Displaying publications 1 - 20 of 1871 in total

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  1. A new step in kinetic proofreading due to misacylated-tRNA during ribosomal peptide bond formation
    Monajemi H, M Zain S, Wan Abdullah WAT
    Nucleosides Nucleotides Nucleic Acids, 2021;40(6):635-646.
    PMID: 34047250 DOI: 10.1080/15257770.2021.1923742
    The translational accuracy in protein synthesis is contributed to by several mechanisms in the ribosome, generally called kinetic proofreading. This process in the ribosome inhibits the non-cognate codon-anticodon interaction. However, it is not sufficient for fidelity of protein synthesis since a wrong amino acid can easily be added to the growing polypeptide chain if a tRNA while cognate to the mRNA, carries a non-cognate amino acid. Therefore, additional to the kinetic proofreading, there must be some hitherto unknown characteristic in misacylated-tRNAs to stop the process of protein synthesis if such misacylated-tRNA is accommodated in the ribosomal A-site. In order to understand this characteristic, we have performed computational quantum chemistry analysis on five different tRNA molecules, each one attached to five different amino acids with one being cognate to the tRNA and the other four non-cognate. This study shows the importance of aminoacyl-tRNA binding energy in ensuring fidelity of protein synthesis.
    Matched MeSH terms: RNA, Messenger; RNA, Transfer*
  2. Editorial: Contemporary siRNA Therapeutics and the Current State-of-Art
    Tekade RK
    Curr Pharm Des, 2015;21(31):4527-8.
    PMID: 26362643
    Matched MeSH terms: RNA Interference*; RNA, Small Interfering/administration & dosage*
  3. Whole genome sequence of moderate halophilic marine bacterium Marinobacter litoralis SW-45: Abundance of non-coding RNAs
    Musa H, Kasim FH, Gunny AAN, Gopinath SCB, Chinni SV, Ahmad MA
    Int J Biol Macromol, 2019 Jul 15;133:1288-1298.
    PMID: 31055112 DOI: 10.1016/j.ijbiomac.2019.05.003
    A report on the de novo Whole Genome Sequence (WGS) of Marinobacter litoralis SW-45, a moderately salt-tolerant bacterium isolated from the seawater in Malaysia is presented. The strain has a genome size of 3.45 Mb and is capable of producing halophilic lipase, protease and esterase enzymes. Computational prediction of non-coding RNA (ncRNA) genes in M. litoralis SW-45 was performed using standalone software known as the non-coding RNA characterization (nocoRNAc). In addition, a phylogenetic tree showing the evolutionary relationship between the strain and other members of the genus Marinobacter was constructed using 16SrRNA sequence information. A total of 385 ncRNA transcripts, 1124 terminator region, and 2350 Stress Induced Duplex Destabilization sites were predicted. The current WGS shotgun project has provided the relevant genetic information that may be useful for the strain's improvement studies. This manuscript gives the first description of M. litoralis with a complete genome.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics; RNA, Untranslated/genetics*
  4. Design, mechanism, delivery and therapeutics of canonical and Dicer-substrate siRNA
    Raja MAG, Katas H, Amjad MW
    Asian J Pharm Sci, 2019 Sep;14(5):497-510.
    PMID: 32104477 DOI: 10.1016/j.ajps.2018.12.005
    Upon the discovery of RNA interference (RNAi), canonical small interfering RNA (siRNA) has been recognized to trigger sequence-specific gene silencing. Despite the benefits of siRNAs as potential new drugs, there are obstacles still to be overcome, including off-target effects and immune stimulation. More recently, Dicer substrate siRNA (DsiRNA) has been introduced as an alternative to siRNA. Similarly, it also is proving to be potent and target-specific, while rendering less immune stimulation. DsiRNA is 25-30 nucleotides in length, and is further cleaved and processed by the Dicer enzyme. As with siRNA, it is crucial to design and develop a stable, safe, and efficient system for the delivery of DsiRNA into the cytoplasm of targeted cells. Several polymeric nanoparticle systems have been well established to load DsiRNA for in vitro and in vivo delivery, thereby overcoming a major hurdle in the therapeutic uses of DsiRNA. The present review focuses on a comparison of siRNA and DsiRNA on the basis of their design, mechanism, in vitro and in vivo delivery, and therapeutics.
    Matched MeSH terms: RNA, Double-Stranded; RNA Interference; RNA, Small Interfering; DEAD-box RNA Helicases
  5. Harnessing the potential of non-coding RNA: An insight into its mechanism and interaction in plant biotic stress
    Othman SMIS, Mustaffa AF, Mohd Zahid NII, Che-Othman MH, Samad AFA, Goh HH, et al.
    Plant Physiol Biochem, 2024 Feb;207:108387.
    PMID: 38266565 DOI: 10.1016/j.plaphy.2024.108387
    Plants have developed diverse physical and chemical defence mechanisms to ensure their continued growth and well-being in challenging environments. Plants also have evolved intricate molecular mechanisms to regulate their responses to biotic stress. Non-coding RNA (ncRNA) plays a crucial role in this process that affects the expression or suppression of target transcripts. While there have been numerous reviews on the role of molecules in plant biotic stress, few of them specifically focus on how plant ncRNAs enhance resistance through various mechanisms against different pathogens. In this context, we explored the role of ncRNA in exhibiting responses to biotic stress endogenously as well as cross-kingdom regulation of transcript expression. Furthermore, we address the interplay between ncRNAs, which can act as suppressors, precursors, or regulators of other ncRNAs. We also delve into the regulation of ncRNAs in response to attacks from different organisms, such as bacteria, viruses, fungi, nematodes, oomycetes, and insects. Interestingly, we observed that diverse microorganisms interact with distinct ncRNAs. This intricacy leads us to conclude that each ncRNA serves a specific function in response to individual biotic stimuli. This deeper understanding of the molecular mechanisms involving ncRNAs in response to biotic stresses enhances our knowledge and provides valuable insights for future research in the field of ncRNA, ultimately leading to improvements in plant traits.
    Matched MeSH terms: RNA, Plant/genetics; RNA, Untranslated/genetics
  6. HnRNP-like proteins as post-transcriptional regulators
    Yeap WC, Namasivayam P, Ho CL
    Plant Sci, 2014 Oct;227:90-100.
    PMID: 25219311 DOI: 10.1016/j.plantsci.2014.07.005
    Plant cells contain a diverse repertoire of RNA-binding proteins (RBPs) that coordinate a network of post-transcriptional regulation. RBPs govern diverse developmental processes by modulating the gene expression of specific transcripts. Recent gene annotation and RNA sequencing clearly showed that heterogeneous nuclear ribonucleoprotein (hnRNP)-like proteins which form a family of RBPs, are also expressed in higher plants and serve specific plant functions. In addition to their involvement in post-transcriptional regulation from mRNA capping to translation, they are also involved in telomere regulation, gene silencing and regulation in chloroplast. Here, we review the involvement of plant hnRNP-like proteins in post-transcription regulation of RNA processes and their functional roles in control of plant developmental processes especially plant-specific functions including flowering, chloroplastic-specific mRNA regulation, long-distance phloem transportation and plant responses to environmental stresses.
    Matched MeSH terms: RNA Processing, Post-Transcriptional*; RNA, Messenger/metabolism*; RNA-Binding Proteins/metabolism; RNA, Plant/metabolism*
  7. Fulltext Biases in small RNA deep sequencing data
    Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS
    Nucleic Acids Res, 2014 Feb;42(3):1414-26.
    PMID: 24198247 DOI: 10.1093/nar/gkt1021
    High-throughput RNA sequencing (RNA-seq) is considered a powerful tool for novel gene discovery and fine-tuned transcriptional profiling. The digital nature of RNA-seq is also believed to simplify meta-analysis and to reduce background noise associated with hybridization-based approaches. The development of multiplex sequencing enables efficient and economic parallel analysis of gene expression. In addition, RNA-seq is of particular value when low RNA expression or modest changes between samples are monitored. However, recent data uncovered severe bias in the sequencing of small non-protein coding RNA (small RNA-seq or sRNA-seq), such that the expression levels of some RNAs appeared to be artificially enhanced and others diminished or even undetectable. The use of different adapters and barcodes during ligation as well as complex RNA structures and modifications drastically influence cDNA synthesis efficacies and exemplify sources of bias in deep sequencing. In addition, variable specific RNA G/C-content is associated with unequal polymerase chain reaction amplification efficiencies. Given the central importance of RNA-seq to molecular biology and personalized medicine, we review recent findings that challenge small non-protein coding RNA-seq data and suggest approaches and precautions to overcome or minimize bias.
    Matched MeSH terms: RNA, Messenger/metabolism; RNA, Messenger/chemistry; Sequence Analysis, RNA/methods*; RNA, Small Untranslated/metabolism*; RNA, Small Untranslated/chemistry
  8. ONIOM and ab-initio calculations on the mechanism of uncatalyzed peptide bond formation
    Monajemi H, Daud MN, Mohd Zain S, Wan Abdullah WA
    Biochem. Cell Biol., 2012 Dec;90(6):691-700.
    PMID: 23016605 DOI: 10.1139/o2012-027
    Finding a proper transition structure for the peptide bond formation process can lead one to a better understanding of the role of ribosome in catalyzing this reaction. Using computer simulations, we performed the potential energy surface scan on the ester bond dissociation of P-site aminoacyl-tRNA and the peptide bond formation of P-site and A-site amino acids. The full fragments of initiator tRNA(i)(met) and elongator tRNA(phe) are attached to both cognate and non-cognate amino acids as the P-site substrate. The A-site amino acid for all four calculations is methionine. We used ONIOM calculations to reduce the computational cost. Our study illustrates the reduced rate of peptide bond formation for misacylated tRNA(i)(met) in the absence of ribosomal bases. The misacylated elongator tRNA(phe), however, did not show any difference in its PES compared with that for the phe-tRNA(phe). This demonstrates the structural specification of initiator tRNA(i)(met) for the amino acids side chain.
    Matched MeSH terms: RNA, Transfer, Amino Acyl/metabolism; RNA, Transfer, Met/metabolism; RNA, Transfer, Met/chemistry*; RNA, Transfer, Phe/metabolism; RNA, Transfer, Phe/chemistry*
  9. Fulltext Evaluation of DNA and RNA extraction methods
    Edwin Shiaw CS, Shiran MS, Cheah YK, Tan GC, Sabariah AR
    Med J Malaysia, 2010 Jun;65(2):133-7.
    PMID: 23756798 MyJurnal
    This study was done to evaluate various DNA and RNA extractions from archival FFPE tissues. A total of 30 FFPE blocks from the years of 2004 to 2006 were assessed with each modified and adapted method. Extraction protocols evaluated include the modified enzymatic extraction method (Method A), Chelex-100 extraction method (Method B), heat-induced retrieval in alkaline solution extraction method (Methods C and D) and one commercial FFPE DNA Extraction kit (Qiagen, Crawley, UK). For RNA extraction, 2 extraction protocols were evaluated including the enzymatic extraction method (Method 1), and Chelex-100 RNA extraction method (Method 2). Results show that the modified enzymatic extraction method (Method A) is an efficient DNA extraction protocol, while for RNA extraction, the enzymatic method (Method 1) and the Chelex-100 RNA extraction method (Method 2) are equally efficient RNA extraction protocols.
    Matched MeSH terms: RNA*
  10. Incorporation of Basic α-Hydroxy Acid Residues into Primitive Polyester Microdroplets for RNA Segregation
    Jia TZ, Bapat NV, Verma A, Mamajanov I, Cleaves HJ, Chandru K
    Biomacromolecules, 2021 04 12;22(4):1484-1493.
    PMID: 33663210 DOI: 10.1021/acs.biomac.0c01697
    Nucleic acid segregation and compartmentalization were likely essential functions that primitive compartment systems resolved during evolution. Recently, polyester microdroplets generated from dehydration synthesis of various α-hydroxy acids (αHA) were suggested as potential primitive compartments. Some of these droplets can differentially segregate and compartmentalize organic dyes, proteins, and nucleic acids. However, the previously studied polyester microdroplets included limited αHA chemical diversity, which may not reflect the chemical diversity available in the primitive Earth environment. Here, we increased the chemical diversity of polyester microdroplet systems by combinatorially adding an αHA monomer with a basic side chain, 4-amino-2-hydroxybutyric acid (4a2h), which was incorporated with different ratios of other αHAs containing uncharged side chains to form combinatorial heteropolyesters via dehydration synthesis. Incorporation of 4a2h in the polymers resulted in the assembly of some polyester microdroplets able to segregate fluorescent RNA or potentially acquire intrinsic fluorescent character, suggesting that minor modifications of polyester composition can significantly impact the functional properties of primitive compartments. This study suggests one process by which primitive chemical systems can increase diversity of compartment "phenotype" through simple modifications in their chemical composition.
    Matched MeSH terms: RNA*
  11. Fulltext Positive aspects of the mRNA platform for SARS-CoV-2 vaccines
    Hajissa K, Mussa A
    Hum Vaccin Immunother, 2021 Aug 03;17(8):2445-2447.
    PMID: 33830862 DOI: 10.1080/21645515.2021.1900713
    The unprecedented need to acquire a safe and effective vaccine for the long-term control of coronavirus disease 2019 (COVID-19) is a global imperative. Researchers have been working urgently and collaboratively to develop vaccines against the causative agent of COVID-19. The use of messenger RNA (mRNA) vaccine platform offers new opportunities for the development of effective vaccines. The first use of COVID-19 mRNA vaccines for individuals outside the clinical trials raised concerns over their safety and future efficacy. In social media, particularly in developing countries, widely shared false claims allege that the current mRNA-based COVID-19 vaccines potentially integrate into the host genome and thus may genetically modify humans. These vaccines are also assumed to lack efficacy due to the emergence of new strains. Such misinformation cause people to hesitate about receiving vaccination against COVID-19. This commentary aimed to outline the structure, mechanism of action and the major motive for the use of COVID-19 mRNA vaccine, with a focus on scientifically addressing challenges associated with conspiracy theories and dispelling misinformation around vaccination.
    Matched MeSH terms: RNA, Messenger/genetics
  12. A link between long non-coding RNA (lncRNA) and thalassaemia: A review
    Sumera A, Radhakrishnan AK, Aziz Baba A, George E
    Malays J Pathol, 2020 Dec;42(3):323-332.
    PMID: 33361713
    The long non-coding RNAs (lncRNAs) are the most prevalent and functionally diverse member of the non-coding RNA (ncRNA). The lncRNA has previously been considered to be a form of transcriptional "noise" but recent studies have found that the lncRNA to be associated with various disease conditions. It has also been found to play important roles in various physiological processes such as haemopoiesis, where lncRNA is reported to act as a fine-tuner of this very important process. To date, the effects of dysregulated lncRNA in thalassaemia has not been fully explored. This review article focuses on the possible roles of dysregulated lncRNAs in the pathogenesis of thalassaemia.
    Matched MeSH terms: RNA, Long Noncoding/genetics*
  13. Circular RNAs as Promising Biomarkers: A Mini-Review
    Abu N, Jamal R
    Front Physiol, 2016;7:355.
    PMID: 27588005 DOI: 10.3389/fphys.2016.00355
    The interest in circular RNAs has resurfaced in the past few years. What was considered as "junk" for nearly two decades is now one of the most interesting molecules. Circular RNAs are non-coding RNAs that are formed by back-splicing events and have covalently closed loops with no poly-adenylated tails. The regulation of circular RNAs is distinctive and they are selectively abundant in different types of tissues. Based on the current knowledge of circular RNAs, these molecules have the potential to be the "next big thing" especially as biomarkers for different diseases. This mini-review attempts to concisely look at the biology of circular RNAs, the putative functional activities, the prevalence of circular RNAs, and the possible role of circular RNA as biomarkers for diagnosis or measuring drug response.
    Matched MeSH terms: RNA Splicing; RNA, Untranslated
  14. Sistem minigenom virus Penyakit Newcastle (NDV) AF2240 sebagai sistem pengekspresan gen sel mamalia
    SHAHRUL HISHAM ZAINAL ARIFFIN, ROSLINA SHAMSUDIN, NURUL ATIKAH AHMAD, ZULKIFLIE ZAMROD
    Sains Malaysiana, 2012;41:423-430.
    Sistem minigenom telah digunakan untuk mengkaji replikasi dan transkripsi virus RNA tidak bersegmen. Objektif kajian ini adalah untuk membina sistem minigenom bagi virus NDV strain tempatan, AF2240 serta bagi mengkaji mekanisme transkripsi dan replikasi virus ini. Bagi tujuan ini lima plasmid digunakan iaitu pMGNDV, pCITENP, pCITEP, pTriEX-T7, dan pGEML. Kesemua plasmid diekstrak secara berskala besar dan dimendakkan menggunakan polietilina glikol. Hasil ekstrak ini digunakan untuk transfeksi ke dalam sel. Translasi in vitro dilakukan dengan menggunakan pCITENP, pCITEP, dan pTriEX-T7 untuk memastikan kesemua konstruk ini berfungsi. Hasil pemblotan western menunjukkan protein bersaiz ~100 kDa (T7), ~53 kDa (NP), ~53 dan 55 kDa (P) berjaya diekspreskan. Protein CAT diperoleh apabila plasmid yang mengekodkan minigenom NDV ditransfeksi bersama plasmid yang mengekodkan protein nukleokapsid (NP), fosfoprotein (P) dan subunit besar polimerase (L) ke dalam sel BHK-21. Dianggarkan 55 pg protein CAT berjaya diperoleh menggunakan kit CAT ELISA. Hasil pemblotan western turut menunjukkan protein CAT bersaiz 25 kDa dihasilkan. Kesimpulannnya, system minigenom ini berupaya untuk berfungsi dan mampu mengekspreskan gen asing di dalam sel mamalia BHK-21.
    Matched MeSH terms: RNA Viruses; RNA, Viral
  15. CircRNA-miRNA interactions in atherogenesis
    Tong KL, Tan KE, Lim YY, Tien XY, Wong PF
    Mol Cell Biochem, 2022 Dec;477(12):2703-2733.
    PMID: 35604519 DOI: 10.1007/s11010-022-04455-8
    Atherosclerosis is the major cause of coronary artery disease (CAD) which includes unstable angina, myocardial infarction, and heart failure. The onset of atherogenesis, a process of atherosclerotic lesion formation in the intima of arteries, is driven by lipid accumulation, a vicious cycle of reactive oxygen species (ROS)-induced oxidative stress and inflammatory reactions leading to endothelial cell (EC) dysfunction, vascular smooth muscle cell (VSMC) activation, and foam cell formation which further fuel plaque formation and destabilization. In recent years, there is a surge in the number of publications reporting the involvement of circular RNAs (circRNAs) in the pathogenesis of cardiovascular diseases, cancers, and metabolic syndromes. These studies have advanced our understanding on the biological functions of circRNAs. One of the most common mechanism of action of circRNAs reported is the sponging of microRNAs (miRNAs) by binding to the miRNAs response element (MRE), thereby indirectly increases the transcription of their target messenger RNAs (mRNAs). Individual networks of circRNA-miRNA-mRNA associated with atherogenesis have been extensively reported, however, there is a need to connect these findings for a complete overview. This review aims to provide an update on atherogenesis-related circRNAs and analyze the circRNA-miRNA-mRNA interactions in atherogenesis. The atherogenic mechanisms and clinical relevance of each atherogenesis-related circRNA were systematically discussed for better understanding of the knowledge gap in this area.
    Matched MeSH terms: RNA, Messenger/metabolism
  16. Role of circular RNAs in determining the fate of mesenchymal stem cells
    Wong RSY, Cheong SK
    Malays J Pathol, 2021 Aug;43(2):241-250.
    PMID: 34448788
    Ribonucleic acid (RNA) has been well-understood for its linear form for many years. With advances in high-throughput sequencing, there is an increasing focus on circular RNAs (circRNAs) recently. Although they were previously regarded as splicing error by-products, research has shown that they play a pivotal role in many cellular processes, one of which is the control of stem cell differentiation and fate. On the other hand, decades of research have demonstrated the promising therapeutic potential of mesenchymal stem cells (MSCs). To this end, there is a growing body of research on the role of circRNAs in the determination of the fate of MSCs. This review critically examines the current evidence and consolidates key findings from studies that explore the involvement of circRNAs in the regulation of MSC differentiation.
    Matched MeSH terms: RNA/genetics
  17. Microcystin production by oscillatorialean cyanobacteria isolated from cryopreserved Antarctic mats
    Usman AS, Merican F, Zaki S, Broady P, Convey P, Muangmai N
    Harmful Algae, 2022 Dec;120:102336.
    PMID: 36470600 DOI: 10.1016/j.hal.2022.102336
    Twenty cyanobacterial strains of eight morphospecies isolated from deep-frozen (-15 °C) mat samples originally collected on Ross Island, in Victoria Land, and on the McMurdo Ice Shelf were screened for the presence of genes encoding for production of anatoxins, cylindrospermopsin, microcystin/nodularin and saxitoxin. One strain of each of Microcoleus autumnalis and Phormidesmis priestleyi and two strains of Wilmottia murrayi were found to produce microcystin. No toxin production was detected in the other 16 strains representing five species. The four toxin-producing strains were characterised using both morphological and molecular approaches. Phylogenetic analyses using partial 16S rRNA sequences were consistent with the morphological identification of all four strains. They were all found to contain a fragment of the mcyE gene, which is involved in microcystin biosynthesis. ELISA analysis of extracts from cultures of these strains confirmed the presence of low concentrations of microcystin: 0.35 μg/L in M. autumnalis, <0.15 μg/L in P. priestleyi, 1.60 μg/L in W. murrayi strain 1 and 0.9 μg/L in W. murrayi strain 2. This study includes the first report of microcystin synthesis by W. murrayi.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  18. Fulltext Immunogenicity mechanism of mRNA vaccines and their limitations in promoting adaptive protection against SARS-CoV-2
    Salleh MZ, Norazmi MN, Deris ZZ
    PeerJ, 2022;10:e13083.
    PMID: 35287350 DOI: 10.7717/peerj.13083
    Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) in late 2019, hundreds of millions of people have been infected worldwide. There have been unprecedented efforts in acquiring effective vaccines to confer protection against the disease. mRNA vaccines have emerged as promising alternatives to conventional vaccines due to their high potency with the capacity for rapid development and low manufacturing costs. In this review, we summarize the currently available vaccines against SARS-CoV-2 in development, with the focus on the concepts of mRNA vaccines, their antigen selection, delivery and optimization to increase the immunostimulatory capability of mRNA as well as its stability and translatability. We also discuss the host immune responses to the SARS-CoV-2 infection and expound in detail, the adaptive immune response upon immunization with mRNA vaccines, in which high levels of spike-specific IgG and neutralizing antibodies were detected after two-dose vaccination. mRNA vaccines have been shown to induce a robust CD8+T cell response, with a balanced CD4+ TH1/TH2 response. We further discuss the challenges and limitations of COVID-19 mRNA vaccines, where newly emerging variants of SARS-CoV-2 may render currently deployed vaccines less effective. Imbalanced and inappropriate inflammatory responses, resulting from hyper-activation of pro-inflammatory cytokines, which may lead to vaccine-associated enhanced respiratory disease (VAERD) and rare cases of myocarditis and pericarditis also are discussed.
    Matched MeSH terms: RNA, Messenger/genetics
  19. Fulltext Optimization of nucleic acid extraction and amplification of a thiamine biosynthesis gene fragment from selected Malaysian seaweeds
    Md Ahaik FA, Mohd Taufik SH, Faiqah Johari NA, Zainal Abidin AA, Balia Yusof ZN
    Genes Genet Syst, 2023 Feb 22;97(5):247-256.
    PMID: 36631109 DOI: 10.1266/ggs.22-00088
    Obtaining high-quality nucleic acid extracted from seaweeds is notoriously difficult due to contamination with polysaccharides and polyphenolic compounds after cell disruption. Specific methods need to be employed for RNA isolation in different seaweed species, and therefore studies of the thiamine biosynthesis pathway have been limited. Two selected Malaysian species which are highly abundant and underutilized, namely Gracilaria sp. and Padina sp., representing the red and brown seaweeds, respectively, were collected to develop optimized total RNA extraction methods. Prior to that, DNA was extracted, and amplification of the 18S rRNA gene and the THIC gene (encoding the first enzyme in the pyrimidine branch of the thiamine biosynthesis pathway) from the DNA template was successful in Gracilaria sp. only. RNA was then extracted from both seaweeds using three different existing methods, with some modifications, using cetyltrimethylammonium bromide, guanidine thiocyanate and sodium dodecyl sulphate. Methods I and III proved to be efficient for Padina sp. and Gracilaria sp., respectively, for the extraction of highly purified RNA, with A260/A280 values of 2.0 and 1.8. However, amplification of the housekeeping gene glyceraldehyde-3-phosphate dehydrogenase and the THIC gene was successful in only Gracilaria sp. cDNA derived from extracted RNA. Further modifications are required to improve the exploitation of nucleic acids from brown seaweeds, which has been proven to be difficult. This work should pave the way for molecular studies of seaweeds generally and for the elucidation, specifically, of the thiamine biosynthesis pathway.
    Matched MeSH terms: RNA/metabolism
  20. Analysis of Coconut cadang-cadang viroid variants on field samples exhibiting variation in orange spotting symptom expression and severity
    Roslan ND, Sundram S, Hong LW, Ling KL, Vadamalai G
    Mol Biol Rep, 2023 Nov;50(11):9699-9705.
    PMID: 37676433 DOI: 10.1007/s11033-023-08771-0
    BACKGROUND: Sequence variation has been attributed to symptom variations but has not been investigated in Orange Spotting-Coconut cadang-cadang viroid (OS-CCCVd) infected palms. Likewise, the relationship between Coconut cadang-cadang viroid (CCCVd) variants, Orange Spotting (OS) severity and the accumulation of the viroid in the palms have not been elucidated. This paper describes the characterization of CCCVd variants by cloning and sequencing, followed by correlation with symptom expression.

    METHODS AND RESULTS: Total nucleic acids were extracted from leaf samples harvested from frond 20 of seven Dura × Pisifera (D × P) African oil palm (Elaeis guineensis Jacq.) aged between 13 and 21 years old collected from local plantations. The nucleic acids were fractionated using 5% non-denaturing polyacrylamide gel electrophoresis (PAGE) before being subjected to detection by reverse transcribed polymerase chain reaction (RT-PCR). The PCR products were cloned into a plasmid vector and the sequence of the clones was analyzed. CCCVd variants were quantified using real-time qPCR assay with CCCVd specific primers. Sixteen randomly selected clones of (OP246) had an arbitrary 100% identity with CCCVdOP246 (GeneBank Accession No: HQ608513). Meanwhile, four clones had >93% similarity with several minor sequence variations forming variants of OP234, OP235, OP251 and OP279.

    CONCLUSION: The OS symptoms observed in the field were characterized into three categories based on the size and morphology of the orange spots on the affected fronds. In addition, there was no direct correlation between disease severity and the accumulation of CCCVd variants in oil palm. This finding is the first report describing the sequence variation of the CCCVd RNA and symptom variation in OS oil palm field samples.

    Matched MeSH terms: RNA, Viral/genetics
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