Science in the Public Mind: sources and consequences of antipathy.

Public attitudes toward science in the United States can profoundly affect national well-being, and even national security. We live in a time when these attitudes are considerably more negative than usual. This critical assessment identifies a number of contributors to public antipathy toward science, some of which are intrinsic to the nature of science and as old as science itself, and some of which are external to science, have arisen recently, and may be unique to the present. Historic examples of scientific developments and challenges and two major current examples (the COVID-19 pandemic and anthropogenic climate change) illustrate the interplay of science and public attitudes and actions, and the development and consequences of antipathy toward science. The problem areas that contribute to public antipathy in turn suggest strategies that may mitigate the antipathy, although some social and political factors will impose limits on possible mitigation. The energy required to sustain an acceptable level of civilization needs to be acknowledged, along with the need to minimize anthropogenic climate change.

Investigating the role of the transcriptional regulator Ure2 on the metabolism of Saccharomyces cerevisiae: a multi-omics approach.

Ure2 regulates nitrogen catabolite repression in Saccharomyces cerevisiae. Deletion of URE2 induces a physiological state mimicking the nitrogen starvation and autophagic responses. Previous work has shown that deletion of URE2 increases the fermentation rate of some wine-producing strains of S. cerevisiae. In this work, we investigated the effect of URE2 deletion (ΔURE2) on the metabolism of S. cerevisiae. During growth on glucose, the ΔURE2 mutant grew at a 40% slower rate than the wild type; however, it produced ethanol at a 31% higher rate. To better under the behavior of this mutant, we performed transcriptomics and metabolomics. Analysis of the RNA sequencing results and metabolite levels indicates that the mutant strain exhibited characteristics of both nitrogen starvation and autophagy, including the upregulation of allantoin, urea, and amino acid uptake and utilization pathways and selective autophagic machinery. In addition, pyruvate decarboxylase and alcohol dehydrogenase isoforms were expressed at higher rates than the wild type. The mutant also accumulated less trehalose and glycogen, and produced more lipids. The induction of a nitrogen starvation-like state and increase in lipid production in nitrogen-rich conditions suggest that URE2 may be a promising target for metabolic engineering in S. cerevisiae and other yeasts for the production of lipids and lipid-derived compounds. KEY POINTS: • Deletion of URE2 increases ethanol and lipid production in Saccharomyces cerevisiae. • Deletion of URE2 reduces glycogen and trehalose production. • Metabolic changes mimic nitrogen starvation and autophagic response.

The pathway of O2to the active site in heme-copper oxidases.

The route of O2to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (CO). Time-resolved and stationary infrared experiments in our laboratories of the fully reduced CO-bound enzymes, as well as transient optical absorption saturation kinetics studies as a function of CO pressure, have provided strong support for CO binding to CuB⁺ on the pathway to and from the high-spin heme. The presence of CO on CuB⁺ suggests that O2binding may be compromised in CO flow-flash experiments. Time-resolved optical absorption studies show that the rate of O2and NO binding in the bovine enzyme (1 × 108M⁻¹s⁻¹) is unaffected by the presence of CO, which is consistent with the rapid dissociation (t½ = 1.5µs) of CO from CuB⁺. In contrast, in Thermus thermophilus (Tt) cytochrome ba3 the O2and NO binding to heme a3 slows by an order of magnitude in the presence of CO (from 1 × 109 to 1 × 108M⁻¹s⁻¹), but is still considerably faster (~10µs at 1atm O2) than the CO off-rate from CuB in the absence of O2(milliseconds). These results show that traditional CO flow-flash experiments do not give accurate results for the physiological binding of O2and NO in Tt ba3, namely, in the absence of CO. They also raise the question whether in CO flow-flash experiments on Tt ba3 the presence of CO on CuB⁺ impedes the binding of O2to CuB⁺ or, if O2does not bind to CuB⁺ prior to heme a3, whether the CuB⁺-CO complex sterically restricts access of O2to the heme. Both possibilities are discussed, and we argue that O2binds directly to heme a3 in Tt ba3, causing CO to dissociate from CuB⁺ in a concerted manner through steric and/or electronic effects. This would allow CuB⁺ to function as an electron donor during the fast (5µs) breaking of the OO bond. These results suggest that the binding of CO to CuB⁺ on the path to and from heme a3 may not be applicable to O2and NO in all heme-copper oxidases. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

Scale-up of microbial lipid and bioethanol production from oilcane.

Microbial oils are a sustainable biomass-derived substitute for liquid fuels and vegetable oils. Oilcane, an engineered sugarcane with superior feedstock characteristics for biodiesel production, is a promising candidate for bioconversion. This study describes the processing of oilcane stems into juice and hydrothermally pretreated lignocellulosic hydrolysate and their valorization to ethanol and microbial oil using Saccharomyces cerevisiae and engineered Rhodosporidium toruloides strains, respectively. A bioethanol titer of 106 g/L was obtained from S. cerevisiae grown on oilcane juice in a 3 L fermenter, and a lipid titer of 8.8 g/L was obtained from R. toruloides grown on oilcane hydrolysate in a 75 L fermenter. Oil was extracted from the R. toruloides cells using supercritical CO2, and the observed fatty acid profile was consistent with previous studies on this strain. These results demonstrate the feasibility of pilot-scale lipid production from oilcane hydrolysate as part of an integrated bioconversion strategy.

Tolerance of engineered Rhodosporidium toruloides to sorghum hydrolysates during batch and fed-batch lipid production.

BACKGROUND: Oleaginous yeasts are a promising candidate for the sustainable conversion of lignocellulosic feedstocks into fuels and chemicals, but their growth on these substrates can be inhibited as a result of upstream pretreatment and enzymatic hydrolysis conditions. Previous studies indicate a high citrate buffer concentration during hydrolysis inhibits downstream cell growth and ethanol fermentation in Saccharomyces cerevisiae. In this study, an engineered Rhodosporidium toruloides strain with enhanced lipid accumulation was grown on sorghum hydrolysate with high and low citrate buffer concentrations. RESULTS: Both hydrolysis conditions resulted in similar sugar recovery rates and concentrations. No significant differences in cell growth, sugar utilization rates, or lipid production rates were observed between the two citrate buffer conditions during batch fermentation of R. toruloides. Under fed-batch growth on low-citrate hydrolysate a lipid titer of 16.7 g/L was obtained. CONCLUSIONS: Citrate buffer was not found to inhibit growth or lipid production in this engineered R. toruloides strain, nor did reducing the citrate buffer concentration negatively affect sugar yields in the hydrolysate. As this process is scaled-up, $131 per ton of hydrothermally pretreated biomass can be saved by use of the lower citrate buffer concentration during enzymatic hydrolysis.

Nature of bonding in complexes containing "supershort" metal-metal bonds. raman and theoretical study of M2(dmp)4 [M = Cr (natural abundance Cr, 50Cr, and 54Cr) and Mo; dmp = 2,6-dimethoxyphenyl].

We report an investigation of complexes of the type M(2)(dmp)(4) (M = Mo, Cr; dmp = 2,6-dimethoxyphenyl) using resonance Raman (RR) spectroscopy, Cr isotopic substitution, and density functional theory (DFT) calculations. Assignment of the Mo-Mo stretching vibration in the Mo(2) species is straightforward, as evidenced by a single resonance-enhanced band at 424 cm(-1), consistent with an essentially unmixed metal-metal stretch, and overtones of this vibration. On the other hand, the Cr(2) congener has no obvious metal-metal stretching mode near 650-700 cm(-1), where empirical predictions based on the Cr-Cr distance as well as DFT calculations suggest that this vibration should appear if unmixed. Instead, three bands are observed at 345, 363, and 387 cm(-1) that (a) have relative RR intensities that are sensitive to the Raman excitation frequency, (b) exhibit overtones and combinations in the RR spectra, and (c) shift in frequency upon isotopic substitution ((50)Cr and (54)Cr). DFT calculations are used to model the vibrational data for the Mo(2) and Cr(2) systems. Both the DFT results and empirical predictions are in good agreement with experimental observations in the Mo(2) complex, but both, while mutually consistent, differ radically from experiment in the Cr(2) complex. Our experimental and theoretical results, especially the Cr isotope shifts, clearly demonstrate that the potential energy of the Cr-Cr stretching coordinate is distributed among several normal modes having both Cr-Cr and Cr-ligand character. The general significance of these results in interpreting spectroscopic observations in terms of the nature of metal-metal multiple bonding is discussed.

Revisiting a model of ontogenetic growth: estimating model parameters from theory and data.

The ontogenetic growth model (OGM) of West et al. provides a general description of how metabolic energy is allocated between production of new biomass and maintenance of existing biomass during ontogeny. Here, we reexamine the OGM, make some minor modifications and corrections, and further evaluate its ability to account for empirical variation on rates of metabolism and biomass in vertebrates both during ontogeny and across species of varying adult body size. We show that the updated version of the model is internally consistent and is consistent with other predictions of metabolic scaling theory and empirical data. The OGM predicts not only the near universal sigmoidal form of growth curves but also the M(1/4) scaling of the characteristic times of ontogenetic stages in addition to the curvilinear decline in growth efficiency described by Brody. Additionally, the OGM relates the M(3/4) scaling across adults of different species to the scaling of metabolic rate across ontogeny within species. In providing a simple, quantitative description of how energy is allocated to growth, the OGM calls attention to unexplained variation, unanswered questions, and opportunities for future research.

Diffuse neurofibrillary tangles with calcification (DNTC): Kosaka-Shibayama disease in America.

Alzheimer's disease and Pick's disease are representative dementias. Cases which do not fit prototypes are termed unclassifiable dementias. New dementia subtypes are identified when a conglomerate of clinical, radiologic and pathologic findings are consistently identified. One such variant is diffuse neurofibrillary tangles with calcification (DNTC), which has been reported almost exclusively from Japan. Significant pathological advances in this decade have established DNTC as a distinct entity. Although initially the diagnosis was neuropathologic, increasing knowledge about DNTC has made it possible for a clinical diagnosis to be made. We report a clinical case of DNTC in a Caucasian American. The diagnosis of DNTC was based on his atypical senile dementia, anomia, apathy and parkinsonian features, normal serum biochemistry, and evidence of basal ganglia and cerebellar calcification with predominant temporal lobe atrophy on neuroimaging. To the best of our knowledge, this is the first clinical description of DNTC from the United States.

FTIR studies of internal proton transfer reactions linked to inter-heme electron transfer in bovine cytochrome c oxidase.

FTIR difference spectroscopy is used to reveal changes in the internal structure and amino acid protonation states of bovine cytochrome c oxidase (CcO) that occur upon photolysis of the CO adduct of the two-electron reduced (mixed valence, MV) and four-electron reduced (fully reduced, FR) forms of the enzyme. FTIR difference spectra were obtained in D(2)O (pH 6-9.3) between the MV-CO adduct (heme a(3) and Cu(B) reduced; heme a and Cu(A) oxidized) and a photostationary state in which the MV-CO enzyme is photodissociated under constant illumination. In the photostationary state, part of the enzyme population has heme a(3) oxidized and heme a reduced. In MV-CO, the frequency of the stretch mode of CO bound to ferrous heme a(3) decreases from 1965.3 cm(-1) at pH*

Fast photoreduction of a heme peptide encapsulated in nanostructured materials.

Microperoxidase-11 has been immobilized on siliceous materials MCM-41 and SBA-15 and on amino-functionalized SBA-15. Resonance Raman spectroscopy has provided solid evidence that the exogenous species occupy the pores of the mesoporous silica materials. Photoreduction of the microperoxidase-11 Fe(III) center has been observed to occur in the immobilized samples and results in a long-lived stable reduced heme. Reoxidation of the heme occurs upon addition of oxygen, and the redox cycle can be repeated numerous times. The source of the electron resulting in reduction of the heme is proposed to originate from the silica matrix, and functionalization of silica surface is suggested to facilitate electron transfer to the heme.

Resonance Raman and X-ray Crystallographic Studies of Intertriad Metal-Metal Bonds. 2. WRu and MoOs Porphyrin Dimers.

Solution ((1)H NMR, Evans method magnetic susceptibility, resonance Raman) and X-ray crystallographic spectroscopic studies of intertriad heterodimeric [(OEP)MoOs(OEP)] (3), [(OEP)WRu(OEP)] (4), [(OEP)MoOs(TPP)]PF(6) (5(+)), and [(OEP)WRu(TPP)]PF(6) (6(+)) metalloporphyrins are reported (OEP = 2,3,7,8,12,13,17,18-octaethylporphyrinato; TPP = 5,10,15,20-tetraphenylporphyrinato). Evans method magnetic susceptibility data indicate that 3 and 4 contain two unpaired electrons in the ground electronic configuration. Resonance Raman spectra of 3, 4, 5(+), and 6(+) suggest that WRu bonds are 5-10% stronger than corresponding MoOs species. Structural characterization of 5(+) and 6(+) demonstrates metal-metal bond lengths of 2.30 (WRu) and 2.24 (MoOs) Å, respectively. The possibility of a special stability associated with polar heterometallic multiple bonds is discussed.

Resonance Raman Spectra of [M(6)X(8)Y(6)](2)(-) Cluster Complexes (M = Mo, W; X, Y = Cl, Br, I).

Resonance Raman spectra of the cubic metal-halide complexes having the general formula [M(6)X(8)Y(6)](2)(-) (M = Mo or W; X, Y = Cl, Br, or I) are reported. The three totally symmetric fundamental vibrations of these complexes are identified. The extensive mixing of the symmetry coordinates that compose the symmetric normal modes expected in these systems is not observed. Instead the "group-frequency" approximation is valid. Furthermore, the force constants of both the apical and face-bridging metal-halide bonds are insensitive to the identity of either the metal or the halide. Raman spectra of related complexes with methoxy and benzenethiol groups as ligands are reported along with the structural data for [Mo(6)Cl(8)(SPh)(6)][NBu(4)](2). Crystal data for [Mo(6)Cl(8)(SPh)(6)][NBu(4)](2) at -156 degrees C: monoclinic space group P2(1)/c; a = 12.588(3), b = 17.471(5), c = 20.646(2) Å; beta = 118.53(1) degrees, V = 3223.4 Å(3); d(calcd) = 1.664 g cm(-)(3); Z = 2.

Resonance Raman, X-ray Crystallographic, and Magnetic Susceptibility Studies of Metal-Metal-Bonded MoRu and WOs Porphyrin Dimers. 1. Evidence for an Unusual MO Diagram.

Solution (VT NMR, Evans method magnetic susceptibility, resonance Raman) and solid-state (SQUID magnetic susceptibility, X-ray crystallography) spectroscopic studies of intertriad heterodimeric [(OEP)MoRu(OEP)] (1), [(OEP)WOs(OEP)] (2), and [(OEP)MoRu(TPP)]PF(6) (3(+)) metalloporphyrins are reported (OEP = 2,3,7,8,12,13,17,18-octaethylporphyrinato; TPP = 5,10,15,20-tetraphenylporphyrinato). Solution and solid-state magnetic susceptibility data indicate that 1 and 2 contain two unpaired electrons in the ground electronic configuration. The presence of a delta bond in 3(+) has been confirmed by structural characterization. The experimental evidence is consistent with a molecular orbital ordering, sigma < pi < delta < pi < delta, which is different from that seen for homologous metalloporphyrin dimers with homometallic or intratriad heterometallic multiple metal-metal bonds. Resonance Raman data suggest that the heterometallic bonds are slightly stronger than isoelectronic homometallic species.

Differential immunotoxicity induced by two different windows of developmental trichloroethylene exposure.

Developmental exposure to environmental toxicants may induce immune system alterations that contribute to adult stage autoimmune disease. We have shown that continuous exposure of MRL+/+ mice to trichloroethylene (TCE) from gestational day (GD) 0 to postnatal day (PND) 49 alters several aspects of CD4(+) T cell function. This window of exposure corresponds to conception-adolescence/young adulthood in humans. More narrowly defining the window of TCE developmental exposure causes immunotoxicity that would establish the stage at which avoidance and/or intervention would be most effective. The current study divided continuous TCE exposure into two separate windows, namely, gestation only (GD0 to birth (PND0)) and early-life only (PND0-PND49). The mice were examined for specific alterations in CD4(+) T cell function at PND49. One potentially long-lasting effect of developmental exposure, alterations in retrotransposon expression indicative of epigenetic alterations, was found in peripheral CD4(+) T cells from both sets of developmentally exposed mice. Interestingly, certain other effects, such as alterations in thymus cellularity, were only found in mice exposed to TCE during gestation. In contrast, expansion of memory/activation cell subset of peripheral CD4(+) T cells were only found in mice exposed to TCE during early life. Different windows of developmental TCE exposure can have different functional consequences.

Acoustic levels of heavy truck tire ruptures.

Transportation vehicles, whether they are passenger vehicles or heavy trucks and transport vehicles, rely upon rubber tires to negotiate the roadways and surfaces on which they are driven. These tires have the potential of sudden rupture resulting from various causes including but not limited to over-pressurization, sidewall failures, or punctures from roadway debris. These rupture events can and do occur while the vehicles are stationary (e.g., during servicing) or are being driven, and often occur without notice. While the phenomenon of sudden tire failure has been documented for several decades, the potential bodily injury which can occur when an individual is in close proximity to such a sudden rupture has only more recently been documented. Aside from anecdotal mention in case studies, there has been little quantitative information available on the acoustic levels during these failures. Our study provides measured acoustic levels as a function of distance for such catastrophic tire failures.

A phenomenological mixture model for biosynthesis and linking of cartilage extracellular matrix in scaffolds seeded with chondrocytes.

A phenomenological mixture model is presented for interactions between biosynthesis of extracellular matrix (ECM) constituents and ECM linking in a scaffold seeded with chondrocytes. A system of three ordinary differential equations for average apparent densities of unlinked ECM, linked ECM and scaffold is developed along with associated initial conditions for scaffold material properties. Equations for unlinked ECM synthesis and ECM linking include an inhibitory mechanism where associated rates decrease as unlinked ECM concentration in the interstitial fluid increases. Linking rates are proposed to depend on average porosity in the evolving tissue construct. The resulting initial value problem contains nine independent parameters that account for scaffold biomaterial properties and interacting mechanisms in the engineered system. Effects of parameter variations on model variables are analyzed relative to a baseline case with emphasis on the evolution of solid phase apparent density, which is often correlated with the compressive elastic modulus of the tissue construct. The new model provides an additional quantitative framework for assessing and optimizing the design of engineered cell-scaffold systems and guiding strategies for articular cartilage tissue engineering.

Energy uptake and allocation during ontogeny.

All organisms face the problem of how to fuel ontogenetic growth. We present a model, empirically grounded in data from birds and mammals, that correctly predicts how growing animals allocate food energy between synthesis of new biomass and maintenance of existing biomass. Previous energy budget models have typically had their bases in rates of either food consumption or metabolic energy expenditure. Our model provides a framework that reconciles these two approaches and highlights the fundamental principles that determine rates of food assimilation and rates of energy allocation to maintenance, biosynthesis, activity, and storage. The model predicts that growth and assimilation rates for all animals should cluster closely around two universal curves. Data for mammals and birds of diverse body sizes and taxa support these predictions.

Scaling of number, size, and metabolic rate of cells with body size in mammals.

The size and metabolic rate of cells affect processes from the molecular to the organismal level. We present a quantitative, theoretical framework for studying relationships among cell volume, cellular metabolic rate, body size, and whole-organism metabolic rate that helps reveal the feedback between these levels of organization. We use this framework to show that average cell volume and average cellular metabolic rate cannot both remain constant with changes in body size because of the well known body-size dependence of whole-organism metabolic rate. Based on empirical data compiled for 18 cell types in mammals, we find that many cell types, including erythrocytes, hepatocytes, fibroblasts, and epithelial cells, follow a strategy in which cellular metabolic rate is body size dependent and cell volume is body size invariant. We suggest that this scaling holds for all quickly dividing cells, and conversely, that slowly dividing cells are expected to follow a strategy in which cell volume is body size dependent and cellular metabolic rate is roughly invariant with body size. Data for slowly dividing neurons and adipocytes show that cell volume does indeed scale with body size. From these results, we argue that the particular strategy followed depends on the structural and functional properties of the cell type. We also discuss consequences of these two strategies for cell number and capillary densities. Our results and conceptual framework emphasize fundamental constraints that link the structure and function of cells to that of whole organisms.

The metabolic basis of whole-organism RNA and phosphorus content.

Understanding the storage, flux, and turnover of nutrients in organisms is important for quantifying contributions of biota to biogeochemical cycles. Here we present a model that predicts the storage of phosphorus-rich RNA and whole-body phosphorus content in eukaryotes based on the mass- and temperature-dependence of ATP production in mitochondria. Data from a broad assortment of eukaryotes support the model's two main predictions. First, whole-body RNA concentration is proportional to mitochondrial density and consequently scales with body mass to the -1/4 power. Second, whole-body phosphorus content declines with increasing body mass in eukaryotic unicells but approaches a relatively constant value in large multicellular animals because the fraction of phosphorus in RNA decreases relative to the fraction in other pools. Extension of the model shows that differences in the flux of RNA-associated phosphorus are due to the size dependencies of metabolic rate and RNA concentration. Thus, the model explicitly links two biological currencies at the individual level: energy in the form of ATP and materials in the form of phosphorus, both of which are critical to the functioning of ecosystems. The model provides a framework for linking attributes of individuals to the storage and flux of phosphorus in ecosystems.

Allometric scaling of metabolic rate from molecules and mitochondria to cells and mammals.

The fact that metabolic rate scales as the three-quarter power of body mass (M) in unicellular, as well as multicellular, organisms suggests that the same principles of biological design operate at multiple levels of organization. We use the framework of a general model of fractal-like distribution networks together with data on energy transformation in mammals to analyze and predict allometric scaling of aerobic metabolism over a remarkable 27 orders of magnitude in mass encompassing four levels of organization: individual organisms, single cells, intact mitochondria, and enzyme molecules. We show that, whereas rates of cellular metabolism in vivo scale as M(-1/4), rates for cells in culture converge to a single predicted value for all mammals regardless of size. Furthermore, a single three-quarter power allometric scaling law characterizes the basal metabolic rates of isolated mammalian cells, mitochondria, and molecules of the respiratory complex; this overlaps with and is indistinguishable from the scaling relationship for unicellular organisms. This observation suggests that aerobic energy transformation at all levels of biological organization is limited by the transport of materials through hierarchical fractal-like networks with the properties specified by the model. We show how the mass of the smallest mammal can be calculated (approximately 1 g), and the observed numbers and densities of mitochondria and respiratory complexes in mammalian cells can be understood. Extending theoretical and empirical analyses of scaling to suborganismal levels potentially has important implications for cellular structure and function as well as for the metabolic basis of aging.