An electrogenetic toggle switch model

Synthetic biology uses molecular biology to implement genetic circuits that perform computations. These circuits can process inputs and deliver outputs according to predefined rules that are encoded, often entirely, into genetic parts. However, the field has recently begun to focus on using mechanisms beyond the realm of genetic parts for engineering biological circuits. We analyse the use of electrogenic processes for circuit design and present a model for a merged genetic and electrogenetic toggle switch operating in a biofilm attached to an electrode. Computational simulations explore conditions under which bistability emerges in order to identify the circuit design principles for best switch performance. The results provide a basis for the rational design and implementation of hybrid devices that can be measured and controlled both genetically and electronically.     

THE FINE STRUCTURE OF THE DNP COMPONENT OF THE NUCLEUS : An Electron Microscopic Study Utilizing Autoradiography to Localize DNA Synthesis

In the present investigation, the sites of deoxyribonucleic acid (DNA) synthesis and the fate of labeled deoxyribonucleoprotein (DNP) were studied in autoradiographs of ultrathin sections viewed with the electron microscope. Tritiated thymidine was employed as a label for DNA in the nuclei of proliferating cells of regenerating salamander limbs. In the autoradiographic method reported here, dilute NaOH was used to remove the gelatin of the emulsion after exposure and development. The exposed silver grains are not displaced by this treatment and the resolution of fine structure in the underlying section is greatly improved. Our observations suggest that the DNP component is a meshwork of interconnected filaments 50 to 75 A in diameter, which may be cross-linked to form what Frey-Wyssling would term a "reticular gel." The filamentous DNP meshwork is dispersed throughout the interphase nucleus during DNA synthesis, whereas in chromosomes, which are relatively inert metabolically, the meshwork is denser and is aggregated into compact masses. Dense chromatin centers in interphase nuclei are similar in fine structure to chromosomes and are also inert with respect to DNA synthesis. In the Discussion, the structure of the filamentous meshwork in chromatin is compared with that in chromosomes, and speculations are made as to the functional significance of the variations in DNP fine structure observed.     

Morphological and Chemical Studies of the Spores and Parasporal Bodies of Bacillus laterosporus

Spores of Bacillus laterosporus were studied to determine the chemical and morphological nature of their basophilic canoe-shaped parasporal bodies. An unusually high phosphorus content of these spores compared to other Bacillus species appeared to be associated with the parasporal body. Preparations of these "canoes" still attached to the spore coats were indeed high in phosphorus, but also in nitrogen. They were free of lipide-soluble and nucleic acid phosphorus and stained for protein. Some 50 per cent of the total nitrogen, but only 6 to 10 per cent of the total P were liberated by extraction with alkali-thioglycollate (pH 11.5) or alkali alone (pH 12.2–12.5). Proteinaceous material was recovered from these alkaline extracts and electron microscopy indicated that there had been a marked loss of "canoe" substance. Extraction with acid, removed some 80 per cent of the phosphorus associated with the "canoes" as orthophosphate. Chromatographic analyses for amino acids indicated some 14 ninhydrin-positive spots in the canoe-coat preparations whereas the whole spores contained at least 16.     

PHYLOGENY OF THE ULVOPHYCEAE (CHLOROPHYTA): CLADISTIC ANALYSIS OF NUCLEAR-ENCODED rRNA SEQUENCE DATA1

Cladistic analysis of nuclear-encoded rRNA sequence data provided us with the basis for some new hypotheses of relationships within the green algal class Ulvophyceae. The orders Ulotrichales and Ulvales are separated from the clade formed by the remaining orders of siphonous and siphonocladous Ulvophyceae (Caulerpales, Siphonocladales /Cladophorales [S/C] complex, and the Dasycladales), by the Chlorophyceae and Pleurastrophyceae. Our results suggest that the Ulvophyceae is not a monophyletic group. Examination of inter- and intra-ordinal relationships within the siphonous and siphonocladous ulvophycean algae revealed that Cladophora, Chaetomorpha, Anadyomene, Microdictyon, Cladophoropsis and Dictyosphaeria form a clade. Thus the hypothesis, based on ultrastructural features, that the Siphonocladales and Cladophorales are closely related is supported. Also, the Caulerpales is a monophyletic group with two lineages; Caulerpa, Halimeda, and Udotea comprise one, and Bryopsis and Codium comprise the other. The Dasycladales (Cymopolia and Batophora) also forms a clade, but this clade is not inferred to be the sister group to the S/C complex as has been proposed. Instead, it is either the sister taxon to the Caulerpales or basal to the Caulerpales and S/C clade The Trentepohliales is also included at the base of the siphonous and siphonocladous ulvophycean clade. The Pleurastrophyceae, which, like the Ulvophyceae, posses a counter-clockwise arrangement of flagellar basal bodies, are more closely related to the Chlorophyceae than to the Ulvophyceae based on rRNA sequences. Thus, the arrangement of basal bodies does not diagnose a monophyletic group. Previously reported hypotheses of phylogenetic relationships of ulvophycean algae were tested. In each case, additional evolutionary steps were required to obtain the proposed relationships. Relationships of ulvophycean algae to other classes of green algae are discussed.     

CONSULTING KU JLOPLE: SOME HISTORIES OF ORACLES IN WEST AFRICA

Historical comparison of oracles in west Africa, mainly during the nineteenth century, shows how divination practices may alter. In the cases explored here, reputation, range of users, economic growth, and political influence interacted as these oracles developed; some at sites with internal and overseas trade access became complex, large-scale operations. But by about 1900, colonialists felt threatened by their secular and their spiritual power and smashed them physically, though not spiritually. Contextualized comparison shows that the many people who were involved as oracle organizers and supplicants must have had different motivations and interests. Some methodological implications of the findings are considered. As in many powerful secular organizations, access to insider knowledge was blocked, but oracular reputation was important, and the oracles had competitors. Success derived partly from collecting intelligence, with simultaneous advertisement that emphasized the mysterious power of their operations.     

Cytokinins and bud morphology in Pinus radiata

Cytokinins (CKs) play essential roles in the regulation of plant growth and development. In the previous paper (Zhang et al. 2001), we reported the detection and identification of a wide spectrum of CKs, including several novel forms, in the buds of Pinus radiata D. Don. In this paper we examine the relationship between the CKs and buds from juvenile and adult trees of P. radiata. During development the morphology of buds alters significantly, from buds bearing primary needles during their juvenile phase to buds sealed in scales at the adult phase. The morphology of adult buds is a very stable character, as fascicle meristems released from apical dominance, or cultured in vitro, produced only secondary needles. However, exogenous CK causes the adult buds to revert to juvenile bud development in vitro . Analyses of the endogenous CKs revealed that juvenile buds had a relatively higher level of isopentenyladenine and isopentenyladenosine, extremely low levels of phosphorylated CKs and a relatively low level of novel CK glycosides. The adult buds contained lower levels of free base and riboside CKs but very high levels of phosphorylated CKs and novel CK glycosides. Possible roles for CKs in the regulation of bud development are discussed.     

The relationship between structure and function for the sulfite reductases

The six-electron reductions of sulfite to sulfide and nitrite to ammonia, fundamental to early and contemporary life, are catalyzed by diverse sulfite and nitrite reductases that share an unusual prosthetic assembly in their active centers, namely siroheme covalently linked to an Fe₄S₄ cluster. The recently determined crystallographic structure of the sulfite reductase hemoprotein from Escherichia coli complements extensive biochemical and spectroscopic studies in revealing structural features that are key for the catalytic mechanism and in suggesting a common symmetric structural unit for this diverse family of enzymes.     

Cadmium replaces calcium in the cell wall ofUlva lactuca

Electron microscopy, in conjunction with X-ray microanalysis, was used to investigate the effects of exposure to cadmium on the elemental composition of the macroalgaUlva lactuca. The cell wall was the only region of the cell to show any marked change in chemical composition as a result of exposure to cadmium, with less calcium evident in cadmium-treated thallus compared with untreated thalli. The cell wall ofU. lactuca is a complex structure made up of polysaccharides consisting of many-branched chains composed mostly of rhamnose and galactose subunits. Some of the hydroxyl groups on the subunits are substituted by sulphate groups. Borate is associated with the rhamnose subunits, which contain no sulphate groups, and calcium binds to borate, cross-linking the rhamnose groups. The borate-calcium complex adds rigidity to the cell wall; the replacement of calcium by cadmium will, therefore, influence the rigidity of the thallus. The ecological significance of this work is discussed with respect to the ability of the alga to withstand grazing or emersion.