John L. Hartman
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View article: Referee report. For: Exploring the anti-aging potential of natural products and plant extracts in budding yeast Saccharomyces cerevisiae: A review [version 1; peer review: 1 approved, 1 approved with reservations]
Referee report. For: Exploring the anti-aging potential of natural products and plant extracts in budding yeast Saccharomyces cerevisiae: A review [version 1; peer review: 1 approved, 1 approved with reservations] Open
View article: University of Alabama at Birmingham Nathan Shock Center: comparative energetics of aging
University of Alabama at Birmingham Nathan Shock Center: comparative energetics of aging Open
View article: A cell-nonautonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism
A cell-nonautonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism Open
Caloric restriction (CR) improves health span and life span of organisms ranging from yeast to mammals. Understanding the mechanisms involved will uncover future interventions for aging-associated diseases. In budding yeast, Saccharomyces …
View article: High-resolution yeast quiescence profiling in human-like media reveals complex influences of auxotrophy and nutrient availability
High-resolution yeast quiescence profiling in human-like media reveals complex influences of auxotrophy and nutrient availability Open
View article: A cell non-autonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism
A cell non-autonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism Open
Caloric restriction (CR) improves healthspan and lifespan of organisms ranging from yeast to mammals. Understanding the mechanisms involved will uncover future interventions for aging associated diseases. In budding yeast, Saccharomyces ce…
View article: High-resolution yeast quiescence profiling in human-like media reveals interacting influences of auxotrophy and nutrient availability
High-resolution yeast quiescence profiling in human-like media reveals interacting influences of auxotrophy and nutrient availability Open
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 knoc…
View article: Interplay of mitochondrial fission-fusion with cell cycle regulation: Possible impacts on stem cell and organismal aging
Interplay of mitochondrial fission-fusion with cell cycle regulation: Possible impacts on stem cell and organismal aging Open
View article: Slowing ribosome velocity restores folding and function of mutant CFTR
Slowing ribosome velocity restores folding and function of mutant CFTR Open
Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR), with approximately 90% of patients harboring at least one copy of the disease-associated variant F508del. We utilized a yeast phenomic system…
View article: A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
View article: A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity
A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity Open
Knowledge about synthetic lethality can be applied to enhance the efficacy of anticancer therapies in individual patients harboring genetic alterations in their cancer that specifically render it vulnerable. We investigated the potential f…
View article: A humanized yeast phenomic model of deoxycytidine kinase to predict genetic buffering of nucleoside analog cytotoxicity
A humanized yeast phenomic model of deoxycytidine kinase to predict genetic buffering of nucleoside analog cytotoxicity Open
Knowledge about synthetic lethality can be applied to enhance the efficacy of anti-cancer therapies in individual patients harboring genetic alterations in their cancer that specifically render it vulnerable. We investigated the potential …
View article: A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Background Saccharomyces cerevisiae represses respiration in the presence of adequate glucose, mimicking the Warburg effect, termed aerobic glycolysis. We conducted yeast phenomic experiments to characterize differential doxorubicin-gene i…
View article: MOESM7 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
MOESM7 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Additional file 7. Systematic comparisons involving genome-wide studies of doxorubicin-gene interaction. Table S9. Genes with deletion-enhancing doxorubicin-gene interaction from Xia et al. 2007 and Westmoreland et al. 2009. Table S10. Sum…
View article: MOESM4 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
MOESM4 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Additional file 4. Interaction plots for HLD. (A, B) Genome-wide and (C, D) validation analyses. (A, C) YKO/KD and (B, D) reference strains in HLD media. See also methods and Additional file 2.
View article: MOESM2 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
MOESM2 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Additional file 2. Doxorubicin-gene interaction data; Tables S1-S8. Tables S1-S4 are the genome-wide experiment: Table S1. YKO/KD strains in HLEG. Table S2. Reference cultures in HLEG. Table S3. YKO/KD strains in HLD. Table S4. Reference c…
View article: MOESM9 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
MOESM9 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Additional file 9. GO term-specific heatmaps for REMc/GTF-enriched clusters. GO term-specific heatmaps for significant GO process terms were generated as described in methods and Figs. 3 and 4. Any related child terms are presented in subs…
View article: MOESM12 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
MOESM12 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Additional file 12. Comparisons between yeast studies of doxorubicin in the context of integrating cancer pharmacogenomics data. Overlapping and unique sets of genes reported from the different studies of doxorubicin, using the YKO/KD libr…
View article: MOESM8 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
MOESM8 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Additional file 8. Quantitative summaries of REMc clusters. File A depicts REMc results, in terms of cluster distributions of L and K interaction (â shiftâ is not used for REMc and thus is not displayed), as a way to visualize cluster diff…
View article: MOESM5 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
MOESM5 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Additional file 5. REMc results with doxorubicin-gene interaction profile heatmaps and Gene Ontology enrichment (GO Term Finder; GTF) results. File A contains REMc results and associated gene interaction and shift data. File B is the heatm…
View article: MOESM11 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
MOESM11 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Additional file 11. Integration of yeast phenomic and cancer cell line pharmacogenomic data to predict human genes that modify doxorubicin toxicity in cancer cells. (A) Tables of UES and OES human genes and whether their yeast homologs wer…
View article: MOESM3 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
MOESM3 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Additional file 3. Interaction plots for HLEG. (A, B) Genome-wide and (C, D) validation analyses for (A, C) YKO/KD and (B, D) reference strains in HLEG. See also methods and Additional file 2.
View article: MOESM6 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
MOESM6 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Additional file 6. Gene Ontology Term Averaging (GTA) results and interactive plots. File A contains all GTA values, cross-referenced with REMc-enriched terms. File B displays GTA values associated with above-threshold GTA scores (see note…
View article: MOESM10 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin
MOESM10 of A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Open
Additional file 10: Table S13. HLD-specific gene deletion enhancement, not associated with ‘shift’ / growth deficiency. Data were selected for yeast-human homologs if the respective YKO/KD strains generated growth curves in both HLD and HL…
View article: Ribosomal Stalk Protein Silencing Partially Corrects the ΔF508-CFTR Functional Expression Defect
Ribosomal Stalk Protein Silencing Partially Corrects the ΔF508-CFTR Functional Expression Defect Open
The most common cystic fibrosis (CF) causing mutation, deletion of phenylalanine 508 (ΔF508 or Phe508del), results in functional expression defect of the CF transmembrane conductance regulator (CFTR) at the apical plasma membrane (PM) of s…
View article: Gene-nutrient interaction markedly influences yeast chronological lifespan
Gene-nutrient interaction markedly influences yeast chronological lifespan Open
View article: Long‐range coupling between the extracellular gates and the intracellular ATP binding domains of multidrug resistance protein pumps and cystic fibrosis transmembrane conductance regulator channels
Long‐range coupling between the extracellular gates and the intracellular ATP binding domains of multidrug resistance protein pumps and cystic fibrosis transmembrane conductance regulator channels Open
The ABCC transporter subfamily includes pumps, the long and short multidrug resistance proteins (MRPs), and an ATP‐gated anion channel, the cystic fibrosis transmembrane conductance regulator (CFTR). We show that despite their thermodynami…
View article: Yeast Phenomics: An Experimental Approach for Modeling Gene Interaction Networks that Buffer Disease
Yeast Phenomics: An Experimental Approach for Modeling Gene Interaction Networks that Buffer Disease Open
The genome project increased appreciation of genetic complexity underlying disease phenotypes: many genes contribute each phenotype and each gene contributes multiple phenotypes. The aspiration of predicting common disease in individuals h…