The Insertion Sequences of Anabaena sp. Strain PCC 7120 and Their Effects on Its Open Reading Frames

Anabaena sp. strain PCC 7120, widely studied, has 145 annotated transposase genes that are part of transposable elements called insertion sequences (ISs). To determine the entirety of the ISs, we aligned transposase genes and their flanking regions; identified the ISs'' possible terminal inverted repeats, usually flanked by direct repeats; and compared IS-interrupted sequences with homologous sequences. We thereby determined both ends of 87 ISs bearing 110 transposase genes in eight IS families (http://www-is.biotoul.fr/) and in a cluster of unclassified ISs, and of hitherto unknown miniature inverted-repeat transposable elements. Open reading frames were then identified to which ISs contributed and others—some encoding proteins of predictable function, including protein kinases, and restriction endonucleases—that were interrupted by ISs. Anabaena sp. ISs were often more closely related to exogenous than to other endogenous ISs, suggesting that numerous variant ISs were not degraded within PCC 7120 but transferred from without. This observation leads to the expectation that further sequencing projects will extend this and similar analyses. We also propose an adaptive role for poly(A) sequences in ISs.Insertion sequences (ISs) are transposable elements found in prokaryotic and eukaryotic genomes (17). A fully functional bacterial IS comprises one or more transposase genes, ends that are often inverted repeats (IRs), and, between the transposase genes and the ends, sequences termed linkers (32). Diverse bacterial ISs have been classified, and a searchable database of ISs has been constructed (ISfinder [http://www-is.biotoul.fr/]) (28). Miniature inverted-repeat transposable elements (MITEs) and even smaller mobile elements lack their own transposases and are also found in Anabaena spp. (11, 12, 33).Anabaena sp. strain PCC 7120 (also known as Nostoc sp. [25], here denoted Anabaena sp.) is widely used to study the patterned differentiation of dinitrogen-fixing cells called heterocysts. Transposition of ISs in Anabaena sp. has been documented (1, 7-9). We earlier reported, with few details, three genes that are intercepted by ISs in Anabaena sp. (23). We here describe the approach more extensively, organize the ISs of Anabaena sp., and present our efforts to identify Anabaena sp. open reading frames (ORFs) interrupted or contributed to by ISs.     

Clustered genes required for synthesis and deposition of envelope glycolipids in Anabaena sp. strain PCC 7120

Photoreduction of dinitrogen by heterocyst-forming cyanobacteria is of great importance ecologically and for subsistence rice agriculture. Their heterocysts must have a glycolipid envelope layer that limits the entry of oxygen if nitrogenase is to remain active to fix dinitrogen in an oxygen-containing milieu (the Fox+ phenotype). Genes alr5354 (hglD), alr5355 (hglC) and alr5357 (hglB) of the filamentous cyanobacterium, Anabaena sp. strain PCC 7120, and hglE of Nostoc punctiforme are required for synthesis of heterocyst envelope glycolipids. Newly identified Fox- mutants bear transposons in nearby open reading frames (orfs) all5343, all5345-asr5349 and alr5351-alr5358. Complementation and other analysis provide evidence that at least orfs all5343 (or a co-transcribed gene), all5345, all5347, alr5348, asr5350-alr5353 and alr5356, but not asr5349, are also required for a Fox+ phenotype. Lipid and sequence analyses suggest that alr5351-alr5357 encode the enzymes that biosynthesize the glycolipid aglycones. Electron microscopy indicates a role of all5345 through all5347 in the normal deposition of the envelope glycolipids.     

Conserved aspartic acid residues 79 and 113 of the beta-adrenergic receptor have different roles in receptor function

Deletion mutagenesis experiments have demonstrated that the binding site of the beta-adrenergic receptor involves the hydrophobic core of the protein (Dixon, R. A. F., Sigal, I. S., Rands, E., Register, R. B., Candelore, M. R., Blake, A. D., and Strader, C. D. (1987) Nature 326, 73-77). Single amino acid replacements for the conserved Asp79 and Asp113 within this putative transmembrane region had profound effects on the ability of the receptor to bind radiolabeled ligands (Strader, C. D., Sigal, I. S., Register, R. B., Candelore, M. R., Rands, E., and Dixon, R. A. F. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4384-4388). In this report we have analyzed the ability of these mutant receptors to stimulate adenylyl cyclase in the presence of agonists. The substitution of Asp79 with Ala caused 10-fold increases in both the Kd for isoproterenol binding and the Kact for adenylyl cyclase stimulation. The substitution of Asp113 by Asn or Glu resulted in 8,000-40,000 and 300-1,500-fold increases, respectively, in the Kact values for agonist stimulation of adenylyl cyclase without altering the maximum level of stimulation. Whereas the binding of antagonists to the receptor was not affected by substitution of Asp79, substitution of Asp113 decreased the affinity for the antagonist propranolol by 10,000-fold. These data are consistent with overlapping but not identical binding sites for agonists and antagonists on the beta-adrenergic receptor, in which the carboxylate group of Asp113 interacts with the amino group of the ligand. The sequence similarity among the family of G-protein-linked receptors suggests that the presence of an Asp residue at the analogous position of one of these receptors is predictive of the ability of the receptor to bind amines as ligands.     

Greater weight loss and hormonal changes after 6 months diet with carbohydrates eaten mostly at dinner

This study was designed to investigate the effect of a low-calorie diet with carbohydrates eaten mostly at dinner on anthropometric, hunger/satiety, biochemical, and inflammatory parameters. Hormonal secretions were also evaluated. Seventy-eight police officers (BMI >30) were randomly assigned to experimental (carbohydrates eaten mostly at dinner) or control weight loss diets for 6 months. On day 0, 7, 90, and 180 blood samples and hunger scores were collected every 4 h from 0800 to 2000 hours. Anthropometric measurements were collected throughout the study. Greater weight loss, abdominal circumference, and body fat mass reductions were observed in the experimental diet in comparison to controls. Hunger scores were lower and greater improvements in fasting glucose, average daily insulin concentrations, and homeostasis model assessment for insulin resistance (HOMA(IR)), T-cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, C-reactive protein (CRP), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) levels were observed in comparison to controls. The experimental diet modified daily leptin and adiponectin concentrations compared to those observed at baseline and to a control diet. A simple dietary manipulation of carbohydrate distribution appears to have additional benefits when compared to a conventional weight loss diet in individuals suffering from obesity. It might also be beneficial for individuals suffering from insulin resistance and the metabolic syndrome. Further research is required to confirm and clarify the mechanisms by which this relatively simple diet approach enhances satiety, leads to better anthropometric outcomes, and achieves improved metabolic response, compared to a more conventional dietary approach.     

Mesh-morphing algorithms for specimen-specific finite element modeling

Despite recent advances in software for meshing specimen-specific geometries, considerable effort is still often required to produce and analyze specimen-specific models suitable for biomechanical analysis through finite element modeling. We hypothesize that it is possible to obtain accurate models by adapting a pre-existing geometry to represent a target specimen using morphing techniques. Here we present two algorithms for morphing, automated wrapping (AW) and manual landmarks (ML), and demonstrate their use to prepare specimen-specific models of caudal rat vertebrae. We evaluate the algorithms by measuring the distance between target and morphed geometries and by comparing response to axial loading simulated with finite element (FE) methods.

First a traditional reconstruction process based on μCT was used to obtain two natural specimen-specific FE models. Next, the two morphing algorithms were used to compute mappings from the surface of one model, the source, to the other, the target, and to use this mapping to morph the source mesh to produce a target mesh. The μCT images were then used to assign element-specific material properties. In AW the mappings were obtained by wrapping the source and target surfaces with an auxiliary triangulated surface. In ML, landmarks were manually placed on corresponding locations on the surfaces of both source and target.

Both morphing algorithms were successful in reproducing the shape of the target vertebra with a median distance between natural and morphed models of 18.8 and 32.2 μm, respectively, for AW and ML. Whereas AW–morphing produced a surface more closely resembling that of the target, ML guaranteed correspondence of the landmark locations between source and target. Morphing preserved the quality of the mesh producing models suitable for FE simulation. Moreover, there were only minor differences between natural and morphed models in predictions of deformation, strain and stress. We therefore conclude that it is possible to use mesh-morphing techniques to produce accurate specimen-specific FE models of caudal rat vertebrae. Mesh morphing techniques provide advantages over conventional specimen-specific finite element modeling by reducing the effort required to generate multiple target specimen models, facilitating intermodel comparisons through correspondence of nodes and maintenance of connectivity, and lends itself to parametric evaluation of “artificial” geometries with a focus on optimizing reconstruction.     

Cooperating in the face of uncertainty: a consistent framework for understanding the evolution of cooperation

The evolution of cooperative behaviour, whereby individuals enhance the fitness of others at an apparent cost to themselves, represents one of the greatest paradoxes of evolution. Individuals that engage in such cooperative behaviour can, however, be favoured by natural selection if cooperative actions confer higher fitness than alternative actions. To understand the evolution of cooperative behaviour, the direct and indirect genetic benefits that individuals accrue in the present and future must be summed - this can be accomplished without any reference to the colorful vocabulary typically associated with studies of cooperation. When benefits are accrued indirectly through relatives or directly in the future individuals must be able to assess and enhance their probability of accruing those benefits and behave accordingly. We suggest that, in the same way that studies of kin recognition systems improved our understanding of how individuals assess and enhance their probability of accruing indirect benefits, studies of various forms of inheritance and reciprocation recognition systems will improve our understanding of how individuals assess and enhance their probability of accruing future benefits. Recognizing the parallel between studies of indirect fitness and future fitness, at multiple levels of analysis, will move us toward a simpler and more consistent framework for understanding the evolution of cooperative behaviour.     

Sperm size of African cichlids in relation to sperm competition

We compared pairs of closely related taxa of cichlid fishesfrom Lake Tanganyika to examine the relationship between spermsize and the presumed intensity of sperm competition. In contrastto previous reports of relatively short sperm in polygamousfishes across a variety of taxa, we found that polygamous cichlidshad significantly longer sperm than their closest monogamousrelatives. In addition, sperm length was significantly relatedto relative testis size (controlling for body size and phylogeny).The site of fertilization may also be correlated with spermlength, as species that fertilize in the female's buccal cavityhad significantly shorter sperm than those that fertilizedeggs on the substrate. Assuming that relatively large testesand polygamous mating are indicative of more intense sperm competition, these results indicate that sperm length is related to the intensityof sperm competition in this clade of cichlids, as has beenfound previously in insects, birds, and mammals.