The nature of inhibition of DNA gyrase by the coumarins and the cyclothialidines revealed by X-ray crystallography.

This study describes the first crystal structures of a complex between a DNA topoisomerase and a drug. We present the structures of a 24 kDa N-terminal fragment of the Escherichia coli DNA gyrase B protein in complexes with two different inhibitors of the ATPase activity of DNA gyrase, namely the coumarin antibiotic, novobiocin, and GR122222X, a member of the cyclothialidine family. These structures are compared with the crystal structure of the complex with an ATP analogue, adenylyl-beta-gamma-imidodiphosphate (ADPNP). The likely mechanism, by which mutant gyrase B proteins become resistant to inhibition by novobiocin are discussed in light of these comparisons. The three ligands are quite dissimilar in chemical structure and bind to the protein in very different ways, but their binding is competitive because of a small degree of overlap of their binding sites. These crystal structures consequently describe a chemically well characterized ligand binding surface and provide useful information to assist in the design of novel ligands.     

Transfer RNA Is the Source of Extracellular Isopentenyladenine in a Ti-Plasmidless Strain of Agrobacterium tumefaciens

Even in the absence of the classical Ti plasmid-encoded cytokinin biosynthetic genes ipt and tzs, Agrobacterium tumefaciens strains still release significant amounts of the cytokinin isopentenyladenine (iP) into the culture medium (R.W. Kaiss-Chapman and R.O. Morris [1977] Biochem Biophys Res Commun 76: 453-459). A potential source of the iP is isopentenylated transfer RNA (tRNA), which, in turn, is synthesized by the activity of tRNA:isopentenyltransferase encoded by the bacterial miaA gene. To determine whether secreted iP had its origin in isopentenylated tRNA, a miaA- deletion/insertion mutant was prepared and reconstructed in Agrobacterium tumefaciens in vivo. The mutant no longer possessed tRNA:isopentenylation activity and no longer released iP into the extracellular medium. Transfer RNA therefore makes a small but significant contribution to the total amount of cytokinin normally secreted by Agrobacterium strains. tRNA-mediated synthesis may also account for cytokinin production by other plant-associated bacteria, such as Rhizobia, that have been reported to secrete similarly low levels of nonhydroxylated cytokinins.     

Torture, Television, and Iranian Culture

The Making of Exile Cultures: Iranian Television in Los Angeles. Hamid Naficy
Torture and Modernity: Self, Society and State in Modern Iran. Darius M. Rejali     

Planar asymmetric lipid bilayers of glycosphingolipid or lipopolysaccharide on one side and phospholipids on the other: membrane potential, porin function, and complement activation.

We have determined some physicochemical properties of the monosaccharide-type fraction (GSL-1) of glycosphingolipids, the major glycolipid components of the outer leaflet of the Gram-negative species Sphingomonas paucimobilis. These properties included the state of order of the hydrocarbon moiety, the effective molecular area, surface charge density, and intrinsic transmembrane potential profile of reconstituted planar asymmetric GSL-1/phospholipid bilayer membranes. We have, furthermore, investigated the insertion into and the function of porin channels in the reconstituted bilayers and the complement-activating capability of GSL-1 surfaces. All results were compared with respective data for deep rough mutant lipopolysaccharide of Salmonella minnesota R595. We found a remarkable agreement in most functional properties of the two glycolipids.     

Effects of substrate limitation on product distribution and H2/CO2 ratio inKlebsiella pneumoniae during anaerobic fermentation of glycerol

Product formation during anaerobic degradation of glycerol byKlebsiella pneumoniae DSM 2026, under glycerol limitation and glycerol excess in continugius cultures, has been investigated. Major and minor products and by-products as well as gaseous products were measured. The results indicated a positive correlation between specific glycerol uptake and most product formation rates under glycerol limitation. The production of 1,3-propanediol, lactate, formate, acetate, succinate and the by-products of anaerobic glycerol degradation byK. pneumoniae, acetoin and 2,3-butanediol, was favoured by glycerol excess, while hydrogen generation and ethanol formation were best under glycerol limitation. It was also found that under glycerol limitation the rate of hydrogen evolution was generally higher than the CO₂ production rate while under excess glycerol the reverse was true. Hence, on the basis of the ratio of the specific rates of evolution of H₂ and CO₂ (q _{H 2}/q _{CO 2}), it is possible to infer the existence of glycerol limitation. On the basis of the carbon and available electron balances, which are independent of metabolic pathways, the data are consistent. The NADH₂ balance, which took into consideration the pathways of product formation, was also tested to check the validity of the assumed pathways and to check critically the consistency of the data. Good balances were also obtained.[     

Structure of REC2, a recombinational repair gene of Ustilago maydis, and its function in homologous recombination between plasmid and chromosomal sequences.

Mutation in the REC2 gene of Ustilago maydis leads to defects in DNA repair, recombination, and meiosis. Analysis of the primary sequence of the Rec2 protein reveals a region with significant homology to bacterial RecA protein and to the yeast recombination proteins Dmc1, Rad51, and Rad57. This homologous region in the U. maydis Rec2 protein was found to be functionally sensitive to mutation, lending support to the hypothesis that Rec2 has a functional RecA-like domain essential for activity in recombination and repair. Homologous recombination between plasmid and chromosomal DNA sequences is reduced substantially in the rec2 mutant following transformation. The frequency can be restored to a level approaching, but not exceeding, that observed in the wild-type strain if transformation is performed with cells containing multiple copies of REC2.     

Poly(3-hydroxybutyrate) granules ofBacillus megaterium

Cells ofBacillus megaterium contain 35–45% of poly(3-hydroxybutyrate) (PHB) at the beginning of the stationary phase. This amount is only slightly affected by the medium composition. The PHB granules are spherical with the mean diameter of 1.15 μm.     

Nutrient balances and phytoplankton dynamics in two agriculturally loaded shallow lakes

The impact of agriculture was estimated on two shallow, eutrophic lakes, Lake Kotojärvi and Lake Villikkalanjärvi in southern Finland. The main emphasis was on phosphorus and nitrogen budgets and on the phytoplankton dynamics. Special attention was paid to internal P loading and blue-green algal blooms. The mean Tot-P load from agricultural land was 1.2 kg ha^-1 a^-1 in both basins and Tot-N loads were 19 kg ha^-1 a^-1 in L. Villikkalanjärvi and 12 kg ha^-1 a^-1 in L. Kotojärvi. The Tot-P input to L. Kotojärvi was on an average 0.62 g m^-2 a^-1 (per lake surface area), and the Tot-N input 9.1 g m^-2 a^-1. The corresponding inputs to L. Villikkalanjärvi were 3.1 and 57 g m^-2 a^-1, respectively. The annual variation followed the runoff volumes. About half of the Tot-P and one third of the Tot-N load was retained in L. Kotojärvi. In L. Villikkalanjärvi the retention was only 24% for Tot-P and 19% for Tot-N. The difference was very probably due to a longer theoretical retention time in L. Kotojärvi. In L. Villikkalanjärvi the mean concentration of Tot-P was 120 µg 1^-1 and that of Tot-N 1700 µg 1^-1 and the corresponding figures in L. Kotojärvi 67 and 990 µg 1^-1, respectively. The mean chlorophyll a concentration was, however, higher in L. Kotojärvi (26 µg 1^-1) than in L. Villikkalanjärvi (20 µg 1^-1). This was probably due to an internal P load in L. Kotojärvi: in 1988 the internal load of dissolved P was estimated to be as much as twofold the external load. In L. Villikkalanjärvi the internal dissolved P load was only up to 50% of the external input. In L. Kotojärvi the high internal P load coupled with a low DIN:DIP ratio resulted in a strong blue-green algal bloom in the summer of 1988. In L. Villikkalanjärvi blue-green algae were observed only in small amounts. Even in August 1990, when the DIN:DIP ratio was low enough to favor the occurrence of blue-green algae, they contributed only up to 10–15% of the total phytoplankton biomass.