Figure 5a shows the HRTEM image of a typical Cs0.33WO3 nanoparticle obtained after grinding for 3 h. The main lattice spacing of 0.375 nm is related to the (002) planes of hexagonal structure. The corresponding electron diffraction pattern was indicated in Figure 5b. Two main fringe patterns with plane distances of 3.25 and 3.71 Å could be observed. They were attributed to the (200) and (002) planes of hexagonal Cs0.33WO3. In addition, the EDX spectrum was also shown in

Figure 5c. Except for C and Cu elements from the Formvar-covered copper grid, only Cs, W, and O elements were observed. No significant peak for the Zr element was found, confirming that the contamination from grinding beads could be neglected. Figure 5 HRTEM image (a), electron diffraction pattern (b), and EDX spectrum (c) of typical Cs 0.33 WO 3 nanoparticle. The absorption spectra for the aqueous dispersions of Cs0.33WO3 powders (0.008 wt.%) before and after grinding

for different times GNS-1480 were indicated in Figure 6. For the samples before grinding and after grinding for 1 and 2 h, 5 wt.% of PEG 6000 was added to avoid the occurrence of precipitation during the measurement. It was found that Cs0.33WO3 powder had no significant absorption PKC412 supplier before grinding. However, after grinding, the Cs0.33WO3 nanoparticles exhibited a significant absorption in the NIR region, owing to the free AZD8931 price electrons or polarons as discussed in the work of Takeda and Adachi [28]. Also, with increasing grinding time, the NIR absorption became more significant while the visible absorption decreased. This revealed that the size reduction to nanoscale indeed made Cs0.33WO3 powder become efficient as a transparent NIR absorption material. In addition, Figure 7 shows absorption spectra for the aqueous dispersions of Cs0.33WO3 Bay 11-7085 nanoparticles with different particle concentrations obtained after grinding for 3 h. It was obvious that NIR

absorption could be enhanced by increasing particle concentration. When the particle concentration was above 0.08 wt.%, the fluctuation of absorbance due to the strong absorption has reached the instrumental detection limit. Figure 6 Absorption spectra for aqueous dispersions of Cs 0.33 WO 3 powder (0.008 wt.%) before and after grinding for different times. For the samples before and after grinding for 1 and 2 h, 5 wt.% of PEG 6000 was added. Figure 7 Absorption spectra for aqueous dispersions of Cs 0.33 WO 3 nanoparticles with different particle concentrations obtained after 3-h grinding. According to Figure 2, the mean hydrodynamic diameters of the Cs0.33WO3 powder before grinding and after grinding for 1, 2, and 3 h were 1,310, 250, 180, and 50 nm, respectively. Their NIR photothermal conversion property in the aqueous dispersions was examined at a fixed particle concentration of 0.008 wt.%. For the samples before grinding and after grinding for 1 and 2 h, 5 wt.% of PEG 6000 was added to avoid the occurrence of precipitation.

​softberry.​com/​, the GeneMark program [67] and the GLIMMER program [68]. We considered an open reading frame (ORF) prediction to be good when it was identified by each of the three prediction tools. Discrepant ORFs were manually verified by the Artemis selleck inhibitor viewer [69] and by identification

of putative ribosomal binding sites. 3MA Each gene was functionally classified by assigning a cluster of orthologous group (COG) number or a Kyoto encyclopedia of genes and genomes (KEGG) number, and each predicted protein was compared against every protein in the non- redundant (nr) protein databases http://​ncbi.​nlm.​nih.​gov. In order to associate a function with a predicted gene, we used a minimum cut-off of 30% identity and 80% coverage of the gene length, checking at least two best hits among the COG, KEGG, and non- redundant protein databases. The rRNA genes were identified by the FGENESB tool on the basis of sequence conservation, while tRNA genes were detected with the tRNAscan-SE program. The BLASTp algorithm AZD1152 nmr was used to search for protein similarities with other pneumococcal genomes or deposited sequences referred in the present study, following these criteria: >50% similarity at the amino acid level and >50% coverage of protein length. Phage characterization AP200 was grown in BHI broth at 37°C to achieve a turbidity corresponding to OD620 0.2-0.3. Mytomycin C (Sigma-Aldrich, St. Louis, MO) was added to a final concentration

of 0.1 μg/ml and the culture was incubated until lysis occurred, as shown by a decrease in turbidity. Cellular debris was pelleted at 16000 g for 15 min. The induced supernatant was filtered through a 0.44-μm pore size filter (Millipore, Billerica, MA). For Ixazomib mouse negative staining, the filtered supernatant was ultracentrifuged at 100,000 g for 2 h at 4°C. Suspensions

of the pellet were placed on Formvar-carbon coated 400 mesh copper grids for 10 s, wicked with filter paper and placed on a drop of 2% sodium phosphotungstate, pH 7.00, for 10 s, wicked again and air-dried. Negatively stained preparations were observed with a Philips 208 electron microscope at 80 kV. To obtain phage DNA, the phage pellet was lysed with sodium dodecyl sulfate (0.5%), EDTA (10 mM) and proteinase K (500 μg/ml) for 2 h at 37°C. Phage DNA was precipitated with a 10% volume of 3 M NaOAc (pH 5.2) and 2 volumes of ethanol at -70°C for 2 h, washed with 70% ethanol and resuspended in deionized H2O. In order to demonstrate the circularization of the excised prophage, a PCR assay using the phage DNA as template and divergent primers pair (FR9 5′- CTAGACTTGCGATAGCAGTTACC- 3′ and FR10 5′- GCTTGAACAATTAAGCCAAGCG-3′) designed on the opposite ends of the prophage sequence, was carried out. The PCR product was purified and submitted to sequencing analysis using a Perkin-Elmer ABI 377 DNA sequencer (PE Applied Byosystem). To demonstrate phage activity, a plaque assay was performed. Briefly, 0.1 ml of filtered induced supernatant was pre-incubated with 0.

The adaptive co-evolution of humans and bacteria has resulted in the establishment of commensal relationships where neither partner is disadvantaged, or symbiotic

relationships where both partners benefit [26]. In our current study, intestinal epithelial cells can secrete IL-10 to find more down-regulate inflammatory cascades through suppressing the secretion of pro-inflammatory cytokines. On the other hand, C. butyricum can drive the secretion of IL-10 to enhance tolerance to bacteria. Such mechanisms allow the host to recognize symbiotic bacteria without eliciting a deleterious immune response, and enable the symbiotic bacteria to reside in the gut, thus providing unique metabolic traits or other benefits. This pathway may be part of an evolutionarily primitive form of adaptive immunity. Conclusions When HT-29 cells were pretreated with

buy HKI-272 anti-IL-10 or siIL-10, C. butyricum induced an excessive immune response and even apoptosis and necrosis compared with control cells. These findings show IWP-2 mw that C. butyricum achieves its beneficial effects on immune modulation through IL-10. On the other hand, C. butyricum may have limited usefulness when the host is deficient in the production of IL-10; this requires further clarification. Acknowledgment This work was supported by the National Natural Science Foundation of China (Grant No. 30901039) and the Ningbo City Bureau of Science and Technology (Grant No. 2009A610155). References 1. Jia W, Li H, Zhao L, Nicholson JK: selleck compound Gut microbiota: a potential new territory for drug targeting. Nat Rev Drug Discov 2008, 7:123–129.PubMedCrossRef 2. Haller D, Bode C, Hammes WP, Pfeifer AM, Schiffrin EJ, Blum S: Nonpathogenic bacteria elicit a differential cytokine response by intestinal epithelial cell/leucocyte co-cultures. Gut 2000, 47:79–87.PubMedCrossRef 3. McCracken VJ, Chun T, Baldeon ME, Ahrne S, Molin G, Mackie RI, Gaskins HR: TNF-alpha sensitizes HT-29 colonic epithelial cells to intestinal lactobacilli. Exp Biol Med 2002, 227:665–670. 4. Shanahan F: Probiotics in inflammatory bowel disease – therapeutic rationale and role.

Adv Drug Deliv Rev 2004, 56:809–818.PubMedCrossRef 5. Sartor RB: Targeting enteric bacteria in treatment of inflammatory bowel diseases: why, how, and when. Curr Opin Gastroenterol 2003, 19:358–365.PubMedCrossRef 6. Kuhn R, Lohler J, Rennick D, Rajewsky K, Muller W: Interleukin-10-deficient mice develop chronic enterocolitis. Cell 1993,75(2):263–274.PubMedCrossRef 7. Lavasani S, Dzhambazov B, Nouri M, Fåk F, Buske S, Molin G, Thorlacius H, Alenfall J, Jeppsson B, Weström B: A novel Probiotic mixture exerts a therapeutic effect on experimental autoimmuneencephalomyelitis mediated by IL-10 producing regulatory T cells. PLoS One 2010,5(2):e9009.PubMedCrossRef 8. Mengheri E: Health, probiotics, and inflammation. J Clin Gastroenterol 2008, 42:s177-s178.PubMedCrossRef 9.

SNP genotyping We searched the HapMap database (http://​hapmap.​ncbi.​nlm.​nih.​gov/​) for SNPs within the genes encoding sirtuin families, and selected 55 SNPs (39 tagging SNPs) for genotyping; 11 in SIRT1 (rs12778366, rs3740051, rs2236318, rs2236319, rs10823108, rs10997868, rs2273773, rs3818292, rs3818291, rs4746720, rs10823116), 7 in

SIRT2 (rs1001413, rs892034, rs2015, rs2241703, rs2082435, rs11575003, rs2053071), 15 in SIRT3 (rs11246002, rs2293168, rs3216, rs10081, rs511744, rs6598074, rs4758633, rs11246007, rs3782117, rs3782116, rs3782115, rs1023430, rs12576565, rs536715, rs3829998), 7 in SIRT4 (rs6490288, rs7298516, rs3847968, rs12424555, rs7137625, rs2261612, rs2070873), 11 in SIRT5 (rs2804923, rs9382227, rs2804916, rs2804918, rs9370232, rs4712047, rs3734674, rs11751539, rs3757261, selleck chemicals rs2253217, rs2841514), and 4 in SIRT6 (rs350852, rs7246235, rs107251, rs350844). We could not identify any confirmed SNPs within SIRT7 in the Japanese population. The genotyping of these SNPs was performed by using multiplex polymerase chain reaction (PCR)-invader assays, as described previously [7–10]. Statistical analyses We tested the genotype distributions for Hardy–Weinberg equilibrium (HWE) proportions by using the chi-squared test. We analyzed

the differences between the case−control groups in terms of the distribution of genotypes with the Cochran–Armitage trend test. The analyses see more for haplotype

structures within each gene were performed using Haploview software version 4.1 [20]. CP673451 in vitro A combined meta-analysis was performed using the Mantel–Haenszel procedure with a fixed effects model after testing for heterogeneity. Results Among the 55 SNPs examined, genotype distributions of 3 SNPs, rs12576565 in SIRT3, and rs2804923 and rs2841514 in SIRT 5, showed significant deviation from HWE proportion in control groups (P < 0.01, Supplementary Table 2), and these 3 SNPs were excluded from the association study. As shown in Table 1, 8 out of 11 SNPs in SIRT1 showed a directionally consistent association with diabetic nephropathy in all 3 studies, although individual associations were not significant (P > 0.05, Supplementary Table 2). In a combined meta-analysis, we could identify a nominally significant association between rs4746720 and proteinuria, and between 4 SNPs, rs2236319, rs10823108, rs3818292, rs4746720, and combined phenotypes (proteinuria + ESRD, P < 0.05). Subsequent haplotype analysis revealed that the 11 SNPs formed one haplotype block (Fig. 1), and 7 common haplotypes covered >99% of the present Japanese population. Among them one haplotype had a stronger association with diabetic nephropathy than selleck single SNPs alone (P = 0.016, odds ratio (OR) 1.31 95% confidence interval (CI) 1.05–1.62].

J Gen Plant Pathol 66:191–201 Kanematsu S, Adachi Y, Ito T (2007) Mating-type loci of heterothallic Diaporthe spp.: homologous genes are present in Fludarabine supplier opposite mating-types.

Curr Genet 52:11–22PubMed Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780PubMedCentralPubMed Kohn LM (2005) Mechanisms of fungal speciation. Annu Rev Phytopathol 43:279–308PubMed Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M et al (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22:5271–5277PubMed Kolomiets T, Mukhina Z, Matveeva T, Bogomaz D, Berner DK, Cavin CA, Castlebury LA (2009) First Everolimus purchase report of stem canker of Salsola tragus caused by Diaporthe eres in Russia. Plant Dis 93:110 Laurence MH, Summerell BA, Burgess LW, Liew EC (2014) Genealogical concordance phylogenetic species recognition in the Fusarium oxysporum species complex. Fungal Biol 118:374–384PubMed Liu K, Warnow TJ, Holder MT, Nelesen S, Yu J, Stamatakis A, Linder RC (2012) SATé-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst Biol 61:90–106PubMed Lombard L, van Leeuwen G,

Guarnaccia V, Polizzi G, van Rijswick P, Rosendahl K, Crous P (2014) Diaporthe species associated with Vaccinium in Europe. Phytopathologia Mediterranea. [S.l.], apr. 2014. selleck kinase inhibitor ISSN 1593–2095. http://​www.​fupress.​net/​index.​php/​pm/​article/​view/​14034. doi:10.14601/Phytopathol_Mediterr 14034 Lopez-Giraldez F, Townsend JP (2011) PhyDesign: an online application for profiling phylogenetic informativeness.

BMC Evol Biol 11:152PubMedCentralPubMed Maddison W P, Maddison DR (2011) Mesquite: a modular system for evolutionary analysis. Version 2.75 http://​mesquiteproject.​org Maharachchikumbura SS, Guo LD, Cai L, Chukeatirote E, Wu WP, Sun X, Dehydratase Hyde KD (2012) A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species. Fungal Divers 56:95–129 Manamgoda DS, Udayanga D, Cai L, Chukeatirote E, Hyde KD (2013) Endophtic Colletotrichum associated with tropical grasses with a new species C. endophytica. Fungal Divers 61:107–115 Matute DR, McEwen JG, Puccia R, Montes BA, San-Blas G, Bagagli E, Taylor JW (2006) Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies. Mol Biol Evol 23:65–73PubMed Mejia LC, Castlebury L, Rossman AY, Sogonov MV, White JF (2008) Phylogenetic placement and taxonomic review of the genus Cryptosporella and its synonyms Ophiovalsa and Winterella. Mycol Res 112:23–35PubMed Mejia LC, Castlebury LA, Rossman AY, Sogonov MV, White JF (2011) A systematic account of the genus Plagiostoma (Gnomoniaceae, Diaporthales) based on morphology, host associations and a four-gene phylogeny.

Our identification of mutants in pbgPE, galE and galU clearly implicates LPS as an important player in the colonization of the IJ by Photorhabdus. In this study we also identified mutations in genes that were not directly associated with LPS metabolism; asmA, hdfR and proQ. The asmA gene was originally identified in E. coli as a site for suppressor mutations of an assembly defective porin, OmpF315 [23]. Although the role of AsmA is still not clear it is likley that this

protein is involved in organising the outer membrane. In the first instance a mutation in asmA has been shown to result in reduced levels of LPS in the outer membrane Lazertinib price of E. coli [12]. In addition a recent study reported that a mutation in asmA in Salmonella enterica serovar Typhimurium resulted in a remodelling selleck kinase inhibitor of the outer membrane that resulted in an GS-9973 supplier increase in the transcription of marAB, encoding a multi-drug efflux pump [24]. The authors further report that the S. enterica

asmA mutant was attenuated in virulence when administered orally to mice and showed a reduced ability to invade epithelial cells thus linking asmA with infection [24]. The hdfR gene was originally annotated as 2 overlapping genes, yifA and pssR, on the E. coli genome but recent analysis confirmed the presence of a sequencing error that resulted in a frameshift and the subsequent mis-annotation [14, 25]. The hdfR gene is predicted to encode a LysR-type regulator that represses the expression of flhDC, and therefore motility, in E. coli [14]. In Proteus mirabilis 2 independent mutations in hdfR were identified in a STM experiment as being important for urinary tract colonization in mice [26]. Motility has been shown to play an important role in P. mirabilis virulence however a role for hdfR in regulating motility (-)-p-Bromotetramisole Oxalate in Proteus has not been determined [27]. Interestingly we have shown that the hdfR mutant does not appear

to affect swimming motility in P. luminescens (data not shown). Finally we identified a mutation in the proQ gene. This gene is predicted to encode a protein that, in E. coli, is involved in the post-translational activation of ProP, an osmoprotectant/proton symporter that is capable of transporting both proline and glycine betaine in response to increases in osmotic pressure [15, 16]. However the genome of P. luminescens is not predicted to encode a ProP homologue suggesting an alternative role for ProQ in Photorhabdus. Interestingly the proQ mutant was the most affected in attachment to an abiotic surface suggesting alterations in the cell surface of the mutant (see Figure 3). However the proQ mutant was not sensitive to CAMPs suggesting that the LPS was not affected (see Figure 5). It is also noteworthy that, unlike the other mutants identified in this study, there is the possibility that the mutation in proQ has a polar affect on the downstream gene, prc (see Figure 2). The proQ and prc genes are separated by 20 bp on both the E.

To ascertain that translation of these two ALA1 mutants was actually initiated

from CGC or CAC, and not from other remedial initiation sites, codons in the leader sequence that have the potential to serve as secondary translation initiation sites and initiate the synthesis of at least part of the mitochondrial targeting sequence were targeted for mutagenesis, and the protein expression and complementation activity of the resultant mutants were then tested. In this regard, TTG(-16) appeared to be a promising candidate on account of its favorable sequence context. To distinguish the protein forms initiated from ACG(-25) and UUG(-16), an 18% polyacrylamide gel was used. As shown in learn more Figure 3, mutation of ACG(-25) to CGC had only a minor effect on mitochondrial activity, but drastically reduced protein expression VE 822 (Figure 3A, B, numbers

selleck compound 1 and 2). The upper and lower protein bands were abolished by the mutation, while the middle band was largely unaffected. This result suggests that both the upper and lower bands were initiated from ACG(-25), and the lower band was derived from cleavage of the upper band possibly by a matrix-processing peptidase. A further mutation that changed TTG(-16) to TTA impaired both the mitochondrial activity and protein expression of the CGC mutant (Figure 3A, B, numbers 2 and 4), suggesting that UUG(-16) served as a remedial initiation

site in the CGC mutant and the middle band was initiated from UUG(-16). As the UUG codon possesses stronger initiating activity in the CGC mutant than in the GGU mutant (Figure 3B, numbers 2 and 3), it is possible that CGC(-25) rescued the initiating activity of UUG(-16). Note that the TTG-to-TTA change is a silent mutation and therefore does not affect the stability of the protein form initiated from ACG(-25). A semiquantitative RT-PCR experiment Selleckchem Erastin further demonstrated that these mutations at codon position -25 or -16 did not affect the stability of the mRNAs derived from these constructs (Figure 3C). Figure 3 Rescuing a cryptic translation initiation site in ALA1. (A) Complementation assays for mitochondrial AlaRS activity. (B) Assay of initiating activity by Western blots. Upper panel, AlaRS-LexA fusion; lower panel, PGK (as loading controls). (C) RT-PCR. Relative amounts of specific ALA1-lexA mRNAs generated from each construct were determined by RT-PCR. As a control, relative amounts of actin mRNAs were also determined. The ALA1 sequences used in the ALA1-lexA constructs 1~4 in (B) were respectively transferred from constructs 1~4 shown in (A). In (C) the numbers 1~4 (circled) denote constructs shown in (B).

The vast MIC differences between MRSA strains, the population heterogeneity within single strains and the dependence of resistance levels on external factors are reflected in these many structural genes and global regulators, which can influence resistance levels. While typically considered nosocomial pathogens, new faster growing and apparently more virulent MRSA have begun spreading in the community. Interestingly, these emerging strains often express very low methicillin resistance, e.g. the MRSA clone spreading amongst intravenous drug users in the Zurich area, which has an in vitro Entospletinib doubling time of 25 min, but oxacillin MICs of only 0.5

to 4 μg/ml [23]. This particular clone’s low-level resistance is partially due to a promoter mutation, leading to tight repression of mecA, but resistance levels appear to be mainly restricted by unknown factors within its genomic background [12]. To identify potential factors involved in mecA regulation

or methicillin resistance levels in such an extremely low level resistant MRSA, we performed DNA-binding protein purification assays, using the mecA operator region as bait. A novel, uncharacterized protein, SA1665, was found to bind to this DNA fragment, and shown to increase methicillin resistance levels when deleted. Results Identification of SA1665 MRSA strain CHE482 is the type strain for APR-246 mw the so-called “”drug clone”" spreading amongst intravenous drug users in the Zurich area [12, 23]. This strain carries mecA and expresses PBP2a, but appears phenotypically methicillin susceptible by conventional phenotypic tests. However, like most other low-level resistant MRSA, it can segregate a small proportion of higher resistant subclones in the presence of β-lactams. We hypothesized that Alpelisib price regulation of methicillin resistance in such low-level resistant clonal lineages may differ qualitatively from classical heterogeneously- or highly-resistant MRSA. A DNA-binding protein purification assay was performed to identify new potential factors involved in the regulation of mecA/PBP2a. The mecA/mecR1 intergenic DNA region, including the 5′

9 bp of mecR1 and the first 52 bp of mecA, was used as bait against crude protein extract from strain CHE482. Proteins why binding to this DNA fragment were analysed by SDS-PAGE. Even though CHE482 contained BlaI, which is known to bind to the mec operator, this band could not be identified on gels due to co-migrating, non-specific bands the same size as BlaI (14.9 KDa) that bound to both the DNA-coated and uncoated control beads. The most prominent protein band of ~16–20 kDa, isolated from DNA-labelled but not from control beads, was identified as the hypothetical protein SA1665 (N315 genome annotation [BA000018]) (Figure 1A). SA1665 encodes a predicted 17-kDa protein with an n-terminal helix-turn-helix (HTH) motif characteristic of DNA-binding transcriptional regulators.

This was in accordance with the SEM observation (Figure 1c) and literature results [45, 46]. The thin hysteresis loops (Figure 3c 1,d1) were due to the slight capillarity phenomenon existing within the very loose nanoarchitectures (Figure 2g,h). As shown in Table 1, with the temperature increasing from 120°C to 150°C, to 180°C, and to 210°C, the corresponding

multipoint BET specific surface area of the nanoarchitecture decreased from 21.3 to 5.2, to 2.6, and to 2.0 m2·g−1, respectively. Meanwhile, the total pore volume changed from 3.9 × 10−2 to 2.9 × 10−2, to 2.9 × 10−2, and to 2.1 × 10−2 cm3·g−1, with a roughly decreasing tendency; the average pore diameter changed from 7.3 to 22.1, to 44.7, and to 40.3 nm, with a roughly increasing tendency. Thus, according to the general recognition of the porous materials [50], nanoarchitectures 3 and 4 selleck inhibitor were determined as the mesoporous structures, whereas the pore diameters were near the macropores category. As a matter of fact, with the temperature increasing from 120°C to 210°C, the evolution of the BET specific surface area, total pore volume, and average pore diameter of the various-morphology pod-like α-Fe2O3 nanoarchitectures agreed with the variation of the D 104 calculated by the AG-120 Debye-Scherrer

equation, also in accordance with the SEM observation (Figure 2d,e,f,g,h). Evolution of the hydrothermal products during hydrothermal process Since the compact pod-like nanoarchitecture obtained at 105°C for 12.0 h (Figure 2c) bridged 1D β-FeOOH nanostructures

and pod-like α-Fe2O3 nanoarchitectures, the composition and morphology of the products hydrothermally treated at 105°C for various times were monitored, as shown in Figure 4. All hydrothermal products obtained at 105°C for 1.0 to 12.0 h Pexidartinib purchase exhibited relatively poor crystallinity (Figure 4a 1,a2,a3). When treated for 1.0 h, the product was composed of β-FeOOH (JCPDS No. 34–1266) and detectable trace amount of maghemite (γ-Fe2O3, JCPDS No. 25–1402) in a nearly amorphous state (Figure 4a 1,b). With the time extending to 3.0 h, the product was only β-FeOOH with improved crystallinity, and γ-Fe2O3 no longer existed (Figure 4a 2,c). Notably, β-FeOOH at that period exhibited very tiny primary 1D morphology (i.e., fibrils, click here Figure 4c 1), and a rudimental pod-like aggregate was also observed (denoted as yellow dotted elliptical region in Figure 4c). When treated for 6.0 h, the hydrothermal products containing trace amount of β-FeOOH and majority of newly formed α-Fe2O3 (Figure 4a 3 were acquired, exhibiting pod-like or ellipsoidal-shaped aggregates entangled with 1D nanostructures (Figure 4d). The enlarged image (Figure 4e) corresponding to the red dot-dashed rectangular region in Figure 4d clearly showed that the selected developing pod-like aggregate was assembled by 1D β-FeOOH nanowhiskers.

Table 2 Swarming and Planktonic Growth of V. paradoxus EPS   Broth Growth (24 h) Swarminga Biofilm Carbon Sources M9 FW M9 FW M9 Casamino acids ++ ++ ++ ++ +++ Glucose ++ +/- + +/- ++ Succinate ++ ++ ++ ++ +++ Benzoate ++ ++ – - +/- Maltose ++ – +* – +/- Sucrose ++ – + – + d-Sorbitol

++ – ++ +/- ++ Maleic acid + – - – +/- Mannitol ++ – ++ – + Malic acid ++ – ++ +/- ++ Nitrogen Sources (with Succinate)           NH4Cl ++ ++ ++ ++ + NH4SO4 ++ ++ ++ ++ + Tryptophan ++ + ++ ++ + Histidine ++ + ++ ++ + Methionine ++ – + + + Cysteine – nd Nd Nd nd Tyrosine ++ – + + + Arginine ++ nd + + + Glycine ++ – +/- + + * swarming was slower with distinct edge (Fig 3, 4) Figure 5 Nutrient dependence of swarming motility. A) Swarm diameter at 24 h (blue bars) or 48 h (red bars) using several carbon sources on FW (F) or M9 (M) base. F/M-S = succinate, F/M-G = glucose, F-G-P = glucose + 2 mM phosphate buffer (pH7), M-M = maltose, F/M-CAA = casamino acids (C+N), VX-689 ic50 M-Ma = malic acid, M-So = sorbitol, M-Su = sucrose. * indicates that NVP-AUY922 cell line swarms merged by 48 h. B) Swarm diameter at 24 h (blue bars) or 48 h (red

bars) using several nitrogen sources on FW (F) or M9 (M) base. All swarms measured in triplicate, with error in all cases ± SEM. Figure 6 Edges of swarms are affected by nutrients, basal medium. Swarming edge images after 24 h on a variety of media. FW base medium was used for (A, B, D, J, K, L) with M8/M9 base medium used for the other panels. Succinate is the C source in all panels except B (glucose) and C (maltose). For growth on PAK6 FW-glucose, 2 mM sodium phosphate buffer (pH 7) was added. NH4Cl was the N source in (A-C), with alternative N sources methionine (D, E), arginine (F), tyrosine (G, J), tryptophan (H, K), and histidine (I, L). Arrows point to extruded material from swarm edges under certain conditions. Scale bar = 25 microns.

Figure 7 Gross swarm morphology is affected by nutrients, basal medium. Colony morphologies after 1d on A) FW-succinate-NH4Cl and B) FW-casamino acids. C) After 3d on FW-succinate-methionine, a “”rare branch”" phenotype was observed. D) Slower swarming on M9-succinate-tyrosine was characterized by a less well defined swarm with altered structure. Stark differences in extent and form of swarming were learn more observed on E) FW-succinate-tryptophan and F) M9-succinate-tryptophan. G) After an extended incubation, swarms on FW-succinate-NH4Cl display a mutually repellent morphology with distinct internal and external edges. Swarming motility on different nitrogen sources When succinate was used as carbon source, all single amino acids tested were permissive for swarming on FW minimal base as well as M8 base (Table 2). When the swarm diameters were measured at 24 h and 48 h, a pattern similar to the carbon source experiments was observed (Fig 5B). Rapid swarming was observed on NH4Cl, tryptophan, histidine, and glycine (Fig 5B).