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Journal articles on the topic 'Gene primers'

Author: Grafiati

Published: 7 June 2025

Last updated: 2 August 2025

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1

Larekeng, Siti Halimah, Firzan Nainu, Muh Restu, Ahmad Rifqi Makkasau, Nasri, and Yuni Fitri Cahyaningsih. "Development and testing of PHYA gene-specific primers in sorghum to detect light-tolerant traits." IOP Conference Series: Earth and Environmental Science 1471, no. 1 (2025): 012020. https://doi.org/10.1088/1755-1315/1471/1/012020.

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Abstract The PHYA gene is one of the genes that play a role in the shade avoidance mechanism. The study aimed to design specific primers for the PHYA gene in sorghum plants and optimize the DNA amplification process. Primers were designed using the Primer3 Plus online tool, and primers were generated and tested on 14 Indonesian sorghum varieties. Gene amplification with PCR technology requires PHYA-specific primers. The amplification rate reached 100% with aneling temperatures ranging from 54-55°C specific to each primer. The resulting band was bright, firm, and specific, and the amplicon size

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Aurora, Dhea Apriano, Wilson Novarino, Djong Hon Tjong, et al. "Primer Design of Sumatran Striped Rabbit (Nesolagus netscheri Schlegel, 1880) using Primer-BLAST and AliView Program." Jurnal Biologi Tropis 25, no. 1 (2025): 599–605. https://doi.org/10.29303/jbt.v25i1.8499.

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The Sumatran striped rabbit (Nesolagus netscheri) lacks specific primers to amplify the chytochrome oxidase 1 (CO1) gene and the chytochrome b (cytb) gene, at present. Therefore, it is important to design primers to amplify the CO1 gene and cytb gene in N. netscheri. The aim of this study is to compare the primer design methods used, namely Primer-BLAST and AliView programs, to design specific primers for the chytochrome oxidase 1 (CO1) and chytochrome b (cytb) genes in N. netscheri. This research was conducted using the descriptive method with molecular observation. In this study, CO1 gene pr

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Khaira, Annisa, Afifatul Achyar, Zulyusri Zulyusri, Yusni Atifah, Dwi Hilda Putri, and Violita Violita. "Primer Design and Optimization of Annealing Temperature for Analysis of Glutathione Reductase Gene Expression in Rice (Oryza sativa L.)." 3BIO: Journal of Biological Science, Technology and Management 5, no. 1 (2023): 142–48. http://dx.doi.org/10.5614/3bio.2023.5.1.3.

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Glutathione Reductase (GR) belongs to the NADPH-dependent flavoprotein oxidoreductase family and is found in both prokaryotes and eukaryotes. The GR gene is considered to play a key role in the elimination of oxidative reaction products by looking at the level of gene expression of GR rice in dealing with drought stress using qPCR. One of the important steps to develop a specific, effective and efficient qPCR is the primer design. Several studies analyzing GR gene expression in rice have also designed primers. However, the primer still lacks an ideal characteristic of primer, as it still has a

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Sozinova, O. I., N. A. Kozub, I. A. Sozinov, and Ya B. Blume. "Genome specificity of primers to puroindoline genes." Faktori eksperimental'noi evolucii organizmiv 22 (September 9, 2018): 191–96. http://dx.doi.org/10.7124/feeo.v22.947.

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Aim. Genome specificity of primers for amplification of complete coding sequences of puroindoline genes was studied. Methods. PCR with gene-specific primers was performed for amplification of puroindoline genes of wheat and related species. Results. The primer pair designated PinaDH is not gene-specific as it yields two products of amplification of the genes Pina-1 and Gsp-1. This primers pair is not specific for the Pina-1 gene of the genome V of D. villosum. The primer pairs designated PinaCM and Pinb are gene-specific as they produce one amplification product of respective length. We have d

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Semenov, V. M., S. K. Yahorau, I. A. Lyatos, et al. "REAL-TIME PCR TEST SYSTEM FOR TTV DNA DETECTION IN BIOLOGICAL MATERIAL." Hepatology and Gastroenterology 8, no. 1 (2024): 36–41. http://dx.doi.org/10.25298/2616-5546-2024-8-1-36-41.

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Background. The study of biological material for the presence of TTV DNA using the PCR method allows for a timely assessment of the functional state of the human liver and immune system. Objective. To develop components for real-time PCR for TTV DNA detection in biological material. Material and methods. The design and selection of optimal primers and probes (taking into account the size (length) of the amplicon, annealing temperature, nucleotide composition, distribution of nucleotides along the length of the primer, length of primers, the possibility of formation of hairpins and dimers by pr

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Mitin, Valentin, and Irina Mitina. "SOME ASPECTS OF PRIMER DESIGN FOR REAL TIME PCR WITH SYBR GREEN AS A DYE." Journal of Engineering Science XXVII (4) (December 15, 2020): 191–96. https://doi.org/10.5281/zenodo.4296193.

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This work considers the sequence of steps for designing primers for real time qPCR analysis with SYBR® Green as fluorescent dye. For primer design, we used Primer-Blast software. As an example, we design primers to fum6 gene, a member of fumonisin biosynthetic gene cluster. The importance of a balance between specificity and efficiency of primers obtained with the help of Primer-Blast software is discussed. Challenges of obtaining specific primers are considered, possible solutions are suggested. BLAST analysis of the primers is discussed, potential approaches to choosing an optimal primer

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Hidayah, Nurul, Yuni Ahda, Afifatul Achyar, and Yusni Atifah. "DESAIN PRIMER GEN EDNRB EKSON 4 DAN OPTIMASI PCR UNTUK ANALISIS MUTASI GEN PADA HIRSCHSPRUNG DISEASE." Jurnal Biogenerasi 10, no. 2 (2025): 1468–76. https://doi.org/10.30605/biogenerasi.v10i2.5954.

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EDNRB gene is a gene located on chromosome 13q22, plays a role in the signaling pathway during the development of the ENS intestinal nerves. Mutations in the EDNRB gene in humans are associated with Hirschsprung Disease (HD). Mutations in the EDNRB gene are the second most common cause after the RET gene in cases of HD with a percentage of 5–10%. To detect mutations, PCR products are needed. Primers are one of the basic components of PCR, while optimization of annealing temperature and optimization of primer concentration are factors in the success of primer attachment to the target gene. This

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Barak, Noga, Eduard Fadeev, Vera Brekhman, Dikla Aharonovich, Tamar Lotan, and Daniel Sher. "Selecting 16S rRNA Primers for Microbiome Analysis in a Host–Microbe System: The Case of the Jellyfish Rhopilema nomadica." Microorganisms 11, no. 4 (2023): 955. http://dx.doi.org/10.3390/microorganisms11040955.

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Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remains a major decision when initiating any new microbiome study. Based on a detailed literature survey of studies focusing on cnidarian microbiomes, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfish Rhopilema nomadica as a model. Although all pr

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Nitovska, І. О. "PECULIARITIES OF GREEN FLUORESCENT PROTEIN TRANSGENE DETECTION IN TOBACCO AND MAIZE PLANTS BY PCR." Biotechnologia Acta 16, no. 4 (2023): 44–49. http://dx.doi.org/10.15407/biotech16.04.044.

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The aim of the work was to investigate detection of different modifications of the green fluorescent protein gene (gfp) in the transgenic tobacco and maize plants by polymerase chain reaction (PCR). Methods. Total DNA isolation, PCR, electrophoresis of DNA in agarose gel, bioinformatic resources. Results. Three pairs of primers were used for PCR analysis of tobacco and maize containing wild-type gfp or mutant synthetic gene S65Tpgfp. The primer pair gfp1F-gfp1R interacted with the wild-type gfp gene only. The gfp2F-gfp2R primers interacted with the gfp gene of different modifications both in t

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Okazaki, Ryuji, Akira Ootsuyama, Yasuhiro Yoshida, and Toshiyuki Norimura. "Establishment of Methylation-Specific PCR for the Mouse p53 Gene." Molecular Biology International 2011 (December 12, 2011): 1–4. http://dx.doi.org/10.4061/2011/938435.

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Methylation-specific PCR (MSP) of the mouse p53 gene has not yet been reported. We searched the CpG islands, sequenced the bisulfited DNA, and designed PCR primers for methylation and unmethylation sites. DNA from a young mouse produced a strong PCR product with the unmethylated primer and a weaker band with the methylated primer. DNA from an old mouse produced bands of similar intensities with both primers. In radiation-induced tumors, DNA from an old mouse yielded similar bands with both types of primers. We suggest that MSP is a valuable technique for the epigenetic study of the mouse p53 g

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Nguyễn, Thị Quý, Trọng Khoa Đào та Thị Huyền Đỗ. "PHÁT HIỆN SỰ BẮT CẶP KHÔNG ĐẶC HIỆU CỦA MỒI 27F, 1527R KHI KHUẾCH ĐẠI GEN 16S rRNA TỪ DNA ĐA HỆ GEN VI KHUẨN TRONG MẪU PHÂN TRẺ EM". Tạp chí Khoa học và Công nghệ Nhiệt đới, № 36 (29 квітня 2025): 55–66. https://doi.org/10.58334/vrtc.jtst.n36.06.

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EFFECT OF ANNEALING TEMPERATURE ON NON-SPECIFIC AMPLIFICATION OF PRIMERS 27F, 1527R FROM METAGENOMIC DNA OF BACTERIA IN CHILDREN FECES Primers 27F and 1527R are universal primers capable of amplifying nearly complete 16S rRNA gene of various bacteria in an environment for diversity analysis. In this study, the primers were used for amplification of multigene 16S rRNA of bacteria extracted from stool samples of a healthy child and a dirrheal child with unknown-pathogenic agent by three PCR programs: specific, tough-up and tough-down. The tough-up amplified DNA fragments of about 250 bp with hig

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Junier, Pilar, Ok-Sun Kim, Ora Hadas, Johannes F. Imhoff, and Karl-Paul Witzel. "Evaluation of PCR Primer Selectivity and Phylogenetic Specificity by Using Amplification of 16S rRNA Genes from Betaproteobacterial Ammonia-Oxidizing Bacteria in Environmental Samples." Applied and Environmental Microbiology 74, no. 16 (2008): 5231–36. http://dx.doi.org/10.1128/aem.00288-08.

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ABSTRACT The effect of primer specificity for studying the diversity of ammonia-oxidizing betaproteobacteria (βAOB) was evaluated. βAOB represent a group of phylogenetically related organisms for which the 16S rRNA gene approach is especially suitable. We used experimental comparisons of primer performance with water samples, together with an in silico analysis of published sequences and a literature review of clone libraries made with four specific PCR primers for the βAOB 16S rRNA gene. With four aquatic samples, the primers NitA/NitB produced the highest frequency of ammonia-oxidizing-bacte

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Ragot, Sabine A., Michael A. Kertesz, and Else K. Bünemann. "phoDAlkaline Phosphatase Gene Diversity in Soil." Applied and Environmental Microbiology 81, no. 20 (2015): 7281–89. http://dx.doi.org/10.1128/aem.01823-15.

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ABSTRACTPhosphatase enzymes are responsible for much of the recycling of organic phosphorus in soils. The PhoD alkaline phosphatase takes part in this process by hydrolyzing a range of organic phosphoesters. We analyzed the taxonomic and environmental distribution ofphoDgenes using whole-genome and metagenome databases.phoDalkaline phosphatase was found to be spread across 20 bacterial phyla and was ubiquitous in the environment, with the greatest abundance in soil. To study the great diversity ofphoD, we developed a new set of primers which targetsphoDgenes in soil. The primer set was validat

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Syamsurizal, S., Hengki Saputra, Dwi Hilda Putri, and Elsa Badriyya. "Primers Designed For Amplifying TCF7L2 Gen." Jurnal Biota 6, no. 2 (2020): 63–70. http://dx.doi.org/10.19109/10.19109/biota.v6i2.5871.

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Diabetes Mellitus (DM) is a disease characterized by high glucose levels because of the lack of insulin hormone in the body. Prevalence of Type-2 Diabetes Mellitus is associated with the variant of the TCF7L2 gene polymorphism, or SNP. The purpose of this study was to construct a specific primer to amplify the TCF7L2 gene fragment and their capabilities to detect the targeted area. This research was a descriptive study that design the primers using Geneious software version 5.4.7. The study was conducted at the Laboratory of Genetics and Biotechnology FMIPA Universitas Negeri Padang. Based on

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Na, Hee Sam, Yuri Song, Yeuni Yu, and Jin Chung. "Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies." Methods and Protocols 6, no. 4 (2023): 71. http://dx.doi.org/10.3390/mps6040071.

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Recent advances in genomic technologies have enabled more in-depth study of the oral microbiome. In this study, we compared the amplicons generated by primers targeting different sites of the 16S rRNA gene found in the Human Oral Microbiome Database (HOMD). Six sets of primer targeting V1–V2, V1–V3, V3–V4, V4–V5, V5–V7 and V6–V8 regions of 16S rRNA were tested via in silico simulation. Primers targeting the V1–V2, V3–V4, and V4–V5 regions generated more than 90% of the original input sequences. Primers targeting the V1–V2 and V1–V3 regions exhibited a low number of mismatches and unclassified

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Irawan, Yulius Dedy, Ilvi Chamalia, Dahlia ,, and Dwi Listyorini. "DOES Beta vulgaris L. HAVE LCYB GENE?" KnE Life Sciences 2, no. 1 (2015): 92. http://dx.doi.org/10.18502/kls.v2i1.122.

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Beta carotene is a pigment that generally shared by all plants. This pigment synthesis is catalized by lycopene beta cyclase enzime. This enzyme is encoded by the LCYB gene. This research aimed to obtain the sequence of LCYB gene isolated from beet (Beta vulgaris L.) leaves. Several experiments have been done to isolate the LCYB gene. In the first experiment, the gene primers are designed using Pick Primer software based on conserved region of Taraxacum officinale (accession no.AB247456.1) and Lilium lancifolium LCYB (accession no. GU471230.1).The forward primer is (5'-TGTCGTGGTGGATCTTGTGG-3')

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Abdullah, Asadatun, Annisaa Putri, and Mala Nurilmala. "Specific Primer Design for Detection of gene Cyt b for Shark Species Prionace glauca and gene COI for Carcharhinus spp. Using Real-Time PCR Method." BIO Web of Conferences 92 (2024): 01008. http://dx.doi.org/10.1051/bioconf/20249201008.

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International market demand for sharks is increasing, thus increasing the number of catches of several shark species that are included in the International Union for Conservation of Nature’s (IUCN) Red List and the Convention International Trade of Endangered Species (CITES) Appendix II. Authentication using biomoleculars by utilizing DNA is necessary. This study was aimed to design specific primers based on cytochrome c oxidase I and cytochrome b marker genes for endangered sharks (Prionace glauca and Carcharhinus spp.) and to apply them in vitro to identify fishery products using real-time P

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Nugroho, Herjuno Ari, Rini Widayanti, Tri Wahyu Pangestiningsih, and Eli Supriyani. "The Development and Optimization of Primer Sets Used to Study the Relative Expression of Androgen Receptor Gene in Turkey (Meleagris gallopavo)." BIO Web of Conferences 33 (2021): 02003. http://dx.doi.org/10.1051/bioconf/20213302003.

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The Androgen Receptor (AR) Gene’s expression is essential during puberty and testes maturation, which is also used as a reference for Turkey’s breeding program. Therefore, this study aims to develop and optimize two primer sets for studying relative expression using qPCR technology. The primers were designed to amplify specific regions in the AR gene as the main target, and the β-actin gene as an internal control. They were tested using in-silico and amplicon sequencing, as well as efficiency calculation with a constructed standard curve from serially diluted reactions. Based on the sequencing

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Löffler, Frank E., Qing Sun, Jieran Li, and James M. Tiedje. "16S rRNA Gene-Based Detection of Tetrachloroethene-Dechlorinating Desulfuromonas andDehalococcoides Species." Applied and Environmental Microbiology 66, no. 4 (2000): 1369–74. http://dx.doi.org/10.1128/aem.66.4.1369-1374.2000.

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ABSTRACT Members of the genera Desulfuromonas andDehalococcoides reductively dechlorinate tetrachloroethene (PCE) and trichloroethene. Two primer pairs specific to hypervariable regions of the 16S rRNA genes of the Dehalococcoides group (comprising Dehalococcoides ethenogenes andDehalococcoides sp. strain FL2) and the acetate-oxidizing, PCE-dechlorinating Desulfuromonas group (comprisingDesulfuromonas sp. strain BB1 and Desulfuromonas chloroethenica) were designed. The detection threshold of a nested PCR approach using universal bacterial primers followed by a second PCR with the Desulfuromona

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Xu, Eugenia Y., Lisa M. Schneper, and Daniel A. Notterman. "A novel metric to improve mismatched primer selection and quantification accuracy in amplifying DNA repeats for quantitative polymerase chain reactions." PLOS ONE 18, no. 10 (2023): e0292559. http://dx.doi.org/10.1371/journal.pone.0292559.

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In quantitative polymerase chain reaction (qPCR) experiments, primers containing mismatches with respect to the template are widely used in measuring repetitive DNA elements. Primer-template mismatches may lead to underestimation of the input sample quantity due to inefficient annealing and amplification. But how primer-template mismatches affect quantification accuracy has not been rigorously investigated. In this study, we performed a series of qPCR experiments in which we tested three pairs of mismatched telomere primers (tel1/tel2, tel1b/tel2b and telg/telc) and two pairs of perfect-match

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Ravindran, Aravind, Julien Levy, Elizabeth Pierson, and Dennis C. Gross. "Development of Primers for Improved PCR Detection of the Potato Zebra Chip Pathogen, ‘Candidatus Liberibacter solanacearum’." Plant Disease 95, no. 12 (2011): 1542–46. http://dx.doi.org/10.1094/pdis-05-11-0386.

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Zebra chip disease poses a major economic threat to potato production. The causative agent is a phloem-limited bacterium identified as ‘Candidatus Liberibacter solanacearum’ that is transmitted by the potato/ tomato psyllid. Currently, there are no effective controls and existing control strategies depend largely on the early detection of the pathogen via polymerase chain reaction (PCR) assays. Most primer sets used for PCR detection target a region of the bacterial 16S rDNA gene, and detection of the pathogen in symptomatic potato tissue with existing primers has been variable depending on th

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ARAÚJO, LEILA G., ANNE S. PRABHU, and MARTA C. FILIPPI. "Identification of rapd marker linked to blast resistance gene in a somaclone of rice cultivar Araguaia." Fitopatologia Brasileira 27, no. 2 (2002): 181–85. http://dx.doi.org/10.1590/s0100-41582002000200010.

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The gene Pi-ar confers resistance to Pyricularia grisea race IB-45 in a somaclone derived from immature panicles of the susceptible rice (Oryza sativa) cultivar Araguaia. RAPD technique was used to identify molecular markers linked to this gene utilizing bulked segregant analysis. Initially, the two parental DNAs from the resistant donor SC09 and 'Araguaia' were analyzed using random primers. Of the 240 primers tested, 203 produced amplification products. The two parental DNAs along with the resistant and susceptible bulks of F2 population were screened using 48 primers that differentiated res

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Doliwa, Annemie, Daniel Grabner, Bernd Sures, and Micah Dunthorn. "Comparing Microsporidia-targeting primers for environmental DNA sequencing." Parasite 30 (2023): 52. http://dx.doi.org/10.1051/parasite/2023056.

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Metabarcoding is a powerful tool to detect classical, and well-known “long-branch” Microsporidia in environmental samples. Several primer pairs were developed to target these unique microbial parasites, the majority of which remain undetected when using general metabarcoding primers. Most of these Microsporidia-targeting primer pairs amplify fragments of different length of the small subunit ribosomal RNA (SSU-rRNA) gene. However, we lack a broad comparison of the efficacy of those primers. Here, we conducted in silico PCRs with three short-read (which amplify a few-hundred base pairs) and two

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Chubarov, Alexey S., Igor P. Oscorbin, Lidiya M. Novikova, Maxim L. Filipenko, Alexander A. Lomzov, and Dmitrii V. Pyshnyi. "Allele-Specific PCR for PIK3CA Mutation Detection Using Phosphoryl Guanidine Modified Primers." Diagnostics 13, no. 2 (2023): 250. http://dx.doi.org/10.3390/diagnostics13020250.

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Phosphoryl guanidine (PG) is the novel uncharged modification of internucleotide phosphates of oligonucleotides. Incorporating PG modification into PCR primers leads to increased discrimination between wild-type and mutated DNA, providing extraordinary detection limits in an allele-specific real-time polymerase chain reaction (AS-PCR). Herein, we used PG-modification to improve the specificity of AS primers with unfavorable Pyr/Pur primer’s 3′-end mismatch in the template/primer complex. Two mutations of the PIK3CA gene (E542K, E545K) were chosen to validate the advantages of the PG modificati

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Alfaruqi, Hamiyawati Qoimatu Dini, Nosa Septiana Anindita, and Arif Bimantara. "KAJIAN MOLEKULER PADA PROBIOTIK ASAL AIR SUSU IBU DALAM SINTESIS EKSOPOLISAKARIDA (EPS)." Jurnal Bioteknologi & Biosains Indonesia (JBBI) 8, no. 1 (2021): 114–23. http://dx.doi.org/10.29122/jbbi.v8i1.4554.

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Molecular Studies on Probiotic of Human Breast Milk in the Synthesis of Exopolysaccharide (EPS) The glucosyltransferase (gtf) gene has an important role in exopolysaccharide (EPS) synthesis in probiotic bacteria. The EPS produced is associated with the adhesion ability of bacteria to the intestinal mucosa. Therefore, the gtf gene can be used as a parameter in the selection of potential probiotic through a molecular approach. This study was conducted to determine the presence of the gtf gene in probiotic from human breast milk using PCR technique. The methods in this study include the following

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Indradewi, Riski. "Teknik Desain Primer untuk Amplifikasi Gen Tujuan Kloning dari DNA Agrobacterium tumefaciens." Perbal: Jurnal Pertanian Berkelanjutan 10, no. 3 (2022): 305–9. http://dx.doi.org/10.30605/perbal.v10i3.2090.

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Penelitian ini bertujuan untuk menghasilkan teknik desain primer untuk amplifikasi gen penyandi enzim dengan tujuan kloning dari DNA genom Agrobacterium tumefaciens. Metode pengumpulan informasi dari penelitian ini dilakukan dengan cara observasi langsung dan melakukan studi pustaka untuk menarik kesimpulan. Prosedur penelitian dimulai dari mengoleksi sekuen DNA genom Agrobacterium tumefasien dari gene bank (NCBI), desain primer menggunakan Genamics expression dan penambahan situs restriksi. Primer yang telah diperoleh dikonfirmasi melalui perangkat lunak past PCR dan amplifikasi gen dengan te

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Sattar, Abu Naser Ibne, Sanjida Khondakar Setu, Ahmed Abu Saleh, and Sharmeen Ahmed. "TRC4 Gene Based PCR Assay in Diagnosis of Tuberculous Meningitis." Bangladesh Journal of Medical Microbiology 8, no. 2 (2017): 19–22. http://dx.doi.org/10.3329/bjmm.v8i2.31094.

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The prevalence of Tuberculous meningitis remains largely underestimated due to nonspecific clinical manifestation at early stages. A total of 20 CSF samples were studied from clinically suspected cases of tuberculous meningitis. All the samples were processed for ZN staining, TB culture on LJ media and TB-PCR using IS6110 and TRC4 primers by standard protocols. Of the total 20 CSF samples, 12 cases were diagnosed as TB meningitis. Most of the tuberculous meningitis cases were found positive by PCR using TRC4 primers (83.33%) followed by IS6110 primer (66.67%) and culture on L-J media(8.33%). N

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Rusch, Antje. "Molecular Tools for the Detection of Nitrogen Cycling Archaea." Archaea 2013 (2013): 1–10. http://dx.doi.org/10.1155/2013/676450.

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Archaea are widespread in extreme and temperate environments, and cultured representatives cover a broad spectrum of metabolic capacities, which sets them up for potentially major roles in the biogeochemistry of their ecosystems. The detection, characterization, and quantification of archaeal functions in mixed communities require Archaea-specific primers or probes for the corresponding metabolic genes. Five pairs of degenerate primers were designed to target archaeal genes encoding key enzymes of nitrogen cycling: nitrite reductases NirA and NirB, nitrous oxide reductase (NosZ), nitrogenase r

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Maciel, Danielli Barreto, Lílian Vieira de Medeiros, Vivian Vieira de Medeiros, Mariele Porto Carneiro Leão, Luis Eduardo Aranha Camargo, and Neiva Tinti de Oliveira. "[NO TITLE AVAILABLE]." Brazilian Archives of Biology and Technology 53, no. 6 (2010): 1255–66. http://dx.doi.org/10.1590/s1516-89132010000600001.

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Studies were performed to analyze the genetic characterization using RFLP-ITS and Intron (primer EI1) markers and the amplification of the cap20 pathogenicity gene by PCR in Colletotrichum gloeosporioides isolates of different hosts plant. The genetic variability was accessed using RFLP-ITS and Intron markers and grouping by UPGMA method. Primers to cap20 gene were constructed using selected sequences of the GenBank (National Center of Biotechnology Information, http://www.ncbi.nlm.nih.gov) with the Primer 3 program. The dendrograms analysis showed that the RFLP-ITS marker was more informative

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Bhuiyan, AR, MM Rahman, JA Begum, MR Islam, and EH Chowdhury. "Comparison of genes as target for molecular diagnosis of peste des petits ruminants in goats." Bangladesh Veterinarian 29, no. 2 (2013): 56–62. http://dx.doi.org/10.3329/bvet.v29i2.14343.

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Peste des petits ruminants (PPR) are an acute viral disease of sheep and goats. Rapid and accurate diagnosis is essential for successful control. Reverse transcriptase polymerase chain reaction (RT-PCR), a molecular diagnostic test based on amplification of the gene target is more sensitive than other tests. The study was to find an efficient primer set and structural gene, which would be more specific and sensitive for detecting PPR virus (PPRV) in field samples. Six primer sets for six structural genes of PPR were used. Primer against NP gene (np3/np4) was specific and sensitive. To ensure e

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Park, S. O., A. Dursun, and D. P. Coyne. "RAPD Markers Linked to Major Genes for Common Bacterial Blight and Purple Flower Color in a Tepary Bean Cross." HortScience 32, no. 3 (1997): 452A—452. http://dx.doi.org/10.21273/hortsci.32.3.452a.

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Common bacterial blight (CBB), incited by Xanthomonas campestris pv. phaseoli (Xcp), is an important disease of common bean (Phaseolus vulgaris L.). Tepary bean (P. acutifolius A. Gray) is of interest to bean breeders because of resistance to CBB. The objective was to identify RAPD markers linked to major dominant genes for CBB resistance and purple flower color using bulked segregant analysis in an F2 population from a tepary bean cross Nebr#19 [resistant (R) to CBB and white flower color] × Nebr#4B [susceptible (S) to CBB and purple flower color]. Ten RAPD primers (600 RAPD primers screened)

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Durham, Richard E., and Schuyler S. Korban. "233 USING RAPDs TO INVESTIGATE GENE INTROGRESSION IN APPLE." HortScience 29, no. 5 (1994): 462g—463. http://dx.doi.org/10.21273/hortsci.29.5.462g.

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DNA was extracted from leaves of various Malus genotypes and used to screen synthetic decamer oligonucleotide primers. Samples from the following two groups were bulked: 1) seven scab-susceptible apple cultivars, and 2) 15 scab-resistant apple genotypes derived by introgressive hybridization from the previous group of cultivars. A third sample consisted of DNA extracted from Malus floribunda Sieb. clone 821, the original source of apple scab resistance for all genotypes in the second group. A total of 59 primers from kits A, L, and R (Operon Technologies) were screened. Amplified fragments wer

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Naqib, Ankur, Trisha Jeon, Kevin Kunstman, et al. "PCR effects of melting temperature adjustment of individual primers in degenerate primer pools." PeerJ 7 (March 4, 2019): e6570. http://dx.doi.org/10.7717/peerj.6570.

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Deep sequencing of small subunit ribosomal RNA (SSU rRNA) gene amplicons continues to be the most common approach for characterization of complex microbial communities. PCR amplifications of conserved regions of SSU rRNA genes often employ degenerate pools of primers to enable targeting of a broad spectrum of organisms. One little noticed feature of such degenerate primer sets is the potential for a wide range of melting temperatures between the primer variants. The melting temperature variation of primers in a degenerate pool could lead to variable amplification efficiencies and PCR bias. Thu

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Hrytseva, N. "DEVELOPMENT OF SPECIFIC PRIMERS FOR 16S rRNA GENE ANALYSIS IN THE DETECTION OF Ralstonia solanacearum SPECIES COMPLEX." Biotechnologia Acta 15, no. 3 (2022): 5–12. http://dx.doi.org/10.15407/biotech15.03.005.

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Members of Ralstonia solanacearum species complex (RSSC) are causal agents of vascular wilt disease in more than 450 crop species, including solanaceous plants such as potatoes, tomatoes, bell pepper, eggplant, etc. These phytopathogens cause serious yield loss mostly in solanaceous crops which are grown in tropical, subtropical, and temperate regions of the world. Yield losses comprise 80%–100% in potato, up to 91% for tomato, 10%–30% in tobacco, 33%–90% in banana, and reduce crop productivity and yield. PCR-methods are specific, sensitive and cost-effective approaches for the detection and i

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Pratap, Chandra Bhan, Gopal Kumar, Saurabh Kumar Patel, et al. "Targeting of putative fimbrial gene for detection of S. Typhi in typhoid fever and chronic typhoid carriers by nested PCR." Journal of Infection in Developing Countries 7, no. 07 (2013): 520–27. http://dx.doi.org/10.3855/jidc.2561.

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Introduction: It is important to identify Salmonella Typhi infection quickly to treat acute fever patients and to prevent transmission by chronic typhoid carriers; therefore, a very specific and sensitive diagnostic technique is highly desirable, especially in endemic areas. The objective of this study was to develop a PCR protocol targeting the putative fimbrial staA gene of S. Typhi. This is a preferred target gene that is specifically amplified in the S. Typhi serotype compared to the commonly targeted fliC gene which may also be amplified from the non-typhoidal Salmonella Munchen serotype.

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Aziz, Saefuddin, Regita Cahaya Sari, Dwi Priyanto, and Tri Ramadhani. "Design and evaluation of degenerate primers targeting the NS3 gene for detection of dengue virus by RT-PCR." Acta Biochimica Indonesiana 8, no. 1 (2025): 190. https://doi.org/10.32889/actabioina.190.

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Background: Dengue fever, caused by the dengue virus, is hyper-endemic in Indonesia. Since no protective vaccine or specific treatments are available, accurate diagnosis is crucial for the early implementation of preventive measures to limit dengue transmission and reduce economic losses. Various diagnostic techniques have been developed, including reverse transcriptase-polymerase chain reaction (RT-PCR) for detecting viral nucleic acids using specific primers. Objective: This study aimed to design and evaluate the effectiveness of a new primer targeting the NS3 gene of the dengue virus for mo

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Rosado, Alexandre S., Gabriela F. Duarte, Lucy Seldin, and Jan Dirk Van Elsas. "Genetic Diversity of nifH Gene Sequences inPaenibacillus azotofixans Strains and Soil Samples Analyzed by Denaturing Gradient Gel Electrophoresis of PCR-Amplified Gene Fragments." Applied and Environmental Microbiology 64, no. 8 (1998): 2770–79. http://dx.doi.org/10.1128/aem.64.8.2770-2779.1998.

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ABSTRACT The diversity of dinitrogenase reductase gene (nifH) fragments in Paenibacillus azotofixans strains was investigated by using molecular methods. The partial nifHgene sequences of eight P. azotofixans strains, as well as one strain each of the close relatives Paenibacillus durum,Paenibacillus polymyxa, and Paenibacillus macerans, were amplified by PCR by using degenerate primers and were characterized by DNA sequencing. We found that there are twonifH sequence clusters, designated clusters I and II, inP. azotofixans. The data further indicated that there was sequence divergence among t

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Kumar, Arbind, and Jagdeep Kaur. "Primer Based Approach for PCR Amplification of High GC Content Gene: Mycobacterium Gene as a Model." Molecular Biology International 2014 (March 24, 2014): 1–7. http://dx.doi.org/10.1155/2014/937308.

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The genome of Mycobacterium is rich in GC content and poses problem in amplification of some genes, especially those rich in the GC content in terminal regions, by standard/routine PCR procedures. Attempts have been made to amplify three GC rich genes of Mycobacterium sp. (Rv0519c and Rv0774c from M. tuberculosis and ML0314c from M. leprae). Out of these three genes, Rv0774c gene was amplified with normal primers under standard PCR conditions, while no amplification was observed in case of Rv0519c and ML0314c genes. In the present investigation a modified primer based approach was successfully

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Toro, Michelle, Loni Pickle, Shrutii Sarda, et al. "Abstract 2940: Somatic hypermutation analysis of chronic lymphocytic leukemia research samples by IGH chain next-generation sequencing." Cancer Research 82, no. 12_Supplement (2022): 2940. http://dx.doi.org/10.1158/1538-7445.am2022-2940.

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Abstract Chronic lymphocytic leukemia (CLL) is a common form of leukemia characterized by clonal expansion of neoplastic B cells and a heterogenous disease course. Somatic hypermutation (SHM) status of the IGHV gene in CLL clinical research samples is important as SHM frequency is an established prognostic biomarker. Conventionally, SHM analysis is performed via Sanger sequencing which is limited by the inability to evaluate more than one rearrangement due to mutations, multiplex constraints, and template input requirements. Ion AmpliSeq™ next generation sequencing (NGS) assays for research in

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Provencher, Cathy, GisÃ¯Â¿Â½le LaPointe, StÃ¯Â¿Â½phane Sirois, Marie-Rose Van Calsteren, and Denis Roy. "Consensus-Degenerate Hybrid Oligonucleotide Primers for Amplification of Priming Glycosyltransferase Genes of the Exopolysaccharide Locus in Strains of the Lactobacillus casei Group." Applied and Environmental Microbiology 69, no. 6 (2003): 3299–307. http://dx.doi.org/10.1128/aem.69.6.3299-3307.2003.

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ABSTRACT A primer design strategy named CODEHOP (consensus-degenerate hybrid oligonucleotide primer) for amplification of distantly related sequences was used to detect the priming glycosyltransferase (GT) gene in strains of the Lactobacillus casei group. Each hybrid primer consisted of a short 3′ degenerate core based on four highly conserved amino acids and a longer 5′ consensus clamp region based on six sequences of the priming GT gene products from exopolysaccharide (EPS)-producing bacteria. The hybrid primers were used to detect the priming GT gene of 44 commercial isolates and reference

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A Rahman, Nur Azizah, Fadhilah Moh Djamil, Vinod RMT Balasubramaniam, Sharifah Syed Hassan, and Wei Boon Yap. "Dengue Virus Non-structural (NS) 1 Gene as A Molecular Marker for Early Detection of in vitro Dengue Virus Infection." Sains Malaysiana 50, no. 10 (2021): 3035–43. http://dx.doi.org/10.17576/jsm-2021-5010-16.

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Serology-based dengue assays at times produce inaccurate results especially in the early phase of disease onset. A more precise diagnostic approach detecting dengue infections in the early phase enables better management of the disease. This helps reduce dengue-associated morbidity and mortality. Besides, an early diagnosis of dengue is also very beneficial in a dengue outbreak and in endemic regions. In this light, this study aimed to determine the potential of the dengue virus (DENV) non-structural 1 (NS1) gene as an early detection biomarker. The cytopathic effects (CPE) were monitored and

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Pahlevi, Dylan R., Edwin De Queljoe, and Beivy J. Kolondam. "AMPLIFIKASI GEN COI DARI SAMPEL DARAH ULAR DENGAN MENGGUNAKAN BEBERAPA PASANGAN PRIMER UNIVERSAL." ZOOTEC 39, no. 2 (2019): 314. http://dx.doi.org/10.35792/zot.39.2.2019.25413.

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AMPLIFICATION OF COI GENE FROM SNAKE BLOOD SAMPLES USING TWO UNIVERSALPRIMER PAIRS. This study aims to amplify COI (Cytochrome Oxidase Subunit I) gene fragments from snake blood. Four samples were obtained from four different snake individuals that were captured in Tapahan Telu Waterfall, Kali Village, Minahasa Regency. Total DNA from the sample was isolated and then the COI gene was amplified through the PCR (Polymerase Chain Reaction) reaction using two primer pairs, LCO1490-HCO2198 and FF2d-FR1d. These four samples were successfully amplified using different primers, i.e. DRP1 and DRP3 by F

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Sai Priya Avuthu, Sri, Bharathi Yelem, Sai Jathin Nunagonda, et al. "TOUCHDOWN PCR FOR INCREASED SENSITIVITY AND SPECIFICITY IN AMPLIFICATION OF MOUSE COGNATE HOMEOBOX." International Journal of Advanced Research 10, no. 08 (2022): 699–703. http://dx.doi.org/10.21474/ijar01/15224.

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Mammalian system have a large genome with a high level of gene sequence identity from other genomic DNA, making assessment difficult and time-consuming.Our findings describe a simple method for rapidly isolating and amplifying HoxA loci in the mouse genome using degenerate primers. For the semi degenerate primers,they were designed based on cognate gene coding regions of consensus sequences. After assembling sequences from different primer matches amplifying the same HoxA loci, the effects of the universal primer-template match on the efficiency of standard PCR amplification were investigated.

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Bhumika, Chauhan, Malti, Misra Monica, and Sharma Bindu. "In Silico PCR Primer Designing using Mitochondrial (cox-1) Gene of Clinostomum marginatum." International Journal of Zoological Investigations 08, no. 02 (2022): 671–73. http://dx.doi.org/10.33745/ijzi.2022.v08i02.081.

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Clinostomum marginatum Rudolphi, 1819 is a digenetic fish trematode parasite. It is commonly known as “yellow grub” as it causes pinhead sized lumps in fishes that are white to yellow or black. Molecular studies employs usage of primer for gene amplification. In silico method helps in designing primers used in amplification of genes which can be further validated using various tools and software to check their specificity and efficiency. The present communication deals with the in silico primer designing of cox-1 gene of helminth trematode parasite, Clinostomum marginatum parasitizing the inte

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Fitriana, Fauziah, Mas Farouq Uz Zaman Al Qodry, Juan Carlos Greevins De Lucas, Dian Ritma Setyorini, and Fatkhanuddin Aziz. "Appropriate Primer Selection Improves Molecular Bird Sexing Accuracy." Buletin Peternakan 47, no. 4 (2023): 215. http://dx.doi.org/10.21059/buletinpeternak.v47i4.83320.

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Birds sexing utilize the Polymerase Chain Reaction (PCR) technique is increasingly being used by researchers and breeders. The PCR technique has high sensitivity, but its success is influenced by the specificity of the DNA template with the oligo primer used. This study aimed to evaluate 5 types of PCR primers P2/P8, 2550F/2718R, CHD1F/CHD1R, 1237L/1272H, and CHD1LF/CHD1LR to determine the sex of Phasianidae, Anatidae, Muscicapidae, and Psittacidae families. This research was conducted by tested primers mentioned above to amplify the target gene chromodomain helicase DNA binding 1 (CHD1) on DN

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Fuadah, Khilmi, Anisa Rahmawati, Fauziah Fitriana, and Fatkhanuddin Aziz. "Evaluation of molecular primers for sexing the magpie robin and green cucak via CHD1 gene amplification." Jurnal Ilmu Peternakan dan Veteriner Tropis (Journal of Tropical Animal and Veterinary Science) 15, no. 2 (2025): 64–71. https://doi.org/10.46549/jipvet.v15i2.557.

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Researchers and breeders are increasingly using the Polymerase Chain Reaction (PCR) method for bird sexing. However, the compatibility of the DNA template and the oligo primer used is the primary key to the success of PCR amplification. In the present study, we evaluated five types of popular PCR primers sexing to determine the sex of a pair of each the magpie robin (Copsychus malabaricus) and green cucak (Chloropsis sonnerati). We used DNA samples from each pair of males and females from the two species above, respectively, to test the five primers listed to amplify the target gene chromodoma

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Shullia, Nurul Insani, Kuswati Kuswati, Aditya Kurniawan, and Hajar Syifa Fiarani. "In Silico Primer Design for geographical detection of Apis florea using Cytochrome c oxidase subunit 1 (COX1) gene." Life Science and Biotechnology 1, no. 1 (2023): 27. http://dx.doi.org/10.19184/lsb.v1i1.40052.

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The yellow dwarf honey bee, Apis florea are well distributed in South Asia to South East Asia. This species is expanded and introduce area from their original distribution. However, the distribution of this honey bee in Indonesia is unexplored. The cytochrome c oxidase subunit 1 (COX1) gene are success to detect original geographic of introduce A. florea found in Egypt. The A. florea specific primer of COX1 gene are needed to produce the molecular marker for geographical origin detection. Thus, this study aims to in silico design the COX1 gene primer of A. florea using Primer3 and Primer-BLAST

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Ovesná, J., L. Dedičová, J. Horáček, E. Sadilová, L. Kučera, and L. Měsková. "Comparison of different PCR-based protocols for detection of Roundup Ready soybean." Czech Journal of Genetics and Plant Breeding 38, No. 1 (2012): 55–63. http://dx.doi.org/10.17221/6111-cjgpb.

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Genetically modified organisms have become a part of our environment and food chain. Roundup Ready soybean is at the moment the most frequent one that man can meet. National regulations require careful monitoring and detection of GMOs. We present in this investigation comparison of several protocols and individual steps, which are included in the whole detection procedure. Currently used CTAB based protocol is suitable for DNA isolation from the green plant tissue but also from the flour. Lectin coding sequence specific primers were suitable for soybean DNA detection unlike leu-tRNA gene speci

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Ben-Dov, Eitan, Orr H. Shapiro, Nachshon Siboni, and Ariel Kushmaro. "Advantage of Using Inosine at the 3′ Termini of 16S rRNA Gene Universal Primers for the Study of Microbial Diversity." Applied and Environmental Microbiology 72, no. 11 (2006): 6902–6. http://dx.doi.org/10.1128/aem.00849-06.

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ABSTRACT To overcome the shortcomings of universal 16S rRNA gene primers 8F and 907R when studying the diversity of complex microbial communities, the 3′ termini of both primers were replaced with inosine. A comparison of the clone libraries derived using both primer sets showed seven bacterial phyla amplified by the altered primer set (8F-I/907R-I) whereas the original set amplified sequences belonging almost exclusively to Proteobacteria (95.8%). Sequences belonging to Firmicutes (42.6%) and Thermotogae (9.3%) were more abundant in a library obtained by using 8F-I/907R-I at a PCR annealing t

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Sysoliatin, Eugeny Nikolaevich, Natalia Vladimirovna Anisimova, and Olga Gennadievna Babak. "Genotyping Lupinus angustifolius cultivars with SRAP molecular markers and degenerate primers." EuroBiotech Journal 1, no. 2 (2017): 200–201. http://dx.doi.org/10.24190/issn2564-615x/2017/02.18.

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Abstract We examined 18 combinations of SRAP primers with resistance gene analog (RGA) and chitinase degenerate primers in order to determine their utility for genotyping L. angustifolius. Primer pairs ResAn51-f/Me8, p-loop/Em5, TM/Me8, Chit3-r/Em5 were the most effective for detection of genetic polymorphism of different narrow-leaved lupine varieties.

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