Recursive use of evolutionary conservation data in molecular modeling of membrane proteins A model of the multidrug H+ antiporter emrE.

Membrane proteins are currently the most biomedically important family of proteins, serving as targets for the majority of pharmaceutical agents. It is also clear that they are invariably abundant in all of the genomes sequence so far, representing up to a third of all open reading frames. Finally, and regrettably, it is clear that they are highly resistant to structural elucidation, representing less than 0.2% of the Protein Data Bank. Recent accomplishments in genome sequencing efforts, however, may help offset this imbalance through the availability of evolutionary conservation data. Herein, we develop a novel approach, utilizing a combination of evolutionary conservation data and global searching molecular dynamics simulations to model membrane proteins, deriving a model for the multidrug H+ antiporter EmrE, a transmembrane four-helix bundle. Structures resulting from an extensive, rotational molecular dynamics search, were evaluated by comparing the residue specific interaction energy and the evolutionary conservation data. Subsequent rounds of molecular dynamics, in which confinement of the search space was undertaken in order to achieve a self consistent result, point to a structure that best satisfies the evolutionary conservation data. As the conservation patterns calculated for each of the helices suggested that the different conservation pattern for helix 3 (as well as being the most conserved) might be due to the oligomeric nature of EmrE, a dodecamer of helices was constructed based on the result of a search of helix 3 as a trimer. The resulting interaction energy per residue in the final model is in reasonable agreement with the evolutionary data and consistent with recent site directed mutagenesis experiments, pointing to the strength of this method as a general tool.     

THE KARYOTYPES OF DIPLOID CESPITOSE ZINNIAS: A METHOD AND ANALYSIS

The karyotypes of the three diploid (n = 10) species of the subg. Diplothrix (Zinnia—Compositae) were compared to determine whether there were any demonstrable differences which could then be sought in their polyploid derivatives. Because many of the chromosomes in a set were too similar to distinguish confidently between them, a method of analysis was developed which measures the similarity of whole sets of chromosomes rather than individual ones. The method consists of measuring the distances between graph-plotted vertices representing arm lengths of chromosomes of real or paper hybrids and then comparing these distances by means of U tests with those similarly derived for the “parents.” This procedure obviates the need of attempting to identify morphologues (morphologically similar chromosomes) in a somatic diploid root-tip cell and to equate corresponding pairs of chromosomes from different cells of a single plant or from different species or hybrids. No demonstrable differences in the karyotypes of diploid cespitose zinnias were found. Analysis of previously published data by this method indicated that there has been a general non-objectivity and non-operationalism in the determination of homologous chromosomes, and a general but unwarranted assumption that morphologues are in reality genologues (genetically corresponding chromosomes).     

Reduction of a Tetrazolium Salt in Determining Growth Activity of Yeast-Phase Histoplasma capsulatum

A colorimetric method using a tetrazolium compound, 3,4,5-dimethylthiozalil-(1 or 2),2,5-diphenyltetrazolium bromide (TTBr), was developed for studying the growth activity of yeast-phase Histoplasma capsulatum. Materials extracted in phosphate buffer, pH 7.0, from cells at different stages of growth reduced TTBr. Colorimetric changes were correlated with enzymatic activity. Under standardized conditions specified herein, the optical density of the reduced tetrazole was an index of the growth activity of the organism.     

Studies on several genetic hematological traits of the Mexican population. XII. Distribution of blood group antigens in twelve Indian tribes

Blood samples from 1090 Mexican Indians belonging to the Chol, Chontal, Totonac, Huastec, Mixe, Mazatec, Zapotec, Mixtec, Chinantec, Nahua, Cora and Huichol linguistic groups, were obtained and examined in regard to the following blood group antigens: A, B. M, N, P, C, c, D, E, e, Fy(a), K and Di(a). The gene frequencies were similar to what has been described for other Amerindians; high values for O, M, CDe, cDE and Duffy; low to absent Kell and presence of Diego in variable amounts. The frequency of chromosomes CDE and cDe/cde was somewhat higher than usual and some of the tribes had relatively high frequencies of the A and B antigens. It was felt that variable degrees of non-Indian admixture was at least partially responsible for this situation. A previous study dealing with the distribution of abnormal hemoglobins and glucose-6-phosphate dehydrogenase deficiency in these same tribes, had strongly suggested the possibility of some Negro admixture in the Chontal, Nahua and Cora tribes. However, this was not specifically reflected in their blood group distribution. This served to emphasize the need of investigating as many markers as possible when trying to characterize a population.     

Effect of Drying on Unexposed Autoradiographic Emulsion in Relation to Background

Unexposed blanks prepared from Kodak AR 10 stripping film were dried by 3 methods: (1) fast, open drying with a fan for 25 min, (2) slow drying in a desiccator for 6 hr, and (3) very slow drying in a desiccator for 24 hr. The number of background grains depended on the mode of drying. Fast drying (method 1) gave 0.7 grain per 100 μ², slow drying (method 2) gave 0.33 grain; very slow drying (method 3), only 0.17 grain. The increase of background after fast drying is assumed to be caused by the rapid shrinkage of wet emulsion. This causes an increase in the intraemulsion pressure which, in turn, sensitizes the silver bromide crystals to cause an increase in the number of developable grains.     

Effects of cesium on in vitro myoblast differentiation: An electron microscopic study

Summary This paper describes the microscopic evidence supporting a cesium-induced delay in the fusion of chick embryo myoblast membranes during in vitro myogenic differentiation. We have recently demonstrated that the sharp decrease in the conductivity and permittivity of the membranes of these myogenic cells at the time of fusion is delayed 30 h by the addition of cesium to the culture medium (Santini et al., Biochim. Biophys. Acta 945:56–64; 1988). We report here that this delay in fusion is substantiated by direct microscopic observation and that cesium also induces ultrastructural changes in the myoblast cells themselves. Possible mechanisms by which cesium may cause both the delay in fusion as well as the ultrastructural changes observed are discussed. This investigation was partially supported by an Italian Consiglio Nazionale delle Ricerche grant 85.00.304.02 (to P. L. I.).     

NOR polymorphism in the Iberian species Chondrostoma lusitanicum (Pisces: Cyprinidae)

Chromosomal polymorphism regarding number of NOR sites in the cyprinid fish Chondrostoma lusitanicum was examined using C-banding, silver-staining (Ag), and fluorescent staining with chromomycin A₃ (CMA₃). The analysis of heterochromatic regions allowed a more precise identification of the centromeric regions and the proposal of a revised haploid chromosome formula (7M: 15S: 3A). We describe variability in the number of NOR regions per genome, number of active NOR sites per cell, and relative size of individual NORs. Individuals expressed two or four NOR-bearing chromosomes. Polymorphism was detected in all the populations studied and sex-related differences were not found. The observed chromosomal NOR phenotypes suggest the occurrence of structural rearrangements during the evolutionary process of this diploid leuciscine cyprinid.     

Humoral anti-idiotypic and anti-anti-idiotypic immune response in cancer patients treated with monoclonal antibody 17-1A

 A group of 96 patients with advanced colorectal carcinoma were treated with the mouse (m) or chimeric (c) (mouse variable regions × human IgG1 constant regions) monoclonal antibody (mAb) 17-1A recognizing the tumour-associated antigen GA733-2. Eighty-two of the 83 patients treated with mmAb17-1A and 69% of the patients given cmAb17-1A (n = 13) developed anti-idiotypic antibodies (ab₂). Auto-antibodies binding to tumour cells expressing GA733-2 were found in 7% of the patients. In a further 38 patients (40%) antitumour-cell antibodies, i.e. anti-anti-idiotypic antibodies (ab₃), were induced by the mAb17-1A therapy. Patients with detectable ab₃ after treatment had significantly higher ab₂ levels than those not developing ab₃. Addition of granulocyte/macrophage-colony-stimulating factor (GM-CSF) to mmAb17-1A significantly enhanced the induction of ab₂ as well as induction of anti-anti-idiotypic antibodies (ab₃), compared to mmAb17-1A alone. Patients with a high increase in antitumour-cell antibodies (ab₃) induced by the therapy lived significantly longer than patients with no or a low level of induction of ab₃ (P = 0.016). The results indicate that induction of an idiotypic network response might be an important effector mechanism in mAb therapy. Received: 20 October 1995 / Accepted: 18 December 1995     

Neural control of the expression of a Ca2+-activated K+ channel involved in the induction of myotonic-like characteristics

Summary 1. Expression of the apamin-sensitive K⁺ channel (SK⁺) in rat skeletal muscle is neurally regulated. The regulatory effect of the nerve over the expression of some muscle ion channels has been attributed to the electrical activity triggered by the nerve and/or to a trophic effect of some molecules transported from the soma to the axonal endings. 2. SK⁺ channels apparently are involved in myotonic dystrophy (MD), therefore understanding the factors that regulate their expression may ultimately have important clinical relevance. 3. To establish if axoplasmic transport is involved in this process, we used two experimental approaches in adult rats: (a) Both sciatic nerves were severed, leaving a short or a long nerve stump attached to the anterior tibialis (AT). (b) Colchicine or vinblastine (VBL), two axonal transport blockers of different potencies, was applied on one leg to the sciatic nerve. To determine whether electrical activity affects the expression of SK⁺ channels, denervated AT were directly stimulated. The corresponding contralateral muscles were used as controls. 4. With these experimental conditions we measured (a) apamin binding to muscle membranes, (b) muscle contractile characteristics, and (c) electromyographic activity. 5. In the short- and long-nerve stump experiments, 5 days after denervation¹²⁵I-apamin binding to AT membranes was 2.0 times higher in the short-stump side. This difference disappeared at longer times. The delayed expression of SK⁺ channels in the muscle left with a longer nerve stump can be attributed to the extra axoplasm contained in the longer stump, which maintains a normally repressive signal for a longer period of time. Ten to 15 days after application of axonal transport blockers we found that the muscle half-relaxation time increased in the drug-treated side and apamin partially reverted the prolonged relaxation. Myotonic-like discharges specifically blockable by apamin were always present in the drug-treated leg.¹²⁵I-Apamin binding, which is undetectable in a microsomal preparation from hind leg control muscles, was increased in the drug-treated preparations. Apamin binding to denervated and stimulated AT muscles was lower than in the contralateral unstimulated muscles [3.3±1.0 vs 6.8±0.8 (n=4) fmol/mg protein]. 6. Our results demonstrate that electrical activity and axoplasmic transport are involved in the control of expression of SK⁺ in rat skeletal muscle. However, the increased expression of this channel induces myotonic-like characteristics that are reversed by apamin. This myotonic activity could be a model for MD.