Jpn J Appl Phys 2009, 48:04C187 CrossRef 18 Huang CH, Igarashi M

Jpn J Appl Phys 2009, 48:04C187.CrossRef 18. Huang CH, Igarashi M, Horita S, Takeguchi CP-868596 manufacturer M, Uraoka Y, Fuyuki T, Yamashita I, Samukawa S: Novel Si nanodisk fabricated by biotemplate and defect-free neutral beam etching for solar cell application. Jpn J Appl Phys 2010, 49:04DL16.CrossRef 19. Huang CH, Wang XY, Igarashi M, Murayama A, Okada Y, Yamashita I, Samukawa S: Optical absorption characteristic

of highly ordered and dense two-dimensional array of silicon nanodiscs. Nanotechnol 2011, 22:105301.CrossRef 20. Hirano R, Miyamoto S, Yonemoto M, Samukawa S, Sawano K, Shiraki Y, Itoh KM: Room-temperature observation of size effects in photoluminescence of Si 0.8 Ge 0.2 /Si nanocolumns prepared by neutral beam etching. Appl Phys Express 2012, 5:082004.CrossRef 21. Budiman MF, Hu W, Igarashi M, Tsukamoto R, Isoda T, Itoh KM, Yamashita I, Murayama A, Okada Y, Samukawa S: Control of optical bandgap energy and optical absorption coefficient by geometric parameters in sub-10 nm silicon-nanodisc array structure. Nanotechnol 2012, 23:065302.CrossRef 22. Igarashi M, Budiman MF, Pan W, Hu W, Tamura Y, Syazwan ME, Usami N, Samukawa S: Effects of formation of mini-bands in two-dimensional array of silicon nanodisks with SiC interlayer

for quantum dot solar cells. Nanotechnol 2013, 24:015301.CrossRef 23. Kuo DMT, Guo GY, Chang YC: Tunneling current through a quantum dot array. Appl Phys Lett 2001, 79:3851.CrossRef Competing interests The authors declare that they have no competing interests. Authors’ contributions

MI and SS conceived NSC 683864 nmr and designed the experiment, fabricated the silicon nanodisk samples, performed electrical and optical measurements, analyzed these data, and wrote the paper. MMR and NU fabricated the solar cell structures and analyzed the I-V data. WH performed the theoretical calculations. All authors discussed the results, commented on the manuscript, and read and approved the final version.”
“Background Dye-sensitized solar cells (DSSCs) have attracted considerable attention as a viable alternative to conventional silicon-based photovoltaic cells [1] because of their Suplatast tosilate low-production cost, high conversion efficiency, environmental friendliness, and easy fabrication procedure [2–5]. A typical DSSC is comprised of a nanocrystalline semiconductor (TiO2), an electrolyte with redox couple (I3 −/I−), and a counter electrode (CE) to collect the electrons and catalyze the redox couple regeneration [6]. Extensive researches have been conducted in order for each component to achieve highly efficient DSSCs with a modified TiO2[7], alternative materials [8, 9], and various structures [10–12]. Usually, Pt-coated fluorine-doped tin oxide (FTO) is used as a counter electrode owing to its superior catalytic activity [13]. However, there are researches reporting that Pt corrodes in an electrolyte containing iodide to generate PtI4[14, 15].

The B-C17 profile was predominant in Scotland in this cohort of i

The B-C17 profile was predominant in Scotland in this cohort of isolates, specifically in learn more the regions of Aberdeenshire, Angus, Borders and Perth and Kinross (Table 1 and see supplementary dataset in Additional file 1 and Additional file 2: Table S1). The C1 profile was more widely spread across

Europe and was found in the Czech Republic, Greece, Finland, The Netherlands, Norway and Spain, (Table 1 and see supplementary dataset in Additional file 1 and Additional file 2: Table S1). Table 1 Combined PFGE, MIRU-VNTR and IS900-RFLP profiles by Map origin Profile     No of isolates Country1-Host2 PFGE 3 MIRU-VNTR 4 IS900-RFLP 5   CZ ES FL GR NL NO SCO [1-1] 1 C1 2 RD       G     [1-1] 2 C1 7 C, RD C C(2)   C, RD     this website [1-1] 2 C18 1     C         [1-1] 2 C5 1         C     [1-1] 6 C1 2         C(2)     [2-1] 1 C1

13 C(4), FD, M C C(2)     G(3), S   [2-1] 1 C9 1 H             [2-1] 1 C17 39           C, S B, C(6), CR, F(2), H, R(13), RK, S(7), ST(3), W, WM [2-1] 2 C17 2             C(2) [2-1] 2 C1 9 C FD     C(2), G, S(4)     [2-1] 2 C5 1         C     [2-1] 2 C36 1         C     [2-1] 5 C10 1 C             [2-1] 19 C17 1             S [2-1] 24 C1 1         S     [2-1] 22 C38 1         G     [2-1] 25 C17 1             R [2-10] 1 C1 1           G   [2-17] 2 C22 1         S     [2-19] 2 C5 2       G, S       [2-30] 1 C16 1         RD     [2-30] 25 C16 1             W [3-2] 1 C17 3             F, G, J [5-2] 1 C17 1             S [9-7] 21 S4 1             S [15-16] 38 C1 1   G           [15-25] 26 C1 7   G(7)           [16-11] 20 I5 1   G           [18-1] 13 C1 1   G           [20-1] 1 C1 1 C             [26-1] 35 C1 1 C             [27-18] 2 C27 1   C           [29-15] 36 C1 1       G       [29-15] 37 C1 3       G(3)       [30-21] 2 C1 1         G     [31-17] 69 C39 1   G           [32-29] 1 C17 1             ST [34-22] 2 C1 2         RD(2)     [34-22] 8 C1 1         RD     [36-27] 1 C1 1 M             [37-23] 29 I4 1 FD             [40-28] 26 C1 1   G           [41-1] 1 C9 1 C             [58-64] 35 C1 1 M

            1. Amino acid Country: CZ Czech Republic, ES Spain, FL Finland, GR Greece, NL The Netherlands, NO Norway, SCO Scotland 2. Host: B badger (Meles meles), C cow (Bos taurus), CR crow (Corvus corone), F fox (Vulpes vulpes), FD fallow deer (Dama dama), G goat (Capra hircus), H hare (Lepus europaeus), J jackdaw (Corvus monedula), M moufflon (Ovis musimon), R rabbit (Oryctolagus cuniculus), RD red deer (Cervus elaphus), RK rook (Corvus frugilegus), S sheep (Ovis aries), ST stoat (Mustela erminea), W weasel (Mustela nivalis), WM wood mouse (Apodemus sylvaticus). The number of isolates obtained from each host species within a country is given in parenthesis. 3. Nomenclature as defined by Stevenson et al. 2002 [11] 4. Nomenclature as defined by Thibault et al. 2007 [56] 5. Nomenclature as defined by Pavlik et al.

Histochem Cell Biol 2006, 126:159–164 CrossRefPubMed 23 Nilsson

Histochem Cell Biol 2006, 126:159–164.CrossRefPubMed 23. Nilsson M, Dahl F, Larsson C, Gullberg M, Stenberg J: Analyzing genes using closing and replicating circles. Trends MLN2238 concentration Biotechnol 2006, 24:83–88.CrossRefPubMed 24. Wang B, Potter SJ, Lin Y, Cunningham AL, Dwyer DE, Su Y, Ma X, Hou Y, Saksena NK: Rapid and sensitive detection of severe acute respiratory syndrome coronavirus by rolling circle amplification. J Clin Microbiol 2005, 43:2339–2344.CrossRefPubMed 25. Kong F, Tong Z, Chen X, Sorrell T, Wang B, Wu Q, Ellis D, Chen S: Rapid identification and differentiation of Trichophyton species, based

on sequence polymorphisms of the ribosomal internal transcribed spacer regions, by rolling-circle amplification. J Clin Microbiol 2008, 46:1192–1199.CrossRefPubMed 26. Zhou X, Kong F, Sorrell TC, Wang H, Duan Y, Chen SC: Practical method for detection and identification of Candida, Aspergillus, and Scedosporium spp. by use of rolling-circle amplification. J Clin Microbiol 2008, 46:2423–2427.CrossRefPubMed 27. Reference method for broth dilution antifungal susceptibility testing of yeasts. Approved standard NCCLS document M27-A3 3 Edition National Committee for Clinical Laboratory Standards:

Wayne, PA 2008. 28. Xiao L, Madison V, Chau AS, Loebenberg D, Palermo RE, McNicholas PM: Three-dimensional models of wild-type and mutated forms of cytochrome P450 14alpha-sterol demethylases from Aspergillus fumigatus and Candida albicans provide insights into posaconazole binding. Antimicrob Agents Chemother 2004, 48:568–574.CrossRefPubMed 29. Asai K, Tsuchimori N, Okonogi K, Perfect JR, Gotoh O, Yoshida Y: Formation of azole-resistant Selleck BI 2536 Candida albicans by mutation of sterol 14-demethylase P450. Antimicrob Agents Chemother 1999, 43:1163–1169.PubMed 30. Yesilkaya H, Meacci Thalidomide F, Niemann S, Hillemann D, Rusch-Gerdes S, Barer MR, Andrew PW, Oggioni MR: Evaluation of molecular-Beacon, TaqMan, and fluorescence resonance energy transfer probes for detection of antibiotic resistance-conferring single

nucleotide polymorphisms in mixed Mycobacterium tuberculosis DNA extracts. J Clin Microbiol 2006, 44:3826–3829.CrossRefPubMed 31. Gibson NJ: The use of real-time PCR methods in DNA sequence variation analysis. Clin Chim Acta; Int J Clin Chem 2006, 363:32–47.CrossRef 32. Coste A, Turner V, Ischer F, Morschhauser J, Forche A, Selmecki A, Berman J, Bille J, Sanglard D: A mutation in Tac1p, a transcription factor regulating CDR1 and CDR2, is coupled with loss of heterozygosity at chromosome 5 to mediate antifungal resistance in Candida albicans. Genetics 2006, 172:2139–2156.CrossRefPubMed 33. MacPherson S, Akache B, Weber S, De Deken X, Raymond M, Turcotte B: Candida albicans zinc cluster protein Upc2p confers resistance to antifungal drugs and is an activator of ergosterol biosynthetic genes. Antimicrob Agents Chemother 2005, 49:1745–1752.CrossRefPubMed 34.

78-fold) and AQY1 (aquaporin water channel, up-regulated by 2 73-

78-fold) and AQY1 (aquaporin water channel, up-regulated by 2.73-fold), which all belong to the group of C. neoformans genes regulated by osmotic stress [49]. It is possible that defects in the plasma membrane resulting from inhibition of ergosterol biosynthesis

Eltanexor by FLC affects transport of small molecules through the membrane. Analysis of the H99 genome sequence [16] predicted 54 ATP-Binding Cassette (ABC) transporters and 159 major facilitator superfamily (MFS) transporters, suggesting wide transport capabilities of this environmental yeast [50]. However, we found only two S. cerevisiae transporter homologues with significant increased expression. One is PDR15 that is a member of the ABC transporter subfamily exporting antifungals and other xenobiotics in fungi [51]. The other gene

is Selleckchem PD0332991 ATR1 that encodes a multidrug resistance transport protein belonging to the MFS class of transporters. ATR1 expression was recently shown to be upregulated by boron and several stress conditions [52]. To date, Afr1 (encoded by AFR1; also termed CneAfr1) and CneMdr1 are the only two efflux pumps associated with antifungal drug resistance in C. neoformans [50]. Since Afr1 is the major efflux pump mediating azole resistance in C. neoformans [11, 15], the absence of altered AFR1 expression could be expected. Not surprisingly, we Oxymatrine noticed downregulated expression (2.35-fold) of FLR1 (for fluconazole resistance) encoding a known MFS multidrug transporter in yeast, that is able to confer resistance to a wide range of dissimilar drugs and other

chemicals [53]. This may suggest that both AFR1 and FLR1 do not participate to the short-term stress induced by FLC in C. neoformans. Effect of FLC on the susceptibility to cell wall inhibitors It was demonstrated that compounds interfering with normal cell wall formation (Congo red, calcofluor white, SDS and caffeine) affect growth of C. neoformans strains with altered cell wall integrity [27]. For instance, several deletion strains for genes involved in the PKC1 signal transduction pathway were found to be sensitive to SDS and Congo red and to a lesser extent caffeine. To test the hypothesis that FLC treatment might induce cell wall stress, we analyzed H99 cells for susceptibility to the cell wall perturbing agents, before and after the cells were exposed for 90 min to FLC at sub-MIC concentration (10 mg/l) at 30°C. Phenotypes of H99 cells on cell wall inhibitor plates are shown in Figure 3. The FLC pre-treated H99 cells were slightly more resistant to all four cell wall inhibitors as compared to untreated cells. These findings are consistent with expression changes of cell wall associated genes identified in our microarray analysis.

B Schematic of VPI-2 excision mechanism and primer pair VPI2attF

B. Schematic of VPI-2 excision mechanism and primer pair VPI2attF and VPI2attR used to detect the VPI-2 attB locus after excision of the entire region. VPI-1 and VPI-2 do

not share any genes in common but do share some functional characteristics such as the ability selleck kinase inhibitor to integrate into the chromosome, specifically at a tRNA site using an integrase belonging to the tyrosine recombinase family [16, 18, 23, 26, 28]. VPI-2 integrates into chromosome 1 at a tRNA-serine locus, whereas VPI-1 is located at the tmRNA locus. Both regions are flanked by direct repeats (DRs) named attL and attR [16, 18, 23, 26, 28]. These integrases, IntV1 (VC0847) and IntV2 (VC1758), are believed to mediate insertion into the host chromosome through site specific recombination between an attachment site attP, present in the pathogenicity island, and attB, present in the bacterial chromosome. Pathogenicity islands have been shown to excise from their host genome in pathogenic Escherichia coli and Yersinia species [29–36]. In E.

coli strain 536, a uropathogenic isolate, Hacker and colleagues have identified six PAIs, all of which encode a tyrosine recombinase integrase and are flanked by DRs [31, 33, 36–39]. They demonstrated that PAI-I, II, III and V can excise from the chromosome by site-specific recombination involving selleckchem their respective DRs (attL and attR) [31, 33]. The PAIs were shown to excise at different frequencies depending on the growth conditions [31, 33]. Likewise, both VPI-1 and VPI-2 have been shown to excise from their host chromosome [23, 28]. Rajanna and colleagues demonstrated that VPI-1 can

excise from V. cholerae N16961 at very low rates [28]. They determined that the integrase IntV1 (VC0847) was not essential for excision since a transposase within the region appeared to compensate for an IntV1 knockout [28]. Recently, Murphy and Boyd demonstrated that VPI-2 from V. cholerae N16961 can excise from chromosome 1, which also occurred at very low frequency under optimal growth conditions [23]. Their study showed that IntV2 (VC1758) was essential for excision and the formation of a circular click here intermediate (CI) [23]. Pathogenicity islands from both E. coli and V. cholerae are non-self mobilizable, they do not encode any proteins such as those for phage structural proteins or conjugation systems needed for cell to cell mobility [23, 28, 31, 33, 36–39]. The mechanism of transfer for most pathogenicity islands remains to be elucidated but likely involves hitchhiking with plasmids, conjugative transposons, Integrative and Conjugative Elements (ICEs), or generalized transducing phages or uptake by transformation. It is known that for some mobile and integrative genetic elements (MIGEs) the presence of a recombination directionality factor (RDF)/excisionase is required for excision [40, 41]. For instance, Xis is required for the excision of the ICE SXT from V.

It also appears that analysis with specialized tools, organized o

It also appears that analysis with specialized tools, organized on a “”one feature at a time”" basis (Lipo SPs, TAT

SPs …), most reliably gives predictions consistent with experimental data. For this purpose, CoBaltDB is a unique and innovative resource. 2-Using CoBaltDB to analyse protein(s) and a proteome One valuable property of CoBaldDB is to recapitulate all pre-computed predictions in a unique A4-formated synopsis. This summary is very helpful for assessing computational data such as the variation and frequency in the predictions of signal peptide cleavage sites: such predictions are sometimes significantly consistent, but often Bioactive Compound Library price SN-38 purchase are not in agreement with each other (Figure 7A). However, correct identification of signal peptide cleavage sites is essential in many situations, especially for producing secreted recombinant proteins. Figure 7 Using CoBaltDB to analyse protein(s) and a proteome. A: Comparative analysis of SP cleavage site predictions (proteinssecreted by P. aeruginosa); B: Discriminating between SPI- and SP II cleavage sites. The CoBaltDB synopsis could also be used to discriminate between SignalPeptidaseII- and SignalPeptidaseI-cleaved signals and between SPs and N-terminal

transmembrane helices. Indeed, most localization predictors have difficulties distinguishing between type I

and type II signal peptidase cleavages. CoBaltDB can be exploited in an interesting way to benchmark this prediction by displaying all cleavage site predictions Methamphetamine in a “”decreasing sensitivity”" arrangement (SpII then Tat-dependant SPI then Sec-SPI). By considering lipoprotein datasets from different organisms, we evidenced two principal profiles (Figure 7B) and found that all experimentally validated lipoproteins score 100% (all tools give the same prediction) or 66% in the CoBaltDB LIPO column (see explanation in the paragraph above). In addition, in almost all of the examined cases, tools dedicated to Twin-arginine SP detection do not identify SpII-dependent SP, whereas the Sec-SP predictors detect both Sec and Tat-type I as well as type II signal-anchor sequences. These observations allow us to propose, for our data set, thresholds for each box: as previously illustrated, lipoproteins have score > 66% in the LIPO prediction box; Tat-secreted proteins have 0% in the LIPO box and 100% for the two TAT-dedicated tools; Sec-secreted proteins have 33% in the LIPO Box (due to the fact that LipoP detects both SpI and SpII [59]), 0% in the TAT-tools, and > 80% in SEC-specialized tools. Rules of this type can be used to check entire proteomes for evaluation of the different secretomes as illustrated in the following case studies.

New J Phys 2010, 12:013020 CrossRef 7 Coey JMD, Venkatesan M, Fi

New J Phys 2010, 12:013020.CrossRef 7. Coey JMD, Venkatesan M, Fitzgerald CB: Donor impurity band exchange in dilute ferromagnetic oxides. Nat Mater 2005, 4:173–179.CrossRef 8. Belghazi Y, Schmerber G, Colis S, Rehspringer JL, Dinia A, Berrada A: Extrinsic origin of ferromagnetism in ZnO and Zn 0.9 Co 0.1 O magnetic semiconductor PRI-724 mouse films prepared by sol-gel technique. Appl Phys Lett 2006, 89:122504.CrossRef 9. Samanta K, Bhattacharya P, Katiyar RS: Optical properties of Zn 1-x Co x O thin

films grown on Al 2 O 3 (0001) substrates. Appl Phys Lett 2005, 87:101903.CrossRef 10. Dinia A, Schmerber G, Mény C, Pierron-Bohnes V, Beaurepaire E: Room-temperature ferromagnetism in Zn 1-x Co x O magnetic semiconductors prepared by sputtering. J Appl Phys 2005, 97:123908.CrossRef 11. Lee H-J,

Park CH, Jeong S-Y, Yee K-J, Cho CR, Jung M-H, Chadi DJ: Hydrogen-induced ferromagnetism in ZnCoO. Appl Phys Lett 2006, 88:062504.CrossRef 12. Lee mTOR inhibitor H-J, Choi SH, Cho CR, Kim HK, Jeong S-Y: The formation of precipitates in the ZnCoO system. Europhys Lett 2005, 72:76–82.CrossRef 13. Lee S, Cho YC, Kim S-J, Cho CR, Jeong S-Y, Kim SJ, Kim JP, Choi YN, Sur JM: Reproducible manipulation of spin ordering in ZnCoO nanocrystals by hydrogen mediation. Appl Phys Lett 2009, 94:212507.CrossRef 14. Kim SJ, Cha SY, Kim JY, Shin JM, Cho YC, Lee S, Kim W-K, Jeong S-Y, Yang YS, Cho MycoClean Mycoplasma Removal Kit CR, Choi HW, Jung MH, Jun B-E, Kwon K-Y, Kuroiwa Y, Moriyoshi C: Ferromagnetism in ZnCoO due to hydrogen-mediated Co–H–Co complexes: how to avoid the formation

of Co metal clusters? J Phys Chem C 2012, 116:12196–12202.CrossRef 15. Lee S, Kim B-S, Cho YC, Shin J-M, Seo S-W, Cho CR, Takeuchi I, Jeong S-Y: Origin of the ferromagnetism in ZnCoO from chemical reaction of Co 3 O 4 . Curr Appl Phys 2013, 13:2005–2009.CrossRef 16. Cho YC, Kim S-J, Lee S, Kim SJ, Cho CR, Nahm H-H, Park CH, Jeong IK, Park S, Hong TE, Kuroda S, Jeong S-Y: Reversible ferromagnetism spin ordering governed by hydrogen in Co-doped ZnO semiconductor. Appl Phys Lett 2009, 95:172514.CrossRef 17. Cho YC, Lee S, Nahm HH, Kim SJ, Park CH, Lee SY, Kim S-K, Cho CR, Koinuma H, Jeong S-Y: Conductive and ferromagnetic contributions of H in ZnCoO using H 2 hot isostatic pressure. Appl Phys Lett 2012, 100:112403.CrossRef 18. Li L, Guo Y, Cui XY, Zheng R, Ohtani K, Kong C, Ceguerra AV, Moody MP, Ye JD, Tan HH, Jagadish C, Liu H, Stampfl C, Ohno H, Ringer SP, Matsukura F: Magnetism of Co-doped ZnO epitaxially grown on a ZnO substrate. Phys Rev B 2012, 85:174430.CrossRef 19. Kim SJ, Lee S, Cho YC, Choi YN, Park S, Jeong IK, Kuroiwa Y, Moriyoshi C, Jeong S-Y: Direct observation of deuterium in ferromagnetic Zn 0.9 Co 0.1 O:D. Phys Rev B 2010, 81:212408.CrossRef 20.

(#) CDRPMI, (##) CDM-C16alone The profound growth arrest of P f

(#) CDRPMI, (##) CDM-C16alone. The profound growth arrest of P. falciparum was investigated further by culturing parasites synchronized at the ring stage in CDM containing different concentrations of C16:0, which was added individually, for 28 h. Suppression of schizogony, particularly the progression of the parasite to the trophozoite stage following the ring stage, was detected in CDM containing C16:0 alone as the NEFA growth factor, regardless of a wide range of concentrations (Figure  8).

On the other hand, all stages of parasites cultured in CDRPMI had comparable development to those ITF2357 price cultured in GFSRPMI (Figure  8). This implies that C18:1 protected the parasite completely from C16:0-induced growth arrest. Figure 8 Modification of P. falciparum development in CDMs containing C16:0 only as a NEFA growth factor. Synchronized parasites at the ring stage were cultured in CDM containing graded concentrations of C16:0 (C16:0–20, 20 μM; C16:0–60, 60 μM; C16:0–160, 160 μM) for 28 h. Each developmental stage was counted after Giemsa staining. Levels of parasitemia were 5.27 ± 0.08 (GFSRPMI), 5.27 ± 0.34 (CDRPMI), 3.61 ± 0.30 (C16:0–20), 3.69 ± 0.60 (C16:0–60), and 3.67 ± (C16:0–160); Caspase inhibitor (*) indicates CDM-C16alone. The morphology of the rings observed in the presence of C16:0 and the schizonts in GFSRPMI and CDRPMI is shown. Although profound growth arrest was detected

in P. falciparum cultured in CDM containing C18:1 alone for a longer period (95 h), all stages of the parasite cultured for 28 h had comparable development to those cultured in CDRPMI and GFSRPMI. However the majority of merozoites were incomplete, resulting in a low growth rate during the longer culture period (Figure  7). Thus, the growth arrest associated with CDM containing C18:1 alone did not involve suppression of schizogony. Developmental C1GALT1 arrest of P. falciparum was detected at the early stage in CDM-C16alone, similar to that with CDRPMI and

GFSRPMI in the presence of Neocuproine and TTM, which cause perturbation of copper homeostasis. We have predicted previously, using genome-wide transcriptome profiling, five transcripts associated with the blockage of trophozoite progression from the ring stage [7], of which one transcript was a putative copper channel (PF3D7_1421900 at PlasmoDB [6]). This suggests a critical function of copper ions and copper-binding proteins in the early developmental arrest of the parasite, in agreement with the results with Neocuproine and TTM. Genes encoding proteins that are involved in the copper pathway and trafficking in various microbes have been identified in P. falciparum. These proteins include: 1) a putative copper channel (XP_001348385 at NCBI), 2) a copper transporter (XP_001348543.1 at NCBI), 3) a putative COX17 (XP_001347536 at NCBI), and 4) a copper-transporting ATPase (XP_001351923 at NCBI).

J Biol Chem 2004, 279:9064–9071 PubMedCrossRef 32 Mellies JL, Ha

J Biol Chem 2004, 279:9064–9071.PubMedCrossRef 32. Mellies JL, Haack KR, Galligan DC: SOS regulation of the type III secretion system of enteropathogenic Escherichia coli . J Bacteriol 2007, 189:2863–2872.PubMedCrossRef 33. Justice SS, Hung C, Theriot JA, Fletcher

DA, Anderson GG, Footer MJ, Hultgren SJ: Differentiation and developmental pathways of uropathogenic Escherichia coli in urinary tract pathogenesis. Proc Natl Acad Sci USA 2004, 101:1333–1338.PubMedCrossRef 34. Dörr T, Lewis K, Vulić M: SOS response induces persistence to fluoroquinolones in Escherichia coli . PLoS Genetics 2009, 5:1–9.CrossRef 35. Keseler IM, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, et al.: EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids BLZ945 in vitro Res 2009, 37:D464–470.PubMedCrossRef 36. Salles B, Weisemann JM, Weinstock GM: Temporal control of colicin E1 induction.

J Bacteriol 1987, 169:5028–5034.PubMed selleck compound 37. Salles B, Weinstock GM: Interaction of the CRP-cAMP complex with the cea regulatory region. Mol Gen Genet 1989, 215:537–542.PubMedCrossRef 38. Chant EL, Summers DK: Indole signaling contributes to the stable maintenance of Escherichia coli multicopy plasmids. Mol Microbiol 2007, 63:35–43.PubMedCrossRef Authors’ contributions SK performed all experiments. ZP contributed to analysis of the results. OG and DŽB participated in the design of the experiments and SK, OG and DŽB in preparation of the manuscript. All authors read and approved the final manuscript.”
“Background Nitrogen-fixing symbiotic bacteria, commonly known as rhizobia, employ a variety of strategies which allow them to exist in the soil and adapt to various environmental conditions

prior to infecting leguminous plant hosts. Rhizobial cell surface components, exopolysaccharide (EPS) and lipopolysaccharide (LPS), play an important role in determining the symbiotic competence of rhizobia, root tissue invasion and induction of nitrogen-fixing nodules on host plants forming indeterminate-type nodules, such as Pisum, Trifolium, Vicia, and Medicago spp. [1–4]. Acidic EPSs secreted in large amounts by rhizobia aminophylline are species-specific compounds consisting of common sugars substituted with non-carbohydrate residues [1, 4–6]. EPS of Rhizobium leguminosarum is a heteropolymer consisting of octasaccharide subunits composed of five glucose residues, one galactose, and two glucuronic acid residues, additionally decorated with acetyl, pyruvyl, and 3-hydroxybutyryl groups [7, 8]. EPS-deficient mutants or those with an altered LPS structure are impaired in nodule cell invasion and nitrogen fixation [1, 6, 9–11]. Biosynthesis of EPS in R. leguminosarum is a multi-step process requiring the expression of several pss genes, located in the major EPS cluster on the chromosome [12, 13].

The arrows indicated sampling (C) Gene expression of SPG1598, SP

The arrows indicated sampling. (C) Gene expression of SPG1598, SPG1592, and SPG1591 in medium supplemented with amino sugars are compared to growth in glucose. Variation of gene expression is shown for genes of bacteria grown in ManNAc (open bars), glucose plus ManNAc (open striped bars), NeuNAc (grey bars), and glucose plus NeuNAc (grey striped bars). Results are represented

as fold changes ± SD of gene expression from 3 to 4 independent experiments. Statistical analysis was carried out using Tukey’s Multiple Comparison Test (ns non significant; *, p < 0.05; **, p < 0.01). Generation time on glucose containing media is 38–45 min, 90 min on NeuNAc and 140 min on ManNAc. Repression of the nanAB locus in the presence of glucose According to the

Belinostat mw presence of three cre sites within the pneumococcal neuraminidase locus, we observed a biphasic growth curve when bacteria grew on glucose plus ManNAc or NeuNAc (Figure 4A,B, open squares). To demonstrate that this phenotype was due to carbon catabolite repression, we investigated the transcriptional behaviour of the neuraminidase locus in the presence or absence of glucose in the medium. Growth Semaxanib molecular weight conditions used were as follows: ManNAc with and without glucose (Figure 4A, open triangles and open squares), NeuNAc with and without glucose (Figure 4B, open triangles and open diamonds) and glucose as the sole carbon source as a reference condition (Figure 4A and 4B, closed circles). Growth curve data show that addition of glucose to both ManNAc and NeuNAc resulted in an initial growth on glucose as a preferred carbon source followed by a second slower growth phase, in which the amino sugars were metabolised. To assess glucose repression during growth on glucose gene expression analysis was carried out by sampling the bacteria at an OD590 of 0.05 (Figure 4A,B, arrows). As shown in Figure 4C, the over-expression of all genes of Prostatic acid phosphatase the nanAB locus occurred during growth on ManNAc or NeuNAc as the sole carbon sources (Figure 4C, open and grey bars), while it was completely repressed in the presence of glucose (Figure 4C, striped bars). Regulation of neuraminidase

A production and activity by ManNAc To assess the production of NanA on the bacterial surface after induction of the nanAB locus by ManNAc or NeuNAc, we performed a cytofluorimetry assay. In these experiments bacteria were harvested at the late exponential phase. In this assay the anti-NanA serum recognises also to a certain extent glucose grown bacteria (Figure 5A). However in culture media with either ManNAc or NeuNAc as the sole carbon sources, the number of NanA expressing bacterial cells significantly increased reaching 73.7% (± 3.4) and 79.6% (± 4.9), respectively. Differences in NanA production between bacterial cells grown with either of the two amino sugars and control cells cultured in glucose or glucose plus ManNAc were statistically significant (Figure 5A).