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.     

De novo-synthesized ceramide signals apoptosis in astrocytes via extracellular signal-regulated kinase.

Recent observations support the importance of ceramide synthesis de novo in the induction of apoptosis. However, the downstream targets of de novo-synthesized ceramide are unknown. Here we show that palmitate incorporated into ceramide and induced apoptotic DNA fragmentation in astrocytes. These effects of palmitate were exacerbated when fatty acid breakdown was uncoupled and were not evident in neurons, which show a very low capacity to take up and metabolize palmitate. Palmitate-induced apoptosis of astrocytes was prevented by L-cycloserine and fumonisin B1, two inhibitors of ceramide synthesis de novo, and by PD098059, an inhibitor of the extracellular signal-regulated kinase (ERK) cascade. Accordingly, palmitate activated ERK by a process that was dependent on ceramide synthesis de novo and Raf-1, but independent of kinase suppressor of Ras. Other potential targets of ceramide in the control of cell fate, namely, c-Jun amino-terminal kinase, p38 mitogen-activated protein kinase, and protein kinase B, were not significantly affected in astrocytes exposed to palmitate. Results show that the Raf-1/ERK cascade is the selective downstream target of de novo-synthesized ceramide in the induction of apoptosis in astrocytes and also highlight the importance of ceramide synthesis de novo in apoptosis of astrocytes, which might have pathophysiological relevance.     

The ACTH-immunoreactive system in the brain of the white-crowned sparrow, Zonotrichia leucophrys gambelii (Passeriformes, Emberizidae)

The ACTH-immunoreactive (ir) system of the avian brain is particularly conspicuous in the male white-crowned sparrow (Zonotrichia leucophrys gambelii). The irperikaryal population is concentrated mainly within the tuberal region, projecting primarily in a dorsal direction: (i) into the striatum; (ii) into rostral diencephalic, septal, hyperstriatal, and thalamic areas; and (iii) into dorsal and ventral areas of the brain stem. Ir-fibers seemingly contact local non-immunoreactive neurons mainly in the accumbens nucleus, septum, dorsal thalamic nuclei, infundibular and interpeduncular nuclei, and in the rostral diencephalon. Neurohemal zones are not supplied by ACTH-ir terminals. Immunocytochemical problems arising from the complexity of the proopiomelanocortin molecule and its derived peptide components are discussed in relation to phylogenetically directed studies, and contradictory results.     

Thermal melting and circular dichroism of DNA complexes with (Lys-Ala-Ala)10 and (Lys-Ala-Ala)n: effect of polypeptide chain length

DNA complexes with polypeptides (Lys-Ala-Ala)₁)] and (Lys-Ala-Ala)₃₄ have been studied using the methods of thermal melting and circular dichroism. Derivative melting curves of (Lys-Ala-Ala)₁₀ DNA differed substantially from those of (Lys-Ala-Ala)₃₄ prepared either by salt gradient dialysis or by direct mixing. Melting curves of the former complex were unimodal or bimodal with T_m increasing continuously withn input lysin-to-DNA phosphate ratio (r); those of the latter complex consisted of three separate transitions with T_m values almost independent of r. Complete reversibility of binding in the (Lys-Ala-Ala)₁₀-DNA system but a slow redistribution of (Lys-Ala-Ala)₃₄ on DNA at low temperature were found in the redistribution experiments Much faster redistribution from denatured to native DNA occurs at the temperature of melting, contributing to the unusual trimodal melting pattern. Circular dichroism curves are very similar for both complexes and indicate little change of DNA conformation upon polypeptide binding.     

The effect of (+) cyanidanol-3 on the Na+-K+-ATP-ase and Mg++-ATP-ase activities of the rat brain in the presence and absence of ascorbic acid

The authors investigated the effects of (+) cyanidanol-3-(Catergen) in vitro on the activities of rat brain plasma membrane and microsomal Na+-K+-ATP-ase and Mg++-ATP-ase, in the presence and absence of ascorbic acid. Due to lipid peroxidation induced by low concentration of ascorbid acid, activity of both ATP-ase decreased. (+) cyanidanol-3 proved to be an effective antioxidant in this system. It inhibited the decrease of ATP-ase activity which occurred as a result of lipid peroxidation promoted by ascorbic acid.     

Dual translational initiation sites control function of the lambda S gene.

Lysis gene S of phage lambda has a 107 codon reading frame beginning with the codons Met1-Lys2-Met3. Genetic data have suggested that translational initiation occurs at both Met1 and Met3, generating two polypeptides, S107 and S105 respectively. We have proposed a model in which the proper scheduling of lysis depends on the partition of translational initiations between the two start codons. Here, using in vitro methods, we show that two stem-loop structures, one immediately upstream of the reading frame and a second approximately 10 codons within the gene, control the partitioning event. Utilizing primer-extension inhibition or 'toeprinting', we show that the two S start codons are served by two adjacent Shine-Dalgarno sequences. Moreover, the timing of lysis supported by the wild-type and a number of mutant alleles in vivo can be correlated with the ratio of ternary complex formation over Met1 and Met3 in vitro. Thus the regulation of the S gene is unique in that the products of two adjacent in-frame initiation events have opposing function.     

Testing of Arg-8-gonadotropin-releasing hormone-directed antisera by immunological and immunocytochemical methods for use in comparative studies

Three polyclonal antisera raised in rabbits against the mammalian molecular form of gonadotropin-releasing hormone (GnRH) were tested in enzyme-linked immunosorbent assays for crossreactivity with naturally occurring GnRHs and with GnRH analogues. Antisera were then tested immunocytochemically in order (i) to identify amino acids essential for the binding of each antiserum, and (ii) to evaluate the specificity of the immunocytochemical reaction in brain sections from various species of cyclostomes, amphibians, reptiles, and birds. Antiserum GnRH 80/1, recognizing mainly a discontinuous determinant including the NH2- and COOH-termini, crossreacts with GnRHs the molecular bending of which enables the spatial approach of both terminal amino acid residues. Antiserum GnRH 80/2, by requiring the COOH-terminus for binding and not tolerating substitutions by aromatic amino acids in the middle region of the molecule, recognizes chicken I GnRH, however, not the salmon form. The use of this antiserum is appropriate in species synthesizing the mammalian and/or the chicken I form of GnRH. GnRH antiserum 81/1 is specific mostly for mammalian GnRH. The results obtained by ELISAs are confirmed by immunocytochemical studies. A comparison between the results obtained in ELISA and in immunocytochemistry involving mammalian-, chicken I-, chicken II-, salmon-, and lamprey-directed GnRH antisera resulted in the following conclusions: (1) An antiserum recognizing the discontinuous antigen determinant including both NH2- and COOH-termini may be reactive in most vertebrate brain sections thus being appropriate for phylogenetically directed immunocytochemical studies. (2) Moreover, this discontinuous determinant seems to be immunocytochemically reactive in all parts of the neurons in the GnRH system, whereas, in some species, determinants located in the middle region of the molecule(s) tend to become reactive only during the axonal transport. (3) A crossreaction between tissue-bound antigen and antibodies recognizing the above cited discontinuous determinant indicates an appropriate bending of the molecule even in case of severe molecular differences, e.g., in lamprey form of GnRH. (4) It follows that in phylogenetic studies, an immunologically well characterized antiserum can be substituted for a species-directed antiserum.     

Progress in the histomorphometry of the microcirculatory system

Following a short review of the limits set to the procedures applied so far to measure quantitative changes in wall tissue of microvessels, a new measuring method is presented. It detect morphological reactions of the microcirculatory system on the grounds of changes in the numerical density of selectively visualized microvessels and their classification according to the external diameter by means of the automatic microscopic image analysing system QUANTIMET. Influences of structurally based and/or postmortal changes of the lumen wideness on the measurement are excluded by the automatic subtraction of the lumen area.     

Changes in auditory evoked brain potentials during ultra-low frequency whole-body vibration of man or of his visual surround

Auditory evoked brain potentials (AEP) were recorded from nine healthy male subjects during three types of condition: A - subject and visual field stationary; B - subject vibrated (z-axis, 0.6 Hz, 1.85 ms-2 rms), visual field stationary; C - subject stationary, visual field vibrated (as for B). The visual surround was confined to a checkerboard pattern in front of the subject. Auditory stimuli (1000 Hz, 86 dB, interstimulus interval 7 s) were delivered via headphones to evoke AEP. Vibration-synchronous activity in the EEG was eliminated by a subtraction technique. In comparison with condition A, conditions B and C caused an attenuation of P2 and N1P2 components of AEP together with an increased latency of N1. Effects of conditions B and C did not differ. Direct vestibular stimulation and mechanisms specific for whole-body vibration were rejected as modes of action. The AEP-changes and the subjective evaluation of experimental conditions, arousal and performance, as well as symptoms of kinetosis (motion sickness) suggest a sensory mismatch, leading to a "latent kinetosis" with de-arousal, as the dominating mechanism by which the processing of information was affected. This suggestion was supported by an additional pilot study. Under real working conditions a similar effect can be expected during relative motion between the driver and his visual surround, i.e. even with perfect vibro-isolation of the driver's seat.     

Somatic characteristics of an Australian population of Oreochromis mossambicus (Pisces: Cichlidae)

Synopsis The Oreochromis mossambicus population of North Pine Dam, Brisbane, Queensland, Australia was studied over three years, from 1985 to 1988. Basic somatic data were obtained and characteristic values of condition factor, sex ratio, gonosomatic index and the relationships between total and standard lengths, and length and weight, were calculated. Standard length is proportional to total length by the formula SL = –0.321 + 0.799 TL. Weight is related to length by the isometric formula W = aL³. Condition factor values spanned the range 0.0254 to 0.0563, with an average of 0.04078 for males and 0.03877 for females. The sex ratio is 1: 1 until maturity is reached (21 cm SL), at which time the catch rate of the sexes varies due to divergent habitat selection behaviour. Average values of gonosomatic index, considered in relation to maturity classification, are similar to those obtained from other populations, however maximum values are generally much lower, at 0.47 for males and 3.62 for females. These characteristic values are compared, with varying degrees of concordance, with those for populations of this species in other countries.