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Thus, the aim of this study was to identify differences between bacterial small RNAs present at the gut level in hypercholesterolemic and normocholesterolemic individuals. Twenty stool samples were collected from hypercholesterolemic and normocholesterolemic subjects. RNA extraction and small RNA sequencing were performed, followed by bioinformatics analyses with BrumiR, Bowtie 2, BLASTn, DESeq2, and IntaRNA, after the filtering of the reads with fastp. In addition, the prediction of secondary structures was obtained with RNAfold WebServer. Most of the small RNAs were of bacterial origin and presented a greater number of readings in normocholesterolemic participants. The upregulation of small RNA ID 2909606 associated with Coprococcus eutactus (family Lachnospiraceae) was presented in hypercholesterolemic subjects. In addition, a positive correlation was established between small RNA ID 2149569 from the species Blautia wexlerae and hypercholesterolemic subjects. Other bacterial and archaeal small RNAs that interacted with the LDL receptor (LDLR) were identified. For these sequences, the prediction of secondary structures was also obtained. There were significant differences in bacterial small RNAs associated with cholesterol metabolism in hypercholesterolemic and normocholesterolemic participants.<\/jats:p>","DOI":"10.3390\/ijms24087213","type":"journal-article","created":{"date-parts":[[2023,4,14]],"date-time":"2023-04-14T02:28:12Z","timestamp":1681439292000},"page":"7213","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Differences in Bacterial Small RNAs in Stool Samples from Hypercholesterolemic and Normocholesterolemic Subjects"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8147-7251","authenticated-orcid":false,"given":"Cristian","family":"Morales","sequence":"first","affiliation":[{"name":"Centro de Biolog\u00eda Molecular y Farmacogen\u00e9tica, N\u00facleo Cient\u00edfico-Tecnol\u00f3gico en Biorecursos BIOREN, Universidad de La Frontera, Temuco 4811230, Chile"},{"name":"Tecnolog\u00eda M\u00e9dica, Facultad de Salud, Universidad Santo Tom\u00e1s, Temuco 4801076, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1698-9282","authenticated-orcid":false,"given":"Raul","family":"Arias-Carrasco","sequence":"additional","affiliation":[{"name":"Programa Institucional de Fomento a la Investigaci\u00f3n, Desarrollo e Innovaci\u00f3n, Universidad Tecnol\u00f3gica Metropolitana, Santiago 8330378, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8873-9381","authenticated-orcid":false,"given":"Vinicius","family":"Maracaja-Coutinho","sequence":"additional","affiliation":[{"name":"Advanced Center for Chronic Diseases\u2014ACCDiS, Facultad de Qu\u00edmica y Ciencias Farmac\u00e9uticas, Universidad de Chile, Santiago 8380494, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0190-8988","authenticated-orcid":false,"given":"Pamela","family":"Seron","sequence":"additional","affiliation":[{"name":"Departamento de Ciencias de La Rehabilitaci\u00f3n, Facultad de Medicina, Universidad de La Frontera, Temuco 4781151, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernando","family":"Lanas","sequence":"additional","affiliation":[{"name":"Departamento de Medicina Interna, Facultad de Medicina, Universidad de La Frontera, Temuco 4781151, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5112-6944","authenticated-orcid":false,"given":"Luis A.","family":"Salazar","sequence":"additional","affiliation":[{"name":"Centro de Biolog\u00eda Molecular y Farmacogen\u00e9tica, N\u00facleo Cient\u00edfico-Tecnol\u00f3gico en Biorecursos BIOREN, Universidad de La Frontera, Temuco 4811230, Chile"},{"name":"Departamento de Ciencias B\u00e1sicas, Facultad de Medicina, Universidad de La Frontera, Temuco 4811230, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3334-5107","authenticated-orcid":false,"given":"Nicol\u00e1s","family":"Saavedra","sequence":"additional","affiliation":[{"name":"Centro de Biolog\u00eda Molecular y Farmacogen\u00e9tica, N\u00facleo Cient\u00edfico-Tecnol\u00f3gico en Biorecursos BIOREN, Universidad de La Frontera, Temuco 4811230, Chile"},{"name":"Departamento de Ciencias B\u00e1sicas, Facultad de Medicina, Universidad de La Frontera, Temuco 4811230, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,4,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1038\/s41580-019-0190-7","article-title":"Mechanisms and regulation of cholesterol homeostasis","volume":"21","author":"Luo","year":"2020","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"158989","DOI":"10.1016\/j.bbalip.2021.158989","article-title":"Cellular cholesterol and how to find it","volume":"1866","author":"Schoop","year":"2021","journal-title":"Biochim. Et Biophys. Acta. Mol. Cell Biol. Lipids"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"3727","DOI":"10.1111\/febs.15727","article-title":"Cholesterol metabolism pathways - are the intermediates more important than the products?","volume":"288","author":"Wang","year":"2021","journal-title":"FEBS J."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.atherosclerosis.2020.12.013","article-title":"New cardiovascular prevention guidelines: How to optimally manage dyslipidaemia and cardiovascular risk in 2021 in patients needing secondary prevention?","volume":"319","author":"Atar","year":"2021","journal-title":"Atherosclerosis"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1038\/s41569-021-00541-4","article-title":"Global epidemiology of dyslipidaemias","volume":"18","author":"Pirillo","year":"2021","journal-title":"Nat. Rev. Cardiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"108878","DOI":"10.1016\/j.steroids.2021.108878","article-title":"Regulation of cholesterol biosynthesis and lipid metabolism: A microRNA management perspective","volume":"173","author":"Bhattarai","year":"2021","journal-title":"Steroids"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"3","DOI":"10.3892\/or.2016.5236","article-title":"Non-coding RNAs as regulators in epigenetics (Review)","volume":"37","author":"Wei","year":"2017","journal-title":"Oncol. Rep."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1007\/s11427-020-1700-9","article-title":"Non-coding RNAs: The new central dogma of cancer biology","volume":"64","author":"Saw","year":"2021","journal-title":"Sci. China Life Sci."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/s41556-022-00880-5","article-title":"Exploring the expanding universe of small RNAs","volume":"24","author":"Shi","year":"2022","journal-title":"Nat. Cell Biol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Xiong, Q., Zhang, Y., Li, J., and Zhu, Q. (2022). Small Non-Coding RNAs in Human Cancer. Genes, 13.","DOI":"10.3390\/genes13112072"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1007\/s11427-017-9167-5","article-title":"Transfer RNA-derived small RNAs in plants","volume":"61","author":"Zhu","year":"2018","journal-title":"Sci. China. Life Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-3-319-42059-2_1","article-title":"Non-coding RNAs: Classification, Biology and Functioning","volume":"937","author":"Hombach","year":"2016","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"16","DOI":"10.3109\/10409238.2013.844092","article-title":"Gene regulation by non-coding RNAs","volume":"49","author":"Patil","year":"2014","journal-title":"Crit. Rev. Biochem. Mol. Biol."},{"key":"ref_14","first-page":"335","article-title":"Non-Coding RNAs: lncRNAs, miRNAs, and piRNAs in Sexual Development","volume":"15","author":"Burgos","year":"2021","journal-title":"Sex. Dev. Genet. Mol. Biol. Evol. Endocrinol. Embryol. Pathol. Sex Determ. Differ."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"El-Mogy, M., Lam, B., Haj-Ahmad, T.A., McGowan, S., Yu, D., Nosal, L., Rghei, N., Roberts, P., and Haj-Ahmad, Y. (2018). Diversity and signature of small RNA in different bodily fluids using next generation sequencing. BMC Genom., 19.","DOI":"10.1186\/s12864-018-4785-8"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"734763","DOI":"10.3389\/fimmu.2021.734763","article-title":"Circulating miRNAs as Potential Biomarkers for Celiac Disease Development","volume":"12","author":"Tan","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e23099","DOI":"10.1002\/jcla.23099","article-title":"Expression profiling and bioinformatics analysis of circulating microRNAs in patients with acute myocardial infarction","volume":"34","author":"Zhong","year":"2020","journal-title":"J. Clin. Lab. Anal."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2704","DOI":"10.1093\/eurheartj\/ehx165","article-title":"Non-coding RNAs in cardiovascular diseases: Diagnostic and therapeutic perspectives","volume":"39","author":"Poller","year":"2018","journal-title":"Eur. Heart J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1007\/978-981-15-1671-9_23","article-title":"Small Interfering RNAs and RNA Therapeutics in Cardiovascular Diseases","volume":"1229","author":"Bansal","year":"2020","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Zeng, J., Gupta, V.K., Jiang, Y., Yang, B., Gong, L., and Zhu, H. (2019). Cross-Kingdom Small RNAs Among Animals, Plants and Microbes. Cells, 8.","DOI":"10.3390\/cells8040371"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Koeppen, K., Hampton, T.H., Jarek, M., Scharfe, M., Gerber, S.A., Mielcarz, D.W., Demers, E.G., Dolben, E.L., Hammond, J.H., and Hogan, D.A. (2016). A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles. PLoS Pathog., 12.","DOI":"10.1371\/journal.ppat.1005672"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"151356","DOI":"10.1016\/j.ijmm.2019.151356","article-title":"sncRNAs packaged by Helicobacter pylori outer membrane vesicles attenuate IL-8 secretion in human cells","volume":"310","author":"Zhang","year":"2020","journal-title":"Int. J. Med. Microbiol. IJMM"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e12292","DOI":"10.1002\/jev2.12292","article-title":"Diverse functional genes harboured in extracellular vesicles from environmental and human microbiota","volume":"11","author":"Zhu","year":"2022","journal-title":"J. Extracell. Vesicles"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1016\/j.tim.2020.12.003","article-title":"Noncoding RNAs: Regulatory Molecules of Host-Microbiome Crosstalk","volume":"29","author":"Malmuthuge","year":"2021","journal-title":"Trends Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1007\/978-3-319-42059-2_12","article-title":"Non-coding RNAs: Therapeutic Strategies and Delivery Systems","volume":"937","author":"Ling","year":"2016","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"9619","DOI":"10.1002\/jcb.27252","article-title":"Synthetic small RNAs: Current status, challenges, and opportunities","volume":"119","author":"Patel","year":"2018","journal-title":"J. Cell. Biochem."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"8127814","DOI":"10.1155\/2017\/8127814","article-title":"Bacterial Community Profile of the Gut Microbiota Differs between Hypercholesterolemic Subjects and Controls","volume":"2017","author":"Rebolledo","year":"2017","journal-title":"BioMed Res. Int."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1007\/s11154-019-09533-9","article-title":"Gut microbiome and cardiometabolic risk","volume":"20","author":"Kappel","year":"2019","journal-title":"Rev. Endocr. Metab. Disord."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1093\/cvr\/cvab030","article-title":"Sequence meets function-microbiota and cardiovascular disease","volume":"118","author":"Kim","year":"2022","journal-title":"Cardiovasc. Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1007\/s00018-018-2943-4","article-title":"An insight into gut microbiota and its functionalities","volume":"76","author":"Adak","year":"2019","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1136\/gutjnl-2020-321747","article-title":"Gut microbiome stability and resilience: Elucidating the response to perturbations in order to modulate gut health","volume":"70","author":"Fassarella","year":"2021","journal-title":"Gut"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"8516","DOI":"10.1038\/s41598-020-65561-5","article-title":"In vitro human colonic microbiota utilises D-\u03b2-hydroxybutyrate to increase butyrogenesis","volume":"10","author":"Sasaki","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.cmet.2016.12.022","article-title":"Multi-dimensional Roles of Ketone Bodies in Fuel Metabolism, Signaling, and Therapeutics","volume":"25","author":"Puchalska","year":"2017","journal-title":"Cell Metab."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Ch\u00e9nard, T., Malick, M., Dub\u00e9, J., and Mass\u00e9, E. (2020). The influence of blood on the human gut microbiome. BMC Microbiol., 20.","DOI":"10.1186\/s12866-020-01724-8"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1016\/j.clnu.2022.04.014","article-title":"Dietary inflammatory potential mediated gut microbiota and metabolite alterations in Crohn\u2019s disease: A fire-new perspective","volume":"41","author":"Tian","year":"2022","journal-title":"Clin. Nutr."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1007\/s10517-017-3700-7","article-title":"Analysis of Gut Microbiota in Patients with Parkinson\u2019s Disease","volume":"162","author":"Petrov","year":"2017","journal-title":"Bull. Exp. Biol. Med."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"4532","DOI":"10.3748\/wjg.v16.i36.4532","article-title":"Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome","volume":"16","author":"Malinen","year":"2010","journal-title":"World J. Gastroenterol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/s13059-020-01989-2","article-title":"A Cas12a ortholog with stringent PAM recognition followed by low off-target editing rates for genome editing","volume":"21","author":"Chen","year":"2020","journal-title":"Genome Biol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1111\/nyas.14566","article-title":"MicroRNA regulation of cholesterol metabolism","volume":"1495","author":"Citrin","year":"2021","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"583","DOI":"10.3920\/BM2014.0133","article-title":"Quantification of Blautia wexlerae and Blautia luti in human faeces by real-time PCR using specific primers","volume":"6","author":"Touyama","year":"2015","journal-title":"Benef. Microbes"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e00857-19","DOI":"10.1128\/mSystems.00857-19","article-title":"Depletion of Blautia Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening","volume":"5","author":"Sanz","year":"2020","journal-title":"mSystems"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"4477","DOI":"10.1038\/s41467-022-32015-7","article-title":"Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota","volume":"13","author":"Hosomi","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2029","DOI":"10.1053\/j.gastro.2021.01.029","article-title":"The Baseline Gut Microbiota Directs Dieting-Induced Weight Loss Trajectories","volume":"160","author":"Jie","year":"2021","journal-title":"Gastroenterology"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.amjcard.2020.08.018","article-title":"Meta-Analysis of Inclisiran for the Treatment of Hypercholesterolemia","volume":"134","author":"Khan","year":"2020","journal-title":"Am. J. Cardiol."},{"key":"ref_45","first-page":"8129513","article-title":"Advantages and Disadvantages of Inclisiran: A Small Interfering Ribonucleic Acid Molecule Targeting PCSK9-A Narrative Review","volume":"2022","author":"Reiner","year":"2022","journal-title":"Cardiovasc. Ther."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1136\/gutjnl-2021-325168","article-title":"Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals","volume":"71","author":"Tarallo","year":"2022","journal-title":"Gut"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/cr.2011.158","article-title":"Exogenous plant MIR168a specifically targets mammalian LDLRAP1: Evidence of cross-kingdom regulation by microRNA","volume":"22","author":"Zhang","year":"2012","journal-title":"Cell Res."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Stanton, B.A. (2021). Extracellular Vesicles and Host-Pathogen Interactions: A Review of Inter-Kingdom Signaling by Small Noncoding RNA. Genes, 12.","DOI":"10.3390\/genes12071010"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1475","DOI":"10.1177\/1535370217723166","article-title":"Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA","volume":"242","author":"Choi","year":"2017","journal-title":"Exp. Biol. Med."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Askenase, P.W. (2022). Exosome Carrier Effects; Resistance to Digestion in Phagolysosomes May Assist Transfers to Targeted Cells; II Transfers of miRNAs Are Better Analyzed via Systems Approach as They Do Not Fit Conventional Reductionist Stoichiometric Concepts. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23116192"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"943609","DOI":"10.3389\/fcimb.2022.943609","article-title":"Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects","volume":"12","author":"Morales","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_53","unstructured":"Babraham Institute (2023, January 11). Babraham Bioinformatics: FastQC. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"giac093","DOI":"10.1093\/gigascience\/giac093","article-title":"BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data","volume":"11","author":"Moraga","year":"2022","journal-title":"GigaScience"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1093\/bioinformatics\/bty648","article-title":"Scaling read aligners to hundreds of threads on general-purpose processors","volume":"35","author":"Langmead","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: A new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"W435","DOI":"10.1093\/nar\/gkx279","article-title":"IntaRNA 2.0: Enhanced and customizable prediction of RNA-RNA interactions","volume":"45","author":"Mann","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"7287","DOI":"10.1073\/pnas.0401799101","article-title":"Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure","volume":"101","author":"Mathews","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"W70","DOI":"10.1093\/nar\/gkn188","article-title":"The Vienna RNA websuite","volume":"36","author":"Gruber","year":"2008","journal-title":"Nucleic Acids Res."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/8\/7213\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:15:34Z","timestamp":1760123734000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/8\/7213"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,13]]},"references-count":60,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2023,4]]}},"alternative-id":["ijms24087213"],"URL":"https:\/\/doi.org\/10.3390\/ijms24087213","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,4,13]]}}}