Review
Biochemistry & Molecular Biology
Ludmila Volozonoka, Anna Miskova, Linda Gailite
Summary: This review provides insight into the performance and drawbacks of WGA techniques such as DOP-PCR, MDA, MALBAC, and hybrid techniques in PGT. The advantages of MDA-based solutions for comprehensive genome coverage and PCR-based solutions for uniformity of coverage are highlighted. The choice of WGA technique should take into consideration the influence of MPS parameters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Jacob Morrison, Julie M. Koeman, Benjamin K. Johnson, Kelly K. Foy, Ian Beddows, Wanding Zhou, David W. Chesla, Larissa L. Rossell, Emily J. Siegwald, Marie Adams, Hui Shen
Summary: This study extensively benchmarked common library preparation protocols for whole-genome DNA methylation sequencing, with NEBNext Enzymatic Methyl-seq and Swift Accel-NGS Methyl-Seq kits showing superior performance quantitatively. The NEBNext Enzymatic Methyl-seq kit is recommended for high-quality DNA samples, while the Swift kit is more suitable for degraded samples.
EPIGENETICS & CHROMATIN
(2021)
Article
Genetics & Heredity
Kyleen Elwick, Patrick Rydzak, James M. Robertson
Summary: This project evaluated the prototype PowerSeq (R) 46GY System using donor DNA and casework-type samples. Modifications to the manufacturer's protocol were tested to improve read coverage and sample results. Different library preparation kits were compared, and the PowerSeq kit was found to be more accurate in quantifying library concentration. The TruSeq library kit provided higher coverage and better overall results compared to the KAPA kit.
Article
Medicine, Legal
Elaine J. Lewis, Erin Weaver, Audrey Hoyle, Robert Lagace, Fabio Oldoni, Daniele Podini
Summary: Genotype profiling is crucial in forensics, with advancements in technology necessitating re-analysis of DNA data from the 1990s to overcome potential confounding factors like paralogous genes.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2022)
Article
Biochemical Research Methods
Fatimah S. Alhamlan, Dana M. Bakheet, Marie F. Bohol, Madain S. Alsanea, Basma M. Alahideb, Faten M. Alhadeq, Feda A. Alsuwairi, Maha A. Al-Abdulkareem, Mohamed S. Asiri, Reem S. Almaghrabi, Sarah A. Altamimi, Maysoon S. Mutabagani, Sahar Althawadi, Ahmed A. Al-Qahtani
Summary: The study developed a cost-effective genome sequencing protocol to identify circulating SARS-CoV-2 variants of concern. Sets of primers were designed and validated using 282 positive samples. The protocol showed 100% specificity and successfully detected alpha, beta, and delta variants in the samples.
Article
Genetics & Heredity
Chunxiao Hua, Lina Liu, Xiangdong Kong
Summary: This study retrospectively analyzed the prenatal genetic diagnosis results of 1408 fetuses at high risk of DMD/BMD, providing information for clinical genetic counseling.
BMC MEDICAL GENOMICS
(2023)
Article
Genetics & Heredity
Xingjian Zhong, Siying Cui, Lina Liu, Yuxia Yang, Xiangdong Kong
Summary: Through 931 prenatal diagnoses for pregnant women with a definite family history of DMD or a history of DMD childbirth, the study found that combining MLPA and Sanger sequencing with STR linkage analysis can provide accurate and rapid prenatal diagnosis. The high de novo rate highlights the importance of prenatal diagnosis and genetic counseling.
BMC MEDICAL GENOMICS
(2021)
Article
Biochemistry & Molecular Biology
Katarzyna Gromek, Tadeusz Kaczorowski
Summary: DNA indexing is a method for amplification and direct analysis of large DNA fragments using a library of oligonucleotide adaptors and type-IIS restriction endonucleases. It can be applied to sequence plasmids, cDNA clones, and longer DNA fragments, as well as fill gaps in genome sequencing projects at the final stage.
ACTA BIOCHIMICA POLONICA
(2021)
Article
Computer Science, Software Engineering
G. Raja, U. Srinivasulu Reddy
Summary: This paper presents a hybrid catfish PSO model for DNA fragment assembly, which incorporates catfish particles and simulated annealing to improve performance and efficiency. Experimental results demonstrate that the proposed model outperforms state-of-the-art models in terms of performance within a shorter time frame.
INTERNATIONAL JOURNAL OF SOFTWARE INNOVATION
(2021)
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)