Identification of NADPH oxidase as a key mediator in the post‐ischemia‐induced sequestration and degradation of the GluA2 AMPA receptor subunit

A hallmark of ischemic/reperfusion injury is a change in subunit composition of synaptic 2‐amino‐3‐(3‐hydroxy‐5‐methylisoazol‐4‐yl)propionic acid receptors (AMPARs). This change in AMPAR subunit composition leads to an increase in surface expression of GluA2‐lacking Ca²⁺/Zn²⁺ permeable AMPARs. These GluA2‐lacking AMPARs play a key role in promoting delayed neuronal death following ischemic injury. At present, the mechanism(s) responsible for the ischemia/reperfusion‐induced subunit composition switch and degradation of the GluA2 subunit remain unclear. In this study, we investigated the role of NADPH oxidase, and its importance in mediating endocytosis and subsequent degradation of the GluA2 AMPAR subunit in adult rat hippocampal slices subjected to oxygen–glucose deprivation/reperfusion (OGD/R) injury. In hippocampal slices pre‐treated with the NADPH oxidase inhibitor apocynin attenuated OGD/R‐mediated sequestration of GluA2 and GluA1 as well as prevent the degradation of GluA2. We provide compelling evidence that NADPH oxidase mediated sequestration of GluA1‐ and GluA2‐ involved activation of p38 MAPK. Furthermore, we demonstrate that inhibition of NADPH oxidase blunts the OGD/R‐induced association of GluA2 with protein interacting with C kinase‐1. In summary, this study identifies a novel mechanism that may underlie the ischemia/reperfusion‐induced AMPAR subunit composition switch and a potential therapeutic target.

     

Within-laboratory and between-laboratory variability in the measurement of anti-müllerian hormone determined within an external quality assurance scheme

Ten laboratories in an external quality assurance scheme used the same assay to measure anti-müllerian hormone concentration (Beckman Coulter Gen II) and received twenty serum samples distributed over a 15 month period. The mean bias for all results was only ?0.089%, but there was large coefficient of repeatability of 38.8% (sample bias ranged from ?37.9% to +54.7%). While each laboratory showed good reproducibility, there was a wide range of average values relative to the consensus value from ?24.0% to +22.7%. This between-laboratory variability suggests clinicians should use the same laboratory to avoid problems with result interpretation.     

A Direct and Efficient Synthesis of 5′-Deoxy-2′, 3′-

Abstract

A direct and efficient synthesis of 5′-deoxy-2′,3′-O-isopropylideneinosine, 7, from readily available inosine is described. An example of a potentially general synthesis of N -substituted-5′-deoxyadenosines from 7 is also described.     

Scientific knowledge is possible with small-sample classification

A typical small-sample biomarker classification paper discriminates between types of pathology based on, say, 30,000 genes and a small labeled sample of less than 100 points. Some classification rule is used to design the classifier from this data, but we are given no good reason or conditions under which this algorithm should perform well. An error estimation rule is used to estimate the classification error on the population using the same data, but once again we are given no good reason or conditions under which this error estimator should produce a good estimate, and thus we do not know how well the classifier should be expected to perform. In fact, virtually, in all such papers the error estimate is expected to be highly inaccurate. In short, we are given no justification for any claims.Given the ubiquity of vacuous small-sample classification papers in the literature, one could easily conclude that scientific knowledge is impossible in small-sample settings. It is not that thousands of papers overtly claim that scientific knowledge is impossible in regard to their content; rather, it is that they utilize methods that preclude scientific knowledge. In this paper, we argue to the contrary that scientific knowledge in small-sample classification is possible provided there is sufficient prior knowledge. A natural way to proceed, discussed herein, is via a paradigm for pattern recognition in which we incorporate prior knowledge in the whole classification procedure (classifier design and error estimation), optimize each step of the procedure given available information, and obtain theoretical measures of performance for both classifiers and error estimators, the latter being the critical epistemological issue. In sum, we can achieve scientific validation for a proposed small-sample classifier and its error estimate.     

On the impoverishment of scientific education

Hannah Arendt, one of the foremost political philosophers of the twentieth century, has argued that it is the responsibility of educators not to leave children in their own world but instead to bring them into the adult world so that, as adults, they can carry civilization forward to whatever challenges it will face by bringing to bear the learning of the past. In the same collection of essays, she discusses the recognition by modern science that Nature is inconceivable in terms of ordinary human conceptual categories - as she writes, ‘unthinkable in terms of pure reason’. Together, these views on scientific education lead to an educational process that transforms children into adults, with a scientific adult being one who has the ability to conceptualize scientific systems independent of ordinary physical intuition. This article begins with Arendt’s basic educational and scientific points and develops from them a critique of current scientific education in conjunction with an appeal to educate young scientists in a manner that allows them to fulfill their potential ‘on the shoulders of giants’. While the article takes a general philosophical perspective, its specifics tend to be directed at biomedical education, in particular, how such education pertains to translational science.     

Conserved WCPL and CX4C Domains Mediate Several Mating Adhesin Interactions in Saccharomyces cerevisiae

Several adhesins are induced by pheromones during mating in Saccharomyces cerevisiae, including Aga1p, Aga2p, Sag1p (Agα1p), and Fig2p. These four proteins all participate in or influence a well-studied agglutinin interaction mediated by Aga1p–Aga2p complexes and Sag1p; however, they also play redundant and essential roles in mating via an unknown mechanism. Aga1p and Fig2p both contain repeated, conserved WCPL and CX₄C domains. This study was directed toward understanding the mechanism underlying the collective requirement of agglutinins and Fig2p for mating. Apart from the well-known agglutinin interaction between Aga2p and Sag1p, three more pairs of interactions in cells of opposite mating type were revealed by this study, including bilateral heterotypic interactions between Aga1p and Fig2p and a homotypic interaction between Fig2p and Fig2p. These four pairs of adhesin interactions are collectively required for maximum mating efficiency and normal zygote morphogenesis. GPI-less, epitope-tagged forms of Aga1p and Fig2p can be co-immunoprecipitated from the culture medium of mating cells in a manner dependent on the WCPL and CX₄C domains in the R1 repeat of Aga1p. Using site-directed mutagenesis, the conserved residues in Aga1p that interact with Fig2p were identified. Aga1p is involved in two distinct adhesive functions that are independent of each other, which raises the possibility for combinatorial interactions of this protein with its different adhesion receptors, Sag1 and Fig2p, a property of many higher eukaryotic adhesins.     

Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults

In the United States, there are persistent and widening socioeconomic gaps in morbidity and mortality from chronic diseases. Although most disparities research focuses on person-level socioeconomic-status, mounting evidence suggest that chronic diseases also pattern by the demographic characteristics of neighborhoods. Yet the biological mechanisms underlying these associations are poorly understood. There is increasing recognition that chronic diseases share common pathogenic features, some of which involve alterations in the composition, diversity, and functioning of the gut microbiota. This study examined whether socioeconomic-status was associated with alpha-diversity of the colonic microbiota. Forty-four healthy adults underwent un-prepped sigmoidoscopy, during which mucosal biopsies and fecal samples were collected. Subjects’ zip codes were geocoded, and census data was used to form a composite indicator of neighborhood socioeconomic-status, reflecting household income, educational attainment, employment status, and home value. In unadjusted analyses, neighborhood socioeconomic-status explained 12–18 percent of the variability in alpha-diversity of colonic microbiota. The direction of these associations was positive, meaning that as neighborhood socioeconomic-status increased, so did alpha-diversity of both the colonic sigmoid mucosa and fecal microbiota. The strength of these associations persisted when models were expanded to include covariates reflecting potential demographic (age, gender, race/ethnicity) and lifestyle (adiposity, alcohol use, smoking) confounds. In these models neighborhood socioeconomic-status continued to explain 11–22 percent of the variability in diversity indicators. Further analyses suggested these patterns reflected socioeconomic variations in evenness, but not richness, of microbial communities residing in the sigmoid. We also found indications that residence in neighborhoods of higher socioeconomic-status was associated with a greater abundance of Bacteroides and a lower abundance of Prevotella, suggesting that diet potentially underlies differences in microbiota composition. These findings suggest the presence of socioeconomic variations in colonic microbiota diversity. Future research should explore whether these variations contribute to disparities in chronic disease outcomes.