Who cares for the protons?

It is tempting to use standard protonation states for the analysis of protein-ligand interactions. Two different pK(a) calculation methods, PROPKA (protein pK(a)) and MCCE (multi conformation continuum electrostatics), were applied to challenge this convenient behavior. As data basis, we selected five recently approved drugs for which structural information of the protein-drug complex is available. We analyzed the pK(a) calculations in terms of a measure termed BIPS (binary protonation states) recently introduced by us. Both methods agree in detecting the majority of the sites with atypical BIPS values. However, when using only one method, some of the atypcial BIPS value would have been missed. Therefore, we recommend using both methods to set such an interpretation on a solid basis.     

Who speaks for the dispossessed?

This commentary articulates three perspectives on race in America: economic determinism, institutionalism and a field-theoretic approach. It argues that William Julius Wilson's masterwork, The Declining Significance of Race, was informed by the first and anticipated the latter two. Wilson's most profound and enduring legacy is his unwavering concern for the dispossessed.     

Our extended genotype—An argument for the study of domesticated microbes

We interpret the domesticated organisms—plants, animals, and the domesticated microbes used for food fermentation—as an extended genotype of humans due to their close relationship with our species. We propose to analyse the role of microbes in traditionally fermented food with the approaches used in the human microbiome project, and we expect to find associations with ethnic groups, explaining part of human (culinary) culture.     

Who should Decide for the Unrepresented?

Unrepresented patients lack the capacity to make medical decisions for themselves, have no clear documentation of preferences for medical treatment, and have no surrogate decision maker or obvious candidate for that role. There is no consensus about who should serve as the decision maker for these patients, particularly regarding whether to continue or to limit life‐sustaining treatment. Several authors have argued that ethics committees should play this role rather than the patient's treating physician, a common current default. We argue that concerns about the adequacy of physicians as surrogates are either empirically unfounded or apply equally to ethics committees. We suggest that physicians should be the primary decision maker for the unrepresented because of their fiduciary duties toward their patients. As part of the process of fulfilling these duties, they should seek the advice of third parties such as ethic committees; but final end‐of‐life decision‐making for the unrepresented should rest with the treating physician.     

Who wants to be a physician? An educational tool for reviewing pulmonary physiology

Traditional review sessions are typically focused on instructor-based learning. However, experts in the field of higher education have long recommended teaching modalities that incorporate student-based active-learning strategies. Given this, we developed an educational game in pulmonary physiology for first-year medical students based loosely on the popular television game show Who Wants To Be A Millionaire. The purpose of our game, Who Wants To Be A Physician, was to provide students with an educational tool by which to review material previously presented in class. Our goal in designing this game was to encourage students to be active participants in their own learning process. The Who Wants To Be A Physician game was constructed in the form of a manual consisting of a bank of questions in various areas of pulmonary physiology: basic concepts, pulmonary mechanics, ventilation, pulmonary blood flow, pulmonary gas exchange, gas transport, and control of ventilation. Detailed answers are included in the manual to assist the instructor or player in comprehension of the material. In addition, an evaluation instrument was used to assess the effectiveness of this instructional tool in an academic setting. Specifically, the evaluation instrument addressed five major components, including goals and objectives, participation, content, components and organization, and summary and recommendations. Students responded positively to our game and the concept of active learning. Moreover, we are confident that this educational tool has enhanced the students' learning process and their ability to understand and retain information.     

Who gets renal bone disease before beginning dialysis?

To identify patients at risk from renal bone disease we compared the demographic characteristics of 243 patients with end stage renal failure grouped according to the presence (97 (40%] or absence of severe renal bone disease as judged by histological criteria. Youth, female sex, tubulointerstitial types of nephropathy, and a long duration of uraemia were all identified as significant independent risk factors for the development of bone disease. The relative risks from being female and having tubulointerstitial renal disease were separately identifiable when the estimated observation of renal failure was short (less than four years). The identification of patients at high risk from bone disease may clarify the pathogenesis and treatment strategies of renal osteodystrophy.     

How different are robust and gracile capuchin monkeys? An argument for the use of sapajus and cebus

Capuchin monkey behavior has been the focus of increasing numbers of captive and field studies in recent years, clarifying behavioral and ecological differences between the two morphological types: the gracile and the robust capuchins (also referred to as untufted and tufted). Studies have tended to focus on the gracile species Cebus capucinus (fewer data are available for C. albifrons, C. olivaceus, and C. kaapori) and on Cebus apella, a name that has encompassed all of the robust capuchins since the 1960s. As a result, it is difficult to ascertain the variation within either gracile or robust types. The phylogenetic relationships between gracile and robust capuchins have also, until now, remained obscure. Recent studies have suggested two independent Pliocene radiations of capuchins stemming from a common ancestor in the Late Miocene, about 6.2 millions of years ago (Ma). The present-day gracile capuchins most likely originated in the Amazon, and the robust capuchins in the Atlantic Forest to the southeast. Sympatry between the two types is explained by a recent expansion of robust capuchins into the Amazon (ca. 400,000 years ago). Morphological data also support a division of capuchins into the same two distinct groups, and we propose the division of capuchin monkeys into two genera, Sapajus Kerr, 1792, for robust capuchins and Cebus Erxleben, 1777, for gracile capuchins, based on a review of extensive morphological, genetic, behavioral, ecological, and biogeographic evidence.     

An evolving paradigm for the secretory pathway?

The paradigm that the secretory pathway consists of a stable endoplasmic reticulum and Golgi apparatus, using discrete transport vesicles to exchange their contents, gained important support from groundbreaking biochemical and genetic studies during the 1980s. However, the subsequent development of new imaging technologies with green fluorescent protein introduced data on dynamic processes not fully accounted for by the paradigm. As a result, we may be seeing an example of how a paradigm is evolving to account for the results of new technologies and their new ways of describing cellular processes.     

Does the immune system of a mouse age faster than the immune system of a human?

One of the characteristics of all somatic cells is a finite life span. Cells may proliferate until they reach a point after which, although they are metabolically active, they can no longer produce daughter cells. This observation is central to the clonal exhaustion hypothesis, a mechanism cited to explain age-associated immune dysfunction. In this hypothesis, repeated division of lymphocytes leads to a replicative limit, after which they enter the senescent phase but are not lost from the pool of T cells. Advancing age would then be associated with an increase in the number of T cells that are unable to proliferate to a stimulus which induces a proliferative response in T cells from younger individuals. This hypothesis seems both logical and reasonable and is supported by data from both humans and mice with the demonstration of an age-related accumulation of senescent T cells in both species. However, there is an apparent paradox. The paradox arises because the onset of immunosenescence appears to be more closely linked to the life span of the animal rather than the life span of the lymphocyte. BioEssays 21:519–524, 1999. © 1999 John Wiley & Sons, Inc.     

γδ-Dioxovalerate as a substrate for the glyoxalase enzyme system

1. Crude gammadelta-dioxovalerate was synthesized from laevulinate by two different methods and was purified by Sephadex chromatography. Some analytical reactions of the compound are described. 2. gammadelta-Dioxovalerate is a substrate for glyoxalase I and the GSH derivative formed by this enzyme is hydrolysed by glyoxalase II to form d-alpha-hydroxyglutarate. The K(m) of glyoxalase I for gammadelta-dioxovalerate is 1.0x10(-3)m at pH5.8.3. The u.v.-absorption spectrum of thiol ester, synthesized enzymically from gammadelta-dioxovalerate and GSH by glyoxalase I, is almost identical with that for S-lactoylglutathione. Some optical properties of this thiol ester were measured. 4. Attempts to show reversibility of the glyoxalase system reactions with d-alpha-hydroxyglutarate as substrate were unsuccessful. 5. The possible metabolic role of the gammadelta-dioxovalerate reaction is discussed. It is suggested that one of the metabolic functions of the glyoxalase system may be to provide a mechanism for the entry of this compound into the tricarboxylic acid cycle.