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.     

Comparative 16S rRNA oligonucleotide analyses and murein types of round-spore-forming bacilli and non-spore-forming relatives

The phylogenetic incoherency of the genus Bacillus as presently described is demonstrated by analysis of both published and new data from comparative 16S rRNA cataloguing of nine Bacillus species and a number of related non-Bacillus taxa, i.e. Caryophanon latum, Filibacter limicola and Planococcus citreus. While the ellipsoidal-spore-forming bacilli, e.g. B. subtilis and allied species, formed a coherent cluster, the round-spore-forming bacilli showed a higher degree of relationship to the non-spore-forming organisms than these bacilli show among each other. Thus B. sphaericus clustered with C. latum, B. globisporus grouped with F. limicola, B. pasteurii with Sporosarcina ureae, and 'B. aminovorans' with P. citreus, respectively. These organisms formed two related subclusters which, in their phylogenetic depth, are comparable to that of the B. subtilis subline. With the exception of 'B. aminovorans', the 16S rRNA phylogeny was entirely consistent with the distribution of murein types. Even more distantly related to and grouping outside the main Bacillus cluster was B. stearothermophilus, which displayed a moderate relationship to Thermoactinomyces vulgaris. Taxonomic problems arising from the new insights into the intrageneric relationships of Bacillus are discussed.     

Isoelectric and mass characterization of human platelet thromboxane A2/prostaglandin H2 receptors

To further characterize the human thromboxane A2 (TXA2)/prostaglandin H2 (PGH2) receptor, preparative isoelectric focusing (IEF) was performed on solubilized platelet membranes. TXA2/PGH2 receptors, assayed by specific binding of the TXA2/PGH2 antagonist [125I]PTA-OH, were electrofocused at pH 5.6. Scatchard analysis of IEF fraction pH 5.6 revealed a 180-fold concentration of TXA2/PGH2 receptors (Bmax = 3650 +/- 228 pM/mg focused, 19 +/- 4 pM/mg unfocused) with no change in binding affinity (Kd = 47 +/- 7 nM focused, 36 +/- 14 nM unfocused). SDS-polyacrylamide gel electrophoresis of photoaffinity-labelled electrofocused receptors revealed concentration of specifically labelled proteins having molecular masses of 49,000 and 27,000 Daltons. These results suggest that the human platelet TXA2/PGH2 receptor has a pI of 5.6, molecular mass of 49,000 Daltons, and may exist as a dimer. Preparative IEF should prove useful in the eventual purification of this receptor.     

Studies on protein kinases involved in regulation of nucleocytoplasmic mRNA transport.

The rate of energy-dependent nucleoside triphosphatase (NTPase)-mediated nucleocytoplasmic translocation of poly(A)-containing mRNA [poly(A)+mRNA] across the nuclear envelope is thought to be regulated by poly(A)-sensitive phosphorylation and dephosphorylation of nuclear-envelope protein. Studying the phosphorylation-related inhibition of the NTPase, we found that phosphorylation of one polypeptide of rat liver envelopes by endogenous NI- and NII-like protein kinase was particularly sensitive to poly(A). This polypeptide (106 kDa) was also phosphorylated by nuclear-envelope-bound Ca2+-activated and phospholipid-dependent protein kinase (protein kinase C). Activation of kinase C by tumour-promoting phorbol esters resulted in inhibition of nuclear-envelope NTPase activity and in a concomitant decrease of mRNA (actin) efflux rate from isolated rat liver nuclei. Protein kinase C, but not nuclear envelope NI-like or NII-like protein kinase, was found to be solubilized from the envelope by Triton X-100, whereas the presumable poly(A)-binding site [the 106 kDa polypeptide, representing the putative carrier for poly(A)+mRNA transport] remained bound to this structure. RNA efflux from detergent-treated nuclei lost its susceptibility to phorbol esters. Addition of purified protein kinase C to these nuclei restored the effect of the tumour promoters. Protein kinase C was found to bind also to isolated rat liver nuclear matrices in the absence but not in the presence of ATP. The NII-like nuclear-envelope protein kinase co-purified together with the 106 kDa polypeptide which specifically binds to poly(A) in an ATP-labile linkage.     

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.     

Third chromosome suppressor of position-effect variegation loci in Drosophila melanogaster

Summary As a result of a genetic analysis of 63 third chromosome suppressor mutations of position-effect variegation 12 different loci showing dominant suppression have been identified and their map positions determined. A compilcation of the genetic data available for each suppressor locus is given. The strong suppressor effects of the mutations have been quantified by measurements of white variegation inw ^m4h /w ^m4h ,w ^m4h /Y andw ^m4h /O flies. Mutant alleles of three loci were found in these studies to dominate over the strong enhancer effect of complete loss of the Y chromosome. Most of the identified loci suppressing position-effect variegation represent essential genetic funtions; only three loci represent nonessential functions. Mutations of two loci display recessive butyrate sensitivity and lethal interaction with the heterochromatic Y chromosome suggesting that these genes affect chromosomal condensation. Studies with deficiencies and triploids revealed that most of the loci represent haplo-abnormal suppressor functions. The use of the isolated mutant material for genetic, developmental and molecular studies of processes connected with gene inactivation in position-effect variegation is discussed.Dedicated to Prof. H.J. Becker on the occasion of his 6th birthday     

Die endokrinen drüsen im embryo von Oncopeltus fasciatus Dallas (Insecta,Heteroptera)

The differentiation of the endocrine glands in the embryo of Oncopeltus fasciatus is described. The function of these glands can be correlated with the embryonic moults. The nuclei of some tissues already become polyploid in the embryo. It is discussed whether the endomitotic growth is dependent upon the function of the endocrine glands.

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Abkürzungen in den Abbildungen A Ca Anlage des Corpus allatum - A Cc Anlage des Corpus cardiacum - A Maxd Anlage der Maxillendrüse - A Meth Anhang des Mesothorax - A Mth Anhang des Metathorax - A Pl Anlage des-Pleuropodiums - A Prd Anlage der Prothoraxdriise - A Pth Anhang des Prothorax - A Spd Anlage der Speicheldrüse - Am Amnion - Ant Antenne - Ao Aorta - Blz Blutzelle - Ca Corpus allatum - Cc Corpus cardiacum - Cul Cuticulinschicht - Cut Cuticula - Des Desmosom - dl denselayer - Do Dotter - Ent Entoderm - Ep Epidermis - Epk Epidermiskern - Fk Fettkörper - fl Do verflüssigter Dotter - Hyp Hypocerebralganglion - Hz Herzschlauch - Kl Kopflappen - La Labrum - Lab Labium - M Mitteldarm mit verschiedenen Abschnitten (I, II, III und IV) - Mal Malpighisches GefäB - Max Maxille - Md Mandibel - Mes Mesoderm - Mik Mikrovilli - Ms Muskel - Mst Mittelstrang - Nbl Neuroblast - NZ Neurosekretorische Zellen - Oen Oenocyt - Oes Oesophagus - Ogl Oberschlundganglion - p Cut Procuticula - Pcz Pericardialzelle - Pi Pleuropodium - Prd Prothoraxdrüse - Pyl Pylorus - Re Rectum - Rk Riesenkern - S Schlüpfakt - Sal Salivarium - Ser Serosa - Sg Segmentgrenze - Spd Speicholdrüse (I = vorderer Lappen, II = scitlicher Lappen, III = hinterer Lappen, IV = akzessorische Drüse und V = Hylus) - Spdg Speicheldrüsengang - St Stechborste - Std Stinkdrüse - Sti Stigma - Stom Stomodaeum - Stt Stechborstentasche - tb E tubuläre Einstülpung des Prothorax - Ugl Unterschlundganglion - V Vakuole Mit Unterstutzung der Deutschen Forschüngsgemcinschaft.     

Isolation and characterization of a 3-chlorobenzoate degrading pseudomonad

A pseudomonad has been isolated from sewage, which can utilize 3-chlorobenzoic acid as a sole carbon source. In cells grown on benzoate the enzymes of the -ketoadipic acid pathway are present. Considerable enzymic activities for chlorinated substrates were found in benzoate grown cells only for the oxygenation of 3-chlorobenzoate and the dehydrogenation of 3- and 5-chloro-3,5-cyclohexadiene-1,2-diol-1-carboxylic acid. 3-Chlorobenzoate grown cells show additional high activities for the turnover of 3- and 4-chlorocatechols and chloromuconic acids.Abbreviations Used DHB (-)-3,5-cyclohexadiene-1,2-diol-1-carboxylic acid (derived from the trivial name, dihydrodihydroxybenzoate) - 3- and 5-Cl-DHB correspondingly 3- and 5-chloro-3,5-cyclohexadiene-1,2-diol-1-carboxylic acid