Article
Agriculture, Dairy & Animal Science
V. Vigolo, M. Franzoi, F. Cendron, G. Salvadore, M. Penasa, M. Cassandro, M. De Marchi
Summary: This study compared different methods and technical engagement for identifying the A1 and A2 variants of 0-casein in milk. The findings showed that automated DNA extraction and chromatoallele-specific PCR techniques are fast and reliable options.
JOURNAL OF DAIRY SCIENCE
(2022)
Review
Oncology
Farzaneh Darbeheshti, Fangyan Yu, G. Mike Makrigiorgos
Summary: Liquid biopsies provide a non-invasive approach to trace tumor-derived biomarkers in blood, and circulating free DNA (cfDNA) is a valuable liquid biopsy-based biomarker for diagnostic, predictive, and prognostic purposes. However, detecting circulating tumor DNA (ctDNA) remains challenging due to its low frequency among excessive cfDNA from normal tissues. Mutation-enrichment methods have emerged to enhance the detection of low-level mutations and pre-PCR enrichment techniques offer advantages in terms of avoiding PCR errors and enabling high multiplexity. This review discusses the recent developments in pre-PCR enrichment methods and their applications in liquid biopsies.
Article
Engineering, Biomedical
Gregory Gydush, Erica Nguyen, Jin H. Bae, Timothy Blewett, Justin Rhoades, Sarah C. Reed, Douglas Shea, Kan Xiong, Ruolin Liu, Fangyan Yu, Ka Wai Leong, Atish D. Choudhury, Daniel G. Stover, Sara M. Tolaney, Ian E. Krop, J. Christopher Love, Heather A. Parsons, G. Mike Makrigiorgos, Todd R. Golub, Viktor A. Adalsteinsson
Summary: Researchers have developed a method called MAESTRO that combines massively parallel mutation enrichment with duplex sequencing to accurately track thousands of distinct mutations with significantly fewer reads per locus than conventional methods. This method has a wide range of applications, including testing for chimaerism, validating mutations, and monitoring minimal residual disease.
NATURE BIOMEDICAL ENGINEERING
(2022)
Article
Chemistry, Analytical
Xiaoxiang Zhou, Zhanping Li, Zhen Zhang, Libo Zhu, Quanjun Liu
Summary: In this study, a 3D electrostatic microfluidic platform was developed to rapidly and label-free enrich viruses from bulky samples at low concentrations. The platform demonstrated a 100-fold increase in the limit of detection based on real-time PCR analysis, making it a simple, rapid, and high-throughput viruses concentration platform with significant utility for various viral detection.
Article
Biochemical Research Methods
Ege Ulgen, Ozan Ozisik, Osman Ugur Sezerman
Summary: We developed PANACEA, a personalized network-based anti-cancer therapy evaluation approach, which extends the protein interaction network with drugs and assigns a driverness score to each altered gene. PANACEA utilizes either a "distance-based" method or a "propagation" method to score drugs. We evaluated PANACEA using multiple datasets and demonstrated its relevance in cancer pharmacotherapy, identification of drugs sensitive to cancer cell lines, and its performance in clinical settings compared to previous approaches.
Article
Multidisciplinary Sciences
Rebecca F. Halperin, Apurva Hegde, Jessica D. Lang, Elizabeth A. Raupach, Christophe Legendre, Winnie S. Liang, Patricia M. LoRusso, Aleksandar Sekulic, Jeffrey A. Sosman, Jeffrey M. Trent, Sampathkumar Rangasamy, Patrick Pirrotte, Nicholas J. Schork
Summary: This study presents a novel statistical approach for detecting splicing outliers and performing differential splicing analysis with higher sensitivity and specificity. The method predicts the protein-level effects of splice alterations by testing differences in percentages of sequence reads representing local splice events. The software package Bisbee can be used to identify tissue-specific splice variants with protein-level expression confirmed by mass spectrometry.
SCIENTIFIC REPORTS
(2021)
Review
Biochemical Research Methods
Jessica Brandi, Roberta Noberini, Tiziana Bonaldi, Daniela Cecconi
Summary: This review provides an overview of the most common post-translational modifications (PTMs) of proteins and discusses enrichment methods for MS-based proteomics analysis. Both traditional affinity strategies and chemical enrichment strategies are detailed, and the challenges and future trends in the field are discussed.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Chemistry, Analytical
Yuanjie Suo, Weihong Yin, Qiangyuan Zhu, Wenshuai Wu, Wenjian Cao, Ying Mu
Summary: In this study, a method for rapid detection of Salmonella typhimurium (S. typhimurium) in food samples was developed. Aptamer-coated magnetic beads were used for specific concentration of S. typhimurium, while a self-priming chip-based digital PCR was used for on-site detection and quantification of S. typhimurium cells. This platform has the advantages of being rapid, sensitive, and convenient, and has potential applications for detecting other target bacteria.
Article
Virology
Dieke Boezen, Marcelle L. Johnson, Alexey A. Grum-Grzhimaylo, Mark P. Zwart, Rene A. A. Van der Vlugt
Summary: Viruses exhibit diverse genome organization, with multipartite viruses packaging their genome segments into separate particles. This seemingly inefficient genome organization allows for flexible changes in gene expression in different environments. The frequency of each genome segment is termed the genome formula (GF). Formal studies have quantified GF using RT-qPCR, but comparison with high-throughput sequencing (HTS) methods is needed to understand GF variation in natural populations or novel virus-host systems. Our study compares several GF quantification methods and highlights the need to tailor the method to the experimental aim, as there is a significant method effect on GF estimates.
Article
Cell Biology
Jiaran Li, Jifeng Wang, Yumeng Yan, Na Li, Xiaoqing Qing, Ailikemu Tuerxun, Xiaojing Guo, Xiulan Chen, Fuquan Yang
Summary: In this study, we comprehensively evaluated different TiO2-based phosphopeptide enrichment and fractionation methods, providing a basis for selecting the proper protocols for comprehensive phosphoproteomics.
Review
Chemistry, Multidisciplinary
Raha Kaviani, Abolghasem Jouyban, Ali Shayanfar
Summary: This review outlines the crucial importance of pharmaceutical cocrystals in chiral resolution techniques of racemic compounds, discussing different cocrystallization methods.
Article
Chemistry, Analytical
Jiayi Luo, Zhaojing Huang, Shunxing Li, Fengying Zheng, Fengjiao Liu, Qianyan Huang, Xuguang Huang, Haijiao Xie
Summary: In this study, an intelligent system is developed to monitor the real-time generation of newly released Fe(III) ions through the photodegradation kinetics-based speciation and bioavailability assessments. The results successfully demonstrate the proof-of-concept for assessing the bioavailability of dissolved metals.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Lara Gibellini, Rebecca Borella, Anna De Gaetano, Giada Zanini, Domenico Lo Tartaro, Gianluca Carnevale, Francesca Beretti, Lorena Losi, Sara De Biasi, Milena Nasi, Mattia Forcato, Andrea Cossarizza, Marcello Pinti
Summary: Coordinated communication between mitochondria and the nucleus is crucial for cellular activities. Recent research has found that the protease Lonp1, previously believed to be exclusively located in the mitochondria, is also present in the nucleus and plays a role in the stress response.
SCIENTIFIC REPORTS
(2022)
Article
Engineering, Biomedical
Wei Chen, Haiqi Xu, Shenbin Dai, Jiayu Wang, Ziyu Yang, Yuewen Jin, Mengbing Zou, Xianjin Xiao, Tongbo Wu, Wei Yan, Bin Zhang, Zhimiao Lin, Meiping Zhao
Summary: Low-frequency DNA mutations can be detected more easily by excising wild-type DNA strands via endonuclease deoxyribonuclease I, guided by single-stranded phosphorothioated DNA. This method allows for the detection of low-frequency mutations in genomic DNA and circulating cell-free DNA at single-nucleotide resolution. It involves a competitive DNA-binding-and-digestion mechanism, using deoxyribonuclease I guided by single-stranded phosphorothioated DNA, to remove wild-type DNA strands.
NATURE BIOMEDICAL ENGINEERING
(2023)
Article
Cell Biology
Masahiro Shin, Hui-Min Yin, Yu-Huan Shih, Takayuki Nozaki, Daneal Portman, Benjamin Toles, Amy Kolb, Kevin Luk, Sumio Isogai, Kinji Ishida, Tomohito Hanasaka, Michael J. Parsons, Scot A. Wolfe, Caroline E. Burns, C. Geoffrey Burns, Nathan D. Lawson
Summary: The zebrafish is a useful model organism for genetic studies, but the lack of conditional deletion alleles has limited the ability to knockout genes at specific developmental stages or in specific cells. In this study, the researchers applied a protocol to establish floxed alleles for several genes, overcoming challenges such as off-target integration and incomplete knockin. They demonstrated the utility of these floxed alleles by successfully deleting genes in specific cell types and showing their involvement in lymphatic valve development. This study provides a framework for generating and using endogenously floxed alleles in zebrafish.
DEVELOPMENTAL CELL
(2023)