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      Reversal of biological age in multiple rat organs by young porcine plasma fraction

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          Abstract

          Young blood plasma is known to confer beneficial effects on various organs in mice and rats. However, it was not known whether plasma from young adult pigs rejuvenates old rat tissues at the epigenetic level; whether it alters the epigenetic clock, which is a highly accurate molecular biomarker of aging. To address this question, we developed and validated six different epigenetic clocks for rat tissues that are based on DNA methylation values derived from n = 613 tissue samples. As indicated by their respective names, the rat pan-tissue clock can be applied to DNA methylation profiles from all rat tissues, while the rat brain, liver, and blood clocks apply to the corresponding tissue types. We also developed two epigenetic clocks that apply to both human and rat tissues by adding n = 1366 human tissue samples to the training data. We employed these six rat clocks to investigate the rejuvenation effects of a porcine plasma fraction treatment in different rat tissues. The treatment more than halved the epigenetic ages of blood, heart, and liver tissue. A less pronounced, but statistically significant, rejuvenation effect could be observed in the hypothalamus. The treatment was accompanied by progressive improvement in the function of these organs as ascertained through numerous biochemical/physiological biomarkers, behavioral responses encompassing cognitive functions. An immunoglobulin G (IgG) N-glycosylation pattern shift from pro- to anti-inflammatory also indicated reversal of glycan aging. Overall, this study demonstrates that a young porcine plasma-derived treatment markedly reverses aging in rats according to epigenetic clocks, IgG glycans, and other biomarkers of aging.

          Supplementary Information

          The online version contains supplementary material available at 10.1007/s11357-023-00980-6.

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          limma powers differential expression analyses for RNA-sequencing and microarray studies

          limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
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            The Hallmarks of Aging

            Aging is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death. This deterioration is the primary risk factor for major human pathologies, including cancer, diabetes, cardiovascular disorders, and neurodegenerative diseases. Aging research has experienced an unprecedented advance over recent years, particularly with the discovery that the rate of aging is controlled, at least to some extent, by genetic pathways and biochemical processes conserved in evolution. This Review enumerates nine tentative hallmarks that represent common denominators of aging in different organisms, with special emphasis on mammalian aging. These hallmarks are: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication. A major challenge is to dissect the interconnectedness between the candidate hallmarks and their relative contributions to aging, with the final goal of identifying pharmaceutical targets to improve human health during aging, with minimal side effects. Copyright © 2013 Elsevier Inc. All rights reserved.
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              Regularization Paths for Generalized Linear Models via Coordinate Descent

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                Author and article information

                Contributors
                shorvath@mednet.ucla.edu
                har.kat@yuvanresearch.com
                Journal
                GeroScience
                Geroscience
                GeroScience
                Springer International Publishing (Cham )
                2509-2715
                2509-2723
                24 October 2023
                24 October 2023
                February 2024
                : 46
                : 1
                : 367-394
                Affiliations
                [1 ]GRID grid.19006.3e, ISNI 0000 0000 9632 6718, Department of Human Genetics, David Geffen School of Medicine, , University of California, ; Los Angeles, CA USA
                [2 ]GRID grid.19006.3e, ISNI 0000 0000 9632 6718, Department of Biostatistics, Fielding School of Public Health, , University of California, ; Los Angeles, CA USA
                [3 ]Altos Labs, Cambridge, UK
                [4 ]GRID grid.444588.1, ISNI 0000 0004 0635 4408, Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, , SVKM’s NMIMS University, ; Mumbai, India
                [5 ]Yuvan Research Inc., Mountain View, CA USA
                [6 ]Institute for Experimental Pharmacology of Cordoba (IFEC), School of Chemical Sciences, National University of Cordoba, ( https://ror.org/056tb7j80) Cordoba, Argentina
                [7 ]Biochemistry Research Institute of La Plata–Histology B, Pathology B, School of Medicine, University of La Plata, ( https://ror.org/018gb4016) La Plata, Argentina
                [8 ]GRID grid.424982.1, Genos Glycoscience Research Laboratory, ; Zagreb, Croatia
                [9 ]Wake Forest University School of Medicine, Medical Center Drive, ( https://ror.org/0207ad724) Winston Salem, NC USA
                [10 ]Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, ( https://ror.org/0011qv509) Memphis, TN USA
                [11 ]GRID grid.19006.3e, ISNI 0000 0000 9632 6718, Department of Neurology, , David Geffen School of Medicine at the University of California, ; Los Angeles, CA USA
                [12 ]Epigenetic Clock Development Foundation, Torrance, CA USA
                [13 ]Faculty of Pharmacy and Biochemistry, University of Zagreb, ( https://ror.org/00mv6sv71) Zagreb, Croatia
                Author information
                http://orcid.org/0000-0002-4110-3589
                Article
                980
                10.1007/s11357-023-00980-6
                10828479
                37875652
                388c4ed6-8d6d-42d9-9154-b1d55865d97a
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 7 August 2023
                : 9 October 2023
                Categories
                Original Article
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                © American Aging Association 2024

                rejuvenation,plasma fraction,epigenetic clock,dna methylation,glycans,rat

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