Novel sugar phosphotransferase system applicable to the efficient labeling of the compounds synthesized via the non-mevalonate pathway in Escherichia coli

It is known that 1-deoxy-D-xylulose taken up by Escherichia coli is used as the precursor of the compounds synthesized via the non-mevalonate pathway, such as isoprenoids, probably after conversion into 1-deoxy-D-xylulose 5-phosphate. In this report, we show that a novel phospho(enol) pyruvate-dependent phosphotransferase system catalyzes the uptake and phosphorylation of 1-deoxy-D-xylulose.     

Expression of CD44 variant 6 and lymphatic invasion: importance to lymph node metastasis in gastric cancer

Lymph node metastasis is a critical prognostic factor for gastric cancer. In the present investigation we examined clinicopathologic factors influencing the metastatic processes to the lymph mode and their prognostic importance. A randomly selected group of 98 patients with adenocarcinomas of the stomach who underwent gastrectomy plus systematic lymph node dissection at Osaka Police Hospital from 1991 to 1996 were analyzed. Altogether 37 (38%) cancers were positive for CD44 variant 6 (v6) staining, 31 (32%) were intermediately stained, and 30 (30%) were negative. CD44-v6 expression correlated well with lymph node metastasis. Expression of CD44-v6 and lymphatic invasion were independent risk factors for metastatic lymph nodes. Among the patients with CD44-v6-positive and lymphatic invasion-positive cancers, 88% had lymph node metastasis, whereas only 13% of patients negative for both factors had lymph node metastasis. Although CD44-v6 expression and lymphatic invasion have been reported to be risk factors for recurrence and a poor prognosis, in this investigation these factors were found not to be significant for hematogenous and lymphatic recurrences or overall survival rates. Thus expression of CD44-v6 and lymphatic invasion may regulate lymph node metastases from gastric cancer.     

Change in fine structure of nylon 6 gut yarn in twisting,annealing, and untwisting processes. I. Observation by WAXD,SAXD, and EM

To obtain information on the change in fine structure of nylon 6 taking place during practical false-twisting processes, the manner of change in the three elemental processes, i.e., twisting, annealing, and untwisting, was studied. For simplicity, nylon 6 gut yarn was used instead of multifilament yarn. Wide- and small-angle x-ray diffraction (WAXD and SAXD) together with electron microscopy (EM) were used here. The degree of molecular orientation in the crystalline region of the twisted yarn gradually decreases with increase of the twist number (TN) in the region of TN ? 100. The long spacing, determined by SAXD, of the twisted yarn increases with increases in TN. The increase in long spacing cannot be interpreted only by macroscopic strain or elongation of the yarn in the twisting process. This difference seems to arise from the contribution of the decrease of lateral size of lamellae to the average long spacing; therefore the increase in long spacing should be attributed to the elongation of the amorphous region, deduced from the crystallinity measured by WAXD and the long spacing diffraction. The angle between the streak line on the surface of twisted yarn observed by EM and the fiber axis agrees well with the twist angle of the yarn. The crystal lamellae are stacked normal to the streak line at the initial stage, i.e., at a low value of TN, but they begin to deviate from the normal direction with increase in TN, accompanied by their partial destruction. Based on SAXD and density measurements, the internal strain of yarn annealed after twisting is fully relaxed. When the yarn is untwisted after twisting and annealing, the crystal orientation recovers gradually to that of the untreated yarn. The chain axis within the lamellae in the center region of the yarn becomes nearly parallel to the fiber axis, but the chain axis in the outer region does not.     

Application of focused ion beam techniques and transmission electron microscopy to thin-film transistor failure analysis

The locations of process-induced defects in hydrogenated amorphous silicon thin-film transistors (a-Si:H TFTs), which are used as elements of active-matrix liquid crystal displays, were investigated by combining focused ion beam techniques with cross-sectional transmission electron microscopy (X-TEM). The FIB technique is applied to TFT failure analysis problems, which require considerable localised etching without inducing mechanical stress or damage at fragile failure locations. We demonstrate the manner in which these techniques are used to characterise TFT defects such as pinholes and portions of the multilayer damaged by mechanical stress. A dramatic improvement brought about by the FIB technique is the increase in temporal efficiency of sample preparations. X-TEM observations also lead to identification of the fault and analysis of its cause, which in turn lead to a marked yield improvement.     

Balanced Scheduling toward Loss-Free Packet Queuing and Delay Fairness

In current networks, packet losses can occur if routers do not provide sufficiently large buffers. This paper studies how many buffers should be provided in a router to eliminate packet losses. We assume a network router has m incoming queues, each corresponding to a single traffic stream, and must schedule at any time on-line from which queue to take the next packet to send out. To exclude packet losses with a small amount of buffers, the maximum queue length must be kept low over the entire scheduling period. We call this new on-line problem the balanced scheduling problem (BSP). By competitive analysis, we measure the power of on-line scheduling algorithms to prevent packet losses. We show that a simple greedy algorithm is Θ(log m)-competitive which is asymptotically optimal, while Round-Robin scheduling is not better than m-competitive, as actually is any deterministic on-line algorithm for BSP. We also give a polynomial time algorithm for solving off-line BSP optimally. We also study another on-line balancing problem that tries to balance the delay among the m traffic streams.     

Purification and characterization of an extracellular beta-agarase from Bacillus sp. MK03

A new beta-agarase was purified from an agarolytic bacterium, Bacillus sp. MK03. The enzyme was purified 129-fold from the culture supernatant by ammonium sulfate precipitation, anion exchange and gel filtration column chromatographic methods. The purified enzyme appeared as a single band on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Estimation of the molecular mass by SDS-PAGE and gel filtration gave values of 92 kDa and 113 kDa, respectively. The N-terminal amino acid sequence of the enzyme showed no homology to those of other known agarases. The optimum pH and temperature for this enzyme were 7.6 and 40 degrees C, respectively. The predominant hydrolysis product of agarose by this enzyme was neoagarotetraose, indicating the cleavage of beta-1,4 linkage. This enzyme could hydrolyze neoagarohexaose to produce neoagarotetraose and neoagarobiose; it could not hydrolyze these products. The enzyme digested agarose by endo-type hydrolysis.     

The relationship between electropermeabilization and cell cycle and cell size of Saccharomyces cerevisiae

Yeast cells (Sacchromyces cerevisiae) in 0.9% NaCl solution containing phloxine B (dye) were treated by an application of a rectangular electric pulse. We input microscopic images of the yeast suspensions after the application into a computer, and measured whether each cell dyes or not, the phase in the cell cycle, and each cell size, using the software we had developed. After those measurements, we discussed the relationship between the yield of electropermeabilization (the ratio of dyed cells to the total cell number) and the phase in the cell cycle, and cell size. From the results, it was found that the yeast cells from S-phase to M-phase (S-M phase) in the cell cycle tend to be more permeated than G1-phase yeast cells, and in both phases the yield decreases with the increase in cell size.     

Strong induction of phytochelatin synthesis by zinc in marine green alga, Dunaliella tertiolecta

Synthesis of phytochelatins (PCs), heavy-metal-sequestering peptides, in the marine green alga, Dunaliella tertiolecta, was evaluated under various conditions of exposure to heavy metals. To investigate the effect of heavy metals on both PC synthesis and their upstream biosynthetic reactions, an ion-pair-HPLC system was developed in this study, by which PCs and their biosynthetic intermediates, cysteine (Cys), gamma-glutamylcysteine (gammaEC) and glutathione (GSH), could be determined simultaneously with high sensitivity. When the cells were exposed to Zn2+, the level of PCs was maximal at 200 microM and significantly higher than that obtained after exposure to 400 microM Cd2+, which is the strongest inducer of PC synthesis in higher plants in vivo and in vitro as well as in microalgae. The predominant PC subtype was PC4, followed by PC3 and PC5, whereas PC2, which is generally abundant in higher plants, has the lowest level among PC2 to PC5. These results suggest that the characteristics of PC synthase in D. tertiolecta including the requirement of heavy metals for its catalysis and substrate specificity towards GSH and PC(n) are considerably different from those in higher plants and other algae. While PC synthesis proceeded in the heavy-metal-treated cells, the level of GSH did not appreciably change. To maintain the same size of the GSH pool, GSH must be newly synthesized to balance the amount consumed for PC synthesis.     

Fast agglomerative hierarchical clustering algorithm using Locality-Sensitive Hashing

The single linkage method is a fundamental agglomerative hierarchical clustering algorithm. This algorithm regards each point as a single cluster initially. In the agglomeration step, it connects a pair of clusters such that the distance between the nearest members is the shortest. This step is repeated until only one cluster remains. The single linkage method can efficiently detect clusters in arbitrary shapes. However, a drawback of this method is a large time complexity of O(n ²), where n represents the number of data points. This time complexity makes this method infeasible for large data. This paper proposes a fast approximation algorithm for the single linkage method. Our algorithm reduces the time complexity to O(nB) by rapidly finding the near clusters to be connected by Locality-Sensitive Hashing, a fast algorithm for the approximate nearest neighbor search. Here, B represents the maximum number of points going into a single hash entry and it practically diminishes to a small constant as compared to n for sufficiently large hash tables. Experimentally, we show that (1) the proposed algorithm obtains clustering results similar to those obtained by the single linkage method and (2) it runs faster for large data than the single linkage method. Hisashi Koga received the M.S. and Ph.D. degree in information science in 1995 and 2002, respectively, from the University of Tokyo. From 1995 to 2003, he worked as a researcher at Fujitsu Laboratories Ltd. Since 2003, he has been a faculty member at the University of Electro-Communications, Tokyo (Japan). Currently, he is an associate professor at the Graduate School of Information Systems, University of Electro-Communications. His research interest includes various kinds of algorithms such as clustering algorithms, on-line algorithms, and algorithms in network communications. Tetsuo Ishibashi received the M.E. degree in information systems design from the Graduate School of Information Systems at the University of Electro-Communications in 2004. Presently, he is a system engineer at Fujitsu Broad Solution & Consulting Inc. Toshinori Watanabe received the B.E. degree in aeronautical engineering in 1971 and the D.E. degree in 1985, both from the University of Tokyo. In 1971, he worked at Hitachi as a researcher in the field of information systems design. His experience includes demand forecasting, inventory and production management, VLSI design automation, knowledge-based nonlinear optimizer, and a case-based evolutionary learning system nicknamed TAMPOPO. He also engaged in FGCS (Fifth Generation Computer System) project of Japan and developed a new hierarchical message-passing parallel cooperative VLSI layout problem solver that ran on PIM (Parallel Inference Machine) in 1991. Since 1992, he has been a professor at the Graduate School of Information Systems, University of Electro-Communications, Tokyo, Japan. His areas of interest include media analysis, learning intelligence, and the semantics of information systems. He is a member of the IEEE.     

Note: Zr(IV)-Immobilized Resin Prepared by Surface Template Polymerization for Fluoride Ion Removal

Abstract

A novel adsorbent Zr(IV)-immobilized resin was prepared to remove fluoride ions from tap water and industrial wastewater. In order to enhance both the kinetics and efficiency, large pathways were formed in the resin for fluoride ion adsorption and the Zr(IV)-phosphate complexes were immobilized on the polymer surface by surface-template polymerization. The Zr(IV)-immobilized resin had a fluoride adsorption capacity of 0.30 mmol/g. The morphology of the Zr(IV)-immobilized resin was evaluated by measuring the specific surface area, pore volume, and pore size distribution. The resin possessed large amounts of large macropores with diameters around 300 nm. The molecular structure at the fluoride adsorption sites was investigated by measuring the amounts of phosphorus, zirconium, and fluoride ion in the resin, and developing a model complex using computational chemistry. On the polymer surface, a fluoride ion/Zr(IV)/dioleyl phosphoric acid complex with an ideal F:Zr:P mole ratio of 3:1:3 could be formed.