Development of a human model for the study of effects of hypoxia, exercise, and sildenafil on cardiac and vascular function in chronic heart failure

Background: Pulmonary hypertension is associated with poor outcome in patients with chronic heart failure (CHF) and may be a therapeutic target. Our aims were to develop a noninvasive model for studying pulmonary vasoreactivity in CHF and characterize sildenafil's acute cardiovascular effects. Methods and Results: In a crossover study, 18 patients with CHF participated 4 times [sildenafil (2 × 20 mg)/or placebo (double-blind) while breathing air or 15% oxygen] at rest and during exercise. Oxygen saturation (SaO2) and systemic vascular resistance were recorded. Left and right ventricular (RV) function and transtricuspid systolic pressure gradient (RVTG) were measured echocardiographically. At rest, hypoxia caused SaO2 (P = 0.001) to fall and RVTG to rise (5 ± 4 mm Hg; P = 0.001). Sildenafil reduced SaO2 (−1 ± 2%; P = 0.043), systemic vascular resistance (−87 ± 156 dyn·s−1·cm−2; P = 0.034), and RVTG (−2 ± 5 mm Hg; P = 0.05). Exercise caused cardiac output (2.1 ± 1.8 L/min; P < 0.001) and RVTG (19 ± 11 mm Hg; P < 0.0001) to rise. The reduction in RVTG with sildenafil was not attenuated by hypoxia. The rise in RVTG with exercise was not substantially reduced by sildenafil. Conclusions: Sildenafil reduces SaO2 at rest while breathing air, this was not exacerbated by hypoxia, suggesting increased ventilation–perfusion mismatching due to pulmonary vasodilation in poorly ventilated lung regions. Sildenafil reduces RVTG at rest and prevents increases caused by hypoxia but not by exercise. This study shows the usefulness of this model to evaluate new therapeutics in pulmonary hypertension

A three-dimensional model for the probabilistic intergranular failure of polycrystalline arrays

A three-dimensional grain model, in which the grains are represented by regular truncated octahedra, has been developed to study probabilistic time-dependent intergranular failure in polycrystalline arrays. In this model, grain boundary facets are assumed to fail randomly in time, as a function of the facet normal stress. A simple approximate method for calculating the load shed by failed facets and a reasonable choice of failure criterion complete the model. This leads to a conceptually simple, but computationally complex, model capable of handling assemblages consisting of relatively large numbers (> 5000) of grains. The predicted scatter in the times-to-failure and the variation in number of failed facets with time are in quite reasonable agreement with available experimental data.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/49082/2/ms6302.pd

Modeling the evolution of a classic genetic switch

Abstract Background The regulatory network underlying the yeast galactose-use pathway has emerged as a model system for the study of regulatory network evolution. Evidence has recently been provided for adaptive evolution in this network following a whole genome duplication event. An ancestral gene encoding a bi-functional galactokinase and co-inducer protein molecule has become subfunctionalized as paralogous genes (GAL1 and GAL3) in Saccharomyces cerevisiae, with most fitness gains being attributable to changes in cis- regulatory elements. However, the quantitative functional implications of the evolutionary changes in this regulatory network remain unexplored. Results We develop a modeling framework to examine the evolution of the GAL regulatory network. This enables us to translate molecular changes in the regulatory network to changes in quantitative network function. We computationally reconstruct an inferred ancestral version of the network and trace the evolutionary paths in the lineage leading to S. cerevisiae. We explore the evolutionary landscape of possible regulatory networks and find that the operation of intermediate networks leading to S. cerevisiae differs substantially depending on the order in which evolutionary changes accumulate; in particular, we systematically explore evolutionary paths and find that some network features cannot be optimized simultaneously. Conclusions We find that a computational modeling approach can be used to analyze the evolution of a well-studied regulatory network. Our results are consistent with several experimental studies of the evolutionary of the GAL regulatory network, including increased fitness in Saccharomyces due to duplication and adaptive regulatory divergence. The conceptual and computational tools that we have developed may be applicable in further studies of regulatory network evolution

Evolution of a Membrane Protein Regulon in Saccharomyces

Expression variation is widespread between species. The ability to distinguish regulatory change driven by natural selection from the consequences of neutral drift remains a major challenge in comparative genomics. In this work, we used observations of mRNA expression and promoter sequence to analyze signatures of selection on groups of functionally related genes in Saccharomycete yeasts. In a survey of gene regulons with expression divergence between Saccharomyces cerevisiae and S. paradoxus, we found that most were subject to variation in trans-regulatory factors that provided no evidence against a neutral model. However, we identified one regulon of membrane protein genes controlled by unlinked cis- and trans-acting determinants with coherent effects on gene expression, consistent with a history of directional, nonneutral evolution. For this membrane protein group, S. paradoxus alleles at regulatory loci were associated with elevated expression and altered stress responsiveness relative to other yeasts. In a phylogenetic comparison of promoter sequences of the membrane protein genes between species, the S. paradoxus lineage was distinguished by a short branch length, indicative of strong selective constraint. Likewise, sequence variants within the S. paradoxus population, but not across strains of other yeasts, were skewed toward low frequencies in promoters of genes in the membrane protein regulon, again reflecting strong purifying selection. Our results support a model in which a distinct expression program for the membrane protein genes in S. paradoxus has been preferentially maintained by negative selection as the result of an increased importance to organismal fitness. These findings illustrate the power of integrating expression- and sequence-based tests of natural selection in the study of evolutionary forces that underlie regulatory change

Interplay between right ventricular function and cardiac resynchronization therapy : an analysis of the CARE-HF trial (cardiac resynchronization–heart failure)

Objectives: The aim of this study was to investigate the impact of cardiac resynchronization therapy (CRT) on right ventricular (RV) function and the influence of RV dysfunction on the echocardiographic and clinical response to CRT among patients enrolled in the CARE-HF (Cardiac Resynchronization-Heart Failure) trial. Background: Cardiac resynchronization therapy prolongs survival in appropriately selected patients with heart failure but the benefit might be diminished in patients with RV dysfunction. Methods: Of 813 patients enrolled in the CARE-HF study, 688 had tricuspid plane systolic excursion (TAPSE) measured at baseline, and 345 of these were assigned to CRT. Their median (interquartile range) age was 66 (58 to 71) years, left ventricular (LV) ejection fraction was 24% (21% to 28%), and TAPSE was 19 (16 to 22) mm. Baseline LV function and size and QRS duration were similar among TAPSE tertiles, but those in the worst tertile (TAPSE < 17.4 mm) were more likely to have ischemic heart disease. Results: Overall, CRT improved LV but not RV structure and function with little evidence of an interaction with TAPSE. During a median (interquartile range) follow-up of 748 (582 to 950) days, 213 deaths occurred. Patients with lower TAPSE had a higher mortality, regardless of assigned treatment (p < 0.001). Greater inter-ventricular mechanical delay, New York Heart Association functional class, mitral regurgitation, and N-terminal pro-B-type natriuretic peptide, lower TAPSE, and assignment to the control group were independently associated with higher mortality. Reduction in mortality with CRT was similar in each tertile of TAPSE. Conclusions: Right ventricular dysfunction is a powerful determinant of prognosis among candidates for CRT, regardless of treatment assigned, but did not diminish the prognostic benefits of CRT among patients enrolled in the CARE-HF trial. (Care-HF CArdiac Resynchronization in Heart Failure; NCT00170300) © 2013 American College of Cardiology Foundation

Natural law, non-voluntary euthanasia, and public policy

© 2019 by Emerald Publishing Limited. Natural Law philosophy asserts that there are universally binding and universally evident principles that can be determined to guide the actions of persons. Moreover, many of these principles have been enshrined in both statute and common law, thus ensuring their saliency for staff and institutions charged with palliative care. The authors examine the often emotive and politicized matter of (non-voluntary) euthanasia – acts or omissions made with the intent of causing or hastening death – with reference to Natural Law philosophy. This leads us to propose a number of important public policy remedies to ensure dignity in dying for the patient, and their associates

Trait Variation in Yeast Is Defined by Population History

A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific genetic variants. Key to such an understanding is the detailed mapping of the natural genomic and phenomic space and a bridging of the gap that separates these worlds. Here we chart a high-resolution map of natural trait variation in one of the most important genetic model organisms, the budding yeast Saccharomyces cerevisiae, and its closest wild relatives and trace the genetic basis and timing of major phenotype changing events in its recent history. We show that natural trait variation in S. cerevisiae exceeds that of its relatives, despite limited genetic variation, and follows the population history rather than the source environment. In particular, the West African population is phenotypically unique, with an extreme abundance of low-performance alleles, notably a premature translational termination signal in GAL3 that cause inability to utilize galactose. Our observations suggest that many S. cerevisiae traits may be the consequence of genetic drift rather than selection, in line with the assumption that natural yeast lineages are remnants of recent population bottlenecks. Disconcertingly, the universal type strain S288C was found to be highly atypical, highlighting the danger of extrapolating gene-trait connections obtained in mosaic, lab-domesticated lineages to the species as a whole. Overall, this study represents a step towards an in-depth understanding of the causal relationship between co-variation in ecology, selection pressure, natural traits, molecular mechanism, and alleles in a key model organism

Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

Funding Information: We want to thank Barbara Roberts from the NCBI Taxonomy Team for providing the update of the current fungal names in NCBI Taxonomic database. Masako Takashima is supported by the Institution for Fermentation, Osaka (IFO). Heide-Marie Daniel is supported by the Belgian Science Policy Office grant C5/00/BCCM. Chris Todd Hittinger is supported by the National Science Foundation under Grant Nos. DEB-1442148 and DEB-2110403, the USDA National Institute of Food and Agriculture (Hatch Project 1020204), in part by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE–SC0018409, and an H.I. Romnes Faculty Fellowship, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation. Research in Antonis Rokas’s lab is supported by grants from the National Science Foundation (DEB-1442113 and DEB-2110404), the National Institutes of Health/National Institute of Allergy and Infectious Diseases (R01 AI153356), and the Burroughs Wellcome Fund. Antonis Rokas acknowledges support from a Klaus Tschira Guest Professorship from the Heidelberg Institute for Theoretical Studies and from a Visiting Research Fellowship from Merton College of the University of Oxford. Marc-André Lachance acknowledges lifelong financial support from the Natural Sciences and Engineering Research Council of Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Carlos A. Rosa is supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq – Brazil, process numbers 408733/2021-7 and 406564/2022-1); Fundação do Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG, process numberAPQ-01525-14). Teun Boekhout is supported by the Distinguished Scientist Fellow Program of King Saud University, Ryadh, Saudi Arabia. Publisher Copyright: © 2023 Westerdijk Fungal Biodiversity Institute.The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.publishersversionpublishe