Article
Biochemical Research Methods
Maria Rain Jennings, Soohyon Min, Grace S. Xu, Kassandra Homayuni, Bhavana Suresh, Yusef Amir Haikal, John Blazeck
Summary: This study successfully produced Homo sapiens adenosine deaminase isoform 1 (HsADA1) and its variants through optimizing the recombinant expression process. The D8N variant of HsADA1 was found to be about 30% less active than the wildtype, but it better retained its activity in human serum. Additionally, the study revealed a previously undescribed phenomenon involving albumin that contributed to the increased activity of HsADA1 and the D8N variant in serum.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Crisciele Fontana, Joao Luiz de Meirelles, Hugo Verli
Summary: By using the GROMOS force field and molecular simulations, this study assessed the dynamics of STA-analogs in aqueous solution and their interaction with water, expanding the knowledge of the conformational space of these ligands and providing potential implications for understanding conformational selection during complexation.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Yufan Lu, Xingmin Guo, Shuya Liu
Summary: This paper investigates how to control the nontrivial topological structures of DNA nanocages by adjusting the number of ssDNA strands. A new algorithm and program are developed to calculate the component number of polyhedral links, filling the gap in computer programs on this aspect. The study provides a complete list of topological structures with different component numbers for DNA octahedrons assembled from one or more ssDNA strands.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Diana Margarita Mojica-Munoz, Karla Lizbeth Macias-Sanchez, Estefania Odemaris Juarez-Hernandez, Aurora Rodriguez-Alvarez, Jean-Michel Grevy, Armando Diaz-Valle, Mauricio Carrillo-Tripp, Jose Marcos Falcon-Gonzalez
Summary: By employing molecular dynamics simulations, we investigated the molecular mechanisms underlying the plasticization of starch. Our study revealed that chain size affects the solubility of starch, temperature influences its diffusivity and elastic properties, and oleic acid shows potential as an alternative plasticizer. Blending glycerol or oleic acid with water enhances the elasticity of starch.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
K. Ramki, G. Thiruppathi, Selva Kumar Ramasamy, P. Sundararaj, P. Sakthivel
Summary: A chromone-based ratiometric fluorescent probe L2 was developed for the selective detection of Hg(II) in a semiaqueous solution. The probe exhibited enhanced fluorescence in its aggregated state and even higher fluorescence when chelated with Hg(II). The probe demonstrated high sensitivity and specificity for Hg(II) detection and was successfully applied for imaging Hg(II) in a living model.
Article
Biochemical Research Methods
Masako Kagawa, Nagayoshi Katsuta, Sayuri Naito, Yuma Masuki, Chikage Yoshimizu, Hitoshi Chiba, Ichiro Tayasu
Summary: In this study, the effect of various sample pretreatments on the delta O-18 and delta S-34 values in sulfate from atmospheric precipitation and aerosols was investigated. The results showed that acidification, heating, concentration, and drying did not significantly affect the delta O-18 and delta S-34 values if HCl was not added before heating and BaSO4 was treated with DTPA for the delta O-18 analysis.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Xi Li, Keisuke Sawada, Hirotaka Shioji
Summary: The article discusses the use of nanoESI-MS and CID-MS/MS to detect and evaluate the stability of unstable metal complexes.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Younis Abiedalla, C. Randall Clark
Summary: The electron ionization (EI)-mass spectroscopy (MS) fragmentation of methoxymethylene substituted benzoate esters was studied. The aliphatic oxygen of the alkoxymethylene group plays a more active role in the fragmentation profile compared to the direct aromatic ring linked oxygen of the ethoxy group.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Yamin Liu, Linnan Li, Zhengtao Wang, Li Yang
Summary: This study developed a rapid and sensitive analytical method using mass spectrometry coupled with ultrahigh-performance liquid chromatography to quantify 14 Ang peptides. The method demonstrated high sensitivity and was validated for linearity, precision, stability, recovery, and matrix effect.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Chaohui Qiu, Xiaolong Li, Zhe Li, Liu Yang, Weimin Wang, Chuan-Fan Ding, Fuxing Xu
Summary: This paper explores three new profile quadrupole ion funnels (QIF) to improve the transmission efficiency of low m/z ions.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Mattia Tagliavento, Sven Hofmann, Michael Ernst Boettcher, Markus Peltz, Jens Fiebig
Summary: This study used an improved Kiel IV device and a pretreatment technique to accurately determine the body temperatures of extinct animals by analyzing the Delta (47) composition of carbonate-bearing bioapatite. The results showed that using water sinks effectively removed water, and the pretreatment technique removed secondary calcite.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Wojciech Jankowski, Marcin Hoffmann, Paulina Polrul, Magdalena Franska
Summary: This study focused on the protonated dimers of cytosine and its nucleoside, using experimental and quantum mechanics methods to investigate their gas-phase stabilities. The results showed that substitution of sugar moiety at N1 cytosine atom decreased the stability of the protonated dimers, and the deoxycytidine dimer was more stable than the cytidine dimer. Quantum chemical calculations suggested that a cytosine aminohydroxy tautomer may play a role in the formation of protonated cytosine-cytosine nucleoside dimers.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Simon Leitner, Kathiravan Meeran, Andrea Watzinger
Summary: The measurement of stable carbon and oxygen isotope ratio of atmospheric CO2 is important for identifying greenhouse gas sources and sinks. This study presents a measuring system that allows a wide range of users to analyze atmospheric CO2 using off-the-bench hardware and software.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Alison Devonshire, Gerwyn Jones, Ana Fernandez Gonzalez, Olga Kofanova, Johanna Trouet, Pamela Pinzani, Stefania Gelmini, Serena Bonin, Carole Foy
Summary: The analysis of circulating cell-free DNA (ccfDNA) in liquid biopsies is becoming increasingly important in clinical practice. However, the accuracy of diagnosis is greatly impacted by the quality of the samples, and standardized approaches for assessing the quality of ccfDNA have not yet been established. This study evaluates the use of nucleic acid spike-in control materials as a quality control (QC) and standardization method for cfDNA isolation in in vitro diagnostic assays.
Article
Biochemical Research Methods
Markus Plass, Rudolf Wittner, Petr Holub, Francesca Frexia, Cecilia Mascia, Matej Gallo, Heimo Mueller, Jorg Geiger
Summary: The development of AI in biotechnology relies on high-quality data and this paper presents a framework for recording and publishing provenance information to meet regulatory requirements. The framework utilizes standardized models and protocols to capture and record provenance information at different stages of the data generation and analysis process. A use case is also provided to illustrate the importance of managing and integrating distributed provenance information.
Article
Biochemical Research Methods
Marina Tumolo, Domenico De Paola, Vito Felice Uricchio, Valeria Ancona
Summary: This study investigated the effects of lactate and yeast extract on the bacterial community in Cr(VI)-polluted microcosms. Results showed that providing electron donors led to the proliferation of specific bacterial species and a decrease in species richness and evenness. Lactate promoted the enrichment of fermentative bacteria, while yeast extract enriched Shewanella. Yeast extract resulted in the quickest Cr(VI) reduction, while lactate supported a slower yet considerable removal of the pollutant.
Article
Biochemical Research Methods
Manon van Daal, Anne-Floor J. de Kanter, Annelien L. Bredenoord, Nienke de Graeff
Summary: Personalized 3D printed scaffolds are a new generation of implants used in tissue engineering and regenerative medicine. This article explores the ethical challenges and opportunities associated with these implants throughout their life cycle, covering topics such as research and clinical practices, privacy issues, and the inclusion of gender in ethical assessments. The article highlights the importance of addressing these ethical issues for the responsible development and implementation of personalized 3D printed scaffolds in the additive manufacturing and tissue engineering field.
Article
Biochemical Research Methods
Roberta Lucchi, Maria C. Lucana, Montserrat Escobar-Rosales, Cristina Diaz-Perlas, Benjami Oller-Salvia
Summary: Antibody therapeutics have potential to treat various diseases, but side effects limit their safe dosage. Conditionally-active antibodies provide additional selectivity for improved safety. In this study, a versatile approach to conditionally mask antibody derivatives was proposed and successfully applied to cancer stem cells in multiple tumors. This method enables rapid activation of antibodies with different internal or external stimuli.
Article
Biochemical Research Methods
Daniel Heinzelmann, Benjamin Lindner, Benjamin Renner, Simon Fischer, Patrick Schulz, Moritz Schmidt
Summary: PCR-based methods, especially droplet digital PCR (ddPCR), have important applications in cell line development. This study demonstrates the use of ddPCR for precise quantification of transgene copies and prediction of assembly and homogeneity of difficult-to-express proteins. The implementation of ddPCR-based assays improves the robustness and comparability of genomic characterization.
Article
Biochemical Research Methods
Monica Estrada, Clara Navarrete, Sonke Moller, Manuel Quiros, Jose L. Martinez
Summary: The halotolerant non-conventional yeast Debaryomyces hansenii has the ability to grow in high salt concentrations, metabolize alternative carbon sources, and withstand different temperatures and pH levels. This yeast can be used to revalue industrial salty by-products and contribute to a circular economy. Experimental results showed that D. hansenii can efficiently grow in different salty by-products and produce recombinant proteins without the need for sterile conditions or additional nutrients, making the process cost-effective and sustainable.
