Back to the future: ribonuclease A

Pancreatic ribonuclease A (EC 3.1.27.5, RNase) is, perhaps, the best-studied enzyme of the 20th century. It was isolated by René Dubos, crystallized by Moses Kunitz, sequenced by Stanford Moore and William Stein, and synthesized in the laboratory of Bruce Merrifield, all at the Rockefeller Institute/University. It has proven to be an excellent model system for many different types of experiments, both as an enzyme and as a well-characterized protein for biophysical studies. Of major significance was the demonstration by Chris Anfinsen at NIH that the primary sequence of RNase encoded the three-dimensional structure of the enzyme. Many other prominent protein chemists/enzymologists have utilized RNase as a dominant theme in their research. In this review, the history of RNase and its offspring, RNase S (S-protein/S-peptide), will be considered, especially the work in the Merrifield group, as a preface to preliminary data and proposed experiments addressing topics of current interest. These include entropy-enthalpy compensation, entropy of ligand binding, the impact of protein modification on thermal stability, and the role of protein dynamics in enzyme action. In continuing to use RNase as a prototypical enzyme, we stand on the shoulders of the giants of protein chemistry to survey the future.     

Back to the future with ubiquitin

Two papers published in 1984 by the Varshavsky laboratory revealed that the ubiquitin/proteasome pathway is the principal system for degradation of short-lived proteins in mammalian cells, setting the stage for future demonstrations of this pathway's many regulatory roles. This perspective discusses the impact of those papers and highlights some of the subsequent insights that have led to our current appreciation of the breadth of ubiquitin-mediated signaling.     

Back to the future: education for systems-level biologists

We describe a graduate course in quantitative biology that is based on original path-breaking papers in diverse areas of biology; each of these papers depends on quantitative reasoning and theory as well as experiment. Close reading and discussion of these papers allows students with backgrounds in physics, computational sciences or biology to learn essential ideas and to communicate in the languages of disciplines other than their own.     

Back to the future: museum specimens in population genetics

Museums and other natural history collections (NHC) worldwide house millions of specimens. With the advent of molecular genetic approaches these collections have become the source of many fascinating population studies in conservation genetics that contrast historical with present-day genetic diversity. Recent developments in molecular genetics and genomics and the associated statistical tools have opened up the further possibility of studying evolutionary change directly. As we discuss here, we believe that NHC specimens provide a largely underutilized resource for such investigations. However, because DNA extracted from NHC samples is degraded, analyses of such samples are technically demanding and many potential pitfalls exist. Thus, we propose a set of guidelines that outline the steps necessary to begin genetic investigations using specimens from NHC.     

Back to the future: genetic correlations, adaptation and speciation

Genetic correlations can affect the course of phenotypic evolution. Although genetic correlations among traits are a common feature of quantitative genetic analyses, they have played a very minor role in recent linkage-map based analyses of the genetic architecture of quantitative traits. Here, we use our work on host-associated races in pea aphids to illustrate how quantitative trait locus (QTL) mapping can be used to test specific hypotheses about how genetic correlations may facilitate ecological specialization and speciation.     

Back to the future: transgenerational transmission of xenobiotic-induced epigenetic remodeling

Epigenetics, or regulation of gene expression independent of DNA sequence, is the missing link between genotype and phenotype. Epigenetic memory, mediated by histone and DNA modifications, is controlled by a set of specialized enzymes, metabolite availability, and signaling pathways. A mostly unstudied subject is how sub-toxic exposure to several xenobiotics during specific developmental stages can alter the epigenome and contribute to the development of disease phenotypes later in life. Furthermore, it has been shown that exposure to low-dose xenobiotics can also result in further epigenetic remodeling in the germ line and contribute to increase disease risk in the next generation (multigenerational and transgenerational effects). We here offer a perspective on current but still incomplete knowledge of xenobiotic-induced epigenetic alterations, and their possible transgenerational transmission. We also propose several molecular mechanisms by which the epigenetic landscape may be altered by environmental xenobiotics and hypothesize how diet and physical activity may counteract epigenetic alterations.     

Mammoth interatrial septal aneurysm in the ICE age

Background

Subaortic and midventricular hypertrophic cardiomyopathy in a patient with extreme segmental hypertrophy exceeding the usual maximum wall thickness reported in the literature is a rare phenomenon.

Case Presentation

A 19-year-old man with recently diagnosed hypertrophic cardiomyopathy (HCM) was referred for sudden death risk assessment. The patient had mild exertional dyspnea (New York Heart Association functional class II), but without syncope or chest pain. There was no family history of HCM or sudden death. A two dimensional echocardiogram revealed an asymmetric type of LV hypertrophy; anterior ventricular septum = 49 mm; posterior ventricular septum = 20 mm; anterolateral free wall = 12 mm; and posterior free wall = 6 mm. The patient had 2 types of obstruction; a LV outflow obstruction due to systolic anterior motion of both mitral leaflets (Doppler-estimated 38 mm Hg gradient at rest); and a midventricular obstruction (Doppler-estimated 43 mm Hg gradient), but without apical aneurysm or dyskinesia. The patient had a normal blood pressure response on exercise test and no episodes of non-sustained ventricular tachycardia in 24-h ECG recording. Cardiac MRI showed a gross late enhancement at the hypertrophied septum. Based on the extreme degree of LV hypertrophy and the myocardial hyperenhancement, an implantation of a cardioverter-defibrillator was recommended prophylactically for primary prevention of sudden death.

Conclusion

Midventricular HCM is an infrequent phenotype, but may be associated with an apical aneurysm and progression to systolic dysfunction (end-stage HCM).     

Back to the future: antibody-based strategies for the treatment of infectious diseases

Before antibiotics, sera from immune animals and humans were used to treat a variety of infectious diseases, often with successful results. After the discovery of antimicrobial agents, serum therapy for bacterial infections was rapidly forsaken. In the last two decades, problems with treatment of newly emerged, reemerged, or persistent infectious diseases necessitated researchers to develop new and/or improved antibody-based therapeutic approaches. This article reviews some information on the use of antibodies for the treatment of infectious diseases, with special reference to the most seminal discoveries and current advances as well as available treatment approaches in this field.     

Back to the future: dynamic full carbon accounting applied to prospective bioenergy scenarios

Purpose

Ongoing debates focus on the role of forest-sourced bioenergy within climate mitigation efforts, due to the long rotation lengths of forest biomass. Valuing sequestration is debated due to its reversibility; however, dynamic modelling of biogenic carbon (C_bio) flows captures both negative and positive emissions. The objective of this work is to respond to the key issue of timing sequestration associated with two opposed modelling choices (historic vs. future) in the context of dynamic life cycle assessment (LCA).

Methods

The outputs of a partial-equilibrium model are used to inform prospective evaluations of the use of forest wood residues in response to an energy transition policy. Dynamic forest carbon modelling represents the carbon cycle between the atmosphere and technosphere: C_bio fixation and release through combustion and/or decay. Time-dependent characterization is used to assess the time-sensitive climate change effects. The two C_bio sequestration perspectives for bioenergy (forest biomass use) and reference (no use) scenarios are contrasted to assess (i) their temporal profiles, (ii) their climatic consequences concerning C-complete (fossil + biogenic C) vs. C-neutral (fossil C) approaches, and (iii) the implications of comparing the two approaches with dynamic LCA.

Results and discussion

Full lifetime carbon accounting confirms that C_bio entering the bioenergy system equals the C_bio leaving it in the net balance, but not within annual dynamic balances, which alter the atmospheric greenhouse gas composition. The impacts of the historic approach differed considerably from those of the future. Moreover, the “no use” scenario yielded higher forcing effects than the “bioenergy” due to the higher methane proportions. The chicken-egg dilemma arises in attributional LCA: as the forcing depends on the timing of the C_bio sequestration and its allocation to a harvest activity. A decision tree supported by case study applications provides general rules for selecting the adequate time-related modelling approach based the criteria of provision of wood and regrowth from managed and unmanaged forests, determined by the origin of biotic resources and related spheres.

Conclusions

Excluding dynamic C_bio introduces under- (future) or over- (historic) estimation of the results, misleading mitigation decisions. Further research is needed to close the gap between forest stand and landscape level, addressing issues beyond the chicken-egg dilemma and developing complete dynamic LCA studies.