We are excited to highlight new research from the IUBMB Journals: IUBMB Life, BioFactors, Biotechnology and Applied Biochemistry, and Biochemistry and Molecular Biology Education.
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Riccardo Delli Ponti, Laura Broglia, Andrea Vandelli, Alexandros Armaos, Marc Torrent Burgas, Natalia Sanchez de Groot, Gian Gaetano Tartaglia
First published: 3 September 2022
RNA molecules undergo a number of chemical modifications whose effects can alter their structure and molecular interactions. Previous studies have shown that RNA editing can impact the formation of ribonucleoprotein complexes and influence the assembly of membrane-less organelles such as stress granules. For instance, N6-methyladenosine (m6A) enhances SG formation and N1-methyladenosine (m1A) prevents their transition to solid-like aggregates. Yet, very little is known about adenosine to inosine (A-to-I) modification that is very abundant in human cells and not only impacts mRNAs but also noncoding RNAs. Here, we introduce the CROSSalive predictor of A-to-I effects on RNA structure based on high-throughput in-cell experiments. Our method shows an accuracy of 90% in predicting the single and double-stranded content of transcripts and identifies a general enrichment of double-stranded regions caused by A-to-I in long intergenic noncoding RNAs (lincRNAs). For the individual cases of NEAT1, NORAD, and XIST, we investigated the relationship between A-to-I editing and interactions with RNA-binding proteins using available CLIP data and catRAPID predictions. We found that A-to-I editing is linked to the alteration of interaction sites with proteins involved in phase separation, which suggests that RNP assembly can be influenced by A-to-I. CROSSalive is available at http://service.tartaglialab.com/new_submission/crossalive.
Xin Jiang, Nieng Yan, Dong Deng, Chuangye Yan
First published: 9 September 2022
Cancer cells shift their glucose catabolism from aerobic respiration to lactic fermentation even in the presence of oxygen, and this is known as the “Warburg effect”. To accommodate the high glucose demands and to avoid lactate accumulation, the expression levels of human glucose transporters (GLUTs) and human monocarboxylate transporters (MCTs) are elevated to maintain metabolic homeostasis. Therefore, inhibition of GLUTs and/or MCTs provides potential therapeutic strategies for cancer treatment. Here, we summarize recent advances in the structural characterization of GLUTs and MCTs, providing a comprehensive understanding of their transport and inhibition mechanisms to facilitate further development of anticancer therapies.
Mariano Sánchez Crespo, Olimpio Montero, Nieves Fernandez
First published: 29 September 2022
Platelet-activating factor (PAF, 1-alkyl-2-acetyl-sn-glycero-3-phosphorylcholine) was discovered when the mechanisms involved in the deposition of immune complex in tissues were being scrutinized in the experimental model of rabbit serum sickness. The initial adscription of PAF to IgE-dependent anaphylaxis was soon extended after disclosing its release from phagocytes stimulated by calcium mobilizing agents, formylated peptides, and phagocytosable particles. This explains why ongoing research in the field turned to the analysis of immune cell types and stimuli involved in PAF production with the purpose of establishing its role in pathology. This was spurred by the identification of the chemical structure of PAF and the enzymic mechanisms involved in its biosynthesis and degradation, which showed commonalities with those involved in eicosanoid production and the Lands’ cycle of phospholipid fatty acid remodeling. The reassignment of PAF function in immunopathology is explained by the finding that the most robust mechanisms leading to PAF production are associated with opsonic and non-opsonic phagocytosis, depending on the cell type. While polymorphonuclear leukocytes exhibit opsonic phagocytosis, monocyte-derived dendritic cells show a marked preference for non-opsonic phagocytosis associated with C-type lectin receptors. This is particularly relevant to the defense against fungal invasion and explains why PAF exerts an autocrine feed-forwarding mechanism required for the selective expression of some cytokines.
Biotechnology and Applied Biochemistry
Pakawat Kongpreecha, Witthawat Phanchai, Theerapong Puangmali, Sineenat Siri
First published: 16 September 2022
Paraquat is a widely used herbicide for controlling weeds and grasses in agriculture, and its contaminated residues in agricultural areas are of increasing concern. This work reports the development of the sensitive and easy-to-use colorimetric aptasensor for screening paraquat residues in agricultural soil. The short DNA fragments derived from the original aptamer were analyzed for their capability to interact with paraquat by molecular dynamic simulation. The paraquat-aptasensor was developed using the selected DNA fragment and gold nanoparticles. Its limit of detection (LOD) for paraquat is 2.76 nM, which is more sensitive than the aptasensor with long-length aptamer (LOD = 12.98 nM). The developed aptasensor shows the selectivity to paraquat, but not to other tested herbicides; ametryn, atrazine, difenzoquat, 2,4-D-dimethyl ammonium, and glufosinate. The recovery rates of paraquat detection in the spiked soil samples were in a range of 99.5%–105.1%, with relative standard deviation values of <4%. The developed aptasensor was used to screen for paraquat residues in agricultural soils, and three out of 23 soil samples were tested positive for paraquat, which was confirmed by a high-performance liquid chromatography analysis. These results suggested the potential application of the developed aptasensor to detect paraquat residues in agricultural sites.
Biochemistry and Molecular Biology Education
Pauline M. Ross, Lucy Mercer-Mapstone, Liana E. Pozza, Philip Poronnik, Tina Hinton, Damien J. Field
First published: 3 October 2022
While biomedical and life science research have embraced interdisciplinarity as the means to solving pressing 21st century complex challenges, interdisciplinarity in undergraduate education has been more difficult to implement. As a consequence, disciplinary rather than interdisciplinary capstones have become ubiquitous. Disciplinary capstones are valuable for students because they enable them to integrate knowledge and skills within the discipline, but they are also limiting because the integration is within rather than across disciplines. In contrast to a capstone, which involves a single discipline, interdisciplinary capstones require two or more disciplines to combine and integrate across disciplinary boundaries. Interdisciplinarity, where two of more disciplines come together, is difficult to implement in the biomedical and life science curricula because student majors and finances are administered in ways, which reinforce institutional organization of schools and faculties and prevent collaboration. Here in this “idea to explore” we provide an interdisciplinary capstone model where students enroll in disciplinary courses, but then these disciplinary courses and students collaborate on interdisciplinary real-world problems. This interdisciplinary capstone model was implemented across two diverse and large biomedical and life science schools within two faculties in a research intensive, metropolitan university. This approach allows for integration of the biomedical, social and ethical perspectives required when solving problems in the real world, such as COVID-19. Interdisciplinary learning also better prepares students for higher degree research and future careers. Overcoming disciplinary curriculum silos and faculty barriers is critical if we are to meet expectations of acquiring interdisciplinarity as a key competency.
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.
Submit your research to the IUBMB Journals today.
Molecular Aspects of Medicine
Volume 87 (October 2022) 101102
by Luis Sobrevia
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!