Review
Biochemistry & Molecular Biology
Andreas Kohler, Antoni Barrientos, Flavia Fontanesi, Martin Ott
Summary: The mitochondrial respiratory chain is an important system for energy conversion in eukaryotic cells. The organization of respiratory chain complexes into supercomplexes provides advantages for cellular energy conversion, although its universality is still debated. Further research is needed to fully understand the functional significance of these supercomplexes.
Article
Biochemical Research Methods
Shakila H. Peli Thanthri, Thomas H. Linz
Summary: This report presents a microfluidic thermal gel transient isotachophoresis (TG-tITP) method for rapid and high-resolution separation of native proteins. By utilizing the viscosity response of thermal gels and temperature gradients, this method achieves a wide mass range separation with 15,000-fold less protein loading and five-fold faster analysis times.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Environmental Sciences
Eugene P. Sokolov, Linda Adzigbli, Stephanie Markert, Amanda Bundgaard, Angela Fago, Doerte Becher, Claudia Hirschfeld, Inna M. Sokolova
Summary: The study found that the mitochondria of mussels exhibit increased respiration flux, reduced oxidative stress, and mitochondrial damage under H/R stress through intrinsic mechanisms such as reversible protein phosphorylation, contributing to their hypoxia-tolerant mitochondrial phenotype.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Miao Chen, Frank Koopmans, Iryna Paliukhovich, Sophie J. F. van der Spek, Jian Dong, August B. Smit, Ka Wan Li
Summary: This study used an interaction proteomics workflow to reveal the existence of GABA(A) receptor subtypes containing both alpha 1 and alpha 6 subunits. Mass spectrometry analysis showed that these receptor subtypes exist in two main forms, with or without Neuroligin-2. Immunocytochemistry confirmed the presence of this synaptic GABA(A)R subtype at the synapse.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Amber N. Rogers, Maya K. Mastronardo, Tsion G. Mekonnen, Ana Maria Soto
Summary: RNA research is an active field that often requires large amounts of purified RNA. One common purification method involves using electroelution to recover RNA from gel pieces. In this study, two electroeluters with different chamber designs were compared and both were found to effectively recover comparable amounts of purified RNA.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Biochemical Research Methods
Christoph J. Burckhardt, John D. Minna, Gaudenz Danuser
Summary: Co-immunoprecipitation is widely used in studying protein-protein interactions, but requires considerable optimization, and results are often presented non-quantitatively. This protocol offers an optimized workflow using semi-quantitative immunoblot densitometry for increased reliability and reproducibility.
Article
Agriculture, Dairy & Animal Science
Larissa Di Marzo, Joice Pranata, David M. Barbano
Summary: The study compared the estimation of milk casein percentage using SDS-PAGE and Kjeldahl methods, finding that Kjeldahl underestimated the proteolytic damage to casein in milk.
JOURNAL OF DAIRY SCIENCE
(2021)
Review
Cell Biology
Huijing Xue, Abhirami Thaivalappil, Kan Cao
Summary: Methylene blue, the first fully man-made medicine, has a wide range of clinical applications and its anti-oxidative properties have brought new attention to this century-old drug. It can bypass Complex I/III activity in mitochondria and diminish oxidative stress to some degree, making it applicable for treating age-related conditions.
Review
Genetics & Heredity
Sabzali Javadov, Sehwan Jang, Xavier R. Chapa-Dubocq, Zaza Khuchua, Amadou K. S. Camara
Summary: Mitochondria are the main source of ATP for cellular energy demands, and the study of ETC complexes has been focused on solid-state and fluid-state models. Respiratory supercomplexes, according to the solid-state model, play a potential role in maintaining energy balance within the cell.
JOURNAL OF MOLECULAR MEDICINE-JMM
(2021)
Article
Biochemistry & Molecular Biology
Gabriel Ing, Andrew M. Hartley, Nikos Pinotsis, Amandine Marechal
Summary: CIV in mitochondria can exist in different forms, and the yeast CIV shows distinct conformational changes and missing subunits compared to mammalian CIV.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2022)
Article
Engineering, Environmental
Dongqi Wang, Yueyun Li, Helen A. Cope, Xiaoxiao Li, Peisheng He, Cong Liu, Guangyu Li, Sheikh M. Rahman, Nicholas B. Tooker, Charles B. Bott, Annalisa Onnis-Hayden, Jyoti Singh, Alistair Elfick, Ricardo Marques, Henning J. Jessen, Adrian Oehmen, April Z. Gu
Summary: This study demonstrated the use of single-cell Raman spectroscopy (SCRS) for characterizing intracellular polyPs in PAOs within complex environmental samples like EBPR systems. SCRS revealed distinct distribution patterns of polyP length in different PAO types and configurations of EBPR systems, as well as distinctive polyP features among PAO phenotypic sub-groups, indicating its potential for microdiversity-level analysis within EBPR communities.
Article
Biochemical Research Methods
Ryo Ishiguro, Tetsuro Fujisawa
Summary: High pressure is an important tool to alter the equilibrium of oligomeric proteins. Native PAGE at high pressure can characterize the dissociation and differentiation of aggregates, but band smearing often hinders detailed analysis. This study focused on band smearing dependent on migration velocity to extract thermodynamic and kinetic parameters.
ANALYTICAL BIOCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Renato Lima Senra, Camilo Jose Ramirez-Lopez, Marcos Jorge Magalhaes-Junior, Joao Gabriel da Silva Neves, Edvaldo Barros, Bruna Waddington, Simone Eliza Facioni Guimaraes, Jose Domingos Guimaraes, Maria Cristina Baracat-Pereira
Summary: This study found that kallikrein proteoforms are involved in the seasonality of horse reproduction. During the breeding season, increased abundance and different types of kallikreins were observed, along with lower sperm motility, increased semen volume, and higher concentrations of glucose and cholesterol.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Masataka Nakagawa, Yui Tomioka, Chiaki Sakuma, Yasunori Kurosawa, Takashi Shibata, Tsutomu Arakawa, Teruo Akuta
Summary: A new protocol for conducting two-dimensional (2D) electrophoresis was developed by combining agarose native gel electrophoresis with sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat SDS agarose gel electrophoresis. The technique utilizes His/MES buffer during the first-dimensional agarose native gel electrophoresis to visualize basic and acidic proteins in their native states or complex structures. The gel strip from the first-dimensional agarose gel electrophoresis is soaked in SDS and placed on top of vertical SDS-PAGE gels or flat SDS-MetaPhor high-resolution agarose gels for the second-dimensional separation.
Article
Engineering, Petroleum
Yingrui Bai, Chengtong Liu, Jinsheng Sun, Kaihe Lv
Summary: This study examines the performance of a polymer gel for well killing in high-pressure gas reservoirs. The gel exhibits high resistance to shear and temperature, making it suitable for long-term isolation of high-temperature formations. However, it is sensitive to high concentrations of salt ions and can be easily oxidized and disintegrated by acidic solutions. The gel also shows excellent well kill capacity and permeability recovery when used in gasflooding scenarios with oxidative degradation. Successful field testing in the Tarim Basin, China confirms its potential for use in high-temperature and high-pressure gas reservoirs.
Article
Chemistry, Physical
Doris Guerra, Luis A. Gomez, Albeiro Restrepo, Jorge David
Article
Biochemical Research Methods
Xuefei Zhong, Xia Wu, Devin K. Schweppe, Juan D. Chavez, Martin Mathay, Jimmy K. Eng, Andrew Keller, James E. Bruce
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2020)
Article
Biochemical Research Methods
John S. Ramsey, Elizabeth L. Chin, Juan D. Chavez, Surya Saha, Darya Mischuk, Jaclyn Mahoney, Jared Mohr, Faith M. Robison, Elizabeth Mitrovic, Yimin Xu, Susan R. Strickler, Noe Fernandez, Xuefei Zhong, MaryLou Polek, Kris E. Godfrey, James J. Giovannoni, Lukas A. Mueller, Carolyn M. Slupsky, James E. Bruce, Michelle Heck
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Pharmacology & Pharmacy
Kirsten M. Wright, Armando Alcazar Magana, Ronald M. Laethem, Caroline L. Moseley, Troy T. Banks, Claudia S. Maier, Jan F. Stevens, Joseph F. Quinn, Amala Soumyanath
DRUG METABOLISM AND DISPOSITION
(2020)
Article
Multidisciplinary Sciences
Juan D. Chavez, Xiaoting Tang, Matthew D. Campbell, Gustavo Reyes, Philip A. Kramer, Rudy Stuppard, Andrew Keller, Huiliang Zhang, Peter S. Rabinovitch, David J. Marcinek, James E. Bruce
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Chemistry, Analytical
Juan D. Chavez, Andrew Keller, Jared P. Mohr, James E. Bruce
ANALYTICAL CHEMISTRY
(2020)
Review
Spectroscopy
Juan D. Chavez, Sung-Gun Park, Jared P. Mohr, James E. Bruce
Summary: This review discusses the development and challenges in studying the interactome using chemical cross-linking and high-performance mass spectrometry technologies. It highlights the application of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and its potential for improving the visualization of the interactome. Further developments in parallel MS array capabilities are also discussed.
MASS SPECTROMETRY REVIEWS
(2022)
Review
Biochemistry & Molecular Biology
Xiaoting Tang, Helisa H. Wippel, Juan D. Chavez, James E. Bruce
Summary: Protein structure is crucial for biological functions, and understanding it is fundamental in biological and biomedical research. Crosslinking mass spectrometry is an emerging technique that can capture transient information on protein interactions in their native environment. Combining XL-MS with traditional techniques has the potential to bridge the gap between structural biology and systems biology approaches.
Article
Medicine, Research & Experimental
Matthew A. Walker, Juan Chavez, Outi Villet, Xiaoting Tang, Andrew Keller, James E. Bruce, Rong Tian
Summary: One hallmark of impaired myocardial energetics in failing hearts is the downregulation of the creatine kinase (CK) system. A study found an inverse relationship between the activity and acetylation of CK muscle form (CKM) in human and mouse failing hearts, where hyperacetylation disrupted MM homodimer formation and reduced enzymatic activity. Deacetylation by sirtuin 2 improved dimer formation and restored CKM activity from failing heart tissue, suggesting a novel mechanism for improving high-energy phosphoryl transfer in heart failure.
Review
Chemistry, Multidisciplinary
Juan D. Chavez, Helisa H. Wippel, Xiaoting Tang, Andrew Keller, James E. Bruce
Summary: Biological systems heavily rely on proteins for various functional roles, and recent advancements in mass spectrometry, chemical labeling, and informatics capabilities have provided insights into the structures of proteins, complexes, and networks within cells. These approaches, which benefit from the molecular detection specificity of mass spectrometry and proteomics, offer systems-level information about conformational changes and protein interactions in response to perturbations.
Review
Biochemistry & Molecular Biology
Helisa H. Wippel, Juan D. Chavez, Xiaoting Tang, James E. Bruce
Summary: This article provides an overview of recent technological developments and applications of qXL-MS, including the design and synthesis of cross-linkers, development of new liquid chromatography-MS methodologies, and computational developments for data interpretation.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Ashish Vaswani, Armando Alcazar Magana, Eric Zimmermann, Wohaib Hasan, Jaishankar Raman, Claudia S. Maier
Summary: The study demonstrates the compatibility of OCT storage with LC-MS/MS lipidomics of heart tissue, enabling the use of biobanked tissue samples for future studies.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Tara K. Bartolec, Joshua J. Hamey, Andrew Keller, Juan D. Chavez, James E. Bruce, Marc. R. Wilkins
Summary: This study investigates the function of histidine protein methyltransferase Hpm1p in yeast and confirms its association with diverse phenotypes, including sugar metabolism regulation, through techniques such as mass spectrometry analysis.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Agronomy
Esther Shiau Ping Yap, Apiradee Uthairatanakij, Natta Laohakunjit, Pongphen Jitareerat, Claudia S. Maier
Summary: This study investigated the effects of maturity stages on secondary compound levels and antioxidant activities in super hot chilies, and found that capsaicin and dihydrocapsaicin were the most abundant compounds, regardless of maturity stage. Capsaicinoid levels in chilies increased from 100% green to 70% red stage, followed by a decrease and subsequent increase at the overripe stage. Total phenolic content was highest at the full red stage, while total flavonoid content was highest at the 90% red stage. Antioxidant activities showed a decreasing trend until the 90% red stage, followed by an increase thereafter. The 80% green stage had the highest capsaicinoid levels, antioxidant properties, and metabolites such as 4-piperidinol.
Article
Biochemistry & Molecular Biology
Helisa H. Wippel, Mariana Fioramonte, Juan D. Chavez, James E. Bruce
Summary: RNA-binding proteins (RBPs) interact with RNAs and other proteins to form ribonucleoprotein (RNP) complexes, which are involved in regulating various cellular processes. Heterogeneous nuclear ribonucleoproteins (hnRNPs) play a crucial role in transcription control and nuclear processing of transcripts, as well as in regulating alternative splicing of pre-mRNAs through spliceosome complex.
Article
Biochemistry & Molecular Biology
Yuri Nagaoka, Kotone Oshiro, Yuta Yoshino, Toshiyuki Matsunaga, Satoshi Endo, Akira Ikari
Summary: This study investigated the effect of intercellular adhesion molecule CLDN1 on the anticancer drug sensitivity of small-cell lung cancer (SCLC) cells. It was found that overexpression of CLDN1 decreased the sensitivity of SCLC cells to anticancer drugs and enhanced their migratory capacity through the activation of the TGF-81/EMT signaling pathway. Treatment with EMT inhibitors showed potential in overcoming the reduced sensitivity to anticancer drugs in CLDN1-overexpressing SCLC cells.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2024)
