We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).

Analysis of cellular components at multiple levels of biological information can provide valuable functional insights. We performed multiple high-throughput measurements to study the response of Escherichia coli cells to genetic and environmental perturbations. Analysis of metabolic enzyme gene disruptants revealed unexpectedly small changes in messenger RNA and proteins for most disruptants. Overall, metabolite levels were also stable, reflecting the rerouting of fluxes in the metabolic network. In contrast, E. coli actively regulated enzyme levels to maintain a stable metabolic state in response to changes in growth rate. E. coli thus seems to use complementary strategies that result in a metabolic network robust against perturbations.

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A new material concept of soft crystals is proposed. Soft crystals respond to gentle stimuli such as vapor exposure and rubbing but maintain their structural order and exhibit remarkable visual changes in their shape, color, and luminescence. Various interesting examples of soft crystals are introduced in the article. By exploring the interesting formation and phase‐transition phenomena of soft crystals through interdisciplinary collaboration, new materials having both the characteristics of ordered hard crystals and those of flexible soft matter are expected.

Central carbon metabolism is a basic and exhaustively analyzed pathway. However, the intrinsic robustness of the pathway might still conceal uncharacterized reactions. To test this hypothesis, we constructed systematic multiple-knockout mutants involved in central carbon catabolism in Escherichia coli and tested their growth under 12 different nutrient conditions. Differences between in silico predictions and experimental growth indicated that unreported reactions existed within this extensively analyzed metabolic network. These putative reactions were then confirmed by metabolome analysis and in vitro enzymatic assays. Novel reactions regarding the breakdown of sedoheptulose-7-phosphate to erythrose-4-phosphate and dihydroxyacetone phosphate were observed in transaldolase-deficient mutants, without any noticeable changes in gene expression. These reactions, triggered by an accumulation of sedoheptulose-7-phosphate, were catalyzed by the universally conserved glycolytic enzymes ATP-dependent phosphofructokinase and aldolase. The emergence of an alternative pathway not requiring any changes in gene expression, but rather relying on the accumulation of an intermediate metabolite may be a novel mechanism mediating the robustness of these metabolic networks.

To examine properties of pentavalent uranium, U(V), we have carried out electrochemical and spectroelectrochemical studies on UO(2)(saloph)L [saloph = N,N'-disalicylidene-o-phenylenediaminate, L = dimethyl sulfoxide (DMSO) or N,N-dimethylformamide (DMF)]. The electrochemical reactions of UO(2)(saloph)L complexes in L were found to occur quasireversibly. The reduction processes of UO(2)(saloph)L complexes were followed spectroelectrochemically by using an optical transparent thin layer electrode cell. It was found that the absorption spectra measured at the applied potentials from 0 to -1.650 V versus ferrocene/ferrocenium ion redox couple (Fc/Fc(+)) for UO(2)(saloph)DMSO in DMSO have clear isosbestic points and that the evaluated electron stoichiometry equals 1.08. These results indicate that the reduction product of UO(2)(saloph)DMSO is [U(V)O(2)(saloph)DMSO](-), which is considerably stable in DMSO. Furthermore, it was clarified that the absorption spectrum of the [U(V)O(2)(saloph)DMSO](-) complex has a very small molar absorptivity in the visible region and characteristic absorption bands due to the 5f(1) orbital at around 750 and 900 nm. For UO(2)(saloph)DMF in DMF, the clear isosbestic points were not observed in the similar spectral changes. It is proposed that the UO(2)(saloph)DMF complex is reduced to [U(V)O(2)(saloph)DMF](-) accompanied by the dissociation of DMF as a successive reaction. The formal redox potentials of UO(2)(saloph)L in L (E(0), vs Fc/Fc(+)) for U(VI)/U(V) couple were determined to be -1.550 V for L = DMSO and -1.626 V for L = DMF.

Extracellular deposition of amyloid beta-protein (beta-AP), or A4 protein (M(r) 4,000), is associated with Alzheimer's disease and with Down's syndrome (trisomy for chromosome 21). The large membrane-bound precursor protein (APP) of beta-AP is normally cleaved within the beta-AP region by a putative proteinase (APP secretase) to release its extracellular portion; beta-AP is produced by an alternative proteolytic processing. Here we demonstrate that APP contains a proteinase inhibitor domain for the matrix metalloproteinase gelatinase A, which is located in the C-terminal glycosylated region of the secretory forms of APP. In addition, we show that the gelatinase has an APP secretase-like activity, which hydrolyses the Lys16-Leu17 bond in the beta-AP sequence. Our results indicate that the proteinase inhibitor domain of APP and gelatinase A may be involved in the formation of beta-AP.

Background Sphingolipids, including sphingosine-1-phosphate (S1P) and ceramide, have emerged as key regulatory molecules that control various aspects of cell growth and proliferation in cancer. Although important roles of sphingolipids in breast cancer progression have been reported in experimental models, their roles in human patients have yet to be determined. The aim of this study is to determine the levels of sphingolipids including S1P, ceramides, and other sphingolipids, in breast cancer and normal breast tissue and to compare the difference in levels of each sphingolipid between the two tissues. Materials and Methods Tumor and non-cancerous breast tissue were obtained from 12 patients with breast cancer. Sphingolipids including S1P, ceramides, and their metabolites of sphingosine, sphingomyelin, and monohexosylceramide were measured by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Results The levels of S1P, ceramides, and other sphingolipids in the tumor were significantly higher than those in normal breast tissue. There was a relatively strong correlation in the levels of S1P between the tumor and that of normal breast tissue from the same person. On the other hand, there was no correlation in the levels of most of the ceramide species between the tumor and that of normal breast tissue from the same person. Conclusions To our knowledge this is the first study to reveal that levels of sphingolipids in cancer tissue are generally higher than normal breast tissue in patients with breast cancer. The correlation of S1P levels in these tissues implicates the role of S1P in interaction between cancer and the tumor microenvironment.