The ontic conception of scientific explanation

Wesley Salmon's version of the ontic conception of explanation is a main historical root of contemporary work on mechanistic explanation. This paper examines and critiques the philosophical merits of Salmon's version, and argues that his conception's most fundamental construct is either fundamentally obscure, or else reduces to a non-ontic conception of explanation. Either way, the ontic conception is a misconception.     

Hispid pocket mouse ( Chaetodipus hispidus ) in east-central and northeastern Nebraska

The hispid pocket mouse ( Chaetodipus hispidus ) occurs throughout the Great Plains, mainly west of the Missouri River. In Nebraska, this species likely occurs throughout the state, but records of occurrence were lacking for east-central and northeastern counties. During a survey in 2008 for the plains pocket mouse ( Perognathus flavescens ) in eastern Nebraska, we documented C. hispidus in 10 new counties, including a modest range expansion into northeastern Nebraska. Many individuals were captured on moderately compact soils consisting of silt, but some also were captured on sandy and other friable soils. Most individuals were captured in areas containing some exposed ground, but this may reflect our trap placement for P. flavescens. Individuals from northeastern and east-central Nebraska best resembled C. h. spilotus from southeastern Nebraska, with black coloration suffused on the dorsum, head, and dorsal side of the tail; however, our individuals generally lacked the characteristic bright ochraceous coloration along lateral lines and on the dorsum. Limited evidence supports a recent expansion in distribution within the region.     

Chromosome 4q DNA rearrangements associated with facioscapulohumeral muscular dystrophy.

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant neuromuscular disorder which maps to chromosome 4qter, distal to the D4S139 locus. The cosmid clone 13E, isolated in a search for homeobox genes, was subsequently mapped to 4q35, also distal to D4S139. A subclone, p13E-11, detects in normal individuals a polymorphic EcoRI fragment usually larger than 28 kilobases (kb). Surprisingly, using the same probe we detected de novo DNA rearrangements, characterized by shorter EcoRI fragments (14-28 kb), in 5 out of 6 new FSHD cases. In 10 Dutch families analysed, a specific shorter fragment between 14-28 kb cosegregates with FSHD. Both observations indicate that FSHD is caused by independent de novo DNA rearrangements in the EcoRI fragment detected by p13E-11.     

Pheromone binding to two rodent urinary proteins revealed by X-ray crystallography.

The principal protein excreted in male rat urine, urinary alpha 2-globulin and the homologous mouse protein, major urinary protein, have been well characterized, although their functions remain unclear. Male rat urine affects the behaviour and sexual response of female rats, leading to the proposal that rodent urinary proteins are responsible for binding pheromones and their subsequent release from drying urine. Urinary alpha 2-globulin is also involved in hyaline droplet nephropathy, an important toxicological syndrome in male rats resulting from exposure to a number of industrial chemicals and characterized by the accumulation of liganded urinary alpha 2-globulin in lysosomes in the kidney, followed by the induction of renal cancer. We now report the three-dimensional structures of mouse major urinary protein (at 2.4 A resolution) and rat urinary alpha 2-globulin (at 2.8 A resolution). The results corroborate the role of these proteins in pheromone transport and elaborate the structural basis of ligand binding.     

The immunodominant site of a synthetic immunogen has a conformational preference in water for a type-II reverse turn

Many short synthetic peptides have now been shown to induce antibodies reactive with their cognate sequences in the intact folded protein. Aside from the usefulness of such antibodies as site-specific reagents, the frequency with which this recognition occurs has raised several theoretical issues, the central one being that of how an antibody to a short synthetic peptide, which represents one of the most disordered states of a site in a protein, can react with the more ordered version of the same sequence in the folded protein. This apparent paradox can be resolved if the target site on the protein approaches disorder or if the peptide in solution or on a carrier adopts, with significant frequency, a conformation compatible with that of the cognate site in the protein. Various studies already suggest that antigenic sites in proteins correspond to regions of high atomic mobility. We now show, using high-field nuclear magnetic resonance (NMR) spectroscopy, that a nonapeptide selected by several monoclonal antibodies as the immunodominant site of a 36-amino-acid immunogen (residues 75-110 of influenza virus haemagglutinin) adopts a highly populated type-II reverse-turn conformation in water. This suggests that in this case the antibodies have selected a sequence possessing a conformational preference. Apart from helping us to understand immunological recognition, anti-peptide antibodies may provide reagents of sufficient precision for an immunological approach to the problem of protein folding.     

Visual motion and cortical velocity

Recent studies have revealed some remarkably simple relationships between visual performance and the neuroanatomy of the visual pathways. The visual field is mapped topographically on the surface of the striate cortex in man; the projection is large for the central visual field and is progressively compressed towards the periphery. Visual acuity decreases with distance from the fovea in proportion to the estimated cortical magnification factor, M (the extent of striate cortex in millimetres corresponding to a degree of arc in visual space). If a stimulus is magnified at peripheral locations in proportion to 1/M, it becomes equally resolvable across the visual field. This scaling procedure (M-scaling) maintains equivalence of the cortical projection of stimuli with different visual field loci. We have used M-scaling to investigate motion perception as a visual field variable. We report here that both the lower threshold of motion and adaptation to motion are uniform for M-scaled stimuli, and are related to the velocity of the 'cortical image'.     

The regulatory peptide system of the large bowel in equine grass sickness

Summary In recent years, distinct changes in regulatory peptides have been found in a number of gastrointestinal diseases. Grass sickness is a fatal disease of horses for which the etiology has yet to be fully ascertained. In this study, the peptide-containing nerves and ganglionic and mucosal endocrine cells of the ileum, colon and rectum were investigated in horses with sub-acute or chronic grass sickness and compared with normal controls using immunocytochemistry, at both the light and electron microscopical levels, and radioimmunoassay. A substantial loss of both peptide-containing cells and nerves was found in all of the sick horses, particularly in the ileum. Electron microscopy revealed marked degeneration of nerves in the gut wall. fibers containing granules immunostained for substance P or VIP, using the immunogold staining technique, underwent extensive degranulation in grass sickness, with the formation of multiple vacuoles.Radioimmunoassay of peptide content also showed that the most drastic changes occurred in the ileum. For example, VIP content was significantly reduced from 109±19.8 (mean±SEM) pmoles/g in controls to 6.8±1.4 pmoles/g in grass sickness (p<0.001) and substance P from 65.9±8.1 to 31.3±9.5 (p<0.02). These results may have applications in the diagnosis and treatment of grass sickness.The authors gratefully acknowledge the financial support of the Wellcome Trust and the Grass Sickness Fund.     

Induction of a novel epidermal growth factor-secreting cell lineage by mucosal ulceration in human gastrointestinal stem cells

Epidermal growth factor, and its human homologue urogastrone (EGF/URO), are secreted by the gut-associated salivary and Brunner's glands. Recombinant EGF/URO is a powerful stimulator of cell proliferation and differentiation in the rodent and neonatal human intestine. But EGF/URO is not absorbed from the adult gut and has no action when given through the gut lumen; thus the role of secreted EGF/URO is unknown. We now report that ulceration of the epithelium anywhere in the human gastrointestinal tract induces the development of a novel cell lineage from gastrointestinal stem cells. This lineage initially appears as a bud from the base of intestinal crypts, adjacent to the ulcer, and grows locally as a tubule, ramifying to form a new small gland, and ultimately emerges onto the mucosal surface. The lineage produces neutral mucin, shows a unique lectin-binding profile and immunophenotype, is nonproliferative, and contains and secretes abundant immunoreactive EGF/URO. We propose that all gastrointestinal stem cells can produce this cell lineage after mucosal ulceration, secreting EGF/URO to stimulate cell proliferation, regeneration and ulcer healing. This cell lineage is very commonly associated with gastrointestinal mucosal ulceration, and we conclude that a principal in vivo role for EGF/URO is to stimulate ulcer healing throughout the gut through induction of this cell lineage in the adjacent mucosa.