Molecular Reclassification of Crohn’s Disease: A Cautionary Note on Population Stratification

Complex human diseases commonly differ in their phenotypic characteristics, e.g., Crohn’s disease (CD) patients are heterogeneous with regard to disease location and disease extent. The genetic susceptibility to Crohn’s disease is widely acknowledged and has been demonstrated by identification of over 100 CD associated genetic loci. However, relating CD subphenotypes to disease susceptible loci has proven to be a difficult task. In this paper we discuss the use of cluster analysis on genetic markers to identify genetic-based subgroups while taking into account possible confounding by population stratification. We show that it is highly relevant to consider the confounding nature of population stratification in order to avoid that detected clusters are strongly related to population groups instead of disease-specific groups. Therefore, we explain the use of principal components to correct for population stratification while clustering affected individuals into genetic-based subgroups. The principal components are obtained using 30 ancestry informative markers (AIM), and the first two PCs are determined to discriminate between continental origins of the affected individuals. Genotypes on 51 CD associated single nucleotide polymorphisms (SNPs) are used to perform latent class analysis, hierarchical and Partitioning Around Medoids (PAM) cluster analysis within a sample of affected individuals with and without the use of principal components to adjust for population stratification. It is seen that without correction for population stratification clusters seem to be influenced by population stratification while with correction clusters are unrelated to continental origin of individuals.     

The influence of diet on the growth of Stenonema vicarium (Walker) (Ephemeroptera: Heptageniidae)

Laboratory studies compared the growth rate of Stenonema vicarium (Walker) nymphs on diets of detritus and natural stream periphyton. In three consecutive runs of the experiment, growth rates were consistently higher on periphyton (mean growth rate = 2.1% wet wt. d⁻¹) than detritus (mean = 1.8% wet wt. d⁻¹). The starting date of each run also significantly influenced growth rates. In each treatment growth rates generally decreased over the course of the 3 runs, and ca. one-half of the nymphs in the last run did not molt or grow. It appeared that growth of S. vicarium may be partially controlled by seasonal factors.     

The effects of substance P and carbachol on inositol tris- and tetrakisphosphate formation and cytosolic free calcium in rat parotid acinar cells. A correlation between inositol phosphate levels and calcium entry

Both substance P and carbachol produced increases in inositol tris- and tetrakisphosphate and increased cytosolic free [Ca2+] in dispersed parotid acinar cells loaded with fura-2. The increase in [Ca2+]i in response to each agonist was due to a combination of mobilization of internal Ca2+ and entry of extracellular Ca2+. Kinetic studies of the initial response to substance P, and measurement of peak [Ca2+]i, demonstrated that the initial rapid rise in [Ca2+]i was due to both internal release and entry of Ca2+. Substance P could evoke a greater initial increase in [Ca2+]i and inositol trisphosphate than could carbachol. However, after 1 min in the presence of external Ca2+, the maintained [Ca2+]i level in response to substance P was considerably smaller than that seen with carbachol, an effect apparently due to homologous desensitization of the substance P receptor. The two agonists each produced a similar 4-5-fold increase in inositol tetrakisphosphate levels within 30 s; this level was maintained in the presence of carbachol, but decreased with substance P. Similarly, the level of inositol (1,4,5)-trisphosphate decreased after prolonged incubation with substance P. Thus, the maintained level of [Ca2+]i, and by deduction Ca2+ entry, correlated with the levels of inositol (1,4,5)-trisphosphate and inositol tetrakisphosphate; a result consistent with a possible role for these inositol phosphates in the control of receptor-mediated Ca2+ channels.     

The cercal sensilla of the blowfly Lucilia cuprina. II. Structure of the enveloping cells and the basal regions of the sensory dendrites

The gustatory, olfactory, touch and stress receptors on the cerci of Lucilia cuprina Wied. (Diptera: Calliphoridae) have either two or three enveloping cells. The gustatory and olfactory sensilla have three enveloping cells: a tormogen, trichogen and thecogen cell. The tormogen and trichogen cells contribute to a sub-cuticular sensillar lumen which divides into two lobes basally. The thecogen cell forms a lumen around the dendrites. Distally the dendrites lie in the contents of the thecogen lumen within the dendritic sheath. Proximally the dendrites embed in the thecogen cell which has an expanded, microlamellate lumen basally. The sensillar lumen of the mechanosensory (trichoid mechanoreceptors and campaniform) sensilla is formed by a single enveloping cell: the presumptive tormogen cell. In trichoid mechanoreceptors the thecogen lumen is restricted to the region of the transitional region of the dendrite whereas the thecogen lumen of campaniform sensilla extends proximally although it is not as well-developed as that of the chemoreceptive sensilla. The dendrites of all sensillum types on the cerci have a granular body in the transitional region: a situation which has not been previously reported in chemoreceptive sensilla although common in the mechanoreceptors of Calliphoridae and Sarcophagidae.     

Cytoplasmic Poly(ADP-Ribose) Polymerase Associated with Free Messenger Ribonucleoprotein Particles in Rat Brain

Poly(ADP-ribose) polymerase associated with free cytoplasmic messenger ribonucleoprotein particles (free mRNP particles) carrying messenger RNA has been characterized in rat brain. There were first-order kinetics for NAD with an apparent Km for NAD of 90.5 +/- 0.70 microM and Vmax of 19.7 +/- 2.8 pmol ADP-ribose incorporated min-1 mg protein-1. Five poly(ADP-ribose) protein acceptors were identified in the Mr 37,000-120,000 range. It is hypothesized that ADP-ribosylation of specific free mRNP proteins might play a role in the derepression and translation of the silent mRNAs of free mRNP particles.     

Genetic structure of natural populations of the red-spotted newt,Notophthalmus viridescens

Genetic variation is described at 15 loci in 2 neotenic and 12 nonneotenic populations of red-spotted newts. Though high levels of genetic similarity (I=0.990) were found among all populations, allele frequencies at six of the eight most polymorphic loci show significant heterogeneity across populations. Change in allele frequencies at two of these loci (Pep-2 and Ldh-1) is significantly correlated with latitude. Interspecific homologies are established for newt peptidases based on substrate specificities and lactate dehydrogenases based on tissue distribution, thermal stability, and kinetic properties. Nonneotenic populations are highly variable (H=0.157) and neotenic populations are only slightly, but significantly, less variable (H=0.120). The high levels of heterozygosity detected in nonneotenic populations may result from large effective population size and/or environmental heterogeneity. The unexpectedly high heterozygosity values obtained for the neotenic populations may indicate adult dispersal or the presence of some previously undetected red efts at these localities. In any case, a major change in life history has apparently had little effect on the genetic structure of these populations.This research was supported by grants from the Blakeslee Fund of Smith College.     

Failure of bacterial endotoxin to produce the generalized Shwartzman reaction in the Syrian hamster

The ability of bacterial endotoxin to produce the generalized Shwartzman reaction (GSR) in pregnant and nonpregnant hamsters was investigated. Endotoxins prepared from Escherichia coli O127:B8, Salmonella enteritidis, and S. typhosa 0-901 did not produce the GSR in nonpregnant hamsters. Injection of lead acetate did not make the hamsters susceptible to the GSR producing effects of endotoxin. Endotoxin administered to hamsters on either or both the 14th and 15th day of the 16-day gestation period caused fetal death, but did not provoke the GSR. The immunization of hamsters with boiled suspensions of gram-negative bacteria isolated from hamster feces did not protect against the GSR produced in pregnant hamsters by the injection of the antimitotic drug colchicine late in the gestation period. It appeared that colchicine was acting to produce the GSR by a mechanism other than the release of endogenous endotoxin through the damaged intestinal wall. Ascitic fluid, amniotic fluid, and serum obtained from pregnant hamsters developing the GSR after the administration of colchicine did not provoke the GSR in other pregnant hamsters.