Especially for new people (lots of people are still confused as to what’s important or what to focus attention on - if we figure out how to get people to focus their attention better, it really drastically increases our ability to solve the coordination problem). There are more papers than time available to read, so choose the ones that summarize the most information with the least filler possible (review papers are often best for this, and are often better than the seminal papers in the field [which often lack insight as to physical mechanism]). The best papers take a big-picture or comparative view (you can use scoping to force a big-picture view even with individual post-translational modifications on specific proteins)
https://www.longevity.technology/targeting-resilience/ (I find the one mentioned here interesting enough to want to understand more - though it uses a not-fully-grounded model)
Also, Redirecting... posts A LOT of good papers and has far higher breadth than most aging researchers
MY FAVORITE ITEMS ON PUBMED (530 items) - Favorites - My NCBI Collection
https://www.frontiersin.org/articles/10.3389/fragi.2021.714926/full#B87 (more than anything else)
- https://www.biorxiv.org/content/10.1101/2022.02.06.479300v2 - Aging clocks, entropy, and the limits of age-reversal
Physical Cell Biology
- https://elifesciences.org/articles/54707 . should be canonical
- see skotheim, sturm papers
Comparative Biology of Aging
- Keane et al. - 2015 - Insights into the evolution of longevity from the bowhead whale genome
- PUFAs in short-lived animals and low PUFAs in NMRs
- The Long Life of Birds: The Rat-Pigeon Comparison Revisited
- The changes in the p53 protein across the animal kingdom pointing to its involvement in longevity
- Universal DNA methylation age across mammalian tissues (Horvath) - https://www.biorxiv.org/content/10.1101/2021.01.18.426733v1
- Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination
- Insights into the evolution of longevity from the bowhead whale genome
Long lifespans have evolved with long and monounsaturated fatty acids in birds.
Translation/Transcription (as naked mole rats show, many protein aggregates form DURING the process of translation/transcription b/c it is when they are in their most vulnerable state, so fix the upstream process)
- Interspecies Differences in Proteome Turnover Kinetics Are Correlated With Life Spans and Energetic Demands - ScienceDirect is a TRULY MUST-READ PAPER. it is super-clear and zooms in all the important proteins/processes at a big-picture comparative view
- https://www.biorxiv.org/content/10.1101/2020.03.09.983213v1.full (Unraveling Oxidative Stress Resistance: Molecular Properties Govern Proteome Vulnerability)
- Santra, Dill, de Graff - 2018 - How Do Chaperones Protect a Cell’s Proteins from Oxidative Damage
- Non-Enzymatic Molecular Damage as a Prototypic Driver of Aging - IMPORTANT
- Ori et al. - 2016 - Spatiotemporal variation of mammalian protein complex stoichiometries
- Catana et al. - 2020 - Implications of Long Non-Coding RNAs in Age-Altered Proteostasis
- Macromolecular deterioration as the ultimate constraint on human lifespan
- Radman - 2020 - Dysfunction and toxicity of damaged proteins in the etiology of aging and age-related degenerative and malignant disease
- Robinson-rechavi et al. - 2020 - Molecular Evolution and Gene Function
- Changes of the proteasomal system during the aging process.
- Mitochondria enter the nucleus (one further problem in chronic alcoholism).
- Protein damage, repair and proteolysis.
- Age-dependent deterioration of nuclear pore assembly in mitotic cells decreases transport dynamics.
- Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation
- Sturm paper on cell size
** Metabolomics **
- Undulating changes in human plasma proteome across lifespan are linked to disease
- Tony Wyss-Corey papers
- Lopes et al. - 2020 - Gene size matters What determines gene length in the human genome
- Title: Aging is associated with a systemic length-driven transcriptome imbalance
- Bartas et al. - 2020 - The changes in the p53 protein across the animal kingdom pointing to its involvement in longevity
- Mariadassou, Pellay - 2014 - Identification of amino acids in mitochondrially encoded proteins that correlate with lifespan
- Studer, Robinson-Rechavi - 2009 - How confident can we be that orthologs are similar, but paralogs differ
- Peto’s Paradox: evolution’s prescription for cancer prevention
- Relaxed Selection Limits Lifespan by Increasing Mutation Load - PubMed
- New Insights into the Role of Histone Changes in Aging - PMC
- Epigenetic Mechanisms Impacting Aging: A Focus on Histone Levels and Telomeres - PMC
- “The Aging Epigenome” (brunet) - REVIEW PAPER
- https://epigenie.com/ (makes each of the histone modifications easier to understand, b/c rly, how tf can ppl tell the dif between H3K9 and H3K27)
Protein/Lipid/Nucleic Acid Aggregation
Neurons (really the most important celltype, so maintain them well)
- https://journals.biologists.com/jcs/article-abstract/134/9/jcs255752/264798/Upregulation-of-APP-endocytosis-by-neuronal-aging?redirectedFrom=fulltext (lists many physical mechanisms thru which neurons shrink). Also https://twitter.com/CGAlmeidaG is very approachable
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4101632/ - Mitochondrial Reactive Oxygen Species (ROS) and ROS-Induced ROS Release
- Mitochondrial Flash: Integrative Reactive Oxygen Species and pH Signals in Cell and Organelle Biology - PMC
Long-Lived Structural Proteins
- Discovery of extremely long-lived proteins may provide insight into cell aging and neurodegenerative diseases - Salk Institute for Biological Studies
- Evolutionary Capacitance and Control of Protein Stability in Protein-Protein Interaction Networks
- Del Giudice, Gangestad - 2018 - Rethinking IL-6 and CRP Why they are more than inflammatory biomarkers, and why it matters
Terpenoids as Potential Geroprotectors.
*** Th**e landscape of the alternatively spliced transcriptome remains stable during aging across different species and tissues
- The emerging role of alternative splicing in senescence and aging - PMC
- Bhadra et al. - 2020 - Alternative splicing in aging and longevity
- Autophagy in aging and longevity.
- The Mechanistic Links Between Proteasome Activity, Aging and Age-related Diseases - PMC
An Overview of the Role of Lipofuscin in Age-Related Neurodegeneration.
Surprisingly Crazy Interventions
(look at chimeric studies, look at T-cell and mitochondrial transfer)
Tangential Insight-Dense Papers
** Chemical-level **
- Chemical biology of mutagenesis and DNA repair: cellular responses to DNA alkylation
- Unraveling Oxidative Stress Resistance: Molecular Properties Govern Proteome Vulnerability
Glucose, glycation and aging
- The nuclear pore complex – structure and function at a glance
- The Cellular Senescence Stress Response in Post-Mitotic Brain Cells: Cell Survival at the Expense of Tissue Degeneration.
- Brain Aging - NCBI Bookshelf (free book with 7 chapters providing an overview. 2007)
- When does age-related cognitive decline begin?
- Neuroanatomical substrates of age-related cognitive decline.
- When neurogenesis encounters aging and disease.
- PSD-95 protects synapses from β-amyloid: Cell Reports
- https://journals.sagepub.com/doi/full/10.1177/0192623310389621 (Histology of the Central Nervous System)
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5966715/ - Neuronal Cell Death [collapse of membrane potentials?]
- Serendipitous discovery could lead to treatment for strokes, cardiac arrest: Researchers identify a mechanism that could lead to new treatments for brain injuries caused by oxygen deprivation -- ScienceDaily - https://www.nature.com/articles/s41467-021-23363-x
I would also look up reperfusion injury and H2S suspended animation - has LOTS of relevance
** General Neuro**
CLASSIFY LATER (unsure of importance)
Wang-michelitsch, Michelitsch - 2015 - Potential of longevity hidden in structural complexity
Recent progress in the biology and physiology of sirtuins.
- Neuronal intrinsic mechanisms of axon regeneration.
Neuronal intrinsic mechanisms of axon regeneration.
- Did Evolution Select a Nonrandom “Alphabet” of Amino Acids?
- Adding new chemistries to the genetic code.
The emerging role of alternative splicing in senescence and aging.