Biological Building Blocks Research Articles

Computational studies of gene regulatory networks: in numero molecular biology

Remarkable progress in genomic research is leading to a complete map of the building blocks of biology. Knowledge of this map is, in turn, setting the stage for a fundamental description of cellular function at the DNA level. Such a description will entail an understanding of gene regulation, in which proteins often regulate their own production or that of other proteins in a complex web of interactions. The implications of the underlying logic of genetic networks are difficult to deduce through experimental techniques alone, and successful approaches will probably involve the union of new experiments and computational modelling techniques.

Travels to the nanoworld: miniature machinery in nature and technology

}Our lives are about to be changed by new technologies that operate on a scale that is smaller than can be seen by the most optical microscopes. Devices inspired by living cells and measured in nanometersbillionths of a meterare the basis of this nanotechnology revolution. In TRAVELS TO THE NANOWORLD, Miniature Machinery in Nature and Technology , Michael Gross takes us to this world to explore natural processes and new technologies that will make modern machines look like relics from the Stone Age.The living cell provides a starting point. All its vital processes, including chemical reactions, catalysis, movement, data storage and processing, and energy conversion, are directed and carried out by structures whose dimensions are on the nanometer scale. As biochemist have come to understand the mechanisms of this nanotechnology of nature, the chances of generating artificial systems of similar performance have grown rapidly. TRAVELS TO THE NANOWORLD provides the nonspecialist reader with an introduction into the background, current state and future prospects of this fascinating subject.We begin this journey into the nanoworld with a guided tour starting from molecules, the all-important building blocks of both biology and technology, that can form complex systems both in the cell and in the reaction tube. Complex molecules make up cells, cells make up organisms that evolve to a variety of species, including one that invented technology as we know it. Technology has returned to the small scale and has arrived at the molecular level once again.We continue this trek, the major developments and success stories in the exploration and utilization of these natural and synthetic nanoworlds. These highlights of cutting-edge research are grouped into the more biological approaches, including workings of proteins, genes, and cells, followed by the development of applications including supramolecular chemistry, small-scale technology, and biotechnology. TRAVELS TO THE NANOWORLD concludes with a discussion of present applications and future prospects for nanotechnology. The exciting revolutionary potential of nanotechnology is balanced by a cautionary note emphasiszing the need for us all to be well informed about the technological path we are heading toward. }

Synthesis of a radioiodinated park nucleotide analog: a new tool for antibacterial screen development

The Park nucleotide is an important biological building block used in the construction of bacterial cell walls. Herein, we describe the synthesis of a radiolabeled Park nucleotide analog, p-iodophenoxyacyl-Ala-(d)-iso-Glu-Lys-(d)-Ala-(d)-Ala-OH-[123I], using electrophilic destannylation. Anti-Park nucleotide antibody binding assays using a scintillation proximity assay (SPA) system showed good recognition of the radiolabeled surrogate. This methodology could be used for establishing a screen to identify inhibitors of peptidoglycan biosynthesis. © 1998 John Wiley & Sons, Ltd.

Inter‐ and Intracultivar Effects of Selection on Heterosis

The effect of selection on heterosis depends on the gene action and the type of selection. Intracultivar (W) selection, full‐sib family selection within each of two cultivars, and intercultivar (R) selection, reciprocal recurrent selection between the two cultivars, were contrasted for their effects on heterosis. The cultivars were considered to be random replicate populations from an ancestral population. The relatedness of individuals within cultivars and the degree of divergence between cultivars were formalized in terms of identity by descent (IBD) measures for two, three, two‐pair, and four genes a locus and joint IBD measures for genes at each of two loci. Quantitative genetic components for a model that is general for additive, dominance, and additive by additive (a ✕ a) effects with an arbitrary number of alleles were defined for the ancestral population, and selection responses were formulated for the cultivars and the hybrid for each selection method with the aid of the IBD measures. A further analysis was made utilizing a biological building block model of gene effects. The contribution of a ✕ a effects was such that they reduced heterosis from W selection, but slightly increased heterosis from R selection. It was concluded that R selection always increased heterosis while W selection could increase or decrease heterosis, but decreased heterosis for a preponderance of the genetic parameters considered.

Electron spin resonance investigation of laser and heated metal‐tip–induced free radical formation in various tissues

The short-lived free radical formation accompanying laser irradiation and laser-heated metal tip contact was examined using electron spin resonance (ESR) spin-trap methodology. Various tissues (canine myocardium, human aorta, liver, and spleen) were irradiated by argon-ion (continuous wave [CW] and pulse) and YAG (CW) lasers employing both naked fiber and a laser-heated metal tip. All showed the formation of primarily carbon-centered, not oxygenated, free radicals, together with some minor unidentified species. This implies that the backbones of amino acids, lipids, or other biological building blocks are cleaved during the irradiation or thermal treatment. Different tissues produce similar radicals but with different amounts when irradiated by argon-ion, YAG, and laser-heated metal tip sources. The amount of the free radicals formed depends on the laser power (within 5-15 W). Compared to the naked fiber, the laser-heated metal tip shows the generation of at least twice the amount of free radicals. The possible relationship of the free radical formation to tissue injury is briefly discussed.

Effects on biological evolution of changes in ocean chemistry.

PERHAPS the most perplexing problem of biological evolution involves explanation of why diversification of life began only after 85% of the lifetime of the Earth while simple life seems to have been present for virtually all of geological time. Recent observations1–2 on the presence of complex organic species in meteoritic debris and in the interstellar medium show that some of the basic biological building blocks may have been available from the earliest times. Chamberlain and Marland3 have commented on the biological consequences of the Hargraves4 model of ocean-crust evolution while others5–6 have reassessed evidence on atmospheric evolution and indicated that changes in oxygen partial pressure may not have been critical to the diversification of life. In this note I suggest that important changes in ocean chemistry must have occurred if our current models of crustal evolution and igneous events have any validity. The evolution of complex life forms requires a high degree of environmental stability and constancy of chemical environment. It is suggested that this condition is closely linked to the spacing of major volcanic centres, and that the modern long wavelength pattern of ocean ridges and subduction zones was necessary to achieve this stability. The distribution of ophiolites or ocean-floor structures of modern type7 indicates that the present pattern may have been initiated about one billion years ago. Furthermore, large scale continental emergence4 may have been necessary to provide oceans with stable chemistry.