aging methylation data, single cell, Transcription factor

Inference of age-associated transcription factor regulatory activity changes in single cells

https://www.nature.com/articles/s43587-022-00233-9#data-availability

 

re we present and validate a TF activity estimation method for single cells from the hematopoietic system that is based on TF regulons, and apply it to a mouse single-cell RNA-sequencing atlas, to infer age-associated differentiation activity changes in the immune cells of different organs

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56046

Series GSE56046 Query DataSets for GSE56046
Status	Public on Nov 24, 2014
Title	Transcriptomics and methylomics of human monocytes [methylome]
Organism	Homo sapiens
Experiment type	Methylation profiling by genome tiling array
Summary	The MESA Epigenomics and Transcriptomics Study has been launched to investigate potential gene expression regulatory methylation sites in humans by examining the association between CpG methylation and gene expression in purified human monocytes from a large study population (community-dwelling participants in the Multi-Ethnic Study of Atherosclerosis (MESA)). The MESA Epigenomics and Transcriptomics Study was funded by a National Heart, Lung and Blood Institute grant (R01HL101250) through the NIH Roadmap Epigenomics Program in 2009.

biological network across scales

 

https://reintegratingbiology.org/wp-content/uploads/2019/12/Netwoks-Across-Scales-Gustavo-Caetano-Anolles.pdf

High-Dimensional Data Analysis with Low-Dimensional Models: Principles, Computation, and Applications

 

High-Dimensional Data Analysis with Low-Dimensional Models:
Principles, Computation, and Applications

John Wright   and   Yi Ma,    Cambridge University Press

https://book-wright-ma.github.io/

to read, yeast paper

 

cell fate

Transcription levels of a noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast

https://pubmed.ncbi.nlm.nih.gov/33472063/

deep learning microscopy

 

https://www.nature.com/articles/s41592-021-01080-z

 

Why Deep Learning Works: A Manifold Disentanglement Perspective

https://ieeexplore.ieee.org/document/7348689

deep learning and fluid dynamics

 

Machine learning accelerated computational fluid dynamics

https://arxiv.org/pdf/2102.01010.pdf

https://twitter.com/dkochkov1/status/1356440834921627650

Fig 1. old velocity goes into CNN block, --> filter constraints, --> advected, advecting velocity components --> tensor product --> divergence --> explicit time step --> pressure projection --> new velocity

flow are considered turbulent if Re >> 1

convection: heated air rise up

advected: horizontally transfer, https://en.wikipedia.org/wiki/Advection 

learned solvers

 

Machine Learning for Fluid Mechanics

https://arxiv.org/abs/1905.11075

Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity

https://www.nature.com/articles/s41598-020-70812-6#Sec2 Article Open Access Published: 19 August 2020 Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity

The proteome landscape of the kingdoms of life

https://www.nature.com/articles/s41586-020-2402-x

hsp70 isoforms in yeast, different functions

• Format: Abstract

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Curr Genet. 2019 Apr 24. doi: 10.1007/s00294-019-00978-8. [Epub ahead of print]

Not quite the SSAme: unique roles for the yeast cytosolic Hsp70s.

Lotz SK1, Knighton LE1, Nitika1, Jones GW2, Truman AW3.

Author information

Abstract

The Heat Shock Protein 70s (Hsp70s) are an essential family of proteins involved in folding of new proteins and triaging of damaged proteins for proteasomal-mediated degradation. They are highly conserved in all organisms, with each organism possessing multiple highly similar Hsp70 variants (isoforms). These isoforms have been previously thought to be identical in function differing only in their spatio-temporal expression pattern. The model organism Saccharomyces cerevisiae (baker's yeast) expresses four Hsp70 isoforms Ssa1, 2, 3 and 4. Here, we review recent findings that suggest that despite their similarity, Ssa isoforms may have unique cellular functions.

KEYWORDS:

Chaperone; Evolution; Hsp70; Isoform; Ssa

PMID:

 

31020385

 

DOI:

 

10.1007/s00294-019-00978-8

medical image analysis

U-net popular for medical image segmentation, but it does not classifiy image. CU-net is proposed in 2018 for do both classification and segmentation.

Life history traits impact the nuclear rate of substitution but not the mitochondrial rate in isopods

https://academic.oup.com/mbe/advance-article-abstract/doi/10.1093/molbev/msy184/5106169?redirectedFrom=fulltext\

Dynamic networks reveal key players in aging

Faisal and Melenkovic 2014  bioinforamtics
https://academic.oup.com/bioinformatics/article/30/12/1721/2748134#supplementary-data


Todo: apply this in yeast. network controllability analysis, -> reliability analysis

neural networks, polynomial regression

https://www.r-bloggers.com/neural-networks-are-essentially-polynomial-regression/

R15 proposals in NIA

1R15AG053879-01
ROLE OF CIRCADIAN CLOCK COMPONENTS IN APOPTOSIS AND TAUOPATHY IN DROSOPHILA

https://projectreporter.nih.gov/project_info_details.cfm?aid=9171076&icde=39147502&ddparam=&ddvalue=&ddsub=&cr=27&csb=default&cs=ASC&pball=

CELL SIGNALING AND RESISTANCE TO OXIDATIVE STRESS: EFFECTS OF AGING AND EXERCISE.
https://projectreporter.nih.gov/project_info_description.cfm?aid=9225339&icde=39147502&ddparam=&ddvalue=&ddsub=&cr=8&csb=FY&cs=DESC&pball=

1R15AG050218-01A1
TESTING DIRECT EFFECTS OF REPRODUCTION ON LIFESPAN WITH CONTROLLED FEEDING IN GRASSHOPPERS
https://projectreporter.nih.gov/project_info_description.cfm?aid=9093113&icde=39147502&ddparam=&ddvalue=&ddsub=&cr=11&csb=FY&cs=DESC&pball=

1R15AG052933-01
THE ROLES OF SPHINGOLIPIDS IN STRESS RESPONSE AND HEALTHY AGING.
https://projectreporter.nih.gov/project_info_description.cfm?aid=9099409&icde=39147502&ddparam=&ddvalue=&ddsub=&cr=16&csb=FY&cs=DESC&pball=

1R15AG052149-01
REGULATION OF THE C. ELEGANS HEAT SHOCK RESPONSE BY LST-3
https://projectreporter.nih.gov/project_info_description.cfm?aid=9022936&icde=39147502&ddparam=&ddvalue=&ddsub=&cr=38&csb=default&cs=ASC&pball=

journal of computational biology

Journal of Computational Biology Special Issue: The 13th International Symposium on Bioinformatics Research and Applications (ISBRA2017) This Special Issue includes a selection of papers presented at the 13th International Symposium on Bioinformatics Research and Applications (ISBRA 2017) which was held in Honolulu, Hawaii on May 30–June 2, 2017. ISBRA provides a forum for the exchange of ideas and results among researchers, developers, and practitioners working on all aspects of bioinformatics and computational biology and their applications. Enjoy FREE ACCESS through April 9, 2018. Read Now: Preface: 13th International Symposium on Bioinformatics Research and Applications (ISBRA 2017) Zhipeng Cai, Pavel Skums, Alexander Zelikovsky  Read Now Reconstructing One-Articulated Networks with Distance Matrices Kuang-Yu Chang, Yun Ciu, Siu-Ming Yiu, Wing-Kai Hon  Read Now ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer Zihao Wang, Yu Chen, Jingrong Zhang, Lun Li, Xiaohua Wan, Zhiyong Liu, Fei Sun, Fa Zhang  Read Now Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry Michał Aleksander Ciach, Mateusz Krzysztof Łącki, Błażej Miasojedow, Frederik Lermyte, Dirk Valkenborg, Frank Sobott, Anna Gambin  Read Now A Median Solver and Phylogenetic Inference Based on Double-Cut-and-Join Sorting Ruofan Xia, Yu Lin, Jun Zhou, Bing Feng, Jijun Tang  Read Now Convolutional Neural Network for Histopathological Analysis of Osteosarcoma Rashika Mishra, Ovidiu Daescu, Patrick Leavey, Dinesh Rakheja, Anita Sengupta  Read Now Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing Albert Ng, Dong Si  Read Now An Optimized Method for Bayesian Connectivity Change Point Model Xiuchun Xiao, Bing Liu, Jing Zhang, Xueli Xiao, Yi Pan  Read Now Unbiased Taxonomic Annotation of Metagenomic Samples Bruno Fosso, Graziano Pesole, Francesc Rosselló, Gabriel Valiente  Read Now

toread: dual activation gene network

Dual gene activation and knockout screen reveals directional dependencies in genetic networks

https://www.nature.com/articles/nbt.4062

UAB, aging biology update

Aging Biology Update is brought to you by the UAB Nathan Shock Center and was compiled by Jessica M. Hoffman, Steven N. Austad, and Heather K. Patterson.

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Featured

• Adults in U.S. South die 3-4 years earlier.
• Women live longer than men even under severe famines and epidemics.
• Do naked mole rats defy Gompertzian laws of aging?

Headline vs Study

• Headline: Scientists discover molecule that could reverse cellular aging.
• Study: Silencing of the lncRNA Zeb2-NAT facilitates reprogramming of aged fibroblasts and safeguards stem cell pluripotency.

Contrary or Null Findings

• Rapamycin supplementation decreases lifespan of long lived growth hormone receptor knock out mice.
• Solanezumab fails to improve cognitive decline in mild Alzheimer’s dementia.
• Circulating IGF-1 levels not associated with Alzheimer’s disease risk.
• Resveratrol fails to extend on life or health in Drosophila.
• Middle-aged HIV positive individuals on antiretroviral therapy show no increased rates of brain aging.

Energetics/Nutrition

• Low protein and high carbohydrate diets are associated with metabolic syndrome in elderly women.
• Expression of methionine sulfoxide reductase extends Drosophila lifespan in a methionine-dependent manner.
• High soybean and isoflavone intake is associated with reduced risk of cognitive impairment.
• Review: Dietary amino acids and healthy aging: lessons from animal nutritionists.

Basic Biology

• The molecular structures of fibroblast growth factors interacting with the aging related proteins -klotho and -klotho.
• Novel SNPs associated with male longevity.
• Deletion of Nrip1 extends female, but not male, mice longevity.
• Overexpression of mitochondrial sirtuin Sirt4 extends life in Drosophila.
• mTOR inhibition protects the blood-brain barrier in mouse models of dementia.
• A pharmaceutical rapalog reduces age- related kidney changes in old rats.
• Transcriptomic aging of mouse astrocytes are brain region specific.
• Supplementation of Torin1 extends life with no fertility reduction in Drosophila.
• Reduction in microRNA-305 extends Drosophila life.
• Telomere length in developmental programming.
• Review: Biology of premature aging in cancer survivors.
• Review: DNA modification in aging research.
• Review: Epigenetics in aging and neurodegenerative disorders.

Ecology & Evolution

• Environmental stress shapes the temporal pattern of investment in reproduction and survival in captive zebra finches.
• Early-life environment affects lifetime fitness in bighorn ewes.
• Fertility trade-offs in male zebrafish with age.

Novel Organisms/Comparative

• Strong social relationships are associated with decreased longevity in the yellow-bellied marmot.
• Life- extending drugs in rotifers.
• More rotifers: Chronic calorie restriction modifies lipid metabolism while decreasing reproduction and increasing lifespan.
• Global protein turnover rate is negatively associated with maximum lifespan across species.
• Meta-analysis: telomere length and mortality in wild bird populations.
• Microbiome diversity changes little with age in a long-lived bat.
• The aging immune system of the cotton rat.
• Long-term hematopoietic stem and progenitor cell output impaired in aged macaques.
• Review: Chronic kidney disease and age associated complications: Insights from the animal kingdom.
• Review: The Chinese tree shrew as a model of Alzheimer’s disease.
• Review: Autophagy in animals, plants, and fungi.

Epidemiology/Demography

• Cancer mortality rates declined 1.5% a year from 2006-2015.
• Among the wealthiest countries, the United States has the highest infant and child mortality rates.
• The effect of temperature on years of life lost across the globe.
• Inverse association between female mortality at ages 45-49 and life expectancy at 60 in three countries.

Policy/Ethics

• Measuring how countries adapt to societal aging.
• Paid family leave reduces nursing home use by 11%.

Clinical

• Up to 75% of nursing home residents may be given potentially inappropriate medications.
• Hypertensive African American men on medication have reduced risk of dementia.
• Interactions between drugs and geriatric syndromes are common in long-term care patients.
• Predicting survival of the elderly based on glomerular filtration rates.
• Preclinical Alzheimer’s disease is associated with circadian rhythm dysfunction.

Care-giving

• The complexities of family caregiving at work.

Commentary

• The benefits of reviewing.

toread, paper on aging, calorie restriction

The Hsp70 homolog Ssb affects ribosome biogenesis via the TORC1-Sch9 signaling pathway Kaivalya Mudholkar1 , Edith Fitzke1 , Claudia Prinz1 , Matthias P. Mayer 2 & Sabine Rospert 1,3
https://www.nature.com/articles/s41467-017-00635-z.pdf

Are aberrant phase transitions a driver of cellular aging?Simon Alberti* and Anthony A. Hyman*
 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5108435/

Protein biogenesis machinery is a driver of replicative aging in yeast. Georges E Janssens1†, Anne C Meinema2†‡, Javier Gonza ́lez3§, Justina C Wolters4, Alexander Schmidt5, Victor Guryev1, Rainer Bischoff4, Ernst C Wit3,
Liesbeth M Veenhoff1*, Matthias Heinemann2.  ELife. 
 https://elifesciences.org/articles/08527

J Cell Biol. 2018 Jan 2;217(1):51-63. doi: 10.1083/jcb.201709072. Epub 2017 Nov 10. Pathways of cellular proteostasis in aging and disease.Klaips CL1, Jayaraj GG2, Hartl FU3.

https://www.ncbi.nlm.nih.gov/pubmed/29127110