Article
Biotechnology & Applied Microbiology
Baryshev Mikhail, Merkulov Dmitrijs, Mironov Ivan
Summary: The study introduces a new method for plasmid miniprep using a centrifuge/mixer-based instrument, which can perform centrifugation, vibration, and rotor oscillation without operator intervention. By applying rotor oscillation-driven mixing, homogeneous mixing of solutions can be achieved within 5 seconds, resulting in the maximum quantity and quality of plasmid DNA.
Article
Chemistry, Analytical
Lohra M. Miller, Benjamin E. Draper, Lauren F. Barnes, Polycarp C. Ofoegbu, Martin F. Jarrold
Summary: Conventional mass spectrometry of nucleic acids is complicated by counter ions, limiting the analysis of DNA size. This study overcomes this limitation using charge detection mass spectrometry to analyze megadalton-sized DNA. Different charge distributions are observed for DNA plasmids, with a low-charge population resembling compact DNA and a higher-charge population with a broad charge range. The high-charge population is attributed to supercoiled plasmids in random coil configuration, while the low-charge population is attributed to a condensed form of the plasmid.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Dawei Li, Xiyu Chen, Rumeng Yan, Zeshan Jiang, Bing Zhou, Bei Lv
Summary: It was found that oligodeoxynucleotides (ODNs) containing G-quadruplexes can efficiently inhibit the activity of DNA topoisomerase I. Among them, the parallel propeller-type G-quadruplex is the most effective inhibitor. Combining G-quadruplexes with duplexes to form hybrids can enhance the inhibition efficiency. Moreover, a circular ODN with a G-quadruplex motif and DNA topoisomerase I binding site showed high inhibitory efficiency.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Physical
Qiang Sun, Gaoqiang Yuan, Zheng Liu, Jingbo Gao, Yiwei Wang, Xuqiang Guo, Lanying Yang
Summary: This study proposes a hydrate-membrane coupling method that utilizes both hydration and membrane permeation as separation driving forces to effectively increase the concentration and recovery rate of H-2 in the product gas, addressing the conflict between H-2 concentration and recovery rate in common separation methods.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2022)
Article
Genetics & Heredity
Diana Habermann, Martin Klempt, Charles M. A. P. Franz
Summary: Sixteen novel circular rep-encoding DNA sequences highly similar to SPHINX and BMMF were discovered from non-bovine foods. Phylogenetic analysis confirmed their relation to known SPHINX/BMMF sequences and differentiation of subtypes. The investigation revealed relationships to rolling circle replication plasmids and discussed the relevance to theta-replicating plasmid reps.
Article
Biochemistry & Molecular Biology
Anastasiia Mereshchuk, Peter S. Johnstone, Joyce S. K. Chew, Melanie J. Dobson
Summary: Partitioning of the 2-micron plasmid in budding yeast involves the association of Rep1 and Rep2 proteins with the STB partitioning locus. This study shows that Rep2 directly participates in plasmid partitioning independent of Rep1 and the RSC2 complex. Mutation of a conserved basic motif in Rep2 impairs plasmid partitioning. These findings reveal the mechanism by which the plasmid is linked to host components during cell division.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Sandra Hui, Rasmus Nielsen
Summary: This study introduces a theoretical framework to accurately call CNAs using tumor evolutionary history, developing a method called SCONCE to analyze read depth data from tumor cells which accurately decodes copy number profiles and provides a useful tool for understanding tumor evolution.
Review
Biochemistry & Molecular Biology
Craig J. Benham
Summary: This article investigates the effects of L on ccDNA molecules and describes a theoretical model of superhelically driven DNA structural transitions. It also examines the changes of unconstrained superhelicity during nucleosome attachment and release.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Instruments & Instrumentation
Behzad Baradaran, Ali Mohammadi, Sara Shamekhi, Nikoo Majidazar, Azita Dilmaghani, Saiedeh Razi Soofiyani, Nigel A. J. McMillan, Farzaneh Lotfipour, Somayeh Hallaj-Nezhadi
Summary: Novel nanoliposomes loaded with murine interleukin-12 (mIL-12) pDNA were successfully prepared using a freeze-drying of a monophase solution method, showing promising physicochemical characteristics and transfection efficiency. In vivo experiments demonstrated significant inhibition of mIL-12 expression in colon carcinoma cells and tumor growth after repeated injections of the nanoliposomes. This study highlights the potential of freeze-drying a monophase solution method for preparing pDNA-loaded nanoliposomes for cancer gene therapy.
DRUG DELIVERY AND TRANSLATIONAL RESEARCH
(2022)
Article
Plant Sciences
Feng Liu, Hongshu Wang, Wenli Song
Summary: Comparative analysis of Ulva species' mitogenomes reveals variations in genome size due to the integration of exogenous DNA fragments, proliferation of introns, and changes in repeat sequences. This study focuses on Ulva meridionalis and compares its mitogenomes with those of other ulvophyceae species. Results show that the main circular mitogenomes of U. meridionalis range from 82.94 to 111.49 kb, with the 111.49-kb mitogenome being the largest among Ulva so far. The expansion of U. meridionalis mitogenomes is primarily due to the integration of a 5.36-kb mitochondrial circular plasmid (pUme) and the proliferation of introns. The integration of plasmids and the rapid divergence of plasmid-derived sequences are important evolutionary forces shaping the diversity of Ulva mitogenomes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Construction & Building Technology
Rezvan Babagoli, Navid Norouzi, Alireza Ameli
Summary: The research findings indicated that asphalt mixtures containing binders V have higher fracture energy compared to mixtures containing binders S, and as the percentage of RAP increases, the fracture energy decreases. High traffic mix designs with higher binder content exhibit higher fracture energy levels.
CONSTRUCTION AND BUILDING MATERIALS
(2021)
Article
Biochemical Research Methods
Nejc Pavlin, Urh Cernigoj, Mojca Bavcar, Tjasa Plesnicar, Jan Mavri, Martin Zidar, Matevz Bone, Urska Kralj Savic, Tadej Sever, Ales Strancar
Summary: A chromatographic method was developed to accurately separate isoforms of <16 kbp pDNA using a weak anion exchange monolithic column with large convective channels. The optimized conditions allowed for baseline separation of OC and SC isoforms, with a recovery rate of >= 95% for OC pDNA. This method has great potential for in-process control monitoring of pDNA production processes.
Article
Biochemistry & Molecular Biology
Xi Wang, Ling Zhao, Xiaoxing Wu, Huaxiu Luo, Di Wu, Meng Zhang, Jing Zhang, Mikhail Pakvasa, William Wagstaff, Fang He, Yukun Mao, Yongtao Zhang, Changchun Niu, Meng Wu, Xia Zhao, Hao Wang, Linjuan Huang, Deyao Shi, Qing Liu, Na Ni, Kai Fu, Kelly Hynes, Jason Strelzow, Mostafa El Dafrawy, Tong-Chuan He, Hongbo Qi, Zongyue Zeng
Summary: Isolation of plasmid DNA (pDNA) from bacterial cells is a critical step in molecular cloning and biomedical research. The use of size selection magnetic beads (SSMBs) in RNA depletion has been shown to be a cost-effective and efficient method for improving the quality and integrity of pDNA samples. The SSMB method can completely deplete contaminating RNA in both small-scale and large-scale pDNA preparations, making it a valuable tool for routine pDNA purification.
Article
Biochemistry & Molecular Biology
Shanru Zuo, Xueguang Li, Yide Yang, Junhua Zhou, Quanyuan He
Summary: EccDNA, a special type of circular DNA, is suggested to have important biological functions in regulating downstream processes. However, the specific functions of individual eccDNAs remain unclear due to limited methods for synthesizing eccDNAs. This study introduces a novel method called QuickLAMA, which enables rapid synthesis of eccDNAs up to 2.6 kb using a simple PCR and ligation approach. The method is efficient, cost-effective, time-efficient, and easily standardized, with the potential to produce a wide range of desired eccDNAs and promote clinical applications of eccDNA research.
Article
Physics, Multidisciplinary
Daqian Wang, Xin Wang, Peifeng Pan, Jun Gao
Summary: Polarimetric imaging has been studied and applied to visibility restoration in scenarios such as haze and underwater, with circular polarized light showing advantages over linear polarized light in certain conditions. However, the performance of both linear and circular polarimetric imaging is affected by factors in complex environments. The propagation of polarized light, especially circular polarized light, is influenced by medium conditions, and while both linear and circular polarimetric imaging can reduce image degradation caused by smoke, differences between orthogonal circular polarization channels may limit circular polarization-based difference imaging and visibility restoration performance in certain conditions.
FRONTIERS IN PHYSICS
(2022)
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)