Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases.     

‘Good Sense’ in context: A response to Kidd

In his response to my (2010), Ian Kidd claims that my argument against Stump’s interpretation of Duhem’s concept of ‘good sense’ is unsound because it ignores an important distinction within virtue epistemology. In light of the distinction between reliabilist and responsibilist virtue epistemology, Kidd argues that Duhem can be seen as supporting the latter, which he further illustrates with a discussion of Duhem’s argument against ‘perfect theory’. I argue that no substantive argument is offered to show that the distinction is relevant and can establish that Duhem’s ‘good sense’ can be understood within responsibilist virtue epistemology. I furthermore demonstrate that Kidd’s attempt to support his contention relies on a crucial misreading of Duhem’s general philosophy of science, and in doing so highlight the importance of understanding ‘good sense’ in its original context, that of theory choice.     

An ‘Ultra’ rapid Golgi method for vertebrate neuroanatomy

Summary A modification of the hardening solution of the rapid Golgi method permits constant successful impregnations of the brain of several vertebrate representatives in only 24 hours.Acknowledgment. Thanks are due to Mr.V. Guglielmotti and Mr.E. Casale for technical assistance.     

Crumbs, the Drosophila homologue of human CRB1/RP12, is essential for photoreceptor morphogenesis

The apical transmembrane protein Crumbs is a central regulator of epithelial apical-basal polarity in Drosophila. Loss-of-function mutations in the human homologue of Crumbs, CRB1 (RP12), cause recessive retinal dystrophies, including retinitis pigmentosa. Here we show that Crumbs and CRB1 localize to corresponding subdomains of the photoreceptor apical plasma membrane: the stalk of the Drosophila photoreceptor and the inner segment of mammalian photoreceptors. These subdomains support the morphogenesis and orientation of the photosensitive membrane organelles: rhabdomeres and outer segments, respectively. Drosophila Crumbs is required to maintain zonula adherens integrity during the rapid apical membrane expansion that builds the rhabdomere. Crumbs also regulates stalk development by stabilizing the membrane-associated spectrin cytoskeleton, a function mechanistically distinct from its role in epithelial apical-basal polarity. We propose that Crumbs is a central component of a molecular scaffold that controls zonula adherens assembly and defines the stalk as an apical membrane subdomain. Defects in such scaffolds may contribute to human CRB1-related retinal dystrophies.     

Substance P-like immunoreactivity in the frog dorsal root ganglia

Summary The distribution of substance P-like immunoreactivity was studied in the thoracic dorsal root ganglia of the frogRana esculenta by immunohistochemistry. Substance P-like immunoreactivity was contained in approximately 50% of primary sensory neurons. The immunoreactive fibers arising from the cell bodies are collected in small bundles within the ganglia neuropil before entering the central and peripheral roots.     

Pierre Duhem’s good sense as a guide to theory choice

This paper examines Duhem’s concept of good sense as an attempt to support a non rule-governed account of rationality in theory choice. Faced with the underdetermination of theory by evidence thesis and the continuity thesis, Duhem tried to account for the ability of scientists to choose theories that continuously grow to a natural classification. I will examine the concept of good sense and the problems that stem from it. I will also present a recent attempt by David Stump to link good sense to virtue epistemology. I will argue that even though this approach can be useful for the better comprehension of the concept of good sense, there are some substantial differences between virtue epistemologists and Duhem. In the light of this reconstruction of good sense, I will propose a possible way to interpret the concept of good sense, which overcomes the noted problems and fits better with Duhem’s views on scientific method and motivation in developing the concept of good sense.     

Fibroblast-to-myofibroblast transition in bronchial asthma

Bronchial asthma is a chronic inflammatory disease in which bronchial wall remodelling plays a significant role. This phenomenon is related to enhanced proliferation of airway smooth muscle cells, elevated extracellular matrix protein secretion and an increased number of myofibroblasts. Phenotypic fibroblast-to-myofibroblast transition represents one of the primary mechanisms by which myofibroblasts arise in fibrotic lung tissue. Fibroblast-to-myofibroblast transition requires a combination of several types of factors, the most important of which are divided into humoural and mechanical factors, as well as certain extracellular matrix proteins. Despite intensive research on the nature of this process, its underlying mechanisms during bronchial airway wall remodelling in asthma are not yet fully clarified. This review focuses on what is known about the nature of fibroblast-to-myofibroblast transition in asthma. We aim to consider possible mechanisms and conditions that may play an important role in fibroblast-to-myofibroblast transition but have not yet been discussed in this context. Recent studies have shown that some inherent and previously undescribed features of fibroblasts can also play a significant role in fibroblast-to-myofibroblast transition. Differences observed between asthmatic and non-asthmatic bronchial fibroblasts (e.g., response to transforming growth factor β, cell shape, elasticity, and protein expression profile) may have a crucial influence on this phenomenon. An accurate understanding and recognition of all factors affecting fibroblast-to-myofibroblast transition might provide an opportunity to discover efficient methods of counteracting this phenomenon.     

The effect of cyclic N-2-O-dibutyryl-adenosine-3′, 5′-monophosphate on neuromuscular transmission and concentration of glycogen in the isolated phrenic nerve-diaphragm preparation of the rat

Résumé Le dérivé dibutyrique du 3, 5-AMP cyclique potentialise les contractions du diaphragme provoquées par stimulation électrique indirecte, alors que l'application du 3,5-AMP cyclique n'a pas un tel effet. D'autre part, ce dérivé diminue le taux de glycogène du diaphragme, ce qui n'est pas le cas pour le 3,5-AMP cyclique.     

Altered proteostasis in aging and heat shock response in C. elegans revealed by analysis of the global and de novo synthesized proteome

Protein misfolding and aggregation as a consequence of impaired protein homeostasis (proteostasis) not only characterizes numerous age-related diseases but also the aging process itself. Functionally related to the aging process are, among others, ribosomal proteins, suggesting an intimate link between proteostasis and aging. We determined by iTRAQ quantitative proteomic analysis in C. elegans how the proteome changes with age and in response to heat shock. Levels of ribosomal proteins and mitochondrial chaperones were decreased in aged animals, supporting the notion that proteostasis is altered during aging. Mitochondrial enzymes of the tricarboxylic acid cycle and the electron transport chain were also reduced, consistent with an age-associated energy impairment. Moreover, we observed an age-associated decline in the heat shock response. In order to determine how protein synthesis is altered in aging and in response to heat shock, we complemented our global analysis by determining the de novo proteome. For that, we established a novel method that enables both the visualization and identification of de novo synthesized proteins, by incorporating the non-canonical methionine analogue, azidohomoalanine (AHA), into the nascent polypeptides, followed by reacting the azide group of AHA by ‘click chemistry’ with an alkyne-labeled tag. Our analysis of AHA-tagged peptides demonstrated that the decreased abundance of, for example, ribosomal proteins in aged animals is not solely due to degradation but also reflects a relative decrease in their synthesis. Interestingly, although the net rate of protein synthesis is reduced in aged animals, our analyses indicate that the synthesis of certain proteins such as the vitellogenins increases with age.