Kobayashi, Kazuo; Kanesaki, Yu
Bacteria have developed various motility mechanisms to adapt to a variety of solid surfaces. A rhizosphere isolate, Paenibacillus sp. NAIST15-1, exhibited unusual motility behavior. When spotted onto 1.5% agar media, Paenibacillus sp. formed many colonies, each of which moved around actively at a speed of 3.6 μm/sec. As their density increased, each moving colony began to spiral, finally forming a static round colony. Despite its unusual motility behavior, draft genome sequencing revealed that both the composition and organization of flagellar genes in Paenibacillus sp. were very similar to those in Bacillus subtilis. Disruption of flagellar genes and flagellar stator operons resulted in loss of motility. Paenibacillus sp. showed increased transcription of flagellar genes and hyperflagellation on hard agar media. Thus, increased flagella and their rotation drive Paenibacillus sp. motility. We also identified a large extracellular protein, CmoA, which is conserved only in several Paenibacillus and related species. A cmoA mutant could neither form moving colonies nor move on hard agar media; however, motility was restored by exogenous CmoA. CmoA was located around cells and enveloped cell clusters. Comparison of cellular behavior between the wild type and cmoA mutant indicated that extracellular CmoA is involved in drawing water out of agar media and/or smoothing the cell surface interface. This function of CmoA probably enables Paenibacillus sp. to move on hard agar media. PMID:27764113
zinc oxide ( ZnO ) thin film as an active channel layer in TFT has become of great interest owing to their specific...630-0192 Japan Phone: +81-743-72-6060 Fax: +81-743-72-6069 E-mail: email@example.com Keywords: zinc oxide , thin film transistors , atomic layer...deposition Symposium topic: Transparent Semiconductors Oxides [Abstract] In this study, we fabricated TFTs using ZnO thin film as the
Otsuka, Yuta; Muto, Ai; Takeuchi, Rikiya; Okada, Chihiro; Ishikawa, Motokazu; Nakamura, Koichiro; Yamamoto, Natsuko; Dose, Hitomi; Nakahigashi, Kenji; Tanishima, Shigeki; Suharnan, Sivasundaram; Nomura, Wataru; Nakayashiki, Toru; Aref, Walid G.; Bochner, Barry R.; Conway, Tyrrell; Gribskov, Michael; Kihara, Daisuke; Rudd, Kenneth E.; Tohsato, Yukako; Wanner, Barry L.; Mori, Hirotada
Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources. PMID:25399415
Detection of pockets on protein surfaces is an important step toward finding the binding sites of small molecules. In a previous study, we defined a pocket as a space into which a small spherical probe can enter, but a large probe cannot. The radius of the large probes corresponds to the shallowness of pockets. We showed that each type of binding molecule has a characteristic shallowness distribution. In this study, we introduced fundamental changes to our previous algorithm by using a 3D grid representation of proteins and probes, and the theory of mathematical morphology. We invented an efficient algorithm for calculating deep and shallow pockets (multiscale pockets) simultaneously, using several different sizes of spherical probes (multiscale probes). We implemented our algorithm as a new program, ghecom (grid-based HECOMi finder). The statistics of calculated pockets for the structural dataset showed that our program had a higher performance of detecting binding pockets, than four other popular pocket-finding programs proposed previously. The ghecom also calculates the shallowness of binding ligands, R(inaccess) (minimum radius of inaccessible spherical probes) that can be obtained from the multiscale molecular volume. We showed that each part of the binding molecule had a bias toward a specific range of shallowness. These findings will be useful for predicting the types of molecules that will be most likely to bind putative binding pockets, as well as the configurations of binding molecules. The program ghecom is available through the Web server (http://biunit.naist.jp/ghecom).
Sentein, Carole; Schuster, Frédéric; Tardif, François
-Tech Innovation Ltd, GB DASKALOS MCERTH/CPERI, GR DE BERARDIS BIstituto Superiore di Sanità, IT DE MIGUEL YTECNALIA, ES DELAHAYE AAd Air Solutions, FR DEMIDOVA TSevertsov Inst. of Ecology and Evolution, RU DENOO KSolae, GR DERROUGH SCEA, FR DOBRZYNSKA E BCentral Institute for Labour Protection, PL DOLEZ PÉcole de technologie supérieure, CA DOUKI TCEA, FR DRAIS EINRS, FR DUFOUR J-PCILAS, FR DURAN NUNICAMP, BR DURAND CCEA, FR DUTOUQUET CINERIS, FR DUVAL-ARNOULD GSaint-Gobain, FR ECKHOFF R KUniv. Bergen, NO ELLENBECKER M JUniv. Massachusetts Lowell, US EMOND CUniv. Montreal, CA ENGEL SBASF, DE ESTRELA-LOPIS ILeipzig Univ., DE FABBRI MJRC, IT FACCINI MLeitat technological center, ES FESSARD VAnses, FR FILIMUNDI ETSI, DE FIRSTOVA VSRCAMB, RU FLEURY DINERIS, FR FRABOULET DCEA, FR FRESNAY CThales Research & Technology, FR GABORIEAU ACEA, FR GAFFET ENanoMaterials Research Group, FR GALLET SCefic, BE GEIGER DBASF, DE GENSDARMES FIRSN, FR GERRITSEN-EBBEN RTNO Quality of Life, NL GKANIS VDemokritos, GR GLUSHKOVA ARIHOPHE, RU GONZALEZ-FERNANDEZ AUniv. Vigo, ES GOOSSENS HPhilips Research Aerasense, NL GRAHNSTEDT SOslo Univ., NO GREENHILL-HOOPER MRio Tinto Minerals, FR GROSSEAU PEcole des Mines de Saint Etienne, FR GUADAGNINI RUniv. Paris 7 Diderot, FR GUIOT ACEA, FR GUIZARD BCEA, FR HAASE AFederal Institute for Risk Assessment, DE HANINI AUniv. Paris 7 Diderot, FR HAYNES LUniv. de los Andes, VE HEJAZI MUniv. Tehran, IR HENRY FINERIS, FR HERRERA HInstitute for Work and Health, CH HOET PKU Leuven, BE HOLE PNanosight, GB HULME JUniv. Cambridge, GB JI XINERIS, FR JOUHANNAUD JCEA, FR JOUZEL J-NCenter for the Sociology of Organizations, FR JURKSCHAT KOxford Univ., GB KAISER J-PEmpa, CH KANAYA FNat. Center for Global Health and Medicine, JP KATALAGARIANAKIS GEuropean Commission, BE KECK LGrimm Aerosol Technik, DE KELLER MFraunhofer Institute, DE KHLEBNIKOVA NRIHOPHE, RU KHODABANDEH MUniv. Tehran, IR KHOLODENKO VSRCAMB, RU KOBAYASHI NAIST, JP KOPONEN INRCWE, DK KOWAL SINERIS, FR KRYSANOV