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Pengehadan kalori, fungsi kognitif dan penuaan: peranan terhadap sistem biologi

Meramat, A. Rajab, N.F. Shahar S, Sharif R

Sains Malaysiana, 2017;46:1625-1633.

Prevalens gangguan kognitif ringan (MCI) di Malaysia mencecah 68% pada tahun 2016. Pelbagai kaedah dijalankan bagi memastikan kelestarian tahap kesihatan warga tua termasuk melalui nutrisi, gaya hidup dan persekitaran. Pengehadan kalori dibuktikan mampu untuk menurunkan kadar mortaliti dan morbiditi warga tua serta memelihara tahap kesihatan warga tua supaya dapat membantu dalam meningkatkan kualiti hidup golongan tersebut. Pengehadan kalori juga merupakan salah satu kaedah yang lebih mudah dan berkesan dalam membantu meningkatkan ingatan dan memelihara kesihatan golongan tersebut. Ia juga membantu mengurangkan kadar inflamasi dan mencantas tindakan radikal bebas yang hadir di dalam sistem tubuh akibat daripada proses penuaan dan faktor persekitaran. Keadaan ini menyediakan tubuh badan yang lebih rentan terhadap kerosakan DNA dan serangan toksin daripada penyakit kronik, pemakanan dan persekitaran. Oleh itu, kajian ini memberikan konsep yang lebih jelas terhadap implikasi pengehadan kalori dalam memelihara fungsi kognitif.

Matched MeSH terms: DNA
Global genetic diversity of Spirometra tapeworms

Hong X, Liu SN, Xu FF, Han LL, Jiang P, Wang ZQ, et al.

Trop Biomed, 2020 Mar 01;37(1):237-250.
PMID: 33612735

Spirometra larvae are etiological agents of human sparganosis. However, the systematics of spirometrid cestodes has long been controversial. In order to determine the current knowledge on the evolution and genetic structure of Spirometra, an exhaustive population diversity analysis of spirometrid cestodes using the mitochondrial gene: cytochrome c oxidase subunit 1 (cox1) was performed. All publicly available cox1 sequences available in the GenBank and 127 new sequencing genes from China were used as the dataset. The haplotype identify, network, genetic differentiation and phylogenetic analysis were conducted successively. A total of 488 sequences from 20 host species, representing four spirometrid tapeworms (S. decipiens, S. ranarum, S. erinaceieuropaei and Sparganum proliferum) and several unclassified American and African isolates from 113 geographical locations in 17 countries, identified 45 haplotypes. The genetic analysis revealed that there are four clades of spirometrid cestodes: Clade 1 (Brazil + USA) and Clade 2 (Argentina + Venezuela) included isolates from America, Clade 3 contained African isolates and one Korean sample, and the remainders from Asia and Australia belonged to Clade 4; unclassified Spirometra from America and Africa should be considered the separate species within the genus; and the taxonomy of two Korea isolates (S. erinaceieuropaei KJ599680 and S. decipiens KJ599679) was still ambiguous and needs to be further identified. In addition, the demographical analyses supported population expansion for the total spirometrid population. In summary, four lineages were found in the spirometrid tapeworm, and further investigation with deeper sampling is needed to elucidate the population structure.

Matched MeSH terms: DNA, Mitochondrial/genetics; DNA, Helminth/genetics
Effects of sirtuins on the riboflavin production in Ashbya gossypii

Kato T, Azegami J, Kano M, El Enshasy HA, Park EY

Appl Microbiol Biotechnol, 2021 Oct;105(20):7813-7823.
PMID: 34559286 DOI: 10.1007/s00253-021-11595-2

This study focuses on sirtuins, which catalyze the reaction of NAD+-dependent protein deacetylase, for riboflavin production in A. gossypii. Nicotinamide, a known inhibitor of sirtuin, made the color of A. gossypii colonies appear a deeper yellow at 5 mM. A. gossypii has 4 sirtuin genes (AgHST1, AgHST2, AgHST3, AgHST4) and these were disrupted to investigate the role of sirtuins in riboflavin production in A. gossypii. AgHST1∆, AgHST3∆, and AgHST4∆ strains were obtained, but AgHST2∆ was not. The AgHST1∆ and AgHST3∆ strains produced approximately 4.3- and 2.9-fold higher amounts of riboflavin than the WT strain. The AgHST3∆ strain showed a lower human sirtuin 6 (SIRT6)-like activity than the WT strain and only in the AgHST3∆ strain was a higher amount of acetylation of histone H3 K9 and K56 (H3K9ac and H3K56ac) observed compared to the WT strain. These results indicate that AgHst3 is SIRT6-like sirtuin in A. gossypii and the activity has an influence on the riboflavin production in A. gossypii. In the presence of 5 mM hydroxyurea and 50 µM camptothecin, which causes DNA damage, especially double-strand DNA breaks, the color of the WT strain colonies turned a deeper yellow. Additionally, hydroxyurea significantly led to the production of approximately 1.5 higher amounts of riboflavin and camptothecin also enhanced the riboflavin production even through the significant difference was not detected. Camptothecin tended to increase the amount of H3K56ac, but the amount of H3K56ac was not increased by hydroxyurea treatment. This study revealed that AgHst1 and AgHst3 are involved in the riboflavin production in A. gossypii through NAD metabolism and the acetylation of H3, respectively. This new finding is a step toward clarifying the role of sirtuins in riboflavin over-production by A. gossypii.Key points• Nicotinamide enhanced the riboflavin production in Ashbya gossypii.• Disruption of AgHST1 or AgHST3 gene also enhanced the riboflavin production in Ashbya gossypii.• Acetylation of H3K56 led to the enhancement of the riboflavin production in Ashbya gossypii.

Matched MeSH terms: DNA Damage
Fulltext Rapid Detection of Porcine DNA in Meatball Using Recombinase Polymerase Amplification Couple with Lateral Flow Immunoassay for Halal Authentication

Yusop MHM, Bakar MFA, Kamarudin KR, Mokhtar NFK, Hossain MAM, Johan MR, et al.

Molecules, 2022 Nov 22;27(23).
PMID: 36500215 DOI: 10.3390/molecules27238122

Point-of-care diagnostic methods for animal species determination are critical for rapid, simple, and accurate enforcement of food labelling. PCR is the most common method for species identification. However, the requirement of using a thermal cycler created drawbacks for the PCR application, particularly in low-resource settings. Hence, in this study, a method for porcine DNA detection using recombinase polymerase amplification (RPA), coupled with nucleic acid lateral flow immunoassay (NALFIA), was developed. Porcine-specific primers targeting pig (Sus scrofa) cytochrome b gene fragments specifically amplify a 197 bp fragment of the mitochondrial gene as being visualized by 2% agarose gel and PCRD NALFIA. The reaction temperature and time were 39 °C and 20 min, respectively. Herein, the specificity of the primers to porcine was confirmed after being assayed against six animal species, namely cow, goat, chicken, duck, dog, and rabbit. The porcine-specific RPA assay shows a high limit of detection of 0.01 ng/µL pork DNA. Based on the preliminary performance data obtained from this study, the potential of this method as a rapid and sensitive tool for porcine DNA detection in meat-based products is foreseen.

Matched MeSH terms: DNA/genetics; DNA Primers/genetics
Fulltext Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea

Strijk JS, Binh HT, Ngoc NV, Pereira JT, Slik JWF, Sukri RS, et al.

PLoS One, 2020;15(5):e0232936.
PMID: 32442164 DOI: 10.1371/journal.pone.0232936

Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile-thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus-a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.

Matched MeSH terms: DNA/genetics; Sequence Analysis, DNA/methods*
Fulltext Silicene Quantum Capacitance Dependent Frequency Readout to a Label-Free Detection of DNA Hybridization- A Simulation Analysis

Rahman MS, Naima RL, Shetu KJ, Hossain MM, Kaiser MS, Hosen ASMS, et al.

Biosensors (Basel), 2021 Jun 01;11(6).
PMID: 34205927 DOI: 10.3390/bios11060178

The use of deoxyribonucleic acid (DNA) hybridization to detect disease-related gene expression is a valuable diagnostic tool. An ion-sensitive field-effect transistor (ISFET) with a graphene layer has been utilized for detecting DNA hybridization. Silicene is a two-dimensional silicon allotrope with structural properties similar to graphene. Thus, it has recently experienced intensive scientific research interest due to its unique electrical, mechanical, and sensing characteristics. In this paper, we proposed an ISFET structure with silicene and electrolyte layers for the label-free detection of DNA hybridization. When DNA hybridization occurs, it changes the ion concentration in the surface layer of the silicene and the pH level of the electrolyte solution. The process also changes the quantum capacitance of the silicene layer and the electrical properties of the ISFET device. The quantum capacitance and the corresponding resonant frequency readout of the silicene and graphene are compared. The performance evaluation found that the changes in quantum capacitance, resonant frequency, and tuning ratio indicate that the sensitivity of silicene is much more effective than graphene.

Matched MeSH terms: DNA/chemistry; DNA Probes*
Fulltext A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library

Lim VC, Ramli R, Bhassu S, Wilson JJ

PLoS One, 2017;12(7):e0179555.
PMID: 28742835 DOI: 10.1371/journal.pone.0179555

Several published checklists of bat species have covered Peninsular Malaysia as part of a broader region and/or in combination with other mammal groups. Other researchers have produced comprehensive checklists for specific localities within the peninsula. To our knowledge, a comprehensive checklist of bats specifically for the entire geopolitical region of Peninsular Malaysia has never been published, yet knowing which species are present in Peninsular Malaysia and their distributions across the region are crucial in developing suitable conservation plans. Our literature search revealed that 110 bat species have been documented in Peninsular Malaysia; 105 species have precise locality records while five species lack recent and/or precise locality records. We retrieved 18 species from records dated before the year 2000 and seven species have only ever been recorded once. Our search of Barcode of Life Datasystems (BOLD) found that 86 (of the 110) species have public records of which 48 species have public DNA barcodes available from bats sampled in Peninsular Malaysia. Based on Neighbour-Joining tree analyses and the allocation of DNA barcodes to Barcode Index Number system (BINs) by BOLD, several DNA barcodes recorded under the same species name are likely to represent distinct taxa. We discuss these cases in detail and highlight the importance of further surveys to determine the occurences and resolve the taxonomy of particular bat species in Peninsular Malaysia, with implications for conservation priorities.

Matched MeSH terms: DNA/genetics*; DNA Barcoding, Taxonomic*
Cellular and DNA Toxicity Study of Triphenyltin Ethyl Phenyl Dithiocarbamate and Triphenyltin Butyl Phenyl Dithiocarbamate on K562, Leukemia Cell Line

Hamid A, Rajab NF, Charmagne Y, Awang N, Jufri NF, Rasli NR

Anticancer Agents Med Chem, 2024;24(1):58-65.
PMID: 37921147 DOI: 10.2174/0118715206266851231025054446

INTRODUCTION: Continuous research for new effective drugs to treat cancer has improved our understanding on the mechanism of action of these drugs and paved new potential for their application in cancer treatments. In this study, organotin compounds known as triphenyltin ethyl phenyl dithiocarbamate and triphenyltin butyl phenyl dithiocarbamate were investigated for their toxicity on leukemia cell line (K562) and non-cancerous cell line (Chang liver cell and lung fibroblast, V79 cell).
METHODS: MTT assay was performed to evaluate the cytotoxic effects of both compounds toward the cells after 24, 48 and 72 hours of exposure or treatment. The alkaline comet assay was conducted to determine the DNA damage on K562 cells after been exposed to both compounds for 30, 60 and 90 minutes.
RESULTS: The IC50 values obtained from K562 cells ranged from 0.01 to 0.30 μM, whereas for both Chang liver cell and lung fibroblast V79 cell, the values ranged from 0.10 to 0.40 μM. For genotoxicity evaluation, the percentage of damaged DNA is measured as an average of tail moment, and was found to be within 1.20 to 2.20 A.U while the percentage of DNA intensity ranging from 1.50 to 3.50% indicating no genotoxic effects.
CONCLUSION: Both compounds are cytotoxic toward leukemia cells and non-cancerous cells but do not exert their genotoxic effects towards leukemia cell.

Matched MeSH terms: DNA Damage
Fulltext Development of triplex real-time PCR and detection of Toxoplasma gondii DNA in infected mice tissues and spiked human samples

Rahumatullah A, Khoo BY, Noordin R

Trop Biomed, 2015 Jun;32(2):376-85.
PMID: 26691266 MyJurnal

Toxoplasma gondii is an important pathogen in veterinary and human medicine. In this study, a new multiplex TaqMan real-time PCR for detection of T. gondii DNA was developed. This assay consisted of new sets of primers and probes which targeted B1 gene and ITS-1 region of T. gondii, with Vibrio cholera gene as internal control. The B1 gene primers were designed to detect T. gondii RH strain, while the ITS-1 region primers detected most T. gondii strains. Specificity test using common protozoal and bacterial DNA revealed that the assay was very specific to T. gondii. Standard curves constructed using human body fluids spiked with T. gondii (RH and ME49 strains) showed that the sensitivity of the assay was one parasite, with R² value of 0.975 to 0.999 and efficiency of 97% to 99% for all types of samples. The assay performed on DNA extracted from tissues of mice infected with T. gondii showed that liver contained the highest parasite load for both strains of T. gondii. The multiplex real-time PCR developed in this study would be potentially useful for detection of T. gondii in human and animal samples.

Matched MeSH terms: DNA, Bacterial/genetics; DNA, Bacterial/chemistry; DNA, Protozoan/genetics; DNA, Protozoan/isolation & purification*; DNA Primers/genetics; DNA, Ribosomal Spacer/genetics; DNA, Ribosomal Spacer/chemistry
Three novel species in the Pseudo-nitzschia pseudodelicatissima complex: P. batesiana sp. nov., P. lundholmiae sp. nov., and P. fukuyoi sp. nov. (Bacillariophyceae) from the Strait of Malacca, Malaysia

Lim HC, Teng ST, Leaw CP, Lim PT

J Phycol, 2013 Oct;49(5):902-16.
PMID: 27007315 DOI: 10.1111/jpy.12101

A study on the morphology and phylogeny of 18 strains of Pseudo-nitzschia established from the Strait of Malacca, Peninsular Malaysia, was undertaken. Morphological data combined with molecular evidence show that they constitute three new species, for which the names, P. batesiana sp. nov., P. lundholmiae sp. nov., and P. fukuyoi sp. nov., are proposed. The three new species closely resemble species in the P. pseudodelicatissima complex sensu lato. Morphologically, P. batesiana differs from other species in the complex by having a smaller part of cell overlapping in the chain, whereas P. lundholmiae differs by having fewer poroid sectors and P. fukuyoi by having a distinct type of poroid sectors. Nucleotide sequences of the LSU rDNA (D1-D3) of the three new species reveal significant nucleotide sequence divergence (0.1%-9.3%) from each other and from other species in the P. pseudodelicatissima complex s.l. The three species are phylogenetically closely related to species in the P. pseudodelicatissima complex, with P. batesiana appearing as a sister taxon to P. circumpora, P. caciantha, and P. subpacifica; whereas P. lundholmiae and P. fukuyoi are more closely related to P. pseudodelicatissima and P. cuspidata. The three species show 2-3 compensatory base changes (CBCs) in their ITS2 transcripts when compared to the closely related species. The ITS2 with its structural information has proven its robustness in constructing a better resolved phylogenetic framework for Pseudo-nitzschia.

Matched MeSH terms: DNA, Ribosomal; DNA, Ribosomal Spacer
Fulltext Rapid detection and identification of human hookworm infections through high resolution melting (HRM) analysis

Ngui R, Lim YA, Chua KH

PLoS One, 2012;7(7):e41996.
PMID: 22844538 DOI: 10.1371/journal.pone.0041996

Hookworm infections are still endemic in low and middle income tropical countries with greater impact on the socioeconomic and public health of the bottom billion of the world's poorest people. In this study, a real-time polymerase chain reaction (PCR) coupled with high resolution melting-curve (HRM) analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on the five human hookworm species.

Matched MeSH terms: DNA, Ribosomal/genetics; DNA, Ribosomal/chemistry; DNA Primers/genetics; DNA, Intergenic/genetics; DNA, Intergenic/chemistry*
Fulltext Chemical reaction of soybean flavonoids with DNA: a computational study using the implicit solvent model

Abdallah HH, Mavri J, Repič M, Lee VS, Wahab HA

Int J Mol Sci, 2012;13(2):1269-83.
PMID: 22408390 DOI: 10.3390/ijms13021269

Genistein, daidzein, glycitein and quercetin are flavonoids present in soybean and other vegetables in high amounts. These flavonoids can be metabolically converted to more active forms, which may react with guanine in the DNA to form complexes and can lead to DNA depurination. We assumed two ultimate carcinogen forms of each of these flavonoids, diol epoxide form and diketone form. Density functional theory (DFT) and Hartree-Fock (HF) methods were used to study the reaction thermodynamics between active forms of flavonoids and DNA guanine. Solvent reaction field method of Tomasi and co-workers and the Langevin dipoles method of Florian and Warshel were used to calculate the hydration free energies. Activation free energy for each reaction was estimated using the linear free energy relation. Our calculations show that diol epoxide forms of flavonoids are more reactive than the corresponding diketone forms and are hence more likely flavonoid ultimate carcinogens. Genistein, daidzein and glycitein show comparable reactivity while quercetin is less reactive toward DNA.

Matched MeSH terms: DNA/chemistry*
Fulltext DNA strand patterns on aluminium thin films

Khatir NM, Banihashemian SM, Periasamy V, Majid WH, Rahman SA, Shahhosseini F

Sensors (Basel), 2011;11(7):6719-27.
PMID: 22163981 DOI: 10.3390/s110706719

A new patterning method using Deoxyribose Nucleic Acid (DNA) strands capable of producing nanogaps of less than 100 nm is proposed and investigated in this work. DNA strands from Bosenbergia rotunda were used as the fundamental element in patterning DNA on thin films of aluminium (Al) metal without the need for any lithographic techniques. The DNA strands were applied in buffer solutions onto thin films of Al on silicon (Si) and the chemical interactions between the DNA strands and Al creates nanometer scale arbitrary patterning by direct transfer of the DNA strands onto the substrate. This simple and cost-effective method can be utilized in the fabrication of various components in electronic chips for microelectronics and Nano Electronic Mechanical System (NEMS) applications in general.

Matched MeSH terms: DNA, Plant/chemistry*
Human papilloma virus 18 detection in oral squamous cell carcinoma and potentially malignant lesions using saliva samples

Goot-Heah K, Kwai-Lin T, Froemming GR, Abraham MT, Nik Mohd Rosdy NM, Zain RB

Asian Pac J Cancer Prev, 2012;13(12):6109-13.
PMID: 23464414

BACKGROUND: Oral cancer has become one of the most prevalent cancers worldwide and human Papillomavirus is one of the risk factors for developing oral cancer. For this study HPV18 was chosen as it is one of the high risk HPV types and may lead to carcinogenesis. However, prevalence of HPV18 infection in Oral Squamous Cell Carcinoma in Malaysia remains unclear.
OBJECTIVE: This study aimed to investigate the viral load of HPV18 DNA in OSCC and potentially malignant lesions using saliva samples.
MATERIALS AND METHODS: Genomic DNAs of thirty saliva samples of normal subjects and thirty saliva samples compromised of 16 samples from potentially malignant lesions and 14 of OSCC patients were amplified for HPV18 DNA using a nested polymerase chain reaction analysis. All PCR products were then analyzed using the Bioanalyzer to confirm presence of HPV18 DNA.
RESULT: From thirty patients examined, only one of 30 (3.3%) cases was found to be positive for HPV18 in this study.
CONCLUSION: The finding of this study revealed that there is a low viral detection of HPV18 in Malaysian OSCC by using saliva samples, suggesting that prevalence of HPV18 may not be important in this group of Malaysian OSCC.

Matched MeSH terms: DNA, Viral/genetics
Fulltext Interaction of DNA with Simple and Mixed Ligand Copper(II) Complexes of 1,10-Phenanthrolines as Studied by DNA-Fiber EPR Spectroscopy

Chikira M, Ng CH, Palaniandavar M

Int J Mol Sci, 2015;16(9):22754-80.
PMID: 26402668 DOI: 10.3390/ijms160922754

The interaction of simple and ternary Cu(II) complexes of 1,10-phenanthrolines with DNA has been studied extensively because of their various interesting and important functions such as DNA cleavage activity, cytotoxicity towards cancer cells, and DNA based asymmetric catalysis. Such functions are closely related to the DNA binding modes of the complexes such as intercalation, groove binding, and electrostatic surface binding. A variety of spectroscopic methods have been used to study the DNA binding mode of the Cu(II) complexes. Of all these methods, DNA-fiber electron paramagnetic resonance (EPR) spectroscopy affords unique information on the DNA binding structures of the complexes. In this review we summarize the results of our DNA-fiber EPR studies on the DNA binding structure of the complexes and discuss them together with the data accumulated by using other measurements.

Matched MeSH terms: DNA; DNA Cleavage
Fulltext Electronic Properties of DNA-Based Schottky Barrier Diodes in Response to Alpha Particles

Al-Ta'ii HM, Periasamy V, Amin YM

Sensors (Basel), 2015;15(5):11836-53.
PMID: 26007733 DOI: 10.3390/s150511836

Detection of nuclear radiation such as alpha particles has become an important field of research in recent history due to nuclear threats and accidents. In this context; deoxyribonucleic acid (DNA) acting as an organic semiconducting material could be utilized in a metal/semiconductor Schottky junction for detecting alpha particles. In this work we demonstrate for the first time the effect of alpha irradiation on an Al/DNA/p-Si/Al Schottky diode by investigating its current-voltage characteristics. The diodes were exposed for different periods (0-20 min) of irradiation. Various diode parameters such as ideality factor, barrier height, series resistance, Richardson constant and saturation current were then determined using conventional, Cheung and Cheung's and Norde methods. Generally, ideality factor or n values were observed to be greater than unity, which indicates the influence of some other current transport mechanism besides thermionic processes. Results indicated ideality factor variation between 9.97 and 9.57 for irradiation times between the ranges 0 to 20 min. Increase in the series resistance with increase in irradiation time was also observed when calculated using conventional and Cheung and Cheung's methods. These responses demonstrate that changes in the electrical characteristics of the metal-semiconductor-metal diode could be further utilized as sensing elements to detect alpha particles.

Matched MeSH terms: DNA/chemistry*
A mesocarp-and species-specific cDNA clone from oil palm encodes for sesquiterpene synthase

Shah FH, Cha TS

Plant Sci, 2000 May 29;154(2):153-160.
PMID: 10729614

The differential display method was used to isolate cDNAs corresponding to transcripts that accumulate during the period of lipid synthesis, 12-20 weeks after anthesis (WAA) in the mesocarp of two oil palms, Elaeis oleifera and Elaeis guineensis, Tenera. DNA-free total RNA from mesocarp and kernel of E. guineensis, Tenera and E. oleifera (15 WAA) were used to obtain differential gene expression patterns between these tissues from the two species. In this report, we describe the isolation and characterization of a specific cDNA clone, MO1 (434 bp) which was shown to be mesocarp-specific as well as species-specific for E. oleifera Sequencing of this fragment showed homology to the enzyme sesquiterpene synthase. Its longer cDNA clone, pMO1 (1072 bp), isolated from a 15-week E. oleifera mesocarp cDNA library confirmed that it encodes for sesquiterpene synthase. The complete sequence of 1976 bp was obtained using 5'RACE method. Northern hybridization showed that MO1 and pMO1 mRNA transcripts are highly expressed only in the mesocarp of E. oleifera from 5 to 20 WAA. No expression was detected in the kernel (12-17 WAA) and vegetative tissues of both species nor in the mesocarp of E. guineensis. This is the first communication to document on the isolation and characterisation of a mesocarp-and species-specific cDNA clone from oil palm.

Matched MeSH terms: DNA; DNA, Complementary
Frequent detection of human herpesvirus 6 in oral carcinoma

Yadav M, Chandrashekran A, Vasudevan DM, Ablashi DV

J Natl Cancer Inst, 1994 Dec 07;86(23):1792-4.
PMID: 7966419
Matched MeSH terms: DNA, Viral/analysis*
Fulltext Designation of a neotype for Enteromiuspallidus (Smith, 1841), an endemic cyprinid minnow from the Cape Fold Ecoregion, South Africa

Martin MB, Chakona A

Zookeys, 2019;848:103-118.
PMID: 31160881 DOI: 10.3897/zookeys.848.32211

Enteromiuspallidus was described by Smith in 1841 without a designated type specimen for the species. Herein, we designate a specimen from the Baakens River system as a neotype for E.pallidus and provide a thorough description for this species to facilitate ongoing taxonomic revisions of southern African Enteromius. Enteromiuspallidus can be distinguished from the other minnows in the "goldie barb group" by having an incomplete lateral line, lack of distinct chevron or tubular markings around lateral line pores, absence of a distinct lateral stripe, absence of wavy parallel lines along scale rows and lack of black pigmentation around the borders of the scales. We provide mtDNA COI sequences for the neotype and an additional specimen from the Baakens River as DNA barcodes of types and topotypes are a fundamental requirement for further taxonomic studies.

Matched MeSH terms: DNA, Mitochondrial; DNA Barcoding, Taxonomic
Silver(I)-mediated base pairing in parallel-stranded DNA involving the luminescent cytosine analog 1,3-diaza-2-oxophenoxazine

Schönrath I, Tsvetkov VB, Zatsepin TS, Aralov AV, Müller J

J Biol Inorg Chem, 2019 08;24(5):693-702.
PMID: 31263954 DOI: 10.1007/s00775-019-01682-1

1,3-Diaza-2-oxophenoxazine (X) has been introduced as a ligand in silver(I)-mediated base pairing in a parallel DNA duplex. This fluorescent cytosine analog is capable of forming stabilizing X-Ag(I)-X and X-Ag(I)-C base pairs in DNA duplexes, as confirmed by temperature-dependent UV spectroscopy and luminescence spectroscopy. DFT calculations of the silver(I)-mediated base pairs suggest the presence of a synergistic hydrogen bond. Molecular dynamics (MD) simulations of entire DNA duplexes nicely underline the geometrical flexibility of these base pairs, with the synergistic hydrogen bond facing either the major or the minor groove. Upon silver(I) binding to the X:X or X:C base pairs, the luminescence emission maximum experiences a red shift from 448 to 460 nm upon excitation at 370 nm. Importantly, the luminescence of the 1,3-diaza-2-oxophenoxazine ligand is not quenched significantly upon binding a silver(I) ion. In fact, the luminescence intensity even increases upon formation of a X-Ag(I)-C base pair, which is expected to be beneficial for the development of biosensors. As a consequence, the silver(I)-mediated phenoxazinone base pairs represent the first strongly fluorescent metal-mediated base pairs.

Matched MeSH terms: DNA/chemistry*

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