@article{Adams2020,
abstract = {The development of the polymerase chain reaction (PCR), for which Kary Mullis received the 1992 Novel Prize in Chemistry, revolutionized molecular biology. At around the time that prize was awarded, research was being carried out by Russel Higuchi which led to the discovery that PCR can be monitored using fluorescent probes, facilitating quantitative real-time PCR (qPCR). In addition, the earlier discovery of reverse transcriptase (in 1970) laid the groundwork for the development of RT-PCR (used in molecular cloning). The latter can be coupled to qPCR, termed RT-qPCR, allowing analysis of gene expression through messenger RNA (mRNA) quantitation. These techniques and their applications have transformed life science research and clinical diagnosis.},
author = {Adams, Grace},
doi = {10.1042/BIO20200034},
issn = {0954-982X},
journal = {The Biochemist},
month = {jun},
number = {3},
pages = {48--53},
title = {{A beginner's guide to RT-PCR, qPCR and RT-qPCR}},
url = {https://doi.org/10.1042/BIO20200034},
volume = {42},
year = {2020}
}
@article{Bak2019,
abstract = {Background: Most genetically modified (GM) plants contain a promoter, P35S, from the plant virus, Cauliflower mosaic virus (CaMV), and many have a terminator, TNOS, derived from the bacterium, Agrobacterium tumefaciens. Assays designed to detect GM plants often target the P35S and/or TNOS DNA sequences. However, because the P35S promoter is derived from CaMV, these detection assays can yield false-positives from non-GM plants infected by this naturally-occurring virus. Results: Here we report the development of an assay designed to distinguish CaMV-infected plants from GM plants in a single multiplexed quantitative PCR (qPCR) reaction. Following initial testing and optimization via PCR and singleplex-to-multiplex qPCR on both plasmid and plant DNA, TaqMan qPCR probes with different fluorescence wavelengths were designed to target actin (a positive-control plant gene), P35S, P3 (a CaMV-specific gene), and TNOS. We tested the specificity of our quadruplex qPCR assay using different DNA extracts from organic watercress and both organic and GM canola, all with and without CaMV infection, and by using commercial and industrial samples. The limit of detection (LOD) of each target was determined to be 1% for actin, 0.001% for P35S, and 0.01% for both P3 and TNOS. Conclusions: This assay was able to distinguish CaMV-infected plants from GM plants in a single multiplexed qPCR reaction for all samples tested in this study, suggesting that this protocol is broadly applicable and readily transferrable to any interested parties with a qPCR platform.},
author = {Bak, Aur{\'{e}}lie and Emerson, Joanne B.},
doi = {10.1186/s12896-019-0571-1},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Bak, Emerson - 2019 - Multiplex quantitative PCR for single-reaction genetically modified (GM) plant detection and identification of fal.pdf:pdf},
issn = {14726750},
journal = {BMC Biotechnology},
keywords = {CaMV,Cauliflower mosaic virus,Detection methods,GM plant,GMO,Multiplex qPCR},
month = {nov},
number = {1},
pages = {1--12},
pmid = {31699075},
publisher = {BioMed Central Ltd.},
title = {{Multiplex quantitative PCR for single-reaction genetically modified (GM) plant detection and identification of false-positive GM plants linked to Cauliflower mosaic virus (CaMV) infection}},
volume = {19},
year = {2019}
}
@misc{Baralle2017,
abstract = {Alternative splicing of eukaryotic transcripts is a mechanism that enables cells to generate vast protein diversity from a limited number of genes. The mechanisms and outcomes of alternative splicing of individual transcripts are relatively well understood, and recent efforts have been directed towards studying splicing networks. It has become apparent that coordinated splicing networks regulate tissue and organ development, and that alternative splicing has important physiological functions in different developmental processes in humans.},
author = {Baralle, Francisco E. and Giudice, Jimena},
booktitle = {Nature Reviews Molecular Cell Biology},
doi = {10.1038/nrm.2017.27},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Baralle, Giudice - 2017 - Alternative splicing as a regulator of development and tissue identity(5).pdf:pdf},
issn = {14710080},
month = {jul},
number = {7},
pages = {437--451},
pmid = {28488700},
publisher = {Nature Publishing Group},
title = {{Alternative splicing as a regulator of development and tissue identity}},
volume = {18},
year = {2017}
}
@article{Busk2014,
abstract = {Background: MicroRNAs are small but biologically important RNA molecules. Although different methods can be used for quantification of microRNAs, quantitative PCR is regarded as the reference that is used to validate other methods. Several commercial qPCR assays are available but they often come at a high price and the sequences of the primers are not disclosed. An alternative to commercial assays is to manually design primers but this work is tedious and, hence, not practical for the design of primers for a larger number of targets.Results: I have developed the software miRprimer for automatic design of primers for the method miR-specific RT-qPCR, which is one of the best performing microRNA qPCR methods available. The algorithm is based on an implementation of the previously published rules for manual design of miR-specific primers with the additional feature of evaluating the propensity of formation of secondary structures and primer dimers. Testing of the primers showed that 76 out of 79 primers (96%) worked for quantification of microRNAs by miR-specific RT-qPCR of mammalian RNA samples. This success rate corresponds to the success rate of manual primer design. Furthermore, primers designed by this method have been distributed to several labs and used successfully in published studies.Conclusions: The software miRprimer is an automatic and easy method for design of functional primers for miR-specific RT-qPCR. The application is available as stand-alone software that will work on the MS Windows platform and in a developer version written in the Ruby programming language. {\textcopyright} 2014 Busk; licensee BioMed Central Ltd.},
author = {Busk, Peter K.},
doi = {10.1186/1471-2105-15-29},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Busk - 2014 - A tool for design of primers for microRNA-specific quantitative RT-qPCR.pdf:pdf},
issn = {14712105},
journal = {BMC Bioinformatics},
keywords = {MicroRNA,Primer design,Quantitative PCR,Software},
month = {jan},
number = {1},
pmid = {24472427},
title = {{A tool for design of primers for microRNA-specific quantitative RT-qPCR}},
volume = {15},
year = {2014}
}
@misc{Bustin2017,
abstract = {Primers are arguably the single most critical components of any PCR assay, as their properties control the exquisite specificity and sensitivity that make this method uniquely powerful. Consequently, poor design combined with failure to optimise reaction conditions is likely to result in reduced technical precision and false positive or negative detection of amplification targets. Despite the framework provided by the MIQE guidelines and the accessibility of wide-ranging support from peer-reviewed publications, books and online sources as well as commercial companies, the design of many published assays continues to be less than optimal: primers often lack intended specificity, can form dimers, compete with template secondary structures at the primer binding sites or hybridise only within a narrow temperature range. We present an overview of the main steps in the primer design workflow, with data that illustrate some of the unexpected variability that often occurs when theory is translated into practice. We also strongly urge researchers to report as much information about their assays as possible in their publications.},
author = {Bustin, Stephen and Huggett, Jim},
booktitle = {Biomolecular Detection and Quantification},
doi = {10.1016/j.bdq.2017.11.001},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Bustin, Huggett - 2017 - qPCR primer design revisited.pdf:pdf},
issn = {22147535},
keywords = {Assay design,MIQE,Oligonucleotides,Real-time PCR},
month = {dec},
pages = {19--28},
publisher = {Elsevier GmbH},
title = {{qPCR primer design revisited}},
volume = {14},
year = {2017}
}
@article{Fu2014,
abstract = {Sequence-specific RNA-binding proteins (RBPs) bind to pre-mRNA to control alternative splicing, but it is not yet possible to read the ‘splicing code' that dictates splicing regulation on the basis of genome sequence. Each alternative splicing event is controlled by multiple RBPs, the combined action of which creates a distribution of alternatively spliced products in a given cell type. As each cell type expresses a distinct array of RBPs, the interpretation of regulatory information on a given RNA target is exceedingly dependent on the cell type. RBPs also control each other's functions at many levels, including by mutual modulation of their binding activities on specific regulatory RNA elements. In this Review, we describe some of the emerging rules that govern the highly context-dependent and combinatorial nature of alternative splicing regulation.},
author = {Fu, Xiang-Dong and Ares, Manuel},
doi = {doi:10.1038/nrg3778},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Fu, Ares - 2014 - Context-dependent control of alternative splicing by RNA-binding proteins.pdf:pdf},
isbn = {8586542555},
journal = {Nat Rev Genet},
keywords = {endothelium,estrogen,estrogen receptors,vascular smooth muscle},
number = {10},
pages = {689--701},
title = {{Context-dependent control of alternative splicing by RNA-binding proteins}},
volume = {15},
year = {2014}
}
@article{Harvey2016,
abstract = {Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semi-quantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We also describe analysis of alternative splicing using a splicing “minigene” in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest.},
author = {Harvey, Samuel E. and Cheng, Chonghui},
doi = {10.1007/978-1-4939-3378-5_18},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Harvey, Cheng - 2016 - Methods for characterization of alternative RNA splicing.pdf:pdf},
isbn = {9781493933785},
issn = {10643745},
journal = {Methods in Molecular Biology},
keywords = {Alternative splicing,Minigene,RNA,RT-PCR,Splicing,Splicing factors,Variable exon,regulation},
pages = {229--241},
pmid = {26721495},
title = {{Methods for characterization of alternative RNA splicing}},
volume = {1402},
year = {2016}
}
@article{Jadav2016,
author = {Jadav, K K and Rajput, N and Singh, A P and Sarkhel, B C and Shrivastav, A B},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Jadav et al. - 2016 - A species-specific ARMS PCR test for detection of Indian wild pig DNA.pdf:pdf},
journal = {Indian Journal of Animal Sciences},
number = {6},
pages = {67--70},
title = {{A species-specific ARMS PCR test for detection of Indian wild pig DNA}},
url = {https://www.researchgate.net/publication/323355376},
volume = {86},
year = {2016}
}
@article{Kalendar2022,
abstract = {Polymerase chain reaction (PCR) is a simple and rapid method that can detect nucleotide polymorphisms and sequence variation in basic research applications, agriculture, and medicine. Variants of PCR, collectively known as allele-specific PCR (AS-PCR), use a competitive reaction in the presence of allele-specific primers to preferentially amplify only certain alleles. This method, originally named by its developers as Kompetitive Allele Specific PCR (KASP), is an AS-PCR variant adapted for fluorescence-based detection of amplification results. We developed a bioinformatic tool for designing probe sequences for PCR-based genotyping assays. Probe sequences are designed in both directions, and both single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) may be targeted. In addition, the tool allows discrimination of up to four-allelic variants at a single SNP site. To increase both the reaction specificity and the discriminative power of SNP genotyping, each allele-specific primer is designed such that the penultimate base before the primer's 3′ end base is positioned at the SNP site. The tool allows design of custom FRET cassette reporter systems for fluorescence-based assays. FastPCR is a user-friendly and powerful Java-based software that is freely available (http://primerdigital.com/tools/). Using the FastPCR environment and the tool for designing AS-PCR provides unparalleled flexibility for developing genotyping assays and specific and sensitive diagnostic PCR-based tests, which translates into a greater likelihood of research success.},
author = {Kalendar, Ruslan and Shustov, Alexandr V. and Akhmetollayev, Ilyas and Kairov, Ulykbek},
doi = {10.3389/fmolb.2022.773956},
file = {:D\:/Dari E/download/fmolb-09-773956.pdf:pdf},
isbn = {0000000262194},
issn = {2296889X},
journal = {Frontiers in Molecular Biosciences},
keywords = {diagnostic system,genotyping assay design software,genotyping system,insertion-deletion polymorphism,polymerase chain reaction-based markers,single nucleotide polymorphism},
number = {March},
pages = {1--13},
title = {{Designing allele-specific competitive-extension PCR-based assays for high-throughput genotyping and gene characterization}},
volume = {9},
year = {2022}
}
@article{Klepikova2016,
abstract = {Arabidopsis thaliana is a long established model species for plant molecular biology, genetics and genomics, and studies of A. thaliana gene function provide the basis for formulating hypotheses and designing experiments involving other plants, including economically important species. A comprehensive understanding of the A. thaliana genome and a detailed and accurate understanding of the expression of its associated genes is therefore of great importance for both fundamental research and practical applications. Such goal is reliant on the development of new genetic and genomic resources, involving new methods of data acquisition and analysis. We present here the genome-wide analysis of A. thaliana gene expression profiles across different organs and developmental stages using high-throughput transcriptome sequencing. The expression of 25 706 protein-coding genes, as well as their stability and their spatiotemporal specificity, was assessed in 79 organs and developmental stages. A search for alternative splicing events identified 37 873 previously unreported splice junctions, approximately 30% of them occurred in intergenic regions. These potentially represent novel spliced genes that are not included in the TAIR10 database. These data are housed in an open-access web-based database, TraVA (Transcriptome Variation Analysis, http://travadb.org/), which allows visualization and analysis of gene expression profiles and differential gene expression between organs and developmental stages.},
author = {Klepikova, Anna V. and Kasianov, Artem S. and Gerasimov, Evgeny S. and Logacheva, Maria D. and Penin, Aleksey A.},
doi = {10.1111/tpj.13312},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Klepikova et al. - 2016 - A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling.pdf:pdf},
issn = {1365313X},
journal = {Plant Journal},
keywords = {Arabidopsis thaliana,RNA-seq,alternative splicing,differentially expressed genes,gene expression analysis,transcription factor},
number = {6},
pages = {1058--1070},
pmid = {27549386},
title = {{A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling}},
volume = {88},
year = {2016}
}
@article{Li2020,
abstract = {In December 2019, a new coronavirus disease (COVID-19) outbreak occurred in Wuhan, China. Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which is the seventh coronavirus known to infect humans, is highly contagious and has rapidly expanded worldwide since its discovery. Quantitative nucleic acid testing has become the gold standard for diagnosis and guiding clinical decisions regarding the use of antiviral therapy. However, the RT-qPCR assays targeting SARS-CoV-2 have a number of challenges, especially in terms of primer design. Primers are the pivotal components of a RT-qPCR assay. Once virus mutation and recombination occur, it is difficult to effectively diagnose viral infection by existing RT-qPCR primers. Some primers and probes have also been made available on the WHO website for reference. However, no previous review has systematically compared the previously reported primers and probes and described how to design new primers in the event of a new coronavirus infection. This review focuses on how primers and probes can be designed methodically and rationally, and how the sensitivity and specificity of the detection process can be improved. This brief review will be useful for the accurate diagnosis and timely treatment of the new coronavirus pneumonia.},
author = {Li, Dandan and Zhang, Jiawei and Li, Jinming},
doi = {10.7150/thno.47649},
file = {:D\:/Dari E/download/thnov10p7150.pdf:pdf},
issn = {18387640},
journal = {Theranostics},
keywords = {Coronavirus,Primer design,Quantitative nucleic acid testing,SARS-CoV-2,Sensitivity},
number = {16},
pages = {7150--7162},
pmid = {32641984},
title = {{Primer design for quantitative real-time PCR for the emerging Coronavirus SARS-CoV-2}},
volume = {10},
year = {2020}
}
@article{Li2014,
abstract = {A continuous-flow microchip with a temperature gradient in microchannels was utilized to demonstrate spatial melting analysis on microbeads for clinical Single Nucleotide Polymorphisms (SNPs) genotyping on animal genomic DNA. The chip had embedded heaters and thermometers, which created a rapid and yet stable temperature gradient between 60 °C and 85 °C in a short distance as the detection region. The microbeads, which served as mobile supports carrying the target DNA and fluorescent dye, were transported across the temperature gradient. As the surrounding temperature increased, the fluorescence signals of the microbeads decayed with this relationship being acquired as the melting curve. Fast DNA denaturation, as a result of the improved heat transfer and thermal stability due to scaling, was also confirmed. Further, each individual microbead could potentially bear different sequences and pass through the detection region, one by one, for a series of melting analysis, with multiplex, high-throughput capability being possible. A prototype was tested with target DNA samples in different genotypes (i.e., wild and mutant types) with a SNP location from Landrace sows. The melting temperatures were obtained and compared to the ones using a traditional tube-based approach. The results showed similar levels of SNP discrimination, validating our proposed technique for scanning homozygotes and heterozygotes to distinguish single base changes for disease research, drug development, medical diagnostics, agriculture, and animal production.},
author = {Li, Kan Chien and Ding, Shih Torng and Lin, En Chung and Wang, Lon and Lu, Yen Wen},
doi = {10.1063/1.4902907},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Li et al. - 2014 - Melting analysis on microbeads in rapid temperature-gradient inside microchannels for single nucleotide polymorphisms.pdf:pdf},
issn = {19321058},
journal = {Biomicrofluidics},
month = {nov},
number = {6},
pages = {1--15},
publisher = {American Institute of Physics Inc.},
title = {{Melting analysis on microbeads in rapid temperature-gradient inside microchannels for single nucleotide polymorphisms detection}},
volume = {8},
year = {2014}
}
@article{Liu2016,
abstract = {Summary Angiosperms and gymnosperms are two major groups of extant seed plants. It has been suggested that gymnosperms lack FLOWERING LOCUS T (FT), a key integrator at the core of flowering pathways in angiosperms. Taking advantage of newly released gymnosperm genomes, we revisited the evolutionary history of the plant phosphatidylethanolamine-binding protein (PEBP) gene family through phylogenetic reconstruction. Expression patterns in three gymnosperm taxa and heterologous expression in Arabidopsis were studied to investigate the functions of gymnosperm FT-like and TERMINAL FLOWER 1 (TFL1)-like genes. Phylogenetic reconstruction suggests that an ancient gene duplication predating the divergence of seed plants gave rise to the FT and TFL1 genes. Expression patterns indicate that gymnosperm TFL1-like genes play a role in the reproductive development process, while GymFT1 and GymFT2, the FT-like genes resulting from a duplication event in the common ancestor of gymnosperms, function in both growth rhythm and sexual development pathways. When expressed in Arabidopsis, both spruce FT-like and TFL1-like genes repressed flowering. Our study demonstrates that gymnosperms do have FT-like and TFL1-like genes. Frequent gene and genome duplications contributed significantly to the expansion of the plant PEBP gene family. The expression patterns of gymnosperm PEBP genes provide novel insight into the functional evolution of this gene family.},
annote = {https://doi.org/10.1111/nph.14066},
author = {Liu, Yan-Yan and Yang, Ke-Zhen and Wei, Xiao-Xin and Wang, Xiao-Quan},
doi = {https://doi.org/10.1111/nph.14066},
issn = {0028-646X},
journal = {New Phytologist},
keywords = {FLOWERING LOCUS T (FT),functional evolution,gene and genome duplication,gymnosperms,molecular phylogeny,phosphatidylethanolamine-binding protein (PEBP) ge,seed plants},
month = {nov},
number = {3},
pages = {730--744},
publisher = {John Wiley & Sons, Ltd},
title = {{Revisiting the phosphatidylethanolamine-binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in gymnosperms and sheds new light on functional evolution}},
url = {https://doi.org/10.1111/nph.14066},
volume = {212},
year = {2016}
}
@article{Mardalisa2021,
abstract = {Bioinformatics has developed into an application tool for basic and applied research in the biomedical and biotechnology field. Polymerase Chain Reaction (PCR) is a common technique in the molecular area that has always involved bioinformatics science. PCR cloning techniques such as TA cloning and PCR-mediated cloning exhibit complex processes with low success rates. One easy, effective, and practical solution is to use a mega-primer with the Overlap Extension PCR Cloning (OEPC) technique. The success of PCR cloning using the mega-primer design in the OEPC technique is strongly influenced by the characteristics of the mega-primer used. Knowledge of mega-primer characteristics is one of the important factors in the success of PCR cloning. The design process for the mega-primer str promoter was characterized based on the principle of a genetic algorithm using the web-based bioinformatics tools such as ClustalW, NetPrimer, and BLAST. The success of the mega-primer construction in producing recombinant pSB1C3 vector has been confirmed by the sequencing method and the function of the reporting protein (AmilCP). DNA analysis shows a 100 % homologous sequence on the str promoter, while E. coli colonies successfully express the purplish-blue color. Mega-primer characters can save costs and time of the research by maintaining the primer parameters that provide optimal values and increase the success value of PCR cloning via bioinformatics software. Hence, implications on biological problems, especially using DNA and amino acid sequences, could solve rapidly.},
author = {Mardalisa and Suhandono, Sony and Yanti, Novi and Rozi, Fazrol and Nova, Fitri and Primawatie},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Mardalisa et al. - 2021 - Bioinformatic Analysis in Designing Mega-primer in Overlap Extension PCR Cloning (OEPC) Technique.pdf:pdf},
journal = {International Journal on Informatics Visualization},
keywords = {Bioinformatics,Overlap Extension PCR Cloning (OEPC),genetic algorithm,mega-primer design},
number = {2},
pages = {139--143},
title = {{Bioinformatic analysis in designing mega-primer in overlap extension PCR cloning (OEPC) technique}},
url = {www.ebi.ac.uk},
volume = {5},
year = {2021}
}
@article{MohdZuhar2019,
abstract = {Basal stern rot (BSR) disease is a major threat to oil palm industry in Malaysia, caused by pathogenic fungus, Ganoderma boninense. Quantitative real-time polymerase chain reaction (VCR) has become a favourable method in quantification the levels of gene expression involved in disease development. In this study, 14 oil palm reference genes were tested for their suitability as reference genes for qPCR analyses using oil palm root taken from six-month old seedlings (nursery sample) and 15-year old mature palms (field sample). Only six reference genes were subjected to stability test via RefFinder. The GRAS and ACTIN genes were ranked as the best reference genes for nursery sample, whereas, GAPDH and GvHK genes for field samples. These reference genes were used in the qpCR analysis for accurate normalisation. Thus, results obtained in this study emphasise the importance of validating the stability of the reference gene and proving the credibility and reliability of RefFinder in determining the most stable reference genes in each specific experiment or biological setting used.},
author = {{Mohd Zuhar}, Liyana},
doi = {10.21894/jopr.2019.0051},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Mohd Zuhar - 2019 - Determination of Reference Genes for Normalisation of Gene Expression Study of Ganoderma-infected Oil Palms.pdf:pdf},
issn = {15112780},
journal = {Journal of Oil Palm Research},
month = {dec},
number = {4},
pages = {550--560},
publisher = {Malaysian Palm Oil Board},
title = {{Determination of reference genes for normalisation of gene expression study of ganoderma-infected oil palms}},
volume = {31},
year = {2019}
}
@incollection{Pal2022,
abstract = {Rapid amplification of cDNA ends (RACE) or “one-sided” polymerase chain reaction (PCR) or “anchored” PCR is a polymerase chain reaction-based technique that results in the cloning of full-length cDNA sequences in case only a partial cDNA sequence is available. The 5′ RACE system is a set of prequalified reagents utilized for the synthesis of first-strand cDNA, purification of first-strand products, homopolymeric tailing, and preparation of target cDNA for subsequent amplification by PCR. The next step is the amplification of tailed cDNA by PCR with a mixture of three primers: a nested gene-specific primer (GSP2), which anneals 3′ to GSP1, a combination of a complementary homopolymer-containing anchor primer and a corresponding adapter primer, which permit amplification from the homopolymeric tail. Outline of the methodology of the individual steps of 5′ RACE is isolation of RNA, design of 5′ RACE primers, design of 5′ RACE primers, first-strand cDNA synthesis from total RNA, removal of RNA template by RNase mix, purification of first-strand product, homopolymeric tailing of cDNA, amplification of target cDNA, cloning 5′ RACE amplification products. Detailed protocol with illustrations has been discussed along with a troubleshooting guide.},
address = {New York, NY},
author = {Pal, Aruna},
booktitle = {Protocols in Advanced Genomics and Allied Techniques},
doi = {10.1007/978-1-0716-1818-9_21},
editor = {Pal, Aruna},
isbn = {978-1-0716-1818-9},
pages = {505--535},
publisher = {Springer US},
title = {{Rapid amplification of cDNA ends (RACE)}},
url = {https://doi.org/10.1007/978-1-0716-1818-9_21},
year = {2022}
}
@inproceedings{Polosoro2020,
author = {Polosoro, Aqwin and Enggarini, Wening and Hadiarto, Toto and Supena, Ence Darmo Jaya and Suharsono},
booktitle = {The 7th International Symposium of Innovative Bioproduction Indonesia on Biotechnology and Bioengineering 2020},
doi = {10.1088/1755-1315/762/1/012063},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Science - 2021 - In silico screening of oil palm early and continuously flowering gene candidates for faster breeding program In silico.pdf:pdf},
pages = {1--8},
publisher = {IOP Publishing},
title = {{In silico screening of oil palm early and continuously flowering gene candidates for faster breeding program}},
year = {2020}
}
@article{Shang2017,
abstract = {Gene expression can be regulated through transcriptional and post-transcriptional mechanisms. Transcription in eukaryotes produces pre-mRNA molecules, which are processed and spliced post-transcriptionally to create translatable mRNAs. More than one mRNA may be produced from a single pre-mRNA by alternative splicing (AS); thus, AS serves to diversify an organism's transcriptome and proteome. Previous studies of gene expression in plants have focused on the role of transcriptional regulation in response to environmental changes. However, recent data suggest that post-transcriptional regulation, especially AS, is necessary for plants to adapt to a changing environment. In this review, we summarize recent advances in our understanding of AS during plant development in response to environmental changes. We suggest that alternative gene splicing is a novel means of regulating the environmental fitness of plants.},
author = {Shang, Xudong and Cao, Ying and Ma, Ligeng},
doi = {10.3390/ijms18020432},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Shang, Cao, Ma - 2017 - Alternative splicing in plant genes A means of regulating the environmental fitness of plants.pdf:pdf},
isbn = {2160801011},
issn = {14220067},
journal = {International Journal of Molecular Sciences},
keywords = {Alternative splicing,Environmental fitness,Gene expression,Plant,Transcriptional regulation},
number = {2},
pages = {1--18},
pmid = {28230724},
title = {{Alternative splicing in plant genes: A means of regulating the environmental fitness of plants}},
volume = {18},
year = {2017}
}
@article{Svec2015,
abstract = {We have examined the imprecision in the estimation of PCR efficiency by means of standard curves based on strategic experimental design with large number of technical replicates. In particular, how robust this estimation is in terms of a commonly varying factors: the instrument used, the number of technical replicates performed and the effect of the volume transferred throughout the dilution series. We used six different qPCR instruments, we performed 1-16 qPCR replicates per concentration and we tested 2-10. $\mu$l volume of analyte transferred, respectively. We find that the estimated PCR efficiency varies significantly across different instruments. Using a Monte Carlo approach, we find the uncertainty in the PCR efficiency estimation may be as large as 42.5% (95% CI) if standard curve with only one qPCR replicate is used in 16 different plates. Based on our investigation we propose recommendations for the precise estimation of PCR efficiency: (1) one robust standard curve with at least 3-4 qPCR replicates at each concentration shall be generated, (2) the efficiency is instrument dependent, but reproducibly stable on one platform, and (3) using a larger volume when constructing serial dilution series reduces sampling error and enables calibration across a wider dynamic range.},
author = {Svec, David and Tichopad, Ales and Novosadova, Vendula and Pfaffl, Michael W. and Kubista, Mikael},
doi = {10.1016/j.bdq.2015.01.005},
file = {:D\:/Download/svec2015.pdf:pdf},
issn = {22147535},
journal = {Biomolecular Detection and Quantification},
keywords = {Amplification efficiency,Dilution series,QPCR,QPCR assay validation,Real-time quantitative PCR,Standard curve},
pages = {9--16},
pmid = {27077029},
publisher = {Elsevier GmbH},
title = {{How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments}},
url = {http://dx.doi.org/10.1016/j.bdq.2015.01.005},
volume = {3},
year = {2015}
}
@misc{Szakonyi2018,
abstract = {Most plant genes are interrupted by introns and the corresponding transcripts need to undergo pre-mRNA splicing to remove these intervening sequences. Alternative splicing (AS) is an important posttranscriptional process that creates multiple mRNA variants from a single pre-mRNA molecule, thereby enhancing the coding and regulatory potential of genomes. In plants, this mechanism has been implicated in the response to environmental cues, including abiotic and biotic stresses, in the regulation of key developmental processes such as flowering, and in circadian timekeeping. The early plant development steps – from embryo formation and seed germination to skoto- and photomorphogenesis – are critical to both execute the correct body plan and initiate a new reproductive cycle. We review here the available evidence for the involvement of AS and various splicing factors in the initial stages of plant development, while highlighting recent findings as well as potential future challenges.},
author = {Szakonyi, D{\'{o}}ra and Duque, Paula},
booktitle = {Frontiers in Plant Science},
doi = {10.3389/fpls.2018.01174},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Szakonyi, Duque - 2018 - Alternative splicing as a regulator of early plant development.pdf:pdf},
issn = {1664462X},
keywords = {Alternative splicing,Early seedling development,Embryogenesis,Photomorphogenesis,Seed dormancy,Seed germination,Seed maturation,Splicing factors},
month = {aug},
pages = {1--9},
publisher = {Frontiers Media S.A.},
title = {{Alternative splicing as a regulator of early plant development}},
volume = {9},
year = {2018}
}
@article{Tellinghuisen2015,
annote = {doi: 10.1021/acs.analchem.5b02057},
author = {Tellinghuisen, Joel and Spiess, Andrej-Nikolai},
doi = {10.1021/acs.analchem.5b02057},
issn = {0003-2700},
journal = {Analytical Chemistry},
month = {sep},
number = {17},
pages = {8925--8931},
publisher = {American Chemical Society},
title = {{Bias and imprecision in analysis of real-time quantitative polymerase chain reaction data}},
url = {https://doi.org/10.1021/acs.analchem.5b02057},
volume = {87},
year = {2015}
}
@article{Tsuji2015,
abstract = {Summary Accumulating evidence indicates that the FLOWERING LOCUS T (FT) protein is the mobile floral signal known as florigen. A rice FT homolog, Heading date 3a (Hd3a), is transported from the phloem to shoot apical cells, where it interacts with 14?3?3 proteins and transcription factor OsFD1 to form a florigen activation complex (FAC) that activates a rice homolog of the floral identity gene APETALA1. Recent studies showed that florigen has roles in plant development beyond flowering; however, the exact nature of these roles is not well understood. It is not clear whether FT is transported to organs outside the shoot apex, and whether FAC formation is required for processes other than flowering. We show here that the Hd3a protein accumulates in axillary meristems to promote branching, and that FAC formation is required. Analysis of transgenic plants revealed that Hd3a promotes branching through lateral bud outgrowth. Hd3a protein produced in the phloem reached the axillary meristem in the lateral bud, and its transport was required for promotion of branching. Moreover, mutant Hd3a proteins defective in FAC formation but competent with respect to transport did not promote branching. Finally, we show that Hd3a promotes branching independently from strigolactone and FC1, a transcription factor that inhibits branching in rice. Together, these results suggest that Hd3a functions as a mobile signal for branching in rice.},
annote = {https://doi.org/10.1111/tpj.12811},
author = {Tsuji, Hiroyuki and Tachibana, Chika and Tamaki, Shojiro and Taoka, Ken-ichiro and Kyozuka, Junko and Shimamoto, Ko},
doi = {https://doi.org/10.1111/tpj.12811},
issn = {0960-7412},
journal = {The Plant Journal},
keywords = {branching,florigen,florigen activation complex,meristem action,organ development,rice (Oryza sativa L.)},
month = {apr},
number = {2},
pages = {256--266},
publisher = {John Wiley & Sons, Ltd},
title = {{Hd3a promotes lateral branching in rice}},
url = {https://doi.org/10.1111/tpj.12811},
volume = {82},
year = {2015}
}
@article{Whankaew2019,
author = {Whankaew, Sukhuman and Ruttajorn, Kedsirin and Madsen, Claus Krogh and Asp, Torben and Xu, Li and Nakkaew, Alisa and Phongdara, Amornrat},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Whankaew et al. - 2019 - An EgHd3a-like and its alternatively spliced transcripts in the oil palm ( Elaeis guineensis ).pdf:pdf},
journal = {J. Sci. Technol.},
keywords = {alternative splicing,floral transition,flowering locus t,heading date,promoter},
number = {2},
pages = {332--340},
title = {{An EgHd3a-like and its alternatively spliced transcripts in the oil palm (Elaeis guineensis)}},
volume = {41},
year = {2019}
}
@article{Wilkinson2020,
abstract = {The spliceosome removes introns from messenger RNA precursors (pre-mRNA). Decades of biochemistry and genetics combined with recent structural studies of the spliceosome have produced a detailed view of the mechanism of splicing. In this review, we aim to make this mechanism understandable and provide several videos of the spliceosome in action to illustrate the intricate choreography of splicing. The U1 and U2 small nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP. Transfer of the 5 splice site (5 SS) from U1 to U6 snRNA triggers unwinding of U6 snRNA from U4 snRNA. U6 folds with U2 snRNA into an RNA-based active site that positions the 5 SS at two catalytic metal ions. The branch point (BP) adenosine attacks the 5 SS, producing a free 5 exon. Removal of the BP adenosine from the active site allows the 3 SS to bind, so that the 5 exon attacks the 3 SS to produce mature mRNA and an excised lariat intron.},
author = {Wilkinson, Max E and Charenton, Cl{\'{e}}ment and Nagai, Kiyoshi},
doi = {10.1146/annurev-biochem-091719},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wilkinson, Charenton, Nagai - 2020 - Annual review of biochemistry RNA splicing by the spliceosome.pdf:pdf},
keywords = {RNA catalysis,cryo-EM,cryo-electron microscopy,crystallography,helicases,pre-mRNA splicing,spliceosome},
pages = {359--388},
title = {{Annual review of biochemistry RNA splicing by the spliceosome}},
url = {https://doi.org/10.1146/annurev-biochem-091719-},
volume = {89},
year = {2020}
}
@article{Wu2019,
abstract = {The transition of meristems is an important developmental process for crop plants. Florigen is considered to be produced in leaves, then moves into the shoot apical meristem (SAM), triggers the transition from the vegetative to the reproductive phase. However, little is known whether Florigen functions in callus development or not. By fused reporter gene $\beta$-glucuronidase (GUS) to 1.7 kb promoter of Heading date 3a (Hd3a), GUS signals were detected in the scutellum cells, as well as in green point of the putative transgenic calli. Quantitative RT-PCR results demonstrated that the expression level of Hd3a was increased gradually over time along with the transition from scutellum-deprived callus to shoot. As reported that ectopic expression of FT-like genes caused earlier flowering, we also found that 80% constitutive expression of Hd3a transgenic callus showed formation floral-like organ structures. However, Hd3a RNA interference (RNAi) transgenic calli did not show any obvious phenotype, although AP1 or AP1-like genes—OsMADS14, OsMADS15, and OsMADS18- expression level is decreased during callus development. Both in Hd3a and RFT1 overexpression transgenic calli, Hd3a also modulated AP1 or AP1-like genes, as well AEPALLATA (SEP)-like gene, OsMADS34 during green point formation. Meanwhile, transgenic calli of RFT1and OsMADS50, but not OsEhd1, shared similar results as Hd3a. All of these findings suggested that florigen genes Hd3a and RFT1 have partial conserved functions in the transition of meristems during callus development.},
author = {Wu, Yunfei and Wei, Jinhuan and Choi, Sang-Chul Chul and Fei, Yongqing and Xiong, Fei},
doi = {10.1007/s11738-019-2914-x},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wu et al. - 2019 - Rice florigen gene Hd3a has conserved functions in callus development(3).pdf:pdf},
isbn = {0123456789},
issn = {1861-1664},
journal = {Acta Physiologiae Plantarum},
keywords = {AP1,Florigen genes,Hd3a,Meristem transition,RFT1},
number = {7},
pages = {125},
publisher = {Springer Berlin Heidelberg},
title = {{Rice florigen gene Hd3a has conserved functions in callus development}},
url = {https://doi.org/10.1007/s11738-019-2914-x},
volume = {41},
year = {2019}
}
@article{Xia2020,
abstract = {Coconut palm has two distinct types—“tall” and “dwarf”—which differ morphologically. Tall coconut varieties need 8–10 years to start flowering, while dwarf coconut varieties only require 3–5 years. We compared seedling and reproductive stage transcriptomes for both coconut types to determine potential molecular mechanisms underlying control of flowering time in coconut. Several key genes in the photoperiod pathway were differentially expressed between seedling and reproductive leaf samples in both tall and dwarf coconut. These genes included suppressor of overexpression of constans (SOC1), flowering locus T (FT), and Apetala 1 (AP1). Alternative splicing analysis of genes in the photoperiod pathway further revealed that the FT gene produces different transcripts in tall compared to dwarf coconut. The shorter alternative splice variant of FT [which included a 6 bp deletion, alternative 3′ splicing sites (A3SS)] was found to be exclusively present in dwarf coconut varieties but absent in most tall coconut varieties. Our results provide a valuable information resource as well as suggesting a probable mechanism for differentiation of flowering time onset in coconut, providing a target for future breeding work in accelerating time to flowering in this crop species.},
author = {Xia, Wei and Liu, Rui and Zhang, Jun and Mason, Annaliese S. and Li, Zhiying and Gong, Shufang and Zhong, Yazhu and Dou, Yajing and Sun, Xiwei and Fan, Haikuo and Xiao, Yong},
doi = {10.1038/s41598-020-68431-2},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Xia et al. - 2020 - Alternative splicing of flowering time gene FT is associated with halving of time to flowering in coconut.pdf:pdf},
isbn = {0123456789},
issn = {20452322},
journal = {Scientific Reports},
number = {1},
pages = {1--11},
pmid = {32669611},
publisher = {Nature Publishing Group UK},
title = {{Alternative splicing of flowering time gene FT is associated with halving of time to flowering in coconut}},
url = {https://doi.org/10.1038/s41598-020-68431-2},
volume = {10},
year = {2020}
}
@article{Yang2014,
abstract = {Alternative splicing (AS) occurs widely in plants and can provide the main source of transcriptome and proteome diversity in an organism. AS functions in a range of physiological processes, including plant disease resistance, but its biological roles and functional mechanisms remain poorly understood. Many plant disease resistance (R) genes undergo AS, and several R genes require alternatively spliced transcripts to produce R proteins that can specifically recognize pathogen invasion. In the finely-tuned process of R protein activation, the truncated isoforms generated by AS may participate in plant disease resistance either by suppressing the negative regulation of initiation of immunity, or by directly engaging in effector-triggered signaling. Although emerging research has shown the functional significance of AS in plant biotic stress responses, many aspects of this topic remain to be understood. Several interesting issues surrounding the AS of R genes, especially regarding its functional roles and regulation, will require innovative techniques and additional research to unravel. {\textcopyright} 2014 by the authors; licensee MDPI, Basel, Switzerland.},
author = {Yang, Shengming and Tang, Fang and Zhu, Hongyan},
doi = {10.3390/ijms150610424},
file = {:D\:/Download/ijms-15-10424.pdf:pdf},
isbn = {1042410445},
issn = {14220067},
journal = {International Journal of Molecular Sciences},
keywords = {Alternative splicing,CC-NBS-LRR,Disease resistance,Post-transcriptional regulation,RNA processing,TIR-NBS-LRR},
number = {6},
pages = {10424--10445},
pmid = {24918296},
title = {{Alternative splicing in plant immunity}},
volume = {15},
year = {2014}
}
@article{Yun2023,
abstract = {Environmental cues regulate the transition of many plants from vegetative to flowering development. Day length, or photoperiod, is one cue that synchronizes flowering by changing seasons. Consequently, the molecular mechanism of flowering control is prominent in Arabidopsis and rice, where essential genes like FLOWERING LOCUS T (FT) homolog, HEADING DATE 3a (Hd3a), have been connected to flowering regulation. Perilla is a nutrient-rich leaf vegetable, and the flowering mechanism remains largely elusive. We identified flowering-related genes under short-day conditions using RNA sequencing to develop an enhanced leaf production trait using the flowering mechanism in the perilla. Initially, an Hd3a-like gene was cloned from the perilla and defined as PfHd3a. Furthermore, PfHd3a is highly rhythmically expressed in mature leaves under short-day and long-day conditions. Ectopic expression of PfHd3a in Atft-1 mutant plants has been shown to complement Arabidopsis FT function, resulting in early flowering. In addition, our genetic approaches revealed that overexpression of PfHd3a in perilla caused early flowering. In contrast, the CRISPR/Cas9 generated PfHd3a-mutant perilla showed significantly late flowering, resulting in approximately 50% leaf production enhancement compared to the control. Our results suggest that PfHd3a plays a vital role in regulating flowering in the perilla and is a potential target for molecular breeding in the perilla.},
author = {Yun, Hee Rang and Chen, Chong and Kim, Jee Hye and Kim, Hae Eun and Karthik, Sivabalan and Kim, Hye Jeong and Chung, Young Soo and Baek, Hee Soon and Sung, Sibum and Kim, Hyun Uk and Heo, Jae Bok},
doi = {10.3389/fpls.2023.1133518},
file = {:C\:/Users/azzam/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Yun et al. - 2023 - Genome-edited HEADING DATE 3a knockout enhances leaf production in Perilla frutescens.pdf:pdf},
issn = {1664462X},
journal = {Frontiers in Plant Science},
keywords = {CRISPR,FT,Hd3a,flowering mechanism,perilla},
pages = {1--12},
publisher = {Frontiers Media S.A.},
title = {{Genome-edited HEADING DATE 3a knockout enhances leaf production in Perilla frutescens}},
volume = {14},
year = {2023}
}
@article{Zhang2022,
abstract = {Background: Oil palm is the most efficient oil-producing crop in the world, and the yield of palm oil is associated with embryonic development. However, a comprehensive understanding of zygotic embryo development at the molecular level remains elusive. In order to address this issue, we report the transcriptomic analysis of zygotic embryo development in oil palm, specifically focusing on regulatory genes involved in important biological pathways. Results: In this study, three cDNA libraries were prepared from embryos at S1 (early-stage), S2 (middle-stage), and S3 (late-stage). There were 16,367, 16,500, and 18,012 genes characterized at the S1, S2, and S3 stages of embryonic development, respectively. A total of 1522, 2698, and 142 genes were differentially expressed in S1 vs S2, S1 vs S3, and S2 vs S3, respectively. Using Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to identify key genes and pathways. In the hormone signaling pathway, genes related to auxin antagonize the output of cytokinin which regulates the development of embryo meristem. The genes related to abscisic acid negatively regulating the synthesis of gibberellin were strongly up-regulated in the mid-late stage of embryonic development. The results were reported the early synthesis and mid-late degradation of sucrose, as well as the activation of the continuous degradation pathway of temporary starch, providing the nutrients needed for differentiation of the embryonic cell. Moreover, the transcripts of genes involved in fatty acid synthesis were also abundantly accumulated in the zygotic embryos. Conclusion: Taken together, our research provides a new perspective on the developmental and metabolic regulation of zygotic embryo development at the transcriptional level in oil palm.},
author = {Zhang, Anni and Jin, Longfei and Yarra, Rajesh and Cao, Hongxing and Chen, Ping and {John Martin}, Jerome Jeyakumar},
doi = {10.1186/s12870-022-03459-2},
file = {:D\:/Dari E/download/12870_2022_Article_3459.pdf:pdf},
issn = {14712229},
journal = {BMC Plant Biology},
keywords = {Carbohydrate,Elaeis guineensis,Embryonic development,Fatty acid biosynthesis,Phytohormone,RNA-Seq,Sucrose and starch metabolism},
number = {1},
pages = {1--13},
pmid = {35279075},
publisher = {BioMed Central},
title = {{Transcriptome analysis reveals key developmental and metabolic regulatory aspects of oil palm (Elaeis guineensis Jacq.) during zygotic embryo development}},
url = {https://doi.org/10.1186/s12870-022-03459-2},
volume = {22},
year = {2022}
}