We find that the metabolome of nutrient-limited yeast varies dramatically with the limiting nutrient's identity. Low glutamine is a hallmark of nitrogen limitation, ATP of phosphorus limitation, and pyruvate of carbon limitation. The availability of these metabolites can quantitatively account for the nutrient-limited yeast's growth rate.

We conducted a phenotypic, transcriptional, metabolic, and genetic analysis of quiescence in yeast induced by starvation of prototrophic cells for one of three essential nutrients (glucose, nitrogen, or phosphate) and compared those results with those obtained with cells growing slowly due to nutrient limitation. These studies address two related questions: (1) Is quiescence a state distinct from any attained during mitotic growth, and (2) does the nature of quiescence differ depending on the means by which it is induced? We found that either limitation or starvation for any of the three nutrients elicits all of the physiological properties associated with quiescence, such as enhanced cell wall integrity and resistance to heat shock and oxidative stress. Moreover, the starvations result in a common transcriptional program, which is in large part a direct extrapolation of the changes that occur during slow growth. In contrast, the metabolic changes that occur upon starvation and the genetic requirements for surviving starvation differ significantly depending on the nutrient for which the cell is starved. The genes needed by cells to survive starvation do not overlap the genes that are induced upon starvation. We conclude that cells do not access a unique and discrete G 0 state, but rather are programmed, when nutrients are scarce, to prepare for a range of possible future stressors. Moreover, these survival strategies are not unique to quiescence, but are engaged by the cell in proportion to nutrient scarcity.

The greatest unmet needs in biomarker discovery are those discoveries that lead to the development of clinical diagnostic tests. These clinical diagnostic tests can provide early intervention when a patient would present otherwise healthy (e.g., cancer or cardiovascular disease) and aid clinical decision making with improved clinical outcomes. The past two decades have seen significant technological improvements in the analytical capabilities of mass spectrometers. Mass spectrometers are unique in that they can directly analyze any biological molecule susceptible to ionization. The biological studies of human metabolites and proteins using contemporary mass spectrometry technology (metabolomics and proteomics, respectively) has been ongoing for over a decade. Some of these studies have resulted in exciting insights into human biology. However, relatively few biomarkers have been translated into clinical tests. This review will discuss some key technological developments that have occurred over this time with an emphasis on technologies that will create new avenues for biomarker discovery.

Survival of yeast during starvation has been shown to depend on the nature of the missing nutrient(s). In general, starvation for "natural" nutrients such as sources of carbon, phosphate, nitrogen, or sulfate results in low death rates, whereas starvation for amino acids or other metabolites in auxotrophic mutants results in rapid loss of viability. Here we characterized phenotype, gene expression, and metabolite abundance during starvation for methionine. Some methionine auxotrophs (those with blocks in the biosynthetic pathway) respond to methionine starvation like yeast starving for natural nutrients such as phosphate or sulfate: they undergo a uniform cell cycle arrest, conserve glucose, and survive. In contrast, methionine auxotrophs with defects in the transcription factors Met31p and Met32p respond poorly, like other auxotrophs. We combined physiological and gene expression data from a variety of nutrient starvations (in both respiratory competent and incompetent cells) to show that successful starvation response is correlated with expression of genes encoding oxidative stress response and nonrespiratory mitochondrial functions, but not respiration per se.U nderstanding global coordination of subcellular processes during adaptation to environmental change is a central challenge in systems biology. The ability of free-living organisms to adapt to changes in their nutritional environment is clearly one of the driving forces of their evolution. In natural environments, yeast are exposed to extreme variations in "natural nutrient" availability, particularly in their sources of carbon (and energy), phosphorus, sulfur, and nitrogen. Unlike wild type strains, auxotrophic mutant yeast strains unable to make an essential metabolite (e.g., leucine or uracil) can also be starved for the missing metabolite, but adaptation to this kind of "nonnatural" starvation has not been subject to evolutionary selection. Starvation of Saccharomyces cerevisiae for a single, growth-limiting nutrient offers the opportunity to study the coordination of nutrient sensing, metabolism, growth, and cell division. Proper coordination results in prolonged survival, concerted cell cycle arrest, and glucose conservation during starvation, and depends strongly on the specific nutrient being depleted. For instance, the survival of auxotrophic yeast starved for leucine, histidine, or uracil is substantially impaired (exhibiting a roughly 10-fold difference in half-life) relative to the same strain starved for the "natural" nutrients sulfate or phosphate (1). Starvation for sulfate or phosphate elicits rapid, nearly uniform G0/G1 cell cycle arrest and slows glucose consumption, whereas starvation for leucine, histidine, or uracil results in incomplete cell cycle arrest and markedly higher rates of glucose consumption.We are interested in understanding what, if any, general principles determine starvation phenotype. Early work on nutrient starvation posited the existence of a starvation "signal" that promotes concerted cell cycle arrest and surviv...

Experimental NMR diffusion measure on polymers and on globular proteins are presented. These results, complemented with results found in the literature, enable a general description of effective fractal dimension for objects such as small organic molecules, sugars, polymers, DNA, and proteins. Results are compared to computational simulations as well as to theoretical values. A global picture of the diffusion phenomenon emerges from this description. A power law relating molecular mass with diffusion coefficients is described and found to be valid over 4 orders of magnitude. From this law, the fractal dimension of the molecular family can be measured, with experimental values ranging from 1.41 to 2.56 in full agreement with theoretical approaches. Finally, a method for evaluating the molecular mass of unknown solutes is described and implemented as a Web page.

Since previous evidence has demonstrated that red blood cell distribution width (RDW) may be a useful prognostic parameter in many critical illnesses and infectious diseases, we investigated the utility of RDW for monitoring patients with coronavirus disease 2019 (COVID-19). The study population consisted of 49 COVID-19 patients, including 16 (32.6%) with severe illness, 12 (24.5%) with severe acute kidney injury (AKI), and 8 (16.3%) requiring renal replacement therapy (RRT). The predictive value of blood tests, performed during emergency department evaluation, was then addressed. A progressive increase of RDW was observed with advancing COVID-19 severity. The area under the curve (AUC) of RDW was 0.73 for predicting severe illness, 0.80 for severe AKI, and 0.83 for RRT, respectively. In multivariate analysis, elevated RDW was associated with 9-fold and 16-fold increased odds of severe COVID-19 and AKI, respectively. The results of this study suggest that RDW should be part of routine laboratory assessment and monitoring of COVID-19.

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Pulsed-field gradient (PFG) 1H and 31P NMR methods were developed to quantitatively estimate the molecular mass of compounds, derivatized with either trichloroacetyl isocyanate (TAI) or 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (chlorophospholane). These agents provide selective analysis with high sensitivity for molecules containing alcohol, amine, carboxylic acid, or thiol functional groups. Tetramethylsilane (TMS) or bisphenol A was used as internal diffusion reference. The empirical relationship between relative diffusivity and molecular mass was established for a set of mono- and difunctional compounds with molecular masses in the range 32-330 g/mol. The utility of the method was demonstrated by analyzing alcohol, phenol, and carboxylic acid components in lubricating oil.