PubMed 35 Visekruna A, Joeris T, Seidel D, Kroesen A, Loddenkemp

PubMed 35. Visekruna A, Joeris T, Seidel D, Kroesen A, Loddenkemper C, Zeitz M, Kaufmann SH, Schmidt-Ullrich

R, Steinhoff U: Proteasome-mediated degradation of IkappaBalpha c-Met inhibitor and processing of p105 in Crohn disease and ulcerative colitis. J Clin Invest 2006, 116:3195–3203.PubMedCrossRef 36. Gyrd-Hansen M, Meier P: IAPs: from caspase inhibitors to modulators of NF-kappaB, inflammation and cancer. Nat Rev Cancer 2010, 10:561–574.PubMedCrossRef 37. Greten FR, Eckmann L, Greten TF, Park JM, Li ZW, Egan LJ, Kagnoff MF, Karin M: IKKbeta links inflammation and tumorigenesis in a mouse model of colitis-associated cancer. Cell 2004, 118:285–296.PubMedCrossRef 38. Varfolomeev E, Vucic D: (Un)expected roles of c-IAPs in apoptotic and NFkappaB signaling pathways. Cell Cycle 2008, 7:1511–1521.PubMedCrossRef 39. Varfolomeev E, Blankenship JW, Wayson SM, Fedorova AV, Kayagaki N, Garg P, Zobel K, Dynek JN, Elliott LO, Wallweber HJ, Flygare JA, Fairbrother WJ, Deshayes K, Dixit VM, Vucic D: IAP antagonists induce autoubiquitination of c-IAPs, NF-kappaB activation, and TNFalpha-dependent apoptosis. Cell

2007, 131:669–681.PubMedCrossRef 40. Vassiliou EK, Kesler OM, Tadros JH, Ganea D: Bone marrow-derived dendritic cells generated in the presence of resolvin E1 induce apoptosis of activated CD4+ T cells. J Immunol 2008, 181:4534–4544.PubMed 41. Arita M, Bianchini F, Aliberti J, Sher A, Chiang N, Hong S, Yang R, Petasis NA, Serhan CN: Stereochemical assignment, antiinflammatory properties, LY2874455 manufacturer and receptor for the omega-3 lipid mediator resolvin E1. J Exp Med 2005, 201:713–722.PubMedCrossRef 42. Harpaz N, Polydorides AD: Colorectal dysplasia in chronic inflammatory bowel disease: pathology, clinical implications, and pathogenesis. Arch Pathol Lab Med 2010,

134:876–895.PubMed 43. Karin M: NF-kappaB as a critical link between inflammation and cancer. Cold Spring Harb Perspect Biol 2009, 1:a000141.PubMedCrossRef 44. Spehlmann ME, Eckmann L: Nuclear factor-kappa B in intestinal protection and destruction. Curr Opin Gastroenterol 2009, 25:92–99.PubMedCrossRef 45. Karrasch T, Jobin C: NF-kappaB and the intestine: friend or foe? Inflamm Bowel Dis 2008, 14:114–124.PubMedCrossRef oxyclozanide 46. Gadjeva M, Wang Y, Horwitz BH: NF-kappaB p50 and p65 subunits control intestinal homeostasis. Eur J Immunol 2007, 37:2509–2517.PubMedCrossRef 47. Schreiber S, Nikolaus S, Hampe J: Activation of nuclear factor kappa B inflammatory bowel disease. Gut 1998, 42:477–484.PubMedCrossRef 48. Ellis RD, Goodlad JR, Limb GA, Powell JJ, Thompson RP, GF120918 concentration Punchard NA: Activation of nuclear factor kappa B in Crohn’s disease. Inflamm Res 1998, 47:440–445.PubMedCrossRef 49. Rogler G, Brand K, Vogl D, Page S, Hofmeister R, Andus T, Knuechel R, Baeuerle PA, Scholmerich J, Gross V: Nuclear factor kappaB is activated in macrophages and epithelial cells of inflamed intestinal mucosa. Gastroenterology 1998, 115:357–369.PubMedCrossRef 50.

b The ratio of rates at which recombination and mutation occur,

b. The ratio of rates at which recombination and mutation occur, representing a measure of how often recombination events happen relative to mutations. The phylogram based on the analysis with correction for recombination revealed that the time to the most recent common ancestor (TMRCA) of L. innocua subgroups A and B was similar (Figure 3), suggesting that these two subgroups appeared at approximately the same time. In addition, our study also showed the TMRCA of L. monocytogenes lineages I and II were similar, consistent with a recent report [24]. Figure 3 A 95% majority-rule consensus tree based on ClonalFrame

output with correction for recombination. The X-axis represents the estimated time to the most recent common ancestors (TMRCA) of the L. innocua-L. monocytogenes clade. Blue dash line shows the estimated time to the most recent common ancestors

of L. innocua subgroups I and II. Distribution of L. innocua isolates among different ABT-737 order sources Of the 29 L. innocua food isolates, 13 were obtained from meat, 8 from milk and 8 from seafoods. The majority of meat isolates (10/13, 76.9%) belonged to subgroup A, while most seafood isolates (5/8, 62.5%) belonged to subgroup B. There were significant associations between subgroups and source of isolation (p < 0.05). L. innocua isolates lack virulence genes found in L. monocytogenes, and were nonpathogenic to mice All L. innocua strains lacked 17 virulence 4EGI-1 genes examined, with the exception of the subgroup D strain (L43) harboring inlJ (87.5%-93.6% nucleotide identities to L. monocytogenes reference strains EGDe and F2365) and two subgroup B strains (1603 and 386) bearing bsh (97.7%-99.4% nucleotide identities to EGDe and F2365). All of these L. innocua strains were Glycogen branching enzyme nonpathogenic to ICR mice (Table 1). Discussion The ecological, biochemical and genetical resemblance as well as the clear differences of virulence between L. monocytogenes and L. innocua make this bacterial clade

attractive as models to examine the evolution of pathogenicity in Listeria genus. L. monocytogenes causes life-threatening infections in animals and human populations, and exhibits a diversity of strains with different pathogenicity [25]. L. innocua has once been postulated as the nonpathogenic variant of L. monocytogenes, and holds the key to understanding the evolutionary history of the L. monocytogenes-L. innocua clade. However, information on the Daporinad concentration phylogenetic structure and microevolution of L. innocua is still lacking. Thus, we characterized L. innocua strains in our laboratory stock from phylogentic perspectives. Profiling of 37 internalin genes grouped the L. innocua strains into five internalin types, IT1 to IT5, with IT1 and IT2 as the major types (Table 2). The MLST scheme identified two major phylogenetic branches containing the majority of sequence types (29/31, 93.5%), and other two bearing one strain each (Fig 1). Consequently, L.

Rev Sci Instrum 2011, 82:113707–113711 CrossRef 18 Kawai H, Yosh

Rev Sci Instrum 2011, 82:113707–113711.CrossRef 18. Kawai H, Yoshimoto Y, Shima H, Nakamura Y, Tsukada M: Time-fluctuation of the dimer structure on a Ge (001) surface studied by a Monte Carlo simulation and a first-principles calculation. J Phys Soc Jpn FDA-approved Drug Library order 2002, 71:2192–2199.CrossRef 19. Yoshimoto Y, Nakamura Y, Kawai H, Tsukada M, Nakayama M: Ge (001) surface reconstruction studied using a first-principles calculation and

a Monte Carlo simulation. Phys Rev B 2000, 61:1965–1970.CrossRef 20. Naitoh Y, Kinoshita Y, Li YJ, Sugawara Y: The influence of a Si cantilever tip with/without tungsten coating on noncontact atomic force microscopy imaging of a Ge (001) surface. Nanotechnology 2009, 20:264011. 1–7CrossRef 21. Leng Y, Williams C, Su L, Stringfellow G: Atomic ordering of GaInP studied by Kelvin probe force microscopy. Appl Phys Lett 2004, 66:1264–1266.CrossRef Competing interests The authors declare that they have BMS345541 cell line no competing interests. Authors’ contributions ZM, JM, JT, HX, and HZ carried out the calculations, performed the experiments, and drafted the manuscript with the help of CX and JL. YL participated in the design of the study and helped to draft the manuscript. All authors read and approved the final manuscript.”
“Background Optical microcavities with tubular geometry exhibit several advantages compared to

other types of optical microcavities [1–4]. They naturally assume a hollow structure and are fully www.selleckchem.com/products/su5402.html integrative into lab-on-chip systems [5]. In the past years, rolled-up tubular microcavities have been used as cell culture devices [6, 7], microlasers [8, 9], sensors [10], and so on. Especially, rolled-up microcavities with (ultra)thin wall thickness are sensitive to tiny alterations and modifications in the vicinity Astemizole of the inner and outer tube wall surfaces [5]. Thus, the microcavities exhibit excellent

potential applications as sensors in the fields of optoelectronics [11], biosensing [6, 12], and integrated optofluidics [10, 13]. Very recently, preliminary results concerning detection of dynamic molecular processes were demonstrated on a self-rolled-up SiO/SiO2 optical microcavity with sub-wavelength wall thickness [14]. In fact, the molecule absorption/desorption are quite complex processes, and their interaction with the evanescent field is even intricate, especially in the nanoscale. Before this sensing technique can be put into practical applications like other label-free methods, more work must be done to disclose the mechanism and to exhibit the general and diverse capability of the approach. In this letter, we focus on the detection of physically and/or chemically absorbed water molecules by using a rolled-up tubular microcavity as a core component. The microcavities used in this work were prepared by releasing prestressed 33.5-nm-thick Y2O3/ZrO2 circular nanomembranes on photoresist sacrificial layers. The influence of surface composition (e.g.

In addition, they require the use of gel electrophoresis to detec

In addition, they require the use of gel electrophoresis to detect amplified products, which is long and tedious. Real-time PCR assays developed for the rapid detection of Xcc [4, 8] have the drawback of requiring an expensive thermal cycler with

a fluorescence detector. Loop-mediated isothermal amplification (LAMP) is a recent DNA amplification technique that amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions [9]. LAMP is based on the principle of autocycling strand displacement DNA synthesis performed by the Bst DNA polymerase, for the detection of a specific DNA sequence [9]. The technique uses four to six primers that recognize six to eight regions of the target DNA and provides very high specificity [9, 10]. The technique can be carried out PS-341 nmr under FG-4592 cell line isothermal conditions ranging between 60 and 65°C and produces large amounts of DNA [9]. The reaction shows high tolerance to biological Elafibranor in vitro contaminants [11],

which can help to avoid false negative results due to the inactivation of the enzyme, a common problem in PCR. Although LAMP amplification products can also be detected by gel electrophoresis, this long procedure reduces the suitability for field applications. For this reason we used SYBRGreen I, an intercalating DNA dye, and a generic lateral flow dipstick (LFD) device to detect the positive amplification by simple visual inspection, as described previously [12–20], with potential field application. We optimized the assay for the amplification of a portion of the pthA gene, a well known pathogenicity determinant of CBC-causing Xanthomonas [21–25]. Various LAMP assays for the detection of animal and human pathogens have been developed [20, 26–33], but this technique remains uncommon for bacterial plant pathogens. Here we describe a sensitive,

specific, fast, and simple LAMP assay for the detection of Citrus Bacterial Canker. Atorvastatin Results Reaction conditions were optimized to establish fast and efficient parameters for amplification. Different temperatures, times and the use of loop primers, which have the capacity to accelerate the reaction, were tested [10]. The optimal amplification of the pthA gene fragment was obtained at 65°C for 30 min using loop primers, as shown by agarose gel electrophoresis (Fig. 1). Amplified products exhibited a typical ladder-like pattern. No products were observed in negative control without DNA (Fig. 1). Specificity of the amplification product was confirmed by sequencing of some bands (data not shown). The samples giving positive reaction show a green color with the addition of SYBRGreen I, while the negative control remained orange (Fig. 2). The lateral flow dipstick shows two clear lines for the positive reaction (the lower line is the sample assay band and the upper one is the control line) while the negative reaction shows only the control line (Fig. 2).

The regulated genes with putative function Among the 302 genes

The regulated genes with putative function Among the 302 genes significantly altered in transcription by root exudates, 44 were annotated to encode a putative enzyme or a hypothetical protein. Similar to the genes with known function, these 44 genes fell into three categories: metabolism of carbohydrates and related molecules, metabolism of amino acids and related https://www.selleckchem.com/CDK.html molecules, and transport/binding proteins and lipoproteins (Additional file 1: Table S2). Some of the 44 genes were closely associated with plant-microbe interactions. For example, the transcription of ydjL, nowadays

renamed bdhA, encoding acetoin reductase/butanediol dehydrogenase [53], was 1.5-fold enhanced by root exudates. 2, 3-Butanediol is a volatile organic compound released by PGPR and able to promote significantly plant growth [54]. The expression of the gene Entospletinib molecular weight epsE, residing in a 15-gene operon epsA-O, was also enhanced by root exudates. EpsE is involved in formation of biofilm by arresting flagellar rotation of cells embedded in biofilm matrix [55]. Another activated gene was dfnY, which encodes a hypothetical protein. Like other induced genes known to be involved in antibiotic production such as dfnF dfnG dfnI and dfnJ (Table 3), dfnY is part of the gene cluster responsible for synthesis

of the polyketide antibiotic difficidin. It is worth mentioning that antibiotic production is energetically very costly and its strict control is a clear evolutionary advantage. In contrast

to a few genes significantly altered during the exponential phase (OD1.0), hundreds of genes were differentially expressed in presence of root exudates during transition to stationary growth phase (OD3.0). Such a difference may not be surprising. The transcription of most bacterial genes during the exponential growth phase is typically initiated by RNA polymerase holoenzyme carrying the housekeeping transcription factor σA, while in the stationary phase, transcription is mainly accomplished by RNAP carrying alternative sigma factors allowing to adapt to a permanently changing environment. The extracytoplasmic-function (ECF) sigma factor W was enhanced in presence of root-exudate (Figure 5). SigW is known as being expressed Baricitinib in early stationary growth-phase and induced by various cell wall antibiotics, alkaline shock, and other stresses affecting the cell envelope. It controls a large “antibiosis” regulon involved in mediating resistance to various antibiotics including P5091 fosfomycin and the antibiotic peptides sublancin and SdpC [56]. It has been observed that many virulence-associated factors influence the colonization, persistence and spreading mechanisms of the human pathogen Streptococcus pyogenes in a growth phase-dependent manner [57–59]. Likewise, rhizobacteria may employ an early stationary phase-related mechanism to favor expression of those genes that mediate rhizosphere competence.

The K2 cps gene cluster of K pneumoniae Chedid contains a total

The K2 cps gene cluster of K. pneumoniae Chedid contains a total number of 19 open reading frames (ORFs) organized into three transcription units, orf1-2 orf3-15, and orf16-17 [16]. In the previous studies, numerous regulatory systems were demonstrated to control the biosynthesis of CPS via regulating the cps transcriptions in K. pneumoniae, Alpelisib concentration such as the Rcs system, RmpA, RmpA2, KvhR, KvgAS, and KvhAS [17–20]. Among these, ferric uptake regulator (Fur) represses the gene expression of rcsA rmpA, and rmpA2 to decrease CPS biosynthesis [21, 22]. Therefore,

overlapping regulons governed the regulation of these assorted virulence genes in response to numerous stress conditions. Bacterial cells are constantly challenged by various environmental stresses from their natural habitats.

Similar to many gastrointestinal (GI) pathogens, K. pneumoniae faces several challenges during infection and colonisation of the human body. These include gastric acid, the immune system, and a limited supply of oxygen and nutrients [23, 24]. Among these, the concentration of iron in the environment is critical for YM155 supplier the control of cellular metabolism. Limitation of iron abolishes bacterial growth, but high intracellular concentrations of iron may damage bacteria because of the formation of undesired reactive oxygen species (ROS). Iron homeostasis maintained by the transport, storage, and metabolism of iron is tightly controlled by Fur

in many gram-negative bacteria [25–27]. To regulate gene transcription, Fur protein functions as a dimer with Fe2+ as a cofactor to bind to a 19-bp consensus sequence, called the Fur box (GATAATGATwATCATTATC; w = A or T), in the promoters of downstream genes [28]. In several gram-negative pathogens, Fur represses the expression of genes involved in iron homeostasis and in the regulation of multiple cellular functions such as oxidative stress, energy metabolism, acid tolerance, and virulence gene production [29–32]. Janus kinase (JAK) In K. pneumoniae, Fur plays a dual role in controlling CPS biosynthesis and iron acquisition [21]. Recently, we also found that type 3 fimbriae expression and bacterial biofilm formation were also controlled by Fur and iron availability [33]. Therefore, the regulatory mechanism of Fur in control of multiple cellular function and virulence factors in K. pneumoniae needs to be further investigated. Although Fur typically acts as a repressor, it also functions as a check details transcriptional activator for the gene expression such as acnA fumA, and sdhCDAB (tricarboxylic acid [TCA] cycle enzymes), bfr and ftnA (iron storage), and sodB (iron superoxide dismutase [FeSOD]) [34–38]. However, positive regulation by Fur is often indirect, mediated by Fur-dependent repression of a small non-coding RNA (sRNA), RyhB [39].

Wiley, Hoboken Leclerc MC, Guillot J, Deville M (2000) Taxonomic

Wiley, Hoboken Leclerc MC, Guillot J, Deville M (2000) Taxonomic and phylogenetic analysis of Saprolegniaceae (Oomycetes) inferred from LSU rDNA and ITS sequence comparisons. Antonie Van Leeuwenhoek 77:369–377PubMed Lee SB, Taylor JW (1992) Phylogeny of five fungus-like protoctistan PI3K inhibitor Phytophthora spp., inferred from the internal transcribed spacers of ribosomal DNA. Mol Biol Evol 9:636–653PubMed Lee TY, Mizubuti E, Fry WE (1999) Genetics of metalaxyl resistance in Phytophthora infestans. Fungal Genet Biol 26:118–130PubMed LéJohn HB (1971) Enzyme regulation, lysine pathways and cell wall structures as indicators of major lines

of evolution in fungi. Nature 231:164–168PubMed Lévesque CA, de Cock AWAM (2004) Molecular phylogeny and taxonomy of the genus Pythium. Mycol Res 108:1363–1383PubMed Lévesque CA, Harlton CE, de Cock AWAM (1998) Identification of some oomycetes by reverse dot blot hybridization. Phytopathology 88:213–222PubMed Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RH, Johnson J, Krajaejun T, Lin H, Meijer HJ,

Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR (2010) Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biology 11(R73):22 Selleck MM-102 Lifshitz R, Dupler M, Elad Y, Baker R (1984) Hyphal interactions between a mycoparasite Pythium nunn and several soil fungi. Can J Microbiol 30:1482–1487 Mao Y, Tyler BM (1991) Genome organization of Phytophthora megasperma f.sp. glycinea. Exp Mycol 15:283–291.

doi:10.​1016/​0147-5975(91)90031-8 Martin FN Thiamet G (1991) Characterization of circular mitochondrial plasmids in three Pythium species. Curr Genet 20:91–97PubMed Martin FN, Kistler HC (1990) Species specific banding patterns of restriction GSK1120212 in vitro endonuclease digested mitochondrial DNA in the genus Pythium. Exp Mycol 14:32–46 Martin FN, Loper JE (1999) Soilborne plant diseases caused by Pythium spp.: ecology, epidemiology, and prospects for biological control. Crit Rev Plant Sci 18:111–181 Martin FN, Tooley PW (2003) Phylogenetic relationships among Phytophthora species inferred from sequence analysis of mitochondrially encoded cytochrome oxidase I and II genes. Mycologia 95:269–284PubMed Martin RR, James D, Lévesque CA (2000) Impacts of molecular diagnostic technologies on plant disease management. Annu Rev Phytopathol 38:207–239PubMed Martin FN, Tooley PW, Blomquist C (2004) Molecular detection of Phytophthora ramorum, the causal agent of sudden oak death in California, and two additional species commonly recovered from diseased plant material.

All pathogenic Y enterocolitica strains harbor ail, which is dif

All pathogenic Y. enterocolitica strains harbor ail, which is different from the inv sequence (which encodes a protein of similar function), and renders Y. enterocolitica capable of invading the intestinal epithelium. In addition, the Ail protein confers a serum resistance phenotype on Y. enterocolitica [5]. In contrast to inv, which exists in non-pathogenic as well as pathogenic strains of Y. enterocolitica, ail only exists in Y. enterocolitica strains epidemiologically

related to human disease [6], and is therefore an important virulence marker. #PRIMA-1MET purchase randurls[1|1|,|CHEM1|]# Environmental isolates not associated with disease have a non-functional inv and no ail [7]. Ferric ion uptake is essential for bacterial growth and survival. The supply of iron and production of the siderophore transport system is a central factor in infections with Yesinia pestis and Y. enterocolitica. IWR-1 molecular weight Pathogenic Y. enterocolitica can be divided into 2 groups, those producing the siderophore, such as biotype 1B/O:8, and those producing no siderophore, as in serotypes O:3 and O:9 [8]; the latter take up ferric ion using ectogenic siderophores, such as ferrioxamin B and ferrioxamin E [9]. The 2 groups have different

ferric ion uptake abilities, which may explain the differences in virulence among serotypes [10]. A 77 kDa receptor on the Y. enterocolitica outer membrane [11] combines with ferrioxamin to take up ferric ion rapidly [12]. This process is energy-dependent and requires the action of the TonB protein, part of a complex known as the Ton system. This complex undergoes a conformational change driven by the proton motive force (PMF), which interacts with the outer membrane receptors and activates Etofibrate transport [13]. The FoxA receptor of Y. enterocolitica, the ferrochrome receptor and the TonB-dependent receptor share high amino acid homology [14, 15]. The foxA was chosen for study because it exists in all Y. enterocolitica strains. Using polymorphic gene analysis,

we show that combined detection of ail and foxA confirms the identity of pathogenic Y. enterocolitica. Methods Bacterial strains and identification of biotype and serotype We chose 271 pathogenic and 27 non-pathogenic Y. enterocolitica strains isolated from diarrhea patients, animals, food and the environment in China. They included 205 strains of serotype O:9, 72 of serotype O:3, 10 of serotype O:8, 5 of serotype O:5, 3 of serotype O:6, 30 and 3 of undetermined serotype (Table 1), together with 11 reference strains from Europe, the United States and Japan (Table 2). The serotypes, biotypes and pathogenesis of these strains were determined as previously described [16–18]. Table 1 Bio-serotypes of the 298 Y.

Such a feedback has a sign-reversed eigenenergy, , and is express

Such a feedback has a sign-reversed eigenenergy, , and is expressed by , where Θ(t), Δ k , γ k and Γ k denote the step function, the particle-hole off-diagonal element, and the scattering rates of the

intermediate and bare-particle states, respectively. The Fourier transform of Σ k (t) gives the frequency representation of the self-energy of the BQPs, (3) Figure 1 shows the ARPES spectra of BQPs for underdoped and overdoped Bi2212 samples with T c = 66 and 80 K (UD66 and OD80, respectively) [8]. As shown in Figure 1b,c, an energy distribution curve was extracted from the minimum PI3K Inhibitor Library gap locus for each off-node angle θ and symmetrized with respect to the Fermi energy ω = 0. These spectra were well fitted with a phenomenological function, (4) except for a featureless background. Equation 4 is deduced from Equation

3 and , neglecting γ k after Norman et al. [11]. Figure 1b,c exemplifies that the superconducting gap energy Δ at each θ is definitely determined by sharp spectral peaks. In Figure 1d,e, the obtained gap energies (small yellow circles) are plotted over the image of spectral intensity as a Mocetinostat research buy function of sin 2θ, so that the deviation from a d-wave gap is readily seen with reference to a straight line. While the superconducting gap of the overdoped sample almost follows the d-wave line, that of the underdoped PXD101 sample is deeply curved against sin 2θ. Furthermore, Figure 1d indicates that the deviation from the d-wave gap penetrates into the close vicinity of the node and that it is difficult to define the pure d-wave region near the node. Therefore, the next-order harmonic term, sin 6θ, has been introduced, so that the smooth experimental gap profile is properly parametrized [12–14]. The next-order high-harmonic function is also expressed as Δ(θ) = ΔN sin 2θ + (Δ∗-ΔN)(3 sin 2θ- sin 6θ)/4, where the antinodal and nodal gap energies are defined as Δ∗ = Δ(θ)| θ=45° and , respectively, so that ΔN/Δ∗ = 1 is satisfied for a pure d-wave gap. Figure 1 Superconducting

gap manifested in BQP spectra. The data are for underdoped and overdoped Bi2212 samples with T c = 66 and 80 K (UD66 and OD80, respectively) [8]. (a) Momentum-space diagram for an off-node Vildagliptin angle, θ, and a bonding-band (BB) Fermi surface along which the ARPES spectra were taken. (b, c) Symmetrized energy distribution curves (colored circles) and their fits (black curves). (d, e) ARPES spectral images as a function of energy ω and sin 2θ. Superimposed are the gap energies (yellow circles) and high-harmonic fit (yellow curve) as functions of sin 2θ. The doping dependences of the superconducting gap parameters are summarized in Figure 2. One can see from Figure 2a that as hole concentration decreases with underdoping, the nodal gap energy 2ΔN closely follows the downward curve of 8.5k B T c in contrast to the monotonic increase in the antinodal gap energy 2Δ∗.

* vGI status for vGI-1b, vGI-19 – vGI-22 either duplicated (dp) o

* vGI status for vGI-1b, vGI-19 – vGI-22 either duplicated (dp) or deleted (dl), else no entry designates present as a single copy region. IS900 insertion site analysis To determine which IS900 sites were absent relative to the K10 reference genome, PCR primers were designed to specifically amplify each of the known 17 IS900 loci (Table  6). These were used

to confirm the insertion of IS900 into each locus in #GM6001 randurls[1|1|,|CHEM1|]# the reference strain K10 and were also all positive in all 316 F strains and a caprine isolate CAM87. Both vaccine strains IIUK2000 and 2eUK2000 were missing IS900(MAP1722) whereas IS900(MAP1033) was also missing from vaccine strain 2eUK2000 but present in all other strains including vaccine strain IIUK2000. Comparative qPCR of IS900 copy number relative to MAP2114c, demonstrated a range of IS900 copies in vaccine strains that corresponded to the trend in hybridisation signals observed in MAPAC scatterplots Ferrostatin-1 in vitro (Figure  1a & 1b). The ratio of copy number however was surprisingly

higher than predicted, with vaccine strains IIUK2000 and 2eUK2000 having only 13 copies whilst MAPK10 and 316 F strains gave signals correspondent with 16–19 relative IS900 copy numbers (Table  7). Functional analysis of tellurite resistance One MAP specific gene predicted to be deleted in vGI-19 was MAP3730 (Table  1), a S-adenosylmethionine-dependent methyltransferase with homologues to tellurite resistance Lck genes (tehB) involved in bacterial virulence and persistence [27, 28]. The functionality of this gene in mycobacteria has not previously been investigated. Using a solid culture plate assay we compared tellurite resistance (MIC) of MAP strains with and without the vGI-19 deletion (Table  7). This demonstrated a wide MIC range (8 – >512 μg/ml) between strains, with significant reductions associated with vGI-19 (316FNOR1960) deletion over full genome complement strains. Of note however was the very low level of tellurite

resistance (8 μg/ml) found in strains containing the vGI-20 (IIUK2000 & 2eUK2000) deletion. Assessment of virulence using a mouse model The virulence of vaccine strains 316FUK2001, IIUK2001 and 2eUK2001 was compared with wild type strain JD87/107 in a mouse model. Ten mice from each of five groups (four inoculated with the different MAP strains and a negative control group inoculated with PBS) were killed at 4, 8 and 12 weeks post inoculation. Body, spleen and liver weights were recorded. Samples of the liver were taken for bacteriological culture and histopathology. Mean bodyweights increased with age, but no statistically significant difference was observed in mean body weight between any of the vaccine strains and the control wild type strain at any of the time points (p=0.11).