Article
Mathematics
Yu-Huei Cheng, Li-Yeh Chuang, Cheng-Hong Yang
Summary: The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) experiment is a low-cost, rapid, simple, convenient, highly sensitive, and specific molecular biotechnology used in various SNPs genotyping works. However, many SNPs lack suitable restriction enzymes for distinguishing specific genotypes, rendering the PCR-RFLP assay unavailable, known as mismatch PCR-RFLP. In order to solve the problem of mismatch PCR-RFLP, a teaching-learning-based optimization (TLBO) multi-point mutagenic primer design algorithm is proposed, combined with REHUNT, to provide a complete and specific solution for restriction enzyme mining. The method introduces several search strategies for multi-point mutagenic primers and enhances the reliability of mutagenic primer design, as well as providing specific solutions for SNP diversity.
Article
Biochemical Research Methods
Cheng-Hong Yang, Yu-Huei Cheng, Emirlyn Cheng Yang, Li-Yeh Chuang, Yu-Da Lin
Summary: This study designed new fitness functions based on user-specified parameters and used the functions in a primer design approach based on the multiobjective particle swarm optimization (MOPSO) algorithm to address the challenge of primer design with user-specified parameters. The algorithms based on fitness functions with user-specified parameters outperformed the algorithms based on general fitness functions for 11 primer constraints.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biology
Priya Jarwar, Yar Muhammad Waryah, Muhammad Rafiq, Ali Muhammad Waryah
Summary: This study analyzed the association between SNP variants in CRYAA and CRYAB genes and Congenital Cataract. The results showed that the rs13053109 G > C variant in CRYAA gene is associated with increased risk of congenital cataract in infants. Haplotype analysis indicated weak linkage disequilibrium between the SNPs rs3761382, rs7278468, and rs13051039 of CRYAA gene. These findings suggest that the variation in CRYAA gene may be a risk factor for congenital cataract in infants.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Food Science & Technology
Asmaa Galal-Khallaf, Doaa Hussein, Sobhy El-Sayed Hassab El-Nabi
Summary: This study focused on the development of genetic techniques for the discrimination of six red meat species, showing low levels of species substitution in tested meat samples. The developed techniques have high potentials to be used as reliable and fast tools to avoid meat species substitutions.
JOURNAL OF FOOD SCIENCE
(2021)
Article
Multidisciplinary Sciences
Jiao Cui, Zhou Jiang, Zerui Wang, Jiaqi Shao, Chuanju Dong, Lei Wang, Xuejun Li, Jinxing Du, Shengjie Li, Zhigang Qiao, Meng Zhang
Summary: This study genotyped largemouth bass fry using PCR-RFLP and identified single nucleotide polymorphisms (SNPs) related to food habit domestication traits and growth traits. These SNPs could serve as a molecular basis for breeding new varieties of largemouth bass.
Article
Entomology
Zhi-Chao Yan, Hai-Qing Hua, Guang-Yuan Qi, Yuan-Xi Li
Summary: We developed a method to detect and identify Trichogramma larvae in their host eggs and successfully differentiated eight Trichogramma species using a PCR-RFLP assay. This study provides a promising approach for conveniently identifying Trichogramma in insectaries and accurately evaluating parasitism rates in the field.
JOURNAL OF ECONOMIC ENTOMOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Owen Higgins, Terry J. Smith
Summary: PCR is crucial for infectious disease detection, especially during the COVID-19 pandemic. Real-time multiplex detection and single-base specificity play key roles in identifying single-nucleotide polymorphisms (SNPs).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Nada K. Sedky, Reem K. Arafa
Summary: Novel Biochemistry lab techniques are rapidly being introduced in scientific research, requiring the development of new labs for undergraduate Biochemistry courses. However, the time limit of Biochemistry labs for undergraduate students poses a major obstacle. This article presents a clear set of laboratory exercises designed to introduce students to the use of PCR-RFLP as a means of detection of genetic variants. Three consecutive lab sessions have been designed for the undergraduate students to learn and practice this technique.
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION
(2022)
Article
Genetics & Heredity
Jing Wang, Yuanlin Ma, Jing Guo, Rong Li, Canquan Zhou, Yanwen Xu
Summary: This study evaluates the feasibility and necessity of using fluorescence Gap-polymerase chain reaction combined with haplotype analysis in preimplantation genetic testing for SEA-type alpha-thalassemia and finds that it is both feasible and necessary.
FRONTIERS IN GENETICS
(2023)
Article
Biotechnology & Applied Microbiology
Sang-Hyuck Park, Seth Alan Steichen, Judith K. Brown
Summary: This study designed specific primers based on the 18S ribosomal RNA sequences of microalgae, enabling rapid detection of 12 microalgae without the need for cloning and sequencing. The use of SNP-mismatch primer pairs successfully identified C. sorokiniana DOE1412 and Scenedesmus among others, offering a cost-effective and easy alternative for routine monitoring of microalgal cultures.
JOURNAL OF APPLIED PHYCOLOGY
(2021)
Article
Plant Sciences
Gunlayarat Bhusudsawang, Ratchanee Rattanawong, Thitaporn Phumichai, Wirulda Pootakham, Sithichoke Tangphatsornruang, Kittipat Ukoskit
Summary: This study performed candidate gene association mapping for girth growth in rubber trees using ILP markers and identified COBL064_1 marker as the strongest associated with girth growth. Through CCS analysis, a SNP in the 3' UTR showing linkage disequilibrium with COBL064_1 was pinpointed. The study demonstrated that ILP gene-based markers can assist in identifying SNPs in candidate genes associated with girth growth and provide useful markers for improvement in rubber tree breeding programs.
Article
Genetics & Heredity
Cesar Fernandez-de-las-Penas, Lars Arendt-Nielsen, Gema Diaz-Gil, Francisco Gomez-Esquer, Antonio Gil-Crujera, Stella M. Gomez-Sanchez, Silvia Ambite-Quesada, Maria A. Palomar-Gallego, Oscar J. Pellicer-Valero, Rocco Giordano
Summary: The study aimed to investigate the association between the Apolipoprotein E (ApoE) gene and long COVID symptoms. The results showed no significant relationship between different genotypes of the ApoE gene (ApoE ε2, ApoE ε3, ApoE ε4) and the presence of long COVID symptoms.
Article
Biochemistry & Molecular Biology
Md. Tareq Bin Salam, Ryota Kataoka
Summary: This study found that the use of insecticides not only negatively affects endophytic bacterial communities, but also leads to a decrease in bacterial diversity and abundance. Additionally, it was observed that plants can regulate and moderate their microbiome during their lifecycle depending on surrounding environmental conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Beata Anna Nowakowska, Katarzyna Pankiewicz, Urszula Nowacka, Magdalena Niemiec, Szymon Kozlowski, Tadeusz Issat
Summary: This review presents the current state of knowledge about the genetic disturbances responsible for fetal growth restriction (FGR) diagnosis, and discusses the fetal, placental, and maternal causes, as well as their impact on prenatal diagnostics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Bo-Ren Wang, Wen-Shin Chang, Cheng-Hsi Liao, Yun-Chi Wang, Jian Gu, Da-Tian Bau, Chia-Wen Tsai
Summary: The association between SNPs in mir146a and mir196a and bladder cancer risk in Taiwan was investigated. The results suggest that mir146a rs2910164 genotypes may serve as a useful biomarker for predicting the risk of bladder cancer, while mir196a rs11614913 genotypes are not associated with bladder cancer risk.
