A Highlights from MBoC Selection: ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin

ChromoShake is a three-dimensional simulator designed to find the thermodynamically favored states for given chromosome geometries. The simulator has been applied to a geometric model based on experimentally determined positions and fluctuations of DNA and the distribution of cohesin and condensin in the budding yeast centromere. Simulations of chromatin in differing initial configurations reveal novel principles for understanding the structure and function of a eukaryotic centromere. The entropic position of DNA loops mirrors their experimental position, consistent with their radial displacement from the spindle axis. The barrel-like distribution of cohesin complexes surrounding the central spindle in metaphase is a consequence of the size of the DNA loops within the pericentromere to which cohesin is bound. Linkage between DNA loops of different centromeres is requisite to recapitulate experimentally determined correlations in DNA motion. The consequences of radial loops and cohesin and condensin binding are to stiffen the DNA along the spindle axis, imparting an active function to the centromere in mitosis.     

Preparation and biological activity of novel tricyclic GPIIb/IIIa antagonists

Antagonists of the glycoprotein GPIIb/IIIa are a promising class of antithrombotic agents offering potential advantages over present antiplatelet agents (i.e., aspirin and ticlopidine). Novel tricyclic nonpeptidal GPIIb/IIIa antagonists have been prepared and evaluated in vitro as antagonists of fibrinogen binding to the purified GPIIb/IIIa receptor and as inhibitors of platelet aggregation. The work presented demonstrates the robustness of the benzodiazepinedione (BZDD) scaffold, which can be functionalized at the N¹---C² amide as well as at C⁷, to provide structural diversity and allow optimization of the physiochemical and pharmacological properties of the BZDD based GPIIb/IIIa antagonists. In addition, the resulting new class of tricyclic GPIIb/IIIa antagonists could be used to probe for additional binding interactions on the GPIIb/IIIa receptor and perhaps lead to BZDD based GPIIb/IIIa antagonists with increased potency. The tricyclic molecules reported herein demonstrate that a heterocyclic ring can be fused to the benzodiazepinedione scaffold with retention of anti-aggregatory potency and in the case of tetrazole 30i, increased potency relative to the bicyclic analogue 1c.     

Cloning and sequence comparison ofAvaI andBsoBI restriction-modification systems

AvaI andBsoBI restriction endonucleases are isoschizomers which recognize the symmetric sequence 5′CYCGRG3′ and cleave between the first C and second Y to generate a four-base 5′ extension. TheAvaI restriction endonuclease gene (avaIR) and methylase gene (avaIM) were cloned intoEscherichia coli by the methylase selection method. TheBsoBI restriction endonuclease gene (bsoBIR) and part of theBsoBI methylase gene (bsoBIM) were cloned by the “endo-blue” method (SOS induction assay), and the remainder ofbsoBIM was cloned by inverse PCR. The nucleotide sequences of the two restriction-modification (RM) systems were determined. Comparisons of the predicted amino acid sequences indicated thatAvaI andBsoBI endonucleases share 55% identity, whereas the two methylases share 41% identity. Although the two systems show similarity in protein sequence, their gene organization differs. TheavaIM gene precedesavaIR in theAvaI RM system, while thebsoBIR gene is located upstream ofbsoBIM in theBsoBI RM system. BothAvaI andBsoBI methylases contain motifs conserved among the N⁴ cytosine methylases.     

Aneuploid epididymal sperm detected in chromosomally normal and Robertsonian translocation-bearing mice using a new three-chromosome FISH method

We present a new method to detect epididymal sperm aneuploidy (ESA) in mice using simultaneous fluorescence in situ hybridization (FISH) with DNA probes specific for mouse chromosomes X, Y and 8. The method was applied to Robertsonian (Rb) translocation (8.14) heterozygotes and homozygotes as well as the chromosomally normal B6C3F1. The sex ratios of sperm did not differ from the expected 1∶1 and the hybridization efficiencies were ≈99.7% for over 60 000 sperm analyzed. Mice heterozygous for Rb (8.14) produced about tenfold higher rates of sperm with chromosome 8 hyperhaploidy than did Rb (8.14) homozygotes or chromosomally normal mice, while frequencies of sperm with hyperhaploidies for chromosomes X and Y were unaffected in all three lines of mice. Hyperhaploid frequencies obtained with the ESA method were consistent with those of the previous testicular FISH method and were validated by published data obtained by conventional cytogenetic analyses (meiotic metaphase II and first cleavage). Thus, the mouse three-chromosome ESA assay together with the previously developed aneuploidy assay for human sperm constitute a promising pair of interspecific biomarkers for comparative studies of the genetic and physiologic mechanisms of the induction and persistence of aneuploidy in male germ cells. Edited by: T. Hassold     

Functional studies of yeast glucokinase.

Glucose phosphorylation capacity is known to be in excess of glucose flux in Saccharomyces cerevisiae wild type but not in a mutant strain lacking the two hexokinases but still having glucokinase. Nonetheless, we show here that in the latter strain, as in the wild type, the internal concentration of glucose is apparently low during growth on glucose and that additional glucokinase activity does not increase glucose flux. The glucokinase-dependent strain accumulates substantial amounts of glucose internally in batch culture after exhaustion of glucose, as well as from maltose. In both of these situations, low concentrations of radioactive glucose provided to the medium are used with incomplete, if any, mixing with the internal pool. Furthermore, in contrast to activity of hexokinase and other enzymes, little glucokinase activity is revealed by toluene treatment of cells. These results may point to a connection between glucose entry and its phosphorylation by glucokinase, but separate explanations for the various findings are also possible.     

Identification of Members of the Family Enterobacteriaceae by the R-B System

The R-B system was evaluated in parallel with conventional bacteriological procedures for the identification of members of the family Enterobacteriaceae by using bacterial strains from a variety of clinical specimens and from stock cultures. The R-B tests found to be reliable were, in decreasing order, the reactions for phenylalanine deaminase, hydrogen sulfide, and indole, the production of gas from glucose, and the decarboxylation of ornithine. The reactions in the R-B system found to be unreliable were motility, the decarboxylation of lysine, and the fermentation of both glucose and lactose. In addition, the reactions of the R-B system were more difficult to read and interpret than those of the conventional system. On the basis of this evaluation, it was concluded that the R-B system is not an acceptable alternative to the conventional methods in the identification of the Enterobacteriaceae.     

Early side effects of intrathoracic BCG therapy in patients with stage I squamous cell carcinoma,adenocarcinoma, or large cell lung cancer

Summary Data are presented on 179 stage I lung cancer patients subjected to resection operations and then given adjuvant intrapleural BCG and subsequent isoniazid (INH) therapy and on 167 control patients given intrapleural saline and placebo pills in a two-arm randomized double-blind study. The predominant immediate response to BCG/INH therapy was hyperpyrexia, which was found to be more pronounced in patients with larger induration in pretreatment PPD skin tests. Subsequently, chemical hepatitis (6 cases after BCG/INH versus 1 case after saline/placebo), peripheral neuropathy (3 versus 1), dermatitis/hives (5 versus 2), pleural thickening (4 versus 0), and persistent fever (10 versus 0) were noted. Analysis of laboratory changes measured at 18 weeks following randomization revealed that patients with BCG/INH lost 1.1 kg in weight and 0.30 g/dl in hemoglobin concentration on average, whereas control patients gained 1.2 kg and 0.33 g/dl, respectively. Modest rises in SGOT and alkaline phosphatase were apparent at 6 weeks after instillation of BCG compared with controls, but these differences were no longer statistically signifikant after 18 weeks. These side effects notwhithstanding, the BCG/INH therapy was well tolerated.Members of the Lung Cancer Study Group include R. T. Eagan*, R. E. Lee, W. S. Payne, R. E. Ritts, and L. Weiland from the Mayo Clinic, Rochester; C. F. Mountain*, H. T. Barkley, O. H. Frazier, K. Hermes, E. Hersh, and M. Valdivieso from M.D. Anderson Hospital, Houston; L. D. Hill*, M. D. Hafermann, and E. Morgan from The Mason Clinic, Seattle; P. W. Wright* and K.-E. Hellstrom from the Hutchinson Cancer Center, Seattle; C. Bagley, L. P. Johnson, H. Kellogg, and R. D. Pinkham from the Swedish Medical Center, Seattle; T. D. Ivey from University Hospital, Seattle; S. Hammar from Virginia Mason Hospital, Seattle; W. Nelems from St. Paul's Hospital, Vancouver; R. Feld*, D. Bergsagel, T. C. Brown, J. Curtis, C. Keen, J. F. Pringle, I. Quirt, and L. Yeoh from The Princess Margaret Hospital, Toronto; M. Blackstein and M. Goldberg from Mount Sinai Hospital, Toronto; F. G. Pearson*, D. W. Chamberlain, J. Cooper, W. Evans, and T. Todd from Toronto General Hospital, Toronto; M. Baker and R. Ginsberg from Toronto Western Hospital, Toronto; R. I. Mitchell from Wellesley Hospital, Toronto; E. C. Holmes*, W. F. Coulson, K. P. Ramming, and T. H. Weisenburger from the University of California, Los Angeles; Z. Petrovich from Wadsworth Veterans Hospital, Los Angeles; R. K. Oldham*, J. T. Forbes, F. A. Greco, D. L. Page, R. Prager, R. L. Richardson, and S. L. Stroup from Vanderbilt University, Nashville; J. M. Lukeman* and S. M. Sajjad from the Pathology Reference Center of M.D. Anderson Hospital, Houston; P. Grifone, A. Lebeck, and T. Voss from the Operations Office, Silver Spring, Maryland; M. Gail, W. McGuire, J. Allegra, and L. Rubinstein from the National Cancer Institute, Bethesda, Maryland; and L. Eirich, W. Heineman, and J. Beach from Information Management Services, Bethesda, Maryland. Asterisks designate principal investigators.     

Growth of Rhizobium japonicum Strains at Temperatures Above 27°C

A study was conducted to examine the growth responses of different Rhizobium japonicum strains to increasing temperatures, determine the degree of variability among strains in those responses, and identify temperature-related growth characteristics that could be used to select temperature-tolerant strains. Each of 42 strains was grown in liquid culture for 96 h at 19 incubation temperatures ranging from 27.4 to 54.1°C in a temperature gradient apparatus. Growth was estimated by measuring the change in optical density over time. Strains differed in their responses to increasing temperatures. Three characteristic temperatures were determined for each strain: the temperature giving the maximum optical density at 96 h (optimum temperature), the maximum temperature allowing a continuous increase in optical density during the 96-h period (maximum permissive temperature), and the maximum temperature allowing growth of the cultures after they were transferred to a uniform incubation temperature of 28°C (maximum survival temperature). The three characteristic temperatures varied among strains and had the following ranges: optimum temperature, from 27.4 to 35.2°C; maximum permissive temperature, from 29.8 to 38.0°C; and maximum survival temperature, from 33.7 to 48.7°C. Significant positive correlations were found between maximum permissive temperature and optimum temperature and between maximum permissive temperature and maximum survival temperature. Eight strains which had the highest maximum permissive temperature, optimum temperature, and maximum survival temperature were considered tolerant of high temperatures and were able to grow at temperatures higher than those previously reported for the most tolerant R. japonicum strains. The strains were of diverse geographical origin, but the response to high temperatures was not related to their origin. Evaluation of the temperature responses in pure culture may be useful in the search for R. japonicum strains better suited to environments in which high soil temperature is a limiting factor.     

Density Centrifugation Method for Recovering Rhizobium spp. from Soil for Fluorescent-Antibody Studies

A density centrifugation procedure has been developed as a replacement for soil flocculation and clarification steps employed in quantitative fluorescent-antibody studies on Rhizobium in soils. Near-quantitative recovery of added cells of two strains of Rhizobium japonicum and two strains of R. phaseoli was achieved from six soils with various properties. It is proposed that this technique may prove useful in separating other soil microorganisms from soil particles in ecological studies employing fluorescent-antibody techniques.     

Ethanol production by immobilized cells of Zymomonas mobilis

Summary Columnar reactors containing immobilized cells of Zymomonas mobilis were utilized for the continuous production of ethanol from glucose. Two different immobilization strategies were investigated. In one case, cells were entrapped in borosilicate glass fiber pads, while in the other, cells were immobilized via flocculation. The reactors were operated in both the fixed-bed and expanded-bed manner. Ethanol productivities as high as 132 g/l·h were achieved. Data obtained from studies employing 5.0 and 10.0% glucose concentrations are presented. Problems encountered during the operation of the continuous, immobilized cell reactors are discussed.Operated by Union Carbide Corporation under contract W-7405-eng-26 with the U.S. Department of Energy.