It clearly shows that the as-synthesized SiNWs on silicon substrate remarkably reduce reflectance throughout the entire wavelength range. This low reflectance of SiNWs mainly comes from the multiple reflection of light among SiNW array, which can lengthen the optical path and increase the capture ratio of photon. In AgNP-decorated cases, the reflectance curves lift up a little more than those in bare SiNW array, indicating the scattering effect

of AgNPs. However, at the same time, it demonstrates a clear dip around 380 nm in the reflectance of AgNP-decorated samples, indicating the plasmon resonance absorption of the AgNPs. Furthermore, with the AgNP average size increasing from 19 to 26 nm, some particles become irregular in shape, which makes the resonance dip to broaden and show a red shift. Nevertheless, because selleck inhibitor the feature size of the particles is in the range of 19 to 26 nm, scattering behavior will be stronger than absorbing behavior on the whole. Figure 4 Optical reflectance spectra of SiNW arrays. The black square line, red dot line, and blue up-triangle line represent the spectra of SiNW arrays decorated with AgNPs with the diameter of 19, 23, and Alisertib datasheet 26 nm, respectively. The green down-triangle line represents the reflectance of bare SiNW array without AgNPs. It is well known that the transmittance of silicon in the wavelength region

of 300 to 1,000 nm is almost zero [1]. Therefore, the absorbance of silicon will be directly related to the reflectance. It should also be noticed that the reflected light only contains the part of scattering light which escapes from the structure. Other scattering light from AgNPs will be absorbed by the adjacent SiNWs or experience multiple reflections in the structure. On the other hand, the scattering effect is relative to the dielectric around the particles. That is to say, only after incorporating the polymer into the space of the structure could the scattering light

be utilized effectively. To make the SiNW and polymer composite together efficiently, we deposited polymer onto SiNWs by spin coating at a relative low rotation speed. Figure 5 shows the SEM image of the SiNW array incorporated by P3HT/PCBM. It can be Janus kinase (JAK) seen that the polymer fills all the space among the SiNWs, which could make the polymer to wrap up all the SiNWs and AgNPs. This structure could provide many benefits for our solar cells. On the one hand, the SiNWs provide high-mobility pathways for carriers. On the other hand, uniformly distributed SiNWs, as supporters of AgNPs, ensure less agglomeration and good dispersity of AgNPs in the organic layer. In device manufacturing process, we directly coated a PEDOT:PSS/ITO/glass substrate on P3HT:PCBM to form a contact. Compared with sputtering, this method could reduce the structure damage of the polymer introduced by particle impact.

, Vantaa, Finland). Values were obtained by comparing these cells with their respective controls. Cell cycle analysis For each analysis, 106 cells were harvested 48 h after treatment and fixed overnight in 70% ethanol at 4°C. Cells were then washed and stained with 5 μg/ml PI in the presence of DNAse free

RNAse (Sigma). After 30 min at room temperature, the cells were analyzed via flow cytometry (Beckman Coulter, Inc., Miami, FL, USA). Assay for apoptosis The samples were washed with phosphate-buffered saline (PBS) twice and re-suspended in 500 μl of binding buffer containing 5 μl of Annexin V-FITC stock solution and 5 μl of PI for determination of phosphatidylserine exposure on the outer plasma membrane. After incubation for 10 min at room temperature in a light-protected area, the samples were quantified by flow cytometry (FASCAria,

find more BD Bioscience, San Jose, CA). Western blot analysis Cells (106) were washed twice in cold PBS, and then lysed by Laemmli sample buffer (Bio-Rad, Hercules, CA, USA). Samples were boiled for 5 min at 100°C. Proteins were separated on 10% or 15% SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred onto nitrocellulose membranes see more (0.45 μm, Mllipore, São Paulo, SP, Brazil). Nonspecific-binding sites were blocked with 5% non-fat dry milk dissolved in TBS (10 mM Tris-HCl, pH 7.6, 137 mM NaCl) with 0.1% Tween 20 (TTBS) for 1 h at room temperature followed by incubation with primary antibody at 4°C overnight. The membranes were then washed 3 times in TTBS and incubated for 1 h at room temperature with secondary horseradish peroxidase (HRP)-conjugated donkey anti-rabbit antibody or HRP-conjugated sheep anti-mouse antibody diluted 1:5000 in TTBS with 5% non-fat milk. Proteins were visualized by ECL plus (Amersham Biosciences, Inc., Piscataway, NJ). All experiments were carried out independently at least 3 times. The level of the GAPDH protein was used as a control of the amount of protein loaded into each lane. Statistical analysis All assays were performed

in triplicate, and data are expressed as mean values ±SD. The Student’s G protein-coupled receptor kinase t-test was used to compare two groups. Results were considered significant with p -value < 0.05. Results Rapamycin and Dex inhibit growth of T-ALL cells synergistically It has been reported that rapamycin can sensitize multiple myeloma cells to apoptosis induced by Dex [9, 11]. In order to evaluate the potential of rapamycin for the treatment of GC-resistant ALL, we selected a panel of four T-ALL cell lines, GC-sensitive CEM-C7-14, and the GC-resistant CEM-C1-15, Molt-4, and Jurkat. Four cell lines were incubated for 48 h with rapamycin and/or Dex. Rapamycin inhibited the growth of all the four T-ALL cell lines. The percentage of viable cells were from the lowest of 46% in Molt-4 to the highest of 66% in CEM-C7-14 as compared to their control group, p < 0.05. The response of the T-ALL cell lines to Dex varied.

At higher levels of physical activity, the risk of recurrent falling decreased, while no association was found see more with fall risk in general. Moreover, the associations did not seem to be modified by level of physical functioning. Acknowledgments This study is based on data from the LASA and is financially supported by the Dutch Ministry of Health, Welfare, and Sports. Conflicts of interest None. Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. References

1. Tromp AM, Smit JH, Deeg DJ, Bouter LM, Lips P (1998) Predictors for falls and fractures in the Longitudinal Aging Study Amsterdam. J Bone Miner Res 13(12):1932–1939CrossRefPubMed

2. Tinetti ME, Speechley M, Ginter SF (1988) Risk factors selleckchem for falls among elderly persons living in the community. N Engl J Med 319(26):1701–1707PubMed 3. Stel VS, Smit JH, Pluijm SM, Lips P (2004) Consequences of falling in older men and women and risk factors for health service use and functional decline. Age Ageing 33(1):58–65CrossRefPubMed 4. Zijlstra GA, van Haastregt JC, van Eijk JT, van Rossum E, Stalenhoef PA, Kempen GI (2007) Prevalence and correlates of fear of falling, and associated avoidance of activity diglyceride in the general population of community-living older people. Age Ageing 36(3):304–309CrossRefPubMed 5. Dunn JE, Rudberg MA, Furner SE, Cassel CK (1992) Mortality, disability, and falls in older persons: the role of underlying disease and disability. Am J Public Health 82(3):395–400CrossRefPubMed 6. Parkkari J, Kannus P, Palvanen M, Natri A, Vainio

J, Aho H, Vuori I, Jarvinen M (1999) Majority of hip fractures occur as a result of a fall and impact on the greater trochanter of the femur: a prospective controlled hip fracture study with 206 consecutive patients. Calcif Tissue Int 65(3):183–187CrossRefPubMed 7. Youm T, Koval KJ, Kummer FJ, Zuckerman JD (1999) Do all hip fractures result from a fall? Am J Orthop 28(3):190–194PubMed 8. O’Loughlin JL, Robitaille Y, Boivin JF, Suissa S (1993) Incidence of and risk factors for falls and injurious falls among the community-dwelling elderly. Am J Epidemiol 137(3):342–354PubMed 9. Gregg EW, Pereira MA, Caspersen CJ (2000) Physical activity, falls, and fractures among older adults: a review of the epidemiologic evidence. J Am Geriatr Soc 48(8):883–893PubMed 10. Tinetti ME, Williams CS (1998) The effect of falls and fall injuries on functioning in community-dwelling older persons. J Gerontol A Biol Sci Med Sci 53(2):M112–M119PubMed 11. Campbell AJ, Borrie MJ, Spears GF (1989) Risk factors for falls in a community-based prospective study of people 70 years and older. J Gerontol 44(4):M112–M117PubMed 12.

However, even with such a high uncertainty, none of the models can predict the plaque productivity selleck kinase inhibitor within the entire range of lysis time used in our study. This is especially true when the lysis time is ~39 min. Discussion The appearance of a plaque is the oldest, but also the most useful and direct way of confirming the presence of a phage. Even with

the advent of modern technologies, such as real-time quantitative PCR and fluorescence-labeling, the simplicity of plaque counting is still the easiest and the most commonly used method for quantifying the number of infectious phages in a sample [28, 29]. Even in the earliest days, researchers have been divining the various idiosyncratic traits of a phage through the size and shape of the plaque it makes [30]. Except for plaques made by phages like T7, most plaques have a definitive size after overnight incubation. One of the most important changes during this typical incubation

period is the switch of host physiology from the initial exponential growth to the eventual stationary stagnation. With few exceptions [3, 4, 31], most phages cannot sustain productive infections when infecting stationary phase cells. Consequently, the plaque size would be limited by the amount of time available for productive infections. The length of productive time can be manipulated by either the initial host density KU57788 or host physiology (e.g., growth rate). For example, in the case of phage ϕ6, the phage made a larger plaque when plated with a lower initial host density [19, 32].

In the most extreme case, addition of sub-lethal amount of antibiotics and/or glycerol in the agar plate, presumably changing the host physiology, greatly improved the appearance of the plaque, second transforming it from small and turbid to large and clear [33]. In our study, however, all the plating conditions were kept constant (except when determining the impact of phage morphology on plaque size, in which we used different host strains), therefore, the differences in plaque size and productivity would simply be due to the differences in phage traits, rather than the amount of time available for productive infection. The life cycle of a phage in an agar plate can be divided into two parts: the extracellular phase for virion diffusion/adsorption and the intracellular phase for progeny production. All else being equal, more time for the extracellular phase would allow the virion to diffuse farther. On the other hand, more time for the intracellular phase would produce more progeny that could be diffused. From this point-of-view, it can be argued that the problems of plaque size and plaque productivity can be seen as a problem of how to optimally allocate the limited time between the extra- and intra-cellular phases. It is possible that the optimal time allocation for maximum plaque size may not be the same for maximum plaque productivity [22].

But this did not associate with C3-dependent internalisation. Most strains studied were resistant to the lytic effects of complement (Table 1). Table 1 Phenotyping of E. coli urine isolates. Strains Internalisation rate (NHS/HIS) Type1-

fimbriae P-fimbriae CNF1 Serum resistance α-Haemolysin J96 25 P P P P P Internalised             U1 9.2 P P P P P U2 6.5 P N P P P U3 14.3 P N P P N U4 5.5 P N N P N U5 5.1 P N N P N U6 15.1 P N N P N U7 23.5 P N N P N Non-internalised             U8 2.1 P N P P P U9 0.55 P N P P P U10 0.83 N P P P P U11 1.5 N N N P N U12 1.2 N PI3K Inhibitor Library N N P N U13 1.9 N N N P N U14 3.25 N N N P N U15 1.375 N N N N N U16

0.47 N N N N N In 16 urine E. coli isolates, bacterial virulence factors (including type-1, P fimbriae, CNF1, serum resistance, and click here α-Haemolysin) were examined to determine their correlation to C3-dependent internalisation (P positive, N negative). All experiments were repeated at least three times. Table 2 The association between virulence factors and C3-dependent internalisation in urine isolates. Bacterial virulence factors Strains demonstrating C3-dependent internalisation Strains not demonstrating C3-dependent internalisation Fischer’s exact test Type 1 fimbriae 7/7 (100%) 2/9 (22.2%) P = 0.0032* P fimbriae 1/7 (14.3%) 1/9 (11.1%) nsd CNF1 3/7 (42.9%) 3/9 (33.3%) nsd Serum resistance 7/7 (100%) 7/9 (77.8%) nsd Haemolysin 2/7 (28.6%) 3/9 (33.3%) nsd The strength of association between virulence factors and C3-dependent internalisation was determined using Fischer’s exact test. In fifteen blood isolates, type 1 fimbriae were also expressed by all of the isolates demonstrating C3-dependent internalisation (P = 0.0338, Fischer’s exact test) (table 3 and 4). A greater proportion of blood isolates expressed invasion factors such as P fimbriae and α-haemolysin than urine isolates, as would be predicted from previous reports [19, 20], however their presence did not correlate selleck products with C3-dependent

internalisation. Table 3 Phenotyping of E. coli blood isolates. Strains Internalisation rate (NHS/HIS) Type 1- fimbriae P- fimbriae CNF1 Serum resistance α-Haemolysin J96 25 P P P P P Internalised             B1 6.3 P P P P P B2 33 P P P P P B3 19 P N N P N Non-internalised             B4 3.5 P P P P P B5 3.3 P P N P P B6 3.0 N P N P P B7 1.2 N P N P P B8 1.5 N P N P N B9 2 N P N P N B10 1.2 N P N P N B11 0.7 N N P P P B12 1.3 N N N P P B13 1 N N N P N B14 0.5 N N N P N B15 2.2 N N N P N In 15 blood isolates, bacterial virulence factors (including type-1, P fimbriae, CNF1, serum resistance, and α-Haemolysin) were examined to determine their correlation to C3-dependent internalisation (P positive, N negative).

04 32.76 aDiluted QDW618 water-based cutting fluid; bDiluted QDW618 water-based cutting fluid with nanographite additive. The cutting fluid owes its lubrication ability from the lubricating film between the cutter and workpiece. Nanographite particles possess the features of high-temperature

resistance and self-lubrication ability which favor the formation and strengthening of the lubricating film. Therefore, the nanographite additive improves apparently the lubrication performance of the water-based cutting fluid. Conclusions In this study, water-soluble nanographite was prepared through in situ emulsion polymerization. The graphite particles could disperse uniformly and steadily in aqueous environment after surface modification. The nanographite additive improved the friction-reducing and antiwear properties of the water-based cutting fluid. The mean friction coefficient

and WSD reduced by 44% (from 0.106 to 0.059) and 49% (from 1.27 to 0.65 mm), respectively. p38 MAPK signaling The P B value increased from 784 to 883 N. Meanwhile, the small surface tension indicated the enhancement of wettability. In general, nanographite additive made up the defect of current water-based cutting fluid whose lubrication ability was not ideal. Authors’ information QC, XW, YL, and TY are graduate students, and ZW is a professor at the College of Science in China University of Petroleum (East China). Acknowledgments This work was supported by the Gold-idea Program of China University of Petroleum (grant no. JD1112-13) and the National University Student Innovation Program

(grant no. 091042514). References Cobimetinib purchase 1. Emma JES, Martin P: Nanographite impurities within carbon nanotubes are responsible for their stable and sensitive response toward electrochemical oxidation of phenols. J Phys Chem C 2011, 115:5530–5534.CrossRef 2. Lee CG, Hwang YJ, Choi YM, Lee JK, Choi C, Oh JM: A study on the tribological characteristics of graphite nano lubricants. Int J Precis Eng Man 2009, 10:85–90.CrossRef 3. Koethen FL: The role of graphite in lubrication. Ind Eng Chem 1926, 18:497–499.CrossRef 4. Chen Q, Wang ZT, Liu S, Liu Y: Synthesis of nanographite/poly(methyl acrylate) compound latex in a water-based fluid. New Chemical Materials 2011, 39:76–77. 5. Dimitrios A, Naga RT, Alberto S: Molecular structure and Nabilone dynamics in thin water films at the silica and graphite surfaces. J Phys Chem C 2008, 112:13587–13599.CrossRef 6. Dandan M, Yildirim EH: Evaporation rate of graphite liquid marbles: comparison with water droplets. Langmuir 2009, 25:8362–8367.CrossRef 7. Alexander P, Michael G: Water-graphite interaction and behavior of water near the graphite surface. J Phys Chem B 2004, 108:1357–1364.CrossRef 8. Julie BZ, Kim FH, Steven JS: Influence of ion accumulation on the emulsion stability and performance of semi-synthetic metalworking fluids. Environ Sci Technol 2004, 38:2482–2490.CrossRef 9. Sun JG, Liu ZC: The essentiality and feasibility of green cutting fluids. Lubr Eng 2001, 2:68–69. 10.

It is therefore possible that commencing exercise in a hyper hydrated state might not confer any significant advantage in terms of exercise performance as found in the studies by Easton et al. (2007), Marino et al. (2003), and Latzka et al. (2000).

In either case, studies with duration and conditions sufficient to induce a higher degree of dehydration should be carried out to examine whether hyper hydration can have a significant effect on exercise performance. Conclusion In comparison to the established hyper hydrating Cr/Gly/Glu supplement, supplement containing Cr/Gly/Ala and decreased amount of Glu provides equal improvements in thermoregulatory and cardiovascular responses during exercise in the

heat. Nevertheless, administration of both supplements had no effect on exercise performance. Acknowledgements The authors acknowledge Selleck VX809 Lukas Beis for his assistance in editing the manuscript. The authors also acknowledge Carlos Celis, Evagelia Daskalaki, Ramzy Ross, Jerome Durassel, Tushar Chatterji, Zeru Bekele and Derisibachew Haile for their major contribution in the data collection as well as John Wilson for his technical assistance. References 1. Sawka MN, Burke LM, Eichner ER, Maughan RJ, Montain SJ, Stachenfeld NS: American college of sports medicine position stand. Exercise and fluid replacement. Med Sci Sports Exerc 2007, 39:377–390.PubMedCrossRef 2. Noakes TD: Fluid replacement during exercise. Exerc Sport Sci Rev 1993, 21:297–330.PubMedCrossRef 3. Easton C, Turner S, Pitsiladis YP: Creatine and glycerol hyperhydration Belinostat solubility dmso in trained subjects before exercise in the heat. Int J Sport Nutr Exerc Metab 2007, 17:70–91.PubMed 4. Beis LY, Polyviou T, Malkova D, Pitsiladis YP: The effects Morin Hydrate of creatine and glycerol hyperhydration on running

economy in well trained endurance runners. J Int Soc Sports Nutr 2011, 8:24.PubMedCrossRef 5. Kilduff LP, Georgiades E, James N, Minnion RH, Mitchell M, Kingsmore D, Hadjicharlambous M, Pitsiladis YP: The effects of creatine supplementation on cardiovascular, metabolic, and thermoregulatory responses during exercise in the heat in endurance-trained humans. Int J Sport Nutr Exerc Metab 2004, 14:443–460.PubMed 6. Nelson JL, Robergs RA: Exploring the potential ergogenic effects of glycerol hyperhydration. Sports Med 2007, 37:981–1000.PubMedCrossRef 7. Haugland RB, Chang DT: Insulin effect on creatine transport in skelatal muscle (38464). Proc Soc Exp Biol Med Soc 1975, 148:1–4. 8. Steenge GR, Lambourne J, Casey A, Macdonald IA, Greenhaff PL: Stimulatory effect of insulin on creatine accumulation in human skeletal muscle. Am J Physiol 1998, 275:E974-E979.PubMed 9. Robinson TM, Sewell DA, Hultman E, Greenhaff PL: Role of submaximal exercise in promoting creatine and glycogen accumulation in human skeletal muscle. J Appl Physiol 1999, 87:598–604.PubMed 10.

Some soil properties respond relatively rapidly to land use and soil management changes, which makes these suitable to serve as soil quality indicators [18]. For instance, the light, labile fraction of soil organic matter, dissolved C and N contents, soil microbial biomass and activity, and bacterial diversity, have all been KU-60019 price proposed to represent suitable early warning indicators of soil quality degradation or improvement [2, 11, 19–23]. However, we are far from having a consolidated set of soil quality indicators, which might allow such monitoring across a range of different soils [24, 25]. Specific groups, such as ammonia oxidizing and denitrifying bacteria, play

basic roles in the N cycling. The study of these groups is very important, mainly in agricultural soil, since nitrification coupled with denitrification are major sources of soil N loss. The use of molecular tools targeting key genes such as amoA and nirK have been widely used to improve the knowledge about this issue. Their

ecology can be more readily understood by exploring the abundance and diversity of key marker genes than through cultivation based approaches [26]. The great majority of studies on effects of different cropping SCH 900776 order systems evaluates just one or a few parameters in soil; thus, stable isotopes are used to better understand C and N dynamics [3], bacterial communities to establish soil quality bioindicators [17] and greenhouse gas fluxes to

evaluate impacts on global warming [15]. On top of this, there is a paucity Fossariinae of knowledge with regard to parameters that might serve as quality indicators for Cerrado soil under sugarcane cultivation, that is, what parameters might serve as quality indicators. Since physical, chemical and biological factors in soil are not independent from each other, it is important to evaluate them together in one system and to attempt to establish the links between them. The main goal of our study was therefore to evaluate the impact of the different management strategies of sugarcane (burnt cane and green cane) on the soil chemical, biological and physical properties (including GHG flow) and to analyze the relationships between these features. Methods Field site The study area (17° 55′ 35″” S 50° 08′ 36″” W) was located in the municipality of Porteirão, state of Goiás, Brazil. The region´s climate is classified as Aw (Köppen), with annual average rainfalls exceeding 1500 mm year-1 and annual average air temperatures of 23.1°C. The soil type is a eutrophic Latossolo vermelho (Ferralsols), which is characterized by high levels of base saturation (>50%). Although the area was very flat, petroplinthite (lateritic nodules or concretions) were found in the subsurface, which may restrict drainage and exhibits a concretionary character. The field had been previously used for cotton, soy and sunflower production, and was converted to sugarcane cultivation in 2002.

The repertoires of sHLA peptides recovered from the plasma of the cancer patients or from the bone marrow plasma were mostly identical. Therefore, the analysis of the blood sHLA peptidome provides an exciting glimpse onto the tumor microenvironment and may facilitate intervening in its immune suppressive properties. O136 Selleckchem VX809 Hypoxia and PMA-Induced Maturation Inhibit TIMP-2 Secretion from Human Monocytes and Enhance Angiogenesis Nitza Lahat 1

, Miri Engelmayer-Goren1, Haim Bitterman2, Doron Rozsenzweig1, Lea Weiss-Cerem2, Michal A. Rahat1 1 Immunology Research Unit, Carmel Medical Center and The Ruth and Bruce Rapapport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel, 2 Ischemia-Shock Laboratory, Carmel Medical Center, Haifa, Israel Hypoxia, characteristic of fast growing solid tumors, recruits www.selleckchem.com/products/Belinostat.html and immobilizes macrophages and enhances angiogenesis. Monocytes extravasation

from the circulation across the basement membrane and extracellular matrix, which is mediated by matrix metalloproteinases (MMPs), is accompanied by their maturation into macrophages. However, the mechanisms evoked by hypoxia that regulate monocyte/macrophage behavior are largely unknown. We show that hypoxia reduces TIMP-2 secretion from primary monocytes or from U937 and THP-1 monocytic cell lines by 3–4 folds (p < 0.01), Morin Hydrate by inhibiting its transcription. PMA-induced maturation of these cells, irrespective of hypoxia, also causes a 2–3- fold reduction of TIMP-2 (p < 0.05), not by enhancing its intracellular or extracellular degradation, but by inhibiting its translation. We demonstrate involvement of SP-1 in transcriptional inhibition of TIMP-2 in monocytes, and suggest that hypoxia-induced enhancement of SP-1 phosphorylation

dissociates it from TIMP-2 promoter, and disrupts coordinative recruitment of other transcription factors, such as NFY. Hypoxia reduces TIMP-2 secretion from endothelial cells by 2-folds (p < 0.05), and increases endothelial cell migration/proliferation in a TIMP-2-dependent manner, whereas the reduced TIMP-2 secretion from monocytes and macrophages do not affect their migration. Thus, we suggest that various mechanisms control TIMPs synthesis and expression in different cell types and processes, and that overall reduced TIMP-2 secretion in the hypoxic tumoral microenvironment contributes to enhance angiogenesis.

In choosing a threshold for the comparisons

used in this study, we noted that the bacterial isolate examined in this paper with the largest genome, Burkholderia xenovorans strain LB400, encodes 8951 ≈ 104 proteins. Thus, a conservative value for n p would be 104. Furthermore, the greatest number of organisms used in a single comparison was n o = 211 (when finding proteins unique to a given genus). Finally, we chose M = 1, since the results of a given comparison would be only negligibly affected by a single spurious match. Thus, the chosen Selumetinib E-value threshold was E = 1/((104)2 × 2112) ≈ 10-13, meaning that two proteins were considered orthologues if the matches between the GDC-0449 price two proteins (in both directions) had E-values less than 10-13, in addition to each being the other’s best BLAST hit. Empirical method To estimate the potential impact of the choice of E-value threshold on our analyses, three pairs of proteomes were arbitrarily selected in each of three categories: isolates from the same species; isolates from different species but the same genus; and isolates from different genera. These three

categories were selected as they span the range of relatedness encountered in our analysis. For each pair of proteomes, the orthologue detection procedure described in the Methods section was used to determine the number of proteins in the first proteome, but not in the second proteome, over the range of E-value thresholds 100, 10-1,…,10-180. Figure 1 shows the number of unique proteins for each comparison for each E-value threshold used. Figure 1 Relationship between the E-value threshold and numbers of unique proteins in pairs of isolates. For a given comparison,

these graphs denote the number of proteins in the first isolate (e.g. Pseudomonas putida GB-1) that are not found in the second isolate (e.g. Pseudomonas putida KT2440). The relationship Rebamipide between pairs of isolates is: (A) same species; (B) same genus but different species; and (C) different genera. As an E-value threshold of 10-13 was ultimately chosen for our analyses, a vertical line corresponding to this E-value is indicated on each graph. For all three comparisons in all three categories, the number of unique proteins differed substantially depending on the E-value threshold chosen. For example, the number of proteins found in the proteome of Pseudomonas putida strain GB-1 but not in that of P. putida strain KT2440 (see Figure 1A) ranged from 3882 when using an E-value threshold of 10-180 to 1075 when using a threshold of 100. The plot for P. putida can be divided into two distinct sections.