The free radical theory of aging posits oxidative damage to macromolecules as a primary determinant of lifespan. Recent studies challenge this theory by demonstrating that in some cases, longevity is enhanced by inactivation of oxidative stress defenses or is correlated with increased, rather than decreased reactive oxygen species and oxidative damage. Here we show that, in Saccharomyces cerevisiae, caloric restriction or inactivation of catalases extends chronological lifespan by inducing elevated levels of the reactive oxygen species hydrogen peroxide, which activate superoxide dismutases that inhibit the accumulation of superoxide anions. Increased hydrogen peroxide in catalase-deficient cells extends chronological lifespan despite parallel increases in oxidative damage. These findings establish a role for hormesis effects of hydrogen peroxide in promoting longevity that have broad implications for understanding aging and age-related diseases.aging | hydrogen peroxide | hormesis | antioxidant enzymes | oxidative damage T he longstanding free radical theory has guided investigations into the causes and consequences of aging for more than 50 y (1). However, the results of a number of recent studies have failed to provide support for the free radical theory or suggest that this theory is at best incomplete (2). Studies of naked mole rats, for example, demonstrated that this extremely long-lived rodent exhibits high levels of oxidative damage compared with mice or rats, whose lifespans are ≈1/10 that of naked mole rats (3). In addition, caloric restriction (CR), which extends the lifespans of a variety of eukaryotic organisms, promotes longevity in Caenorhabditis elegans by a mechanism that involves increased oxidative stress (4). In fact, in contrast to the destructive effects of reactive oxygen species (ROS), recent evidence indicates that in mammals, hydrogen peroxide (H 2 O 2 ) and other forms of ROS function as essential secondary messengers in the regulation of a variety of physiological processes (reviewed in ref. 5). For example, H 2 O 2 activates prosurvival signaling pathways mediated by p53, NF-κB, AP-1, and other molecules (6). Furthermore, increases in the intracellular steady-state production of H 2 O 2 by SOD2 overexpression can block the activation of cellular processes required for programmed cell death (7). However, a causal relationship between CR and effects on oxidative stress has been difficult to establish.To better understand how CR impacts oxidative stress and longevity in the model organism Saccharomyces cerevisiae, in this study we examined intracellular levels of H 2 O 2 and superoxide anions (O 2 − ), which are two forms of ROS implicated in aging in all eukaryotes, under CR and other conditions. Our findings indicate that CR or inactivation of catalases extends chronological lifespan (CLS) by inducing elevated levels of H 2 O 2 , which activate superoxide dismutases that inhibit the accumulation of O 2 − . These findings establish a role for hormesis effects of H 2 O 2 in promoting l...

Human pluripotent stem cell-based in vitro models that reflect human physiology have the potential to reduce the number of drug failures in clinical trials and offer a cost-effective approach for assessing chemical safety. Here, human embryonic stem (ES) cell-derived neural progenitor cells, endothelial cells, mesenchymal stem cells, and microglia/ macrophage precursors were combined on chemically defined polyethylene glycol hydrogels and cultured in serum-free medium to model cellular interactions within the developing brain. The precursors self-assembled into 3D neural constructs with diverse neuronal and glial populations, interconnected vascular networks, and ramified microglia. Replicate constructs were reproducible by RNA sequencing (RNA-Seq) and expressed neurogenesis, vasculature development, and microglia genes. Linear support vector machines were used to construct a predictive model from RNA-Seq data for 240 neural constructs treated with 34 toxic and 26 nontoxic chemicals. The predictive model was evaluated using two standard hold-out testing methods: a nearly unbiased leave-one-out cross-validation for the 60 training compounds and an unbiased blinded trial using a single holdout set of 10 additional chemicals. The linear support vector produced an estimate for future data of 0.91 in the cross-validation experiment and correctly classified 9 of 10 chemicals in the blinded trial.organoid | machine learning | tissue engineering | differentiation | toxicology T here is a pressing need for improved methods to assess the safety of drugs and other compounds (1-5). Success rates for drug approval are declining despite higher research and development spending (6), and clinical trials often fail due to toxicities that were not identified through animal testing (7). In addition, most of the chemicals in commerce have not been rigorously assessed for safety despite growing concerns over the potential impact of industrial and environmental exposures on human health (2-5). Animal models are costly, time consuming, and fail to recapitulate many aspects of human physiology, which has motivated agencies such as the National Institutes of Health (NIH) and the US Environmental Protection Agency (EPA) to initiate programs that emphasize human cellular approaches for assessing the safety of drugs (1) and environmental chemicals (2, 3). In vitro cellular models that accurately reflect human physiology have the potential to improve the prediction of drug toxicity early in the development pipeline (1) and would provide a cost-effective approach for testing other sources of chemical exposure, including food additives, cosmetics, pesticides, and industrial chemicals (2-5).The human brain is particularly sensitive to toxic insults during development and early childhood (8), and there is growing concern that exposure to environmental chemicals may be linked to the rising incidence of neurodevelopmental disorders worldwide (4). Human brain development is mediated by highly coordinated cellular interactions between functionally ...

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The past few years have seen a surge of interest in the field of probabilistic logic learning and statistical relational learning. In this endeavor, many probabilistic logics have been developed. ProbLog is a recent probabilistic extension of Prolog motivated by the mining of large biological networks. In ProbLog, facts can be labeled with probabilities. These facts are treated as mutually independent random variables that indicate whether these facts belong to a randomly sampled program. Different kinds of queries can be posed to ProbLog programs. We introduce algorithms that allow the efficient execution of these queries, discuss their implementation on top of the YAP-Prolog system, and evaluate their performance in the context of large networks of biological entities.

Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research.

The inositolphosphosphingolipid phospholipase C (Isc1p) of Saccharomyces cerevisiae belongs to the family of neutral sphingomyelinases that generates the bioactive sphingolipid ceramide. In this work the role of Isc1p in oxidative stress resistance and chronological lifespan was investigated. Loss of Isc1p resulted in a higher sensitivity to hydrogen peroxide that was associated with an increase in oxidative stress markers, namely intracellular oxidation, protein carbonylation, and lipid peroxidation. Microarray analysis showed that Isc1p deficiency up-regulated the iron regulon leading to increased levels of iron, which is known to catalyze the production of the highly reactive hydroxyl radicals via the Fenton reaction. In agreement, iron chelation suppressed hydrogen peroxide sensitivity of isc1⌬ mutants. Cells lacking Isc1p also displayed a shortened chronological lifespan associated with oxidative stress markers and aging of parental cells was correlated with a decrease in Isc1p activity. The analysis of DNA fragmentation and caspase-like activity showed that Isc1p deficiency increased apoptotic cell death associated with oxidative stress and aging. Furthermore, deletion of Yca1p metacaspase suppressed the oxidative stress sensitivity and premature aging phenotypes of isc1⌬ mutants. These results indicate that Isc1p plays an important role in the regulation of cellular redox homeostasis, through modulation of iron levels, and of apoptosis.

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Quercetin, the major flavonol found in several fruits and vegetables, is a natural antioxidant with potential anticancer and antiaging activities. In this paper, the effect of quercetin in Sacharomyces cerevisiae cells submitted to oxidative stress was studied. Hydrogen peroxide resistance increased in cells pretreated with quercetin. Cellular protection was correlated with a decrease in oxidative stress markers, namely, levels of reactive oxygen species, glutathione oxidation, protein carbonylation, and lipid peroxidation. The acquisition of H2O2 resistance was not associated with the induction of antioxidant defenses or with iron chelation. Oxidative stress is a limiting factor for longevity. In agreement, quercetin also increased 60% chronological life span. These results support the utilization of yeast as a useful model to screen in vivo for natural antioxidants with putative health beneficial effects.