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We are excited to highlight new research from the IUBMB Journals: IUBMB Life, BioFactors, Biotechnology and Applied Biochemistry, and Biochemistry and Molecular Biology Education.
Please also consider submitting your own research to the IUBMB Journals. You can expect to work with distinguished Editorial Board members and benefit from worldwide circulation and readership through our publishing partnership with Wiley. For more information about the journal and submissions, feel free to peruse the IUBMB journals website.
For now, please enjoy highlights of our recent content. Happy reading!
IUBMB Life
New Special Issue: Volume 74, Issue 11
Issue Highlights
David L. Brautigan
First published: 14 October 2022
Glycogen is a polymerized form of glucose that serves as an energy reserve in all types of organisms. In animals glycogen synthesis and degradation, especially in liver and skeletal muscle, are regulated by hormonal and physiological signals that reciprocally control the opposing activities of glycogen synthase and glycogen phosphorylase. These enzymes are under allosteric control by binding of metabolites (e.g., ATP, AMP, G6P) and covalent control by reversible phosphorylation by kinase and phosphatase all assembled together on glycogen. More than 50 years ago Edmond Fischer and colleagues showed “flash activation” of phosphorylase in glycogen particles. This involved transient and extensive inhibition of protein phosphatase but even today the phenomenon is not understood. Phosphatase regulation is known to rely on regulatory subunits including glycogen binding subunits that serve as scaffolds, binding catalytic subunit, glycogen, and substrates. This tribute article to Edmond Fischer highlights his thoughts and ideas about the transient inhibition of phosphorylase phosphatase during flash activation of phosphorylase and speculates that phosphatase regulation in glycogen particles might involve a/b hybrids of phosphorylase.
Machine learning applications for transcription level and phenotype predictions
Juthamard Chantaraamporn, Pongpannee Phumikhet, Sarintip Nguantad, Todsapol Techo, Varodom Charoensawan
First published: 7 November 2022
Predicting phenotypes and complex traits from genomic variations has always been a big challenge in molecular biology, at least in part because the task is often complicated by the influences of external stimuli and the environment on regulation of gene expression. With today’s abundance of omic data and advances in high-throughput computing and machine learning (ML), we now have an unprecedented opportunity to uncover the missing links and molecular mechanisms that control gene expression and phenotypes. To empower molecular biologists and researchers in related fields to start using ML for in-depth analyses of their large-scale data, here we provide a summary of fundamental concepts of machine learning, and describe a wide range of research questions and scenarios in molecular biology where ML has been implemented. Due to the abundance of data, reproducibility, and genome-wide coverage, we focus on transcriptomics, and two ML tasks involving it: (a) predicting of transcriptomic profiles or transcription levels from genomic variations in DNA, and (b) predicting phenotypes of interest from transcriptomic profiles or transcription levels. Similar approaches can also be applied to more complex data such as those in multi-omic studies. We envisage that the concepts and examples described here will raise awareness and promote the application of ML among molecular biologists, and eventually help improve a framework for systematic design and predictions of gene expression and phenotypes for synthetic biology applications.
New Special Issue: Volume 74, Issue 12
A special issue of IUBMB Life celebrating the 50th anniversary of FAOBMB (1972–2022)
Akira Kikuchi, Zengyi Chang, Paul A Gleeson
First published: 7 November 2022
The December issue of IUBMB Life is dedicated to the 50th anniversary of FAOBMB (the Federation of Asian and Oceanian Biochemists and Molecular Biologists), which was founded in 1972. At the foundation, the Federation consisted of only three national biochemical societies, and has now grown to incorporate 20 Biochemical and Molecular Biology Societies within the Asian and Oceanic regions. Included in this special issue is a long and very informative article (written by Prof. Phillip Nagley et al) on the 50-year history of FAOBMB.
BioFactors
New Special Issue: Volume 48, Issue 5
Issue Highlights
Satoshi Yano, Katsuhiko Suzuki, Taichi Hara
First published: 7 November 2022
Exosomes are extracellular vesicles primarily responsible for intercellular communication, and they contain nucleic acids and proteins. Exosome secretion has been observed in the intestines, suggesting their physiological effects on the receptor cells of target tissues. It is possible that intestinal epithelial cells recognize food components as ligands, resulting in exosome secretion. However, research on intestine-derived exosomes regulated by food ingredients is limited. In this study, Caco-2 cells were utilized as an intestinal epithelial model for proteomic profiling. NanoLC-MS/MS analysis revealed the alteration of exosome properties by epigallocatechin gallate (EGCG) in differentiated Caco-2 cells. This natural polyphenol reduced both the number and size of secreted exosomes and altered the expression of exosomal proteins. The enriched proteins in exosomes were involved in immune response and cell proliferation. In contrast, those in the EGCG-treated group had distinctive functions in the maintenance of skin homeostasis. We also found variable expression of galectin-3-binding protein and fibronectin as molecular signatures in exosomes derived from EGCG-treated cells. These results could help elucidate the expression and mechanism of exosomal proteins related to food components./p>
Carson J. Rohan, Rushabh P. Lohade, Chad Brewer, Jeffrey B. Travers
First published: 7 November 2022
Thermal burn injuries (TBIs) in patients who are alcohol-intoxicated result in greater morbidity and mortality. The systemic toxicity found in human patients, which includes both immediate systemic cytokine generation with multiple organ failure and a delayed systemic immunosuppression, has previously been replicated in mouse models combining ethanol and localized TBI. Though considerable insights have been provided with these models, the exact mechanisms for these pathologic effects are unclear. In this review, we highlight the roles of the lipid mediator platelet-activating factor (PAF) and subcellular microvesicle particle (MVP) release in response to intoxicated thermal burn injury (ITBI) as effectors in the pathology. Particularly, MVP is released from keratinocytes in response to PAF receptor (PAFR) activation due to excess PAF produced by ITBI. These subcellular particles carry and thus protect the metabolically labile PAF which enable binding of this potent lipid mediator to several key sites. We hypothesize that PAF carried by MVP can bind to PAFR within the gut, activating myosin light chain kinase (MLCK). The subsequent gut barrier dysfunction in response to MLCK activation then allows bacteria to invade the lymphatic system and, eventually, the bloodstream, resulting in sepsis and resultant dysregulated inflammation in multiple organs. PAF in MVP also activate the skin mast cell PAFR resulting in migration of this key effector cell to the lymph nodes to induce immunosuppression. This review thus provides a mechanism and potential therapeutic approaches for the increased toxicity and immunosuppressive outcomes of TBI in the presence of acute ethanol exposure.
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Biotechnology and Applied Biochemistry
Issue Highlights
Effect on the conformations of the spike protein of SARS-CoV-2 due to mutation
Aayatti Mallick Gupta, Jaydeb Chakrabarti
First published: 31 October 2022
The spike protein of SARS-CoV-2 mediates receptor binding and cell entry and is the key immunogenic target for virus neutralization and the present attention of many vaccine layouts. It exhibits significant conformational flexibility. We study the structural fluctuations of spike protein among the most common mutations that appeared in the variant of concerns (VOC). We report the thermodynamics of conformational changes in mutant spike protein with respect to the wild-type from the distributions of the dihedral angles obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. We find that the mutation causes the increase in distance between the N-terminal domain and receptor binding domain, leading to an obtuse angle cosine θ distribution in the trimeric structure in spike protein. Thus, an increase in open state is conferred to the more infectious variants of SARS-CoV-2. The thermodynamically destabilized and disordered residues of receptor binding motif among the mutant variants of spike protein are proposed to serve as better binding sites for the host factor. We identify a short stretch of region connecting the N-terminal domain and receptor binding domain forming a linker loop where many residues undergo stabilization in the open state compared to the closed one.
Biochemistry and Molecular Biology Education
New Virtual Issue on Teaching in the Time of COVID-19
Issue Highlights
Hosein Ameri, Mina Mahami-Oskouei, Simin Sharafi, Saeede Saadatjoo, Maryam Miri, Morteza Arab-Zozani
First published: 7 Novembver 2022
This study aimed to explore the strengths and weaknesses of e-learning during the COVID-19 pandemic from the perspective of its primary stakeholders, namely professors and students, and to provide practical solutions. Design is a qualitative study. We enrolled 22 faculty members and 58 students purposively. Research data were collected through a data collection checklist and via email and continued until the data were saturated. The qualitative content analyses were the basis of analysis in this study. Strengths were presented in 6 themes and 26 subthemes, weaknesses in 5 themes and 23 subthemes, and solutions were presented in 5 themes and 20 subthemes. Save money, time and energy; use modern software and educational technologies; and the ability to individualize education were among the strengths of e-learning. The most important weaknesses related to e-learning include infrastructure difficulties, problems related to the ability of professors and students to use educational systems. The most beneficial solutions offered included improving and upgrading the e-learning infrastructure, empowering professors and students to use educational systems. We concluded that using online teaching has many strengths as well as some weaknesses. Identifying these strengths and weaknesses can help policymakers plan better.
Did you know? Wiley and Jisc just signed an agreement that allows UK authors to publish Open Access in the IUBMB Journals at no cost to them.
Thanks to a partnership our publisher Wiley has signed with Jisc, certain UK institutions now have full access to journals published by Wiley, including the IUBMB Journals. Further, the partnership enables authors at participating UK institutions to publish open access at no cost to them in the IUBMB Journals. Payment of the associated Article Publication Charges (APC) would be covered via the partnership, and authors will not need to cover the APCs from their own pockets.
Wiley has also signed similar agreements with universities in Germany, the Netherlands, Austria, Norway, Hungary, Finland, Sweden, and with the US-based OhioLink And VIVA.
Submit your research to the IUBMB Journals today.
Molecular Aspects of Medicine
Details in IUBMB Newsletter: Issue 14
Should you have a proposal or an idea for a thematic issue for Molecular Aspects of Medicine, please complete the thematic issue proposal form and send it to Dr. Angelo Azzi (angelo.azzi@tufts.edu)
Aspects of Molecular Medicine
Aspects of Molecular Medicine is accepting submissions! Submit your paper to the new open access companion of Molecular Aspects of Medicine by October 31, 2023 and the Article Publishing Charge will be waived!
International Union of Biochemistry and Molecular Biology