Freshly prepared MHB, before bacterial inoculation, contained relatively low levels of free glucose (0.38 mM), which were rapidly depleted (<0.001 mM) during the pre-shock growth period, as found in other studies [48, 49]. Extracellular starch levels, an abundant component of MHB, which was looked as a potential glucose-providing source, remained absolutely constant (assayed as 1.2–1.3 mg/ml of glucose equivalent) throughout bacterial growth. This suggested that S. aureus could not use starch as a nutrient source

presumably BGB324 molecular weight because of the lack of extracellular amylolytic activity. Collectively, our transcriptomic and physiological data strongly indicated that, after glucose exhaustion from the medium, S. aureus was forced to use the most abundant alternative carbon sources that were amino acid or peptide mixtures provided in the casein acid hydrolysate component of MHB. Recent metabolic studies indicate that the catabolism of several amino acids can feed both TCA cycle and gluconeogenesis pathways by producing essential intermediates oxaloacetate, oxoglutarate, phosphoenolpyruvate, and pyruvate [44, 49, 50]. These metabolic studies also indicate that glucose depletion leads to derepression

of TCA cycle components [44], as confirmed by our transcriptomic data showing their high expression levels at 37°C. While significant selleck compound levels (3.0–3.5 mM) of acetate were detected in MHB just before and after temperature up-shifts, these levels remained marginal

compared to those (ca. 15–20 mM) recorded in other studies [44, 48, 51], and were not sufficient to significantly acidify the growth medium. In contrast to gene activities of the glycolytic, pentose phosphate shunt, and TCA cycle pathways, most nitrate/nitrite reductase components were down-regulated at both 43°C and 48°C. Furthermore, several major fermentative pathway components were markedly PLEKHB2 down-regulated by heat stress at both 43°C and 48°C, in particular alcohol (adhE, adh1), lactate (ldhA, ldhB) and formate (fdh) dehydrogenases. Biochemical assays confirmed the marginal levels of L-lactate (0.3–0.5 mM) and D-lactate (< 0.15 mM) in MHB. The down-regulation of energy-providing fermentative pathways suggests that they may be energetically less efficient for heat-exposed S. aureus. Adjustment of ATP-consuming pathways in heat-shocked S. aureus Two categories of ATP-requiring biosynthetic pathways showed a significant, global reduction in transcript levels. The first category included the purine and pyrimidine synthetic pathways whose fifteen and nine components, respectively, were down-regulated to the same extent (Additional files 4 and 2). In contrast, transcript levels of drm (phosphopentomutase) and pnp (purine nucleoside phosphorylase), coding for salvage pathways, were markedly increased.

5 M), sorbitol

(1.5 M) or caffeine (0.2%). Conidia spread on only PDA plates served as control. For cold stress experiments, conidia at a concentration of 1e + 06 ml-1 in sterile water was incubated at 4°C for 3 days, 6 days or 9 days and then spread on PDA plates. Frequency of conidial germination was determined post 16 h of spreading by counting the number of germinating and non-germinating conidia using microscope. Two hundred to three hundred conidia were counted for each treatment. Each experiment had 3 biological replicates and was repeated 2 times. Mycelial hydrophobicity of C. rosea strains were assayed on PDA plates post 3 days or 10 days of inoculation using water or SDS following the procedure described before [34]. The hydrophobicity Decitabine mw of conidia was assayed using MATH [34], and hydrophobic index was calculated following the formula described before [10]. For extracellular protein concentration determination, fungal strains were grown for 10 days in liquid PDB medium at 25°C, mycelial debris were removed by filtering through four layers of Miracloth, followed by protein precipitation using an acetone precipitation protocol as described elsewhere. The protein Rapamycin nmr pellets

were dissolved in water and total extracellular protein concentration was determined using the quick start Bradford protein assay kit following the manufacturer’s instruction (Bio-Rad, Hercules, CA). Antagonism test Antagonistic behaviour against phytopathogenic fungi B. cinerea, F. graminearum and R. solani was tested using an in vitro plate confrontation assay on PDA medium. An agar plug of C. rosea was inoculated 2 cm from the edge in a 9 cm PDA plate. After 7 days of incubation at 25°C, a plug of B. cinerea, F. graminearum or R. solani was placed

at equal distance to the opposite edge of plate. To test the tolerance of C. rosea WT, deletion or complemented strains against secreted factors of B. cinerea, F. graminearum and R. solani, agar plugs of phytopathogenic fungi were inoculated on PDA plates covered with cellophane and incubated at 25°C in darkness. The plates covered with cellophane, without inoculation, were used as control. The cellophane was removed when fungal mycelia covered the plates, followed by inoculation with C. rosea WT, deletion or complementation strains. Linear growth 3-mercaptopyruvate sulfurtransferase was recorded daily in 3 replicates. For secretion assay, C. rosea strains were grown for 10 days in liquid PDB medium on rotary shaker at 25°C. Culture filtrate was collected after removing mycelia by filtering through four layers of Miracloth. The filtrate was further purified by passing through a 0.45 μM pore size nylon membrane. Agar plugs of B. cinerea, F. graminearum or R. solani was inoculated in conical flasks (50 ml) with 20 ml culture filtrate and incubated at 25°C under constant shaking condition (100 rpm). Biomass production in culture filtrates was analysed by determining mycelial dry weight post 3 days of inoculation. Detached leaf bioassay B.

The identification of novel targets may prove useful in the development of new antimicrobials effective against chlamydiae. Chlamydial genomic studies have identified three Ser/Thr protein kinases, Pkn1, Pkn5, and PknD. Our laboratory has shown previously that C. pneumoniae PknD is a dual-specific protein kinase that autophosphorylates on threonine and tyrosine residues and phosphorylates serine and tyrosine residues of the

FHA-2 domain of Cpn0712, a putative Yersinia YscD ortholog called CdsD [45]. In this report we show that a 3′-pyridyl oxindole compound, a known inhibitor of Janus kinase 3 (JAK3), inhibits C. pneumoniae PknD activity. Selleck Osimertinib This compound prevented PknD autophosphorylation and phosphorylation of CdsD, a type III secretion apparatus protein. When added to infected HeLa cells, the compound retarded C. pneumoniae growth and significantly reduced the amount of infectious C. pneumoniae produced suggesting that PknD plays an important role in chlamydial replication.

Results Identification of an inhibitor of C. pneumoniae PknD protein kinase activity We have recently shown that C. pneumoniae contains three Ser/Thr protein kinases [46] and that one of these, PknD, phosphorylates CdsD, a structural component of the type III secretion Midostaurin solubility dmso system (T3SS) [45]. In order to determine whether PknD plays an essential role in Chlamydia development, we screened an existing library Resveratrol of 80 small molecule kinase inhibitors, including inhibitors of eukaryotic receptor tyrosine kinases and atypical kinases, for their ability to inhibit PknD autophosphorylation in vitro. Recombinant GST-tagged PknD kinase domain (GST-PknD KD) was pre-incubated with 10 μM of each compound

and reactions initiated with the addition of kinase assay buffer containing Mn2+ and ATP. SDS-PAGE and Western blotting followed by autoradiography was used to visualize the extent of PknD autophosphorylation in the presence of each compound. Nine compounds (EMD designations: D7, E8, F4, F5, F6, F7, G5, H10, and H11) of the 80 tested exhibited some level of inhibition of PknD autophosphorylation when tested at 10 μM (data not shown). Of these nine compounds only one, compound D7, a 3′-pyridyl oxindole, completely inhibited PknD autophosphorylation. Fig. 1A shows a dose response for PknD inhibition. At 1 μM compound D7 reduced PknD autophosphorylation by greater than 50% (fig. 1A). Similar results were obtained with two different lots of the inhibitor. Compound D4, a pan-specific inhibitor of the Janus kinase (JAK) family, did not significantly inhibit PknD autophosphorylation at concentrations of 0.2 to 10 μM (figs. 1A and 1B). Similarly, two other JAK3 inhibitors, compounds D5 and D6, did not inhibit PknD autophosphorylation at concentrations of 1 or 10 μM (fig. 1B). Figure 1 Inhibition of PknD by compound D7.

In addition, it should be noted that we analyzed samples from 35 of the 43 patients who completed the study because serum samples were not obtained from eight patients. Our previous

study using the same sample demonstrated that glucose fluctuations in 43 type 2 diabetic Japanese patients were reduced by switching from acarbose or voglibose to miglitol for 3 months. In this study, we obtained the same result in 35 patients. Thus, missing data from the eight patients would this website be less likely to affect the results of this study. It should be noted that our study is relatively small in scale. It has been reported that an increase of the postprandial

incremental area under the curve of blood glucose in a single oral meal test in eight type 2 diabetic patients was reduced by miglitol treatment at doses of 50, 75, 100, and 200 mg [29]. An RCT of 36 type 2 diabetic patients found that postprandial blood glucose levels were reduced by ~50 % in patients treated with miglitol compared with those treated with placebo [30]. A double-blind, crossover design in 15 type 2 diabetic patients found that treatment with miglitol (300 mg/day) effectively reduced postprandial blood glucose levels over 8 weeks [31]. In addition, a previous selleck chemicals llc study reported that treatment with miglitol in 24 viscerally obese subjects reduced glucose fluctuations and circulating IL-6 concentrations versus acarbose treatment [17]. In addition, our previous study reported that the switch of α-GI from acarbose or voglibose to miglitol in 43 type 2 diabetic patients reduced glucose fluctuations and expression of inflammatory

cytokine genes, such as IL-1β and TNF-α, in peripheral leukocytes and the circulating protein concentrations of TNF-α [19]. From these studies, we considered that our sample of 35 type 2 diabetic Japanese patients is comparable; however, a large-scale RCT is needed to examine whether miglitol reduces glucose fluctuations and circulating Depsipeptide order concentrations of CVD risk factors in type 2 diabetic patients compared with other α-GIs. We assessed glucose fluctuations by SMBG. Recent studies have suggested that blood glucose profiles monitored by SMBG are not always correlated with continuous glucose monitoring (CGM), particularly given that measurement of blood glucose concentrations by SMBG often omit hypoglycemic events entirely [32, 33]. A study of ten type 2 diabetic patients hospitalized for 4 days found that glucose fluctuations, which were monitored by CGM, in a standard meal loading were reduced effectively by treatment with miglitol (50 mg) compared with acarbose (100 mg) [34].

3-Methyladenine (3-MA) was purchased from Sigma (Sigma-Aldrich, USA) and prepared as a stock solution of 100 mM in phosphate buffered saline (PBS). Paclitaxel, monodansyl cadaverine (MDC), and bafilomycin A1 were purchased from Sigma. U0126 was purchased from LC laboratories (LC Labs, USA).

GFP-LC3 plasmid was obtained from Addgene (Addgene plasmid 24920). HT TiterTACSTM Assay Kit was purchased from TREVIGEN (TREVIGEN, USA), Beclin 1 siRNA was purchased from Invitrogen (Invitrogen Life Technologies, NY, USA). Antibodies used in this study included the following: Anti-cleaved Caspase-3, anti-MEK1/2, anti-phospho-MEK1/2, anti-phospho-ERK1/2, anti-p62 and anti-Beclin 1 (Cell Signaling Technology, USA); anti- LC3 polyclonal (Thermo Fisher Scientific, USA); anti-FLCN antibody (Obtained from the Van Andel Research Institute). Cell culture Two pairs of cell lines were used: FLCN Etoposide nmr siRNA-silenced ACHN-5968 cell line and scrambled ACHN line (ACHN-sc); FLCN-null UOK257 cell line and UOK257-2 line restored with ectopic expression of FLCN. ACHN was purchased from ATCC, and ACHN-5968 was generated in our lab. UOK257 cell line was obtained from NCI, and UOK257-2 Dactolisib chemical structure was prepared in our lab. All of these cell lines were cultured in DMEM medium, supplemented with 10% fetal bovine serum (FBS) and maintained at 37°C with 5% CO2. Cell viability assay The viability of cells was measured by MTT

assay. Approximately 2 × 103 cells were cultured in 96-well plates and treated with various reagents. MTT (5 mg/ml) was added to each well and cells were cultured at 37°C for 4 hours. Supernatant was

removed and 200 μl DMSO per well was added to dissolve the formazan. Absorbance was measured at 570 nm Etomidate using a microplate reader (BioTek). Western blot Cells were harvested and lysed on ice for 45 min in RIPA lysis buffer (1 M Tris, PH7.4, 50 mM; NaCl 150 mM; 1%NP-40; EDTA 1 mM, plus standard protease inhibitor). The concentration of protein was measured by Nanodrop (Thermo). Equal amounts of total protein extracts were loaded and separated in 10% -15% SDS-PAGE gel and transferred to PVDF membranes. The membranes were blocked in Tris-buffered saline-Tween-20 (TBST) with 5% milk for 1 hour and incubated overnight at 4°C with different primary antibodies: mouse monoclonal anti-FLCN at a dilution of 1:1000, rabbit polyclonal anti-LC3-I/II (1:2000), rabbit polyclonal anti-p62 (1:2000), rabbit monoclonal anti-cleaved caspase-3 antibody (1:1500); mouse polyclonal anti-MEK (1:2000), rabbit polyclonal anti-phospho-MEK (1:2000); rabbit polyclonal anti-phospho-ERK (1:2000) or mouse monoclonal anti-Beclin 1(1:2000). The membranes were washed in TBST and incubated with secondary antibody at room temperature for two hours. Proteins were detected with ChemiDoc detection system (Bio-Rad). DAPI stain and TUNEL assay Cell apoptosis was detected using DAPI stain and TUNEL assay.

Mullen JO, Mullen NL (1992) Hip fracture mortality. A prospective, multifactorial study to predict and minimize death risk. Clin Orthop Relat Res 280:214–22PubMed 30. Nightingale S, Holmes J, Mason J, House A (2001) Psychiatric illness and mortality

after hip fracture. Lancet 357:1264–1265CrossRefPubMed 31. Inouye SK (1994) The dilemma of delirium: clinical and research controversies regarding diagnosis and evaluation of delirium in hospitalized elderly medical patients. Am J Med 97:278–288CrossRefPubMed 32. Blacker DJ, Flemming KD, Link MJ, Brown RD Jr (2004) The preoperative cerebrovascular https://www.selleckchem.com/autophagy.html consultation: common cerebrovascular questions before general or cardiac surgery. Mayo Clin Proc 79:223–229CrossRefPubMed”
“Introduction A history of non-vertebral fracture (NVF) is associated with a doubling of the risk of a subsequent fracture, and the subsequent fracture risk is quadrupled after a vertebral fracture [1, 2]. This subsequent fracture risk is not constant over time and is driven by the high, three to fivefold increase in the years immediately after a first fracture, followed by a gradual waning off later on [3]. This has been shown for

repeat morphometric vertebral fractures [4], subsequent clinical spine, forearm and hip fractures in patients who were hospitalised with a vertebral fracture [5], repeat low-trauma fractures in subjects older than 60 years [6], repeat clinical vertebral and non-vertebral fractures from menopause onwards [3, 7, 8] and repeat hip fractures [9]. As a result, it has been shown in long-term follow-up studies that 40% buy RG7420 to 50% of ATR inhibitor all subsequent fractures occur within 3 to 5 years after a first fracture. The clinical implication is that patients older than 50 years presenting with a fracture need immediate attention to reduce reversible risk factors of a subsequent fracture. This indicates that to undertake immediate care in fracture patients is necessary, such as the Fracture Liaison Service, the involvement of a fracture nurse and other initiatives in the field of post-fracture

care [10–13]. It also indicates that treatment, which has been shown to reduce fracture risk within short term, should be started as soon as possible in patients with a high fracture risk [14]. An increased risk of mortality has been documented after hip, vertebral and several non-hip, non-vertebral fractures [15]. Similar to subsequent fracture risk, this increase in mortality is higher immediately after fracture than later on. In women and men older than 60 years, nearly 90% of excess deaths related to fracture over the 18 years of observation occurred in the first 5 years. Of the 5-year post-fracture excess mortality, approximately one third of deaths were associated to hip, vertebral and non-hip, non-vertebral fractures, respectively. The major causes of death were related to cardiovascular and respiratory comorbidity and infections [15].

3 ± 1.8 45.5 ± 1.9 1.8 <0.0001 17.51 ± 0.81 16.64 ± 0.23 1.81 VX-809 molecular weight 0.0174 pRG198 76.9 ± 1.7 35.7 ± 1.6 2.2 <0.0001 17.48 ± 0.08 16.27 ± 0.06 2.24 0.0013 #volume of the unoccupied space available under the signal is quantitated *p-value of ≤ 0.05 is significant EMSA analysis of upstream sequences of p28-Omp14 and p28-Omp19 promoters Electrophoretic mobility shift assay (EMSA) experiments utilizing the complete promoter regions of the p28-Omp14 and p28-Omp19 of E. chaffeensis showed promoter-specific

binding of tick cell- or macrophage-derived E. chaffeensis proteins (not shown). Addition of 50 ng of specific competitor DNAs consisting of unlabeled full length promoter DNA of p28-Omp14 or p28-Omp19 abolished the shift of DNA-protein complex migration for both promoter regions. To further assess the interactions of Ehrlichia proteins with putative upstream sequences, five biotin-labelled short upstream DNA segments of p28-Omp14 (probes Selleck Vemurafenib P1 to P5) (Figure 8A) and two DNA segments of p28-Omp19 (P6 and P7) (Figure 8B) promoters

were prepared and used in the EMSA experiments. The promoter sequences of genes 14 and 19 included direct repeats and palindromic sequences [25]. The probes included one or more of the sequences. Three of the five probes for the p28-Omp14 promoter region exhibited significant shift in mobility in the presence of protein lysate from macrophage derived E. chaffeensis compared to the controls which contained probe alone with no lysate added or when non-specific protein was added to the probe fragments (Figure 9A). A shift in mobility was also noted in the interaction with one probe segment of the p28-Omp19 promoter region when

the protein lysate was added (Figure 9B). Addition of a 50-fold excess of unlabeled specific-competitors in the binding reactions significantly reduced the mobility shift of the probes. Densitometry analysis of the mobility shifted fragments differed for each probe compared to the non-shifted fragments. The P1 probe had 84% shift which reduced to 29% when competitor DNA was added; P2 and P3 probes had about 31%, and 27% shifts, respectively, and the shifts for these probes were completely FER abolished in the presence of specific competitors. The p28-Omp19 promoter region probe had about 23% shift which was reduced to 10% in the presence of specific competitor. Figure 8 Sequences of EMSA probes used in this study. Sequences of p28-Omp14 P1-P5 (panel A) and p28-Omp19 P6 and P7 (panel B) represent promoter segments utilized in the EMSA experiments. Figure 9 EMSA using short segments of three biotin-labeled probes of p28-Omp14 (panel A) and one p28-Omp19 (panel B) promoter segments. Addition of E.

Neurology 66(9):1318–1324PubMedCrossRef

20. van den Brand MW, Samson MM, Pouwels S, van Staa TP, Thio B, Cooper C, Leufkens HG, Egberts AC, Verhaar HJ, de Vries F (2009) Use of anti-depressants and the risk of fracture of the hip or femur. Osteoporos Int 20(10):1705–1713PubMedCrossRef 21. Pouwels S, van Staa TP, Egberts AC, Leufkens HG, Cooper C, de Vries F (2009) Antipsychotic use and the risk of hip/femur fracture: a population-based case–control study. Osteoporos Int 20(9):1499–1506PubMedCrossRef 22. Haney EM, Chan BK, Diem SJ, Ensrud KE, Cauley JA, Barrett-Connor E, Orwoll E, Bliziotes MM, Osteoporotic Fractures in Men Study Group (2007) Association Protein Tyrosine Kinase inhibitor of low bone mineral density with selective serotonin reuptake inhibitor use by older men. Arch Intern Med 167(12):1246–1251PubMedCrossRef 23. Diem SJ, Blackwell TL, Stone KL, Yaffe K, Haney EM, Bliziotes MM, Ensrud KE (2007) Use of antidepressants and rates of hip bone

loss in older women: the study of osteoporotic fractures. Arch Intern Med 167(12):1240–1245PubMedCrossRef 24. Walley T, Mantgani A (1997) The UK General Practice Research Database. Lancet 350:1097–1099PubMedCrossRef 25. Van Staa TP, Abenhaim L (1994) The quality of information recorded on a UK database of primary care records: a study of hospitalization due to hypoglycemia and other conditions. Pharmacoepidemiol Drug Saf 3:15–21CrossRef 26. Van Staa TP, Abenhaim L, Cooper C, Begaud B, Zhang B, Leufkens HG (2000) The use of a large pharmaco-epidemiological

database to study exposure to oral glucocorticoids and risk of fractures: validation of find more study population and results. Pharmacoepidemiol Drug Saf 9:359–366PubMedCrossRef 27. Jaretzki why JA 3rd, Barohn RJ, Ernstoff RM, Kaminski HJ, Keesey JC, Penn AS, Sanders DB (2000) Myasthenia gravis: recommendations for clinical research standards. Task force of the medical scientific advisory board of the Myasthenia Gravis Foundation of America. Ann Thorac Surg 70(1):327–334PubMedCrossRef 28. Kanis JA, Johnell O, Oden A, Johansson H, McCloskey E (2008) FRAX and the assessment of fracture probability in men and women from the UK. Osteoporos Int 19(4):385–397PubMedCrossRef 29. Sata T, Abe T, Chida D, Nakamoto N, Hori N, Kokabu S, Sakata Y, Tomaru Y, Iwata T, Usui M, Aiko K, Yoda T (2010) Functional role of acetylcholine and the expression of cholinergic receptors and components in osteoblasts. FEBS Lett 584(4):817–824CrossRef 30. En-Nosse M, Hartmann S, Trinkaus K, Alt V, Stigler B, Heiss C, Kilian O, Schnettler R, Lips KS (2009) Expression of non-neuronal cholinergic system in osteoblast-like cells and its involvement in osteogenesis. Cell Tissue Res 338(2):203–215PubMedCrossRef 31. Wakata N, Nemoto H, Sugimoto H, Nomoto N, Konno S, Hayashi N, Araki Y, Nakazato A (2004) Bone density in myasthenia gravis patients receiving long-term prednisolone therapy. Clin Neurol Neurosurg 106(2):139–141PubMedCrossRef 32.

A decreased TMRE Ruxolitinib order signal corresponding

to decreased membrane potential was observed in a significant number of S20-3 peptide-treated (20%) and CH-11–treated (22%) cells as early as 4 hours after treatment, relative to treatment with buffer or the control S8-2 peptide (Additional file 1: Figure S1). The S20-3 peptide is effective against various hematological cancer cell lines We further investigated whether the S20-3 peptide would be effective in inducing cell death in HHV-8–positive cancer cell lines (KS-1, BC-3, BCBL-1), which have been shown to express K1 [10]. All HHV-8–infected cell lines tested were sensitive to the S20-3 peptide, which induced death in about 20–35% of cells, whereas no significant effect on cell death was detected with the S8-2 control peptide (Figure 2A). Figure 2 The HHV-8 K1-derived peptide S20-3 induces cell death

in K1-positive and K1-negative hematological cancer cells but not in PBMCs from healthy donors. Indicated cell lines (1 × 106 cells/mL) were incubated with 100 μM peptide S20-3 or buffer for 1 hour. Cells were washed and incubated in complete medium for 24 hours before flow cytometry analysis. (A) HHV-8– and K1-positive cell lines KS-1, BC-3, BCBL-1; (B) HHV-8 and K1-negative cell lines BJAB, Jurkat, Daudi; (C) Jurkat cells and PBMCs from healthy donors. Data in (A) and (B) are shown as the means ± SD of triplicate wells. Double asterisks indicate significant differences compared with control treatments; **P < 0.01. Panel (C) shows representative results of selleck chemical 2 experiments

with samples Ketotifen analyzed in triplicates. To evaluate whether the peptides were able to modulate the interaction between Fas and K1, 293T cells were transiently transfected with the vector expressing Flag-tagged K1 protein, lysed, and subjected to co-immunoprecipitation analysis used previously to show a direct physical interaction of Fas with K1 [8]. We observed that K1-Fas interaction was not disrupted by incubation of cells with the S20-3 or other K1-derived peptides with the exception of the shorter peptide S10-1 (Additional file 1: Figure S2). The lack of S20-3 peptide’s effect on the K1-Fas interaction suggested a possible cell-killing mechanism independent of K1. To confirm this hypothesis, we tested the peptide’s ability to kill K1-negative cell lines. The S20-3 peptide was able to induce significant levels of cell death in K1-negative BJAB cells (30%) and in the T-cell leukemia Jurkat cell line (25%) (Figure 2B). Quite surprisingly, the S20-3 peptide was equally effective in killing Daudi cells (35%), which express low levels of Fas on the cell surface and are considered Fas-resistant [17]. In contrast, human PBMCs from healthy donors, treated with S20-3 peptide, showed no significant amount of cell death (Figure 2C). Overall, S20-3 peptide treatment induced a 4.6 ± 1.

CF122 [15]. Whole genome comparison of related species would provide clues on the divergence mechanisms involved in speciation. Numerical estimates such as average nucleotide identity (ANI) and genome conservation estimates have been found useful to globally compare genomes [22], and we use them here. In this work we present 1) an improved version of the R. grahamii CCGE502 genome, selleck compound 2) a genomic comparison of ERs in related

rhizobia, 3) evidence of the natural integration of an ER in the R. grahamii CCGE502 chromosome, and 4) an evaluation of the conjugative transfer ability of the R. grahamii CCGE502 symbiotic plasmid and megaplasmid to other Rhizobium species. Methods Bacterial strains and growth conditions The bacterial strains and plasmids used in this work are described in Table 1. Rhizobium and Agrobacterium tumefaciens strains were grown at 30°C on PY medium [23]. Escherichia coli cells were grown on LB medium [24] at 37°C. When required, antibiotics were added at the following concentrations (in μg ml-1): nalidixic acid (Nal) 20, spectinomycin (Sp) 75, kanamycin (Km) 15, neomycin (Nm) 60, rifampicin (Rif) 100, streptomycin (Sm) 50, gentamicin (Gm) 30. Table 1 Bacterial strains, plasmids and primers Strain Relevant characteristics Source Rhizobia     R. grahamii CCGE502 Wild type strain [10] R. mesoamericanum CCGE501 Wild type

strain [10] R. mesoamericanum CCGE501-1 mini-Tn5 SmR/SpR This work R. grahamii CCGE502a:GFP CCGE502 carrying a Gm: GFP cassette at pRgrCCGE502a This work R. grahamii find more CCGE502b:Km CCGE502 carrying pK18mob:sacB at This work R. grahamii CCGE502ΔtraI CCGE502 carrying a deletion of traI. This work R. grahamii CCGE502ΔtraI::nodC CCGE502ΔtraI with pG18mob2 inserted at nodC This work R. etli CFN2001 CFN42 derivative (pRetCFN42a-pRetCFN42d-) [25] S. fredii GR64-4

GR64 cured of pSfrGR64a and pSfGRr64b, RifR GNA12 [26] S. meliloti SmA818R 2011 cured of pSymA, RifR [27] R. phaseoli Ch24-10 Tn5mob, NeoR Rosenblueth, M, unpublished Rhizobium sp. LPU83 SmR [27] R. endophyticum CCGE2052 Endophyte of P. vulgaris [11] Agrobacterium     GMI9023 C-58 cured of its native plasmids [28] GMI9023 (pRgrCCGE502a:GFP) GMI9023 carrying pRgrCCGE502a with a Gm-GFP cassette This work GMI9023 (pRgrCCGE502b:Km) GMI9023 carrying pRgrCCGE502b with a pK18mob:sacB insertion This work GMI9023 (pRgrCCGE502a:GFP, pRgrCCGE502b:Km) GMI9023 carrying pRgrCCGE502a with a Gm: GFP cassette and pRgrCCGE502b with a pK18mob:sacB insertion This work GMI 9023 (SpR) GMI9023 with a mTn5SSgusA40 This work GMI 9023(pRgrCCGE502a:GFP, pBBR1MCS2::traI) GMI9023 carrying pRgrCCGE502a with a Gm-GFP cassette and pBBR1MCS2::traI overexpressing AHLs of R. grahamii This work Escherichia coli     DH5α Recipient for transformation, supE44 ΔlacU169 ϕ80lacΔZM15) hsdR17 recA1 endA1 gyrA96 thi-1 relA1 [29] S17-1 E.