Evidence map›Paper›PMID 33015753›Full record

ArticleGeroScience2021

High-resolution yeast quiescence profiling in human-like media reveals complex influences of auxotrophy and nutrient availability.

Sean M Santos, Samantha Laflin, Audrie Broadway, Cosby Burnet, Joline Hartheimer, John Rodgers, Daniel L Smith, John L Hartman

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in GeroScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed, 1 pooled it
0.5field-weighted citation impact, top 37% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed, 1 synthesis or guideline pooled it, 10 citations in OpenAlex.

  1. Pooled it
  2. Review
  3. BY4741 cannot enter quiescence from rich medium.microPublication biology · 2023
    Article
  4. Review
  5. Quiescence inAnnual review of genetics · 2022
    Review
  6. Cellular quiescence in budding yeast.Yeast (Chichester, England) · 2021
    Review
  7. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 1 institution in 1 country.

Sean M SantosDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
Samantha LaflinDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
Audrie BroadwayDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
Cosby BurnetDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
Joline HartheimerDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
John RodgersDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
Daniel L SmithDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
John L HartmanDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA. jhartman@uab.edu.ORCID http://orcid.org/0000-0003-1176-6469
University of Alabama at Birmingham · US

Funding

Why is the prevalence of obesity so high in U.S. Southern States? Regional predictors of BMI and obesity treatment response.P30DK056336 · NIDDK · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI BARBARA A GOWER · 2000 to 2026
$31.9M
Constructing gene-regulatory networks to reveal the metabolic basis of lifespan in yeastR01AG043076 · NIA · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI HARTMAN, JOHN L · 2012 to 2016
$1.9M
Systems level analysis of the interplay between metabolism, cell-cell communication, and agingR56AG059590 · NIA · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI HARTMAN, JOHN L, SMITH, JEFFREY SCOTT · 2018 to 2018
$377k
NIA NIH HHS R01 AG043076NIA NIH HHS R56 AG059590NIDDK NIH HHS P30 DK056336
6 · The paper itself

Abstract

Yeast cells survive in stationary phase culture by entering quiescence, which is measured by colony-forming capacity upon nutrient re-exposure. Yeast chronological lifespan (CLS) studies, employing the comprehensive collection of gene knockout strains, have correlated weakly between independent laboratories, which is hypothesized to reflect differential interaction between the deleted genes, auxotrophy, media composition, and other assay conditions influencing quiescence. This hypothesis was investigated by high-throughput quiescence profiling of the parental prototrophic strain, from which the gene deletion strain libraries were constructed, and all possible auxotrophic allele combinations in that background. Defined media resembling human cell culture media promoted long-term quiescence and was used to assess effects of glucose, ammonium sulfate, auxotrophic nutrient availability, target of rapamycin signaling, and replication stress. Frequent, high-replicate measurements of colony-forming capacity from cultures aged past 60 days provided profiles of quiescence phenomena such as gasping and hormesis. Media acidification was assayed in parallel to assess correlation. Influences of leucine, methionine, glucose, and ammonium sulfate metabolism were clarified, and a role for lysine metabolism newly characterized, while histidine and uracil perturbations had less impact. Interactions occurred between glucose, ammonium sulfate, auxotrophy, auxotrophic nutrient limitation, aeration, TOR signaling, and/or replication stress. Weak correlation existed between media acidification and maintenance of quiescence. In summary, experimental factors, uncontrolled across previous genome-wide yeast CLS studies, influence quiescence and interact extensively, revealing quiescence as a complex metabolic and developmental process that should be studied in a prototrophic context, omitting ammonium sulfate from defined media, and employing highly replicable protocols.

Indexed as

LongevitySaccharomyces cerevisiaeAgedCulture MediaGlucoseHumansNutrientsCulture MediaGlucoseNutrientsGene-nutrient interactionHuman-like (HL) yeast mediaQuantitative high-throughput cell array phenotyping (Q-HTCP)Quiescence profilingYeast chronological lifespan (CLS)

Identifiers

PMID33015753
PMCPMC8110628
OpenAlexW3091288620

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.