; Vaccines, DNA/genetics; Vaccines, DNA/immunology
  4. Zainudin H, Caszo BA, Knight VF, Gnanou JV
    Eurasian J Med, 2019 Jun;51(2):116-120.
    PMID: 31258349 DOI: 10.5152/eurasianjmed.2019.18106
    Objective: Regular moderate-intensity exercise has beneficial health effects, whereas regular strenuous exercise increases the production of oxidants that may lead to DNA, skeletal, and cardiac muscle damages. Triathletes experience strenuous muscular activity both during competition and training, being at risk of developing these tissue damages. The objective of the present study was to estimate DNA, skeletal, and cardiac muscle damages using blood biomarkers, 8-hydroxy-2'-deoxyguanosine (8-OHdG), myoglobin, and cardiac troponin I (cTnI) among young triathletes.

    Materials and Methods: Age-matched seven male and seven female triathletes were recruited for the study. They were on a standardized training regimen and on average competed in at least one endurance event every month for the past 3-4 years. Serum biomarkers were measured using enzyme-linked immunosorbent assay at the start and at end of the racing season.

    Results: Both male and female triathletes showed a statistically significant increase in 8-OHdG. A similar pattern of increase was seen with serum myoglobin, which was not statistically significant in both male and female triathletes. cTnI levels did not show any change in both sexes.

    Conclusion: Our study shows that there could be an increased evidence of DNA damage among triathletes. However, similar effects were not observed with skeletal and cardiac muscle biomarkers.

    Matched MeSH terms: DNA; DNA Damage
  5. Cheah PL, Li J, Looi LM, Koh CC, Lau TP, Chang SW, et al.
    Malays J Pathol, 2019 Aug;41(2):91-100.
    PMID: 31427545
    Since 2014, the National Comprehensive Cancer Network (NCCN) has recommended that colorectal carcinoma (CRC) be universally tested for high microsatellite instability (MSI-H) which is present in 15% of such cancers. Fidelity of resultant microsatellites during DNA replication is contingent upon an intact mismatch repair (MMR) system and lack of fidelity can result in tumourigenesis. Prior to commencing routine screening for MSI-H, we assessed two commonly used methods, immunohistochemical (IHC) determination of loss of MMR gene products viz MLH1, MSH2, MSH6 and PMS2 against PCR amplification and subsequent fragment analysis of microsatellite markers, BAT25, BAT26, D2S123, D5S346 and D17S250 (Bethesda markers) in 73 unselected primary CRC. 15.1% (11/73) were categorized as MSI-H while deficient MMR (dMMR) was detected in 16.4% (12/73). Of the dMMR, 66.7% (8/12) were classified MSI-H, while 33.3% (4/12) were microsatellite stable/low microsatellite instability (MSS/MSI-L). Of the proficient MMR (pMMR), 95.1% (58/61) were MSS/MSI-L and 4.9% (3/61) were MSI-H. The κ value of 0.639 (standard error =0.125; p = 0.000) indicated substantial agreement between detection of loss of DNA mismatch repair using immunohistochemistry and the detection of downstream microsatellite instability using PCR. After consideration of advantages and shortcomings of both methods, it is our opinion that the choice of preferred technique for MSI analysis would depend on the type of laboratory carrying out the testing.
    Matched MeSH terms: DNA Replication; DNA Mismatch Repair
  6. Radzi R, Muangmai N, Broady P, Wan Omar WM, Lavoue S, Convey P, et al.
    PLoS One, 2019;14(11):e0224395.
    PMID: 31682631 DOI: 10.1371/journal.pone.0224395
    Terrestrial cyanobacteria are very diverse and widely distributed in Antarctica, where they can form macroscopically visible biofilms on the surfaces of soils and rocks, and on benthic surfaces in fresh waters. We recently isolated several terrestrial cyanobacteria from soils collected on Signy Island, South Orkney Islands, Antarctica. Among them, we found a novel species of Nodosilinea, named here as Nodosilinea signiensis sp. nov. This new species is morphologically and genetically distinct from other described species. Morphological examination indicated that the new species is differentiated from others in the genus by cell size, cell shape, filament attenuation, sheath morphology and granulation. 16S rDNA phylogenetic analyses clearly confirmed that N. signiensis belongs to the genus Nodosilinea, but that it is genetically distinct from other known species of Nodosilinea. The D1-D1´ helix of the 16S-23S ITS region of the new species was also different from previously described Nodosilinea species. This is the first detailed characterization of a member of the genus Nodosilinea from Antarctica as well as being a newly described species.
    Matched MeSH terms: DNA, Bacterial/isolation & purification
  7. Tuma J, Eggleton P, Fayle TM
    Biol Rev Camb Philos Soc, 2020 06;95(3):555-572.
    PMID: 31876057 DOI: 10.1111/brv.12577
    Animal interactions play an important role in understanding ecological processes. The nature and intensity of these interactions can shape the impacts of organisms on their environment. Because ants and termites, with their high biomass and range of ecological functions, have considerable effects on their environment, the interaction between them is important for ecosystem processes. Although the manner in which ants and termites interact is becoming increasingly well studied, there has been no synthesis to date of the available literature. Here we review and synthesise all existing literature on ant-termite interactions. We infer that ant predation on termites is the most important, most widespread, and most studied type of interaction. Predatory ant species can regulate termite populations and subsequently slow down the decomposition of wood, litter and soil organic matter. As a consequence they also affect plant growth and distribution, nutrient cycling and nutrient availability. Although some ant species are specialised termite predators, there is probably a high level of opportunistic predation by generalist ant species, and hence their impact on ecosystem processes that termites are known to provide varies at the species level. The most fruitful future research direction will be to evaluate the impact of ant-termite predation on broader ecosystem processes. To do this it will be necessary to quantify the efficacy both of particular ant species and of ant communities as a whole in regulating termite populations in different biomes. We envisage that this work will require a combination of methods, including DNA barcoding of ant gut contents along with field observations and exclusion experiments. Such a combined approach is necessary for assessing how this interaction influences entire ecosystems.
    Matched MeSH terms: DNA/analysis
  8. Mohd Safwan Ibrahim, Ahmad Azuhairi Ariffin, Sri Ganesh Muthiah
    MyJurnal
    Introduction: Workers in health sector are exposed 5 times more workplace violence as compared to workers in other sectors. Their consequences can range from mild to severe, affecting the victim, quality of services and orga-nization. The objective is to evaluate the effectiveness of educational intervention on workplace violence among healthcare workers in health clinics. Methods: This study is a single blinded cluster randomized trial to see the ef-fectiveness of education intervention on coping with workplace violence involving 10 cluster clinics with total 82 respondents in each control and intervention group. Data was collected using pretested questionnaire at baseline, 1-month and 6-months post intervention. The analysis used were descriptive, compared mean at baseline, repeated measures of variance and Mixed Model. Results: Response rate 94% at 1-month due to loss to follow up. Majority of the respondents were female (82.3%), and Malays (83.5%). The prevalence of workplace violence was 27.4% and mostly involved psychological violence (95.6%). There were no significant different between control and interven-tion group characteristic at baseline. Repeated measures MANOVA test was conducted to test intervention effect on dependent variables. The results until 1-month time showed significant difference between intervention and control group on combination of the dependent variables over time in coping (F(1,162)=9.51, p=0.002, and η2=0.06), knowledge (F(1,162)=10.47, p=0.001, and η2=0.061) and confidence (F(1,162)=15.65, p
    Matched MeSH terms: DNA-Directed DNA Polymerase
  9. Ng HF, Ngeow YF
    Pathog Dis, 2020 11 11;78(8).
    PMID: 32945880 DOI: 10.1093/femspd/ftaa055
    The subspecies classification of Mycobacteroides abscessus complex into M. abscessus, M. massiliense and M. bolletii requires the amplification and sequencing of multiple genes. The objective of this study was to evaluate the possibility of subspecies classification using a single PCR target. An in silico study was performed to classify 1613 strains deposited in a public database using 9 genes (partial gene sequences of hsp65, rpoB, sodA, argH, cya, glpK, gnd, and murC, and the full gene sequence of MAB_3542c). We found the housekeeping gene gnd to be able to classify the M. abscessus subspecies with high accuracy (99.94%). A single-gene PCR approach based on gnd would be a suitable replacement for the more expensive, labor-intensive and time-consuming multi-gene PCR analysis currently in use for the subspecies identification of M. abscessus.
    Matched MeSH terms: DNA, Bacterial; Sequence Analysis, DNA
  10. Kumar Singla S, Muthuraman A, Sahai D, Mangal N, Dhamodharan J
    Front Biosci (Elite Ed), 2021 01 01;13:158-184.
    PMID: 33048780
    Transdermal drug-delivery systems (TDDS) offer an attractive alternative to the oral route for delivery of biotherapeutics. Technological advancements in the past few decades have revolutionized the fabrication of micro-structured devices including creation of microneedles (MC). These devices are used for delivering peptides, macromolecules such as proteins and DNA, and other therapeutics through the skin. Here, we review the current use of MCs as a cost effective method for the self-administration of therapeutics. We will then review the current and common use of MCs as an effective treatment strategy for a broad range of diseases and their utility in the generation of effective vaccination delivery platforms. Finally, we will summarize the currently FDA approved MCs and their applications, along with the ongoing clinical trials that use such devices.
    Matched MeSH terms: DNA/administration & dosage
  11. Madhaiyan M, Saravanan VS, See-Too WS
    Int J Syst Evol Microbiol, 2020 Jun;70(6):3924-3929.
    PMID: 32441614 DOI: 10.1099/ijsem.0.004217
    Phylogenetic analysis based on 16S rRNA gene sequences of the genus Streptomyces showed the presence of six distinguishable clusters, with 100 % sequence similarity values among strains in each cluster; thus they shared almost the same evolutionary distance. This result corroborated well with the outcome of core gene (orthologous gene clusters) based genome phylogeny analysis of 190 genomes including the Streptomyces species in those six clusters. These preeminent results led to an investigation of genome-based indices such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) for the strains in those six clusters. Certain strains recorded genomic indices well above the threshold values (70 %, 95-96 % and >95 % for dDDH, ANI and AAI, respectively) determined for species affiliation, suggesting only one type strain belongs to described species and the other(s) may need to be reduced in taxa to a later heterotypic synonym. To conclude, the results of comprehensive analyses based on phylogenetic and genomic indices suggest that the following six reclassifications are proposed: Streptomyces flavovariabilis as a later heterotypic synonym of Streptomyces variegatus; Streptomyces griseofuscus as a later heterotypic synonym of Streptomyces murinus; Streptomyces kasugaensis as a later heterotypic synonym of Streptomyces celluloflavus; Streptomyces luridiscabiei as a later heterotypic synonym of Streptomyces fulvissimus; Streptomyces pharetrae as a later heterotypic synonym of Streptomyces glaucescens; and Streptomyces stelliscabiei as a later heterotypic synonym of Streptomyces bottropensis.
    Matched MeSH terms: DNA, Bacterial/genetics
  12. Kannan A, Rama Rao S, Ratnayeke S, Yow YY
    PeerJ, 2020;8:e8755.
    PMID: 32274263 DOI: 10.7717/peerj.8755
    Invasive apple snails, Pomacea canaliculata and P. maculata, have a widespread distribution globally and are regarded as devastating pests of agricultural wetlands. The two species are morphologically similar, which hinders species identification via morphological approaches and species-specific management efforts. Advances in molecular genetics may contribute effective diagnostic tools to potentially resolve morphological ambiguity. DNA barcoding has revolutionized the field of taxonomy by providing an alternative, simple approach for species discrimination, where short sections of DNA, the cytochrome c oxidase subunit I (COI) gene in particular, are used as 'barcodes' to delineate species boundaries. In our study, we aimed to assess the effectiveness of two mitochondrial markers, the COI and 16S ribosomal deoxyribonucleic acid (16S rDNA) markers for DNA barcoding of P. canaliculata and P. maculata. The COI and 16S rDNA sequences of 40 Pomacea specimens collected from six localities in Peninsular Malaysia were analyzed to assess their barcoding performance using phylogenetic methods and distance-based assessments. The results confirmed both markers were suitable for barcoding P. canaliculata and P. maculata. The phylogenies of the COI and 16S rDNA markers demonstrated species-specific monophyly and were largely congruent with the exception of one individual. The COI marker exhibited a larger barcoding gap (6.06-6.58%) than the 16S rDNA marker (1.54%); however, the magnitude of barcoding gap generated within the barcoding region of the 16S rDNA marker (12-fold) was bigger than the COI counterpart (approximately 9-fold). Both markers were generally successful in identifying P. canaliculata and P. maculata in the similarity-based DNA identifications. The COI + 16S rDNA concatenated dataset successfully recovered monophylies of P. canaliculata and P. maculata but concatenation did not improve individual datasets in distance-based analyses. Overall, although both markers were successful for the identification of apple snails, the COI molecular marker is a better barcoding marker and could be utilized in various population genetic studies of P. canaliculata and P. maculata.
    Matched MeSH terms: DNA, Ribosomal; DNA Barcoding, Taxonomic
  13. Jeon AJ, Kellogg D, Khan MA, Tucker-Kellogg G
    Biochem Mol Biol Educ, 2021 01;49(1):140-150.
    PMID: 32746505 DOI: 10.1002/bmb.21414
    Laboratory pedagogy is moving away from step-by-step instructions and toward inquiry-based learning, but only now developing methods for integrating inquiry-based writing (IBW) practices into the laboratory course. Based on an earlier proposal (Science 2011;332:919), we designed and implemented an IBW sequence in a university bioinformatics course. We automatically generated unique, double-blinded, biologically plausible DNA sequences for each student. After guided instruction, students investigated sequences independently and responded through IBW writing assignments. IBW assignments were structured as condensed versions of a scientific research article, and because the sequences were double blinded, they were also assessed as authentic science and evaluated on clarity and persuasiveness. We piloted the approach in a seven-day workshop (35 students) at Perdana University in Malaysia. We observed dramatically improved student engagement and indirect evidence of improved learning outcomes over a similar workshop without IBW. Based on student feedback, initial discomfort with the writing component abated in favor of an overall positive response and increasing comfort with the high demands of student writing. Similarly, encouraging results were found in a semester length undergraduate module at the National University of Singapore (155 students).
    Matched MeSH terms: DNA/genetics
  14. Gangathraprabhu B, Kannan S, Santhanam G, Suryadevara N, Maruthamuthu M
    Microb Pathog, 2020 Oct;147:104352.
    PMID: 32592823 DOI: 10.1016/j.micpath.2020.104352
    Salmonellosis continues to remain a health problem as the causative organism Salmonella spp. developed resistance to many of the antibiotics. As per World Health Organization (WHO), it is estimated that enteric fever, accounts for almost 16 million cases annually and over 600,000 deaths worldwide. Recent data revealed that the multi-drug resistance (MDR) rate of enteric fever was as high as 70% in Asian countries, as compared with the overall reported incidence of 50%. Emergence of MDR typhoid fever demands the use of newer antibiotics which also not offer promising effect in recent days. Effective antimicrobial therapy is required to control morbidity and prevent death from typhoid fever. The studies on PhoP/Q regulation revealed it as a best-characterized transcriptional regulation; a two-component system required for Salmonella pathogenesis which controls the expression of more than 40 genes. The PhoP DNA binding proteins possess positively charged amino acids such as arginine, lysine and histidine which present in the DNA binding site. Prevention of PhoP binding in phoP box may ultimately prevent the expression of many regulatory mechanism which plays vital role in Salmonella virulence. Deepness study of PhoP protein and various mutation swots may offer effectual controlling of MDR Salmonella.
    Matched MeSH terms: DNA; DNA-Binding Proteins
  15. Al Amin M, Mahfujur Rahman M, Razimi MSA, Chowdhury ZZ, Hussain MNM, Desa MNM
    J Food Compost Anal, 2020 Sep;92:103565.
    PMID: 32546895 DOI: 10.1016/j.jfca.2020.103565
    Determination of feline meat in food products is an important issue for social, health, economic and religious concern. Hence this paper documented the application of species specific polymerase chain reaction-restriction fragment length polymorphism (SP-PCR-RFLP) assay targeting a short-fragments (69 bp) of mitochondrial cytochrome b (cytb) gene to screen feline meat in commercial meat products using lab-on-a-chip. The SP-PCR assay proved its specificity theoretically and experimentally while testing with different common animal, aquatic and plant species of DNA. The feline specific (69 bp, 43- and 26-bp) characteristic molecular DNA pattern was observed by SP-PCR and RFLP analysis. For assay performance, it was tested in three different types of commercial dummy meat products such as frankfurters, nuggets and meatballs and digested with AluI-restriction enzyme. The highest sensitivity of the assay using lab-on-a-chip was as low as 0.1 pg or 0.01 % (w/w) in commercial dummy meat products. We have also applied this assay to screen three important commercial meat products of six different brand from six supermarket chains located at three different states of Malaysia. Thus total 378 samples were tested to validate the specificity, sensitivity, stability of the assay and utilization of it for commercial meat product screening.
    Matched MeSH terms: DNA; DNA Restriction Enzymes
  16. Chua KH, Tan EW, Chai HC, Puthucheary SD, Lee PC, Puah SM
    PeerJ, 2020;8:e9238.
    PMID: 32518734 DOI: 10.7717/peerj.9238
    Background: Burkholderia pseudomallei causes melioidosis, a serious illness that can be fatal if untreated or misdiagnosed. Culture from clinical specimens remains the gold standard but has low diagnostic sensitivity.

    Method: In this study, we developed a rapid, sensitive and specific insulated isothermal Polymerase Chain Reaction (iiPCR) targeting bimA gene (Burkholderia Intracellular Motility A; BPSS1492) for the identification of B. pseudomallei. A pair of novel primers: BimA(F) and BimA(R) together with a probe were designed and 121 clinical B. pseudomallei strains obtained from numerous clinical sources and 10 ATCC non-targeted strains were tested with iiPCR and qPCR in parallel.

    Results: All 121 B. pseudomallei isolates were positive for qPCR while 118 isolates were positive for iiPCR, demonstrating satisfactory agreement (97.71%; 95% CI [93.45-99.53%]; k = 0.87). Sensitivity of the bimA iiPCR/POCKIT assay was 97.52% with the lower detection limit of 14 ng/µL of B. pseudomallei DNA. The developed iiPCR assay did not cross-react with 10 types of non-targeted strains, indicating good specificity.

    Conclusion: This bimA iiPCR/POCKIT assay will undoubtedly complement other methodologies used in the clinical laboratory for the rapid identification of this pathogen.

    Matched MeSH terms: DNA Primers; DNA, B-Form
  17. Rashid AA, Ghazali SS, Mohamad I, Mawardi M, Musa H, Roslan D
    PLoS One, 2020;15(7):e0235685.
    PMID: 32678838 DOI: 10.1371/journal.pone.0235685
    INTRODUCTION: House Officer (HO) Preparatory Courses in Malaysia are designed to prepare medical graduates to work as a HO. The courses are designed to address the issues related to lack of confidence and readiness to work, which could lead to stress and HO dropping out of work. The modules focus on how to prepare medical graduates into the real-life working scenario. Hence, we determined the effectiveness of a HO Preparatory Course on the level of confidence and readiness to work among medical graduates.

    METHODOLOGY: A quasi-experimental study was conducted at three time-points (pre-intervention, post-intervention and one-month after working as a HO) on the level of confidence and readiness of medical graduates. The intervention was the Medicorp module, which included information and training needed for the HO such as common clinical cases in the wards, case referrals, experience sharing and hands on clinical training. We recruited eligible participants undergoing the course between April-November 2018. The adapted IMU Student Competency Survey was used to measure the confidence and readiness levels, which were scored from a Likert scale of 1-5. The higher score indicated higher levels of confidence or readiness.

    RESULTS: A total of 239 participants were recruited at baseline (90% response rate). They were mostly female (77.8%), Malays (79.1%), single (90.0%), graduated overseas (73.6%), in 2018 (65.3%). The mean (SE) confidence scores significantly increased from 2.18 (1.00) pre-course to 3.50 (0.75) immediately after course and 3.79 (0.92) after one-month of work (p <0.001, η2 = 0.710). The mean (SE) readiness scores at pre-course, immediately and one-month post work were 2.36 (1.03), 3.46(0.78) and 3.70(0.90), respectively (p< 0.001, η2 = 0.612).

    CONCLUSION: The HO Preparatory Course module was effective in increasing levels of confidence and readiness for medical graduates, most of whom are overseas graduates; namely Egypt, Russia and Indonesia.

    Matched MeSH terms: DNA-Directed DNA Polymerase
  18. Chan KO, Hutter CR, Wood PL, Grismer LL, Das I, Brown RM
    Mol Ecol, 2020 10;29(20):3970-3987.
    PMID: 32808335 DOI: 10.1111/mec.15603
    Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  19. Cree SL, Chua EW, Crowther J, Dobson RCJ, Kennedy MA
    Biochimie, 2020 Aug 14.
    PMID: 32805304 DOI: 10.1016/j.biochi.2020.07.022
    Next generation DNA sequencing and analysis of amplicons spanning the pharmacogene CYP2D6 suggested that the Nextera transposase used for fragmenting and providing sequencing priming sites displayed a targeting bias. This manifested as dramatically lower sequencing coverage at sites in the amplicon that appeared likely to form G-quadruplex structures. Since secondary DNA structures such as G-quadruplexes are abundant in the human genome, and are known to interact with many other proteins, we further investigated these sites of low coverage. Our investigation revealed that G-quadruplex structures are formed in vitro within the CYP2D6 pharmacogene at these sites, and G-quadruplexes can interact with the hyperactive Tn5 transposase (EZ-Tn5) with high affinity. These findings indicate that secondary DNA structures such as G-quadruplexes may represent preferential transposon integration sites and provide additional evidence for the role of G-quadruplex structures in transposition or viral integration processes.
    Matched MeSH terms: DNA; Sequence Analysis, DNA
  20. Ahmed A, Ijaz M, Ghauri HN, Aziz MU, Ghaffar A, Naveed M, et al.
    PMID: 32829184 DOI: 10.1016/j.cimid.2020.101524
    Feline anaplasmosis is considered as an emerging tick-borne disease of zoonotic potential. The aim of current study was to investigate the molecular prevalence of anaplasmosis, associated risk factors, and alterations in hematological parameters of domestic cats from Lahore, Pakistan. Blood samples of 100 domestic cats from district Lahore were examined microscopically and the extracted genomic DNA from each sample was processed for the amplification of 16 S rRNA gene of Anaplasma. PCR confirmed isolates were purified for sequencing. The data regarding the risk factors was collected in a predesigned questionnaire and statistically analyzed by logistic regression analysis. The study found a molecular prevalence of 13% (13/100) among analyzed blood samples. The nucleotide analysis of Anaplasmataceae species sequences amplified by PCR showed high resemblance (99%) with isolates from Korea, Japan, Malaysia, Philippines, and India. The potential risk factors found to be significantly associated (p 
    Matched MeSH terms: DNA, Bacterial/genetics
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