Plant Sci 1999, 148:131–138.CrossRef 41. Roxas VP, Lodhi SA, Garrett DK, Mahan JR, Allen RD: Stress tolerance in transgenic tobacco seedlings that overexpress glutathione

S-transferase/glutathione peroxidase. Plant Cell Reports 2000, 42:1229–1234. 42. Schmitt ME, Brown TA, Trumpower BL: A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res 1990, 18:3091–3092.CrossRefPubMed 43. Del Aguila EM, Dutra MB, Silva JT, Paschoalin VM: Comparing protocols for preparation of DNA-free total yeast RNA suitable for RT-PCR. BMC Mol Biol 2005, 6:9–15.CrossRefPubMed 44. Hoffman CS, Winston F: A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 1987, 57:267–72.CrossRefPubMed 45. Tarutina MG, Tolstorukov II: Development of a method for the vector transformation of the methylotrophic yeast see more Pichia methanolica. Russian J of Genetics 1994, 30:689–695. 46. Chattopadhyay MK, Tabor CW, Tabor H: Polyamine deficiency leads to accumulation of reactive oxygen species in a spe2 mutant

of Saccharmyces cerevisiae. Yeast 2006, 23:751–761.CrossRefPubMed Authors’ contributions HFC planned and designed the study, performed the experiments and analyzed the results and drafted the manuscript. YFY contributed equally. MSBK initiated and supervised the study, assisted in Wnt inhibitor data analysis and revised the manuscript. All authors read and approved the final manuscript.”
“Background Aerobic bacteria use oxygen as a terminal electron acceptor in oxygen-containing environments for their metabolism. Although aerobic growth Fossariinae has its obvious advantages (e. g. high energy efficiency, abundance of oxygen in the atmosphere, etc), bacteria must deal with the undesired consequences from exposure to oxygen and oxidative environments. Oxygen and

its derivatives, such as superoxide and hydrogen peroxide, are often highly reactive and pose a threat to many macromolecules, such as enzymes with iron-sulfur centers, nucleic acids, and lipids. Therefore, bacteria undergoing aerobic growth must be able to sense, respond to, and detoxify reactive oxygen species (ROS), and maintain their structural and functional integrities. The principle mechanism through which bacteria respond to environmental signals is through two-component and other regulatory systems [1, 2]. At least four global regulatory systems -OxyRS, SoxRS, Fnr and ArcAB – are identified to respond to oxygen and its derivatives [3, 4]. OxyRS and SoxRS systems control the response of bacteria to hydrogen peroxide and superoxide, respectively [3–12]. Fnr (fumarate and nitrate reduction) controls the transition from aerobic growth to anaerobic growth [13–17]. Fnr is believed to directly sense oxygen [18–20] and regulate at least 100 operons [21–23].

Conclusions Our work demonstrates a novel, real-time monitoring system for Salmonella enterica serotypes that is stable and has potential use for in in vivo and in vitro trials.

Our results show the efficiency of plasmid pBEN276 to confer bioluminescence to eleven wild-type Salmonella enterica isolates by inserting the luxCDABE operon into the attTn7 site on the chromosome. Chromosomal insertion of the gene is significant SN-38 in that external antibiotic pressure is not required for perpetuation of the luxCDABE cassette. This system has the potential to eventually be utilized for the evaluation of potential pathogen mitigation strategies upon Salmonella under different environmental conditions over extended time courses, which was not previously www.selleckchem.com/products/AZD8931.html possible due to limitations of plasmid-based reporter systems. Detection was successful following metabolic inactivity due to refrigeration temperatures and results provide support for application of our model in trials simulating

processing plant environmental conditions. Future experiments are planned using this system to evaluate the efficacy of various AMCs. We expect this research may provide a foundation for future work to understand the mechanism of attachment of Salmonella to chicken skin and its ability to persist during the poultry processing continuum. Methods Bacterial serotypes and growth media As part of a previous study, Salmonella enterica isolates from five different sites along the broiler production continuum (day one placement, end of growout, arrival at the plant, pre-chill tank, and post-chill tank) were cataloged [25]. In the current study, 11 Salmonella enterica serotypes (S. Alachua, S. Braenderup, S. Enteritidis, S. Heidelberg, S. Kentucky, S. Mbandaka,

S. Montevideo, S. Newport, S. Schwarzengrund, S. Seftenberg, S. Typhimurium) were selected. Salmonella enterica serotypes were cultured using Luria-Bertani broth and agar plates at 37°C. Ampicillin (100 μg mL-1) and was used for selection Cepharanthine and 0.1% arabinose was used for transposition induction. Construction of plasmid pBEN276 The luxCDABE operon was amplified from the genome of Photorhabdus luminescens using primers PG131 (GATGCTACCTCGAGGTACAACCAGTTTGCAAGATG) and PG132 (TACGCTCAGGATCCGAATTCACTCCCTTGCCATC) and cloned in pCR2.1 (Invitrogen) to yield plasmid pBEN139. Primers PG131 and PG132 were added to include XhoI and BamHI restriction sites. A XhoI-BamHI restriction fragment from plasmid pBEN139 carrying luxCDABE was subcloned into plasmid pBEN129, a derivative of plasmid pACYC184 [26] containing XhoI and BamHI sites, yielding plasmid pBEN135. A XhoI-NotI fragment from plasmid pBEN135 carrying the luxCDABE operon was subcloned into plasmid pGRG25 [20] to give plasmid pBEN275. The promoter of the housekeeping gene frr [27] was amplified from the E.

The Φ24B ::Kan genome is 57.6 kb in size and is identical in all aspects to its wild-type parental phage other than the stxA gene interruption [14, 18]. The majority of genes and coding sequences (CDS) carried by Φ24B are simply annotated as hypothetical [GenBank: HM_208303]. Bacteriophages tightly regulate expression of their genes involved in maintenance

of lysogeny versus replication of viral progeny, and the differentiation of gene expression associated with each state needed to be carefully Temsirolimus chemical structure determined in order to definitively associate expressed proteins and their genes with either the temperate or the lytic cycle. Results The rate of spontaneous lysis in an E. coli MC1061(Φ24B) culture at different stages of growth Spontaneous induction, defined as the induction of prophages from lysogens in the absence of an applied stimulus [19], occurs constantly in a proportion of the lysogen population in any culture, and this could seriously interfere with the differentiation of gene expression between lytic and lysogenic states. In this study, it was necessary to determine culture conditions under which the number of spontaneous PFT�� induction events was low whilst the cell density was high, enabling the consistent harvesting of sufficient

amounts of cell-associated protein for downstream analyses. Lysogen cultures were sampled at hourly intervals beginning two hours post inoculation, and the c.f.u. ml-1 and p.f.u. ml-1 determined. The lowest ratio of infective phages to cells, 1:50, occurred at both 2 h and 3 h of lysogen growth. However the c.f.u. ml-1 during these times was relatively low; OD600 = 0.184 (± 0.003) and OD600 = 0.651 (± 0.008), respectively. The ratio Sorafenib nmr of phage to host cells increased sharply after 4 h of growth, before dropping after 5 h to 1:33 (OD600 = 1.192 [± 0.011]). The ratio of phage to cells in the culture remained stable at 1:33 through to 6 hours of growth. Lysogen growth conditions

were therefore standardised for MC1061 (Φ24B) at 5-6 hours when the cells were grown to an OD600 of 1.2-1.3. Phage-encoded, lysogen-culture gene expression identified by CMAT A total of 13,519 clones were subjected to CMAT primary screening, and taking efficiency of the library into account, this equates to a 3.3x coverage of the phage genome. Of these, 330 were identified by the lysogen-specific antiserum and chosen for further analyses and secondary screening. After two rounds of secondary screening, 250 clones were removed from the study and PCR analysis of the remaining 80 clones demonstrated that 46 possessed vector DNA only. The remaining 34 recombinant transformants produced a peptide recognised by antibodies in the lysogen specific antiserum. The cloned inserts were sequenced, and the DNA sequences translated in all six possible reading frames. Twenty-three of the clones possessed sequences from twenty different Φ24B CDS (Table 1, Figure 1).

In addition, IGF-1 is able to counteract the effects of myostatin, a member of the TGFβ family

involved in muscle atrophy [23]. The hypothesis that Akt is implicated also in OP-related muscle atrophy is supported by our Western blot analysis, showing a significant reduction of Akt levels in OP atrophic muscles, compared to OA muscles. In fact, similarly to other metabolic myopathies, the decline of specific 3-Methyladenine in vitro hormones, including IGF-1, occurring in OP might downregulate IGF-1/PI3K/Akt activity, leading to muscle atrophy. Moreover, since IGF-1/PI3K/Akt controls glucose uptake in skeletal muscle [10], its downregulation could affect mainly glycolytic fibers (type II), whereas oxidative fibers (type I) tend to be more resistant to atrophy, because of their capacity of utilizing

other substrates than glucose to produce energy. Downstream mediators of Akt, such as mTOR, p70S6K, FoxO1, GSK3b, are to be studied to better clarify the IGF-1/PI3K/Akt role in OP-related muscle atrophy. An involvement of IGF-1/PI3K/Akt in OP, rather than in www.selleckchem.com/products/Ispinesib-mesilate(SB-715992).html OA patients, could explain the muscle morphological differences found in those diseases. In fact, in OP patients, type II fiber atrophy is more prominent and selective as compared to OA and is related to severity of bone mass reduction. All patients in the OP group were examined for the first time on admission because of the hip fracture and did not refer any important

limitation in their physical daily activity. This leads to the hypothesis that OP muscle atrophy is independent from muscle disuse. The reduced bone density occurring in OP patients is due mainly to a decrease click here of circulating hormones, and according to the reduced Akt levels found in OP, we believe that OP muscle atrophy has the same pathogenesis. Conversely, our OA patients complained of a decline in their physical activity due to pain and functional impairment in the affected joint for some time before surgery, suggesting that their muscle atrophy could be mainly due to disuse. In confirmation of that, OA-related muscle atrophy was of lower extent, more homogeneous among fiber types (even if type II fibers are more liable to size variations), and correlated to the HHS and disease duration. Whether other factors, such as myostatin, systemic or local inflammatory mediators, cytokines, or inflammatory transcription factors, can contribute to the muscle atrophy present in OP and OA should be matter for further investigation. Our morphological study on vastus lateralis muscles failed to show, in both groups of patients, denervation features such as type grouping or angulated fibers, reported to be present in distal senescent muscle [24] but not in proximal muscle [25].

As shown in the figure, the obtained energy of the coupled electron-positron pair – a positronium – is much smaller than the energy of separately quantized particles. Note that the jump between the energy curves corresponding to strong and weak SQ regimes is precisely conditioned by the formation of Ps atom. This is the criterion of the formation of a Ps as a whole at the particular value of the QD radius. It is seen from the figure that in the case of Kane’s dispersion law, the jump of the energy is significantly greater than that in the parabolic case. In other words, more energy is emitted at the formation of a Ps in a QD. Consequently,

the binding energy of the Ps is much higher than in the case of parabolic dispersion law. As it was https://www.selleckchem.com/MEK.html noted above, this is a consequence

of the Coulomb quantization enhancement due to the interaction of bands. Figure 5 Dependences of ground-state energies on a QD radius. They are for the Ps in weak SQ regime and for separately quantized electron and positron in strong SQ regime. Conclusions In the present paper, size-quantized states of the pair of particles – electron and positron – in the strong SQ regime ICG-001 and the atom of Ps in the weak SQ regime were theoretically investigated in spherical and circular QDs with two-band approximation of Kane’s dispersion law as well as with parabolic dispersion law of CC. An additional influence of SQ on Coulomb quantization of a Ps was considered both in 3D and 2D QDs for both dispersion laws. The analytical expressions for the wave functions and energies of the electron-positron pair in the strong SQ regime and for the Ps as in the weak SQ regime and in the absence of

SQ were obtained in the cases of the two dispersion laws and two types of QDs. The fundamental differences between the physical properties of a Ps as well as separately quantized electron and positron in the case of Kane’s dispersion law, in contrast to the parabolic case, were revealed. For the atom of Ps, the stability was obtained in a spherical QD and instability in all states with m = 0 in a circular QD in the case of Kane’s dispersion law. It was shown that the instability (annihilation) is a consequence of dimensionality Non-specific serine/threonine protein kinase reduction and does not depend on the presence of SQ. More than a fourfold increase in the binding energy for the Ps in a circular QD with parabolic dispersion law was revealed compared to the binding energy in a spherical QD. The convergence of the ground-state energies and binding energies to the free Ps energies for both cases of dispersion laws were shown. The jump between the energy curves corresponding to the cases of strong and weak SQ regimes (which is significantly greater in the case of Kane’s dispersion law), which is the criterion of the electron and positron coupled state formation – a positronium – at a particular radius of a QD, was also revealed.

The relative growth rate (RGR,  % day−1) of the projected total leaf area was obtained by multiplying b by 100. Carbohydrate assay Leaf samples for carbohydrate assay were harvested after 10 h of illumination by different light regimes on the second and fifth day of the treatments. As described for the

Chl fluorescence analysis, only mature leaves, which had existed before starting the experiments, were used for the analysis. After excision, leaves were quickly weighed, frozen in liquid N2, and stored at −80 °C until extraction. Soluble sugars (glucose, fructose and sucrose) and starch were extracted from the leaves as described by Czech et al. (2009). Concentrations of soluble sugars were determined according to Jones et al. (1977). Starch concentration was measured as glucose after enzymatic digestion with α-amylase and amyloglucosidase (Czech et al. 2009). Carbohydrate contents were expressed relative to leaf fresh weight (μmol g−1 selleck FW). Analysis SBE-��-CD purchase of photosynthetic pigments Leaf disks (0.77 cm2) were taken from mature leaves early in the morning on day 0 (before

the treatments) and on day 7 (after 7 days under different light regimes) to analyze photosynthetic pigments. The mature leaves used for sampling on day 7 were those that existed already on day 0. Two samples were collected from each plant: a “dark” sample taken at the end of the night period and a “light” sample taken after exposure of plants to halogen lamps (Haloline; Osram) of ca. 1,000 μmol photons m−2 s−1 for 5 min. The latter condition is comparable with the actinic illumination used for NPQ measurements in the second experiment. Leaf disks were immediately frozen in liquid N2 and stored at −80 °C until pigment extraction. Photosynthetic pigments were extracted by grinding frozen leaf disks in 1 mL acetone. The homogenate was then centrifuged at 13,000 rpm for 5 min and filtered (0.45-μm True Syringe Filter; Alltech Associates) before injection (20 μL) into the HPLC system. Chlorophylls and carotenoids

were separated with an Allsphere ODS-1 column (5 μm, 250 × 4.6 mm; Alltech Associates) at a constant flow rate of 1 mL min−1 Vitamin B12 according to the method modified from Gilmore and Yamamoto (1991). Pigments were detected using a Waters 996 photodiode array detector (Waters Corporation) and the peak area of chromatograms was integrated at 440 nm with the Empower software (Waters Corporation). Western blot analysis Leaf samples for PsbS protein analysis were taken early in the morning on day 0 and day 7 in parallel with the “dark” samples of pigment analysis. The leaves were frozen in liquid N2 and stored at −80 °C. Proteins were extracted by homogenizing frozen leaves in a strongly denaturing buffer (7 M urea, 5 % SDS, 50 mM Tris–HCl (pH 7.6), and 5 % β-mercaptoethanol) followed by centrifugation at 13,000 rpm for 10 min at 4 °C. Samples from three replicate plants were pooled together for each treatment and accession.

All other allelic variants differed from the founder alleles at four or more sites and were considered as putative recombinational imports. Ignoring alleles with one non-unique

and two nucleotide changes, the estimated ratio of recombinational events to mutational events per gene fragment is 11:1. If we include non-unique changes as recombinational imports, and unique changes as point mutations, the ratio is 15:2. We therefore conclude that new alleles were 7.5 to 11 times more likely to be generated by recombination than by point mutation. This is a conservative estimate because single nucleotide changes were attributed to point mutation and not to recombination, although recombination between similar Dinaciclib alleles could result in a single nucleotide change. Further, a high rate of recombination is consistent with the observed incongruence between the four gene tree topologies (Additional file 3). Intragenic recombination is another process that may contribute to the origin of new Wolbachia genotypes. We detected intragenic recombination within the trmD and wsp genes (Figure 3). The alignment of wsp genes shows that the polymorphic sites are not randomly distributed, but clearly shows a mosaic pattern consistent with recombination. Intragenic recombination is not restricted to Wolbachia strains from the same host

species, but also involves strains infecting different host species. For example, the wsp sequence obtained from Wolbachia in B. sarothamni (all populations) is a recombinant between selleck the wsp sequences obtained from Wolbachia in B. kissophila (FR13) and T. urticae (T3) (Figure 3). Cospeciation of Wolbachia

and host species Examination of the concatenated Wolbachia phylogeny reveals that there is generally a lack of cospeciation between host and parasite (Figure 4). Wolbachia strains obtained from a single host species do not clearly cluster. For example, strains from B. rubrioculus are found at different places in the phylogeny. The same is true for strains from B. spec. I. On the other hand, the Wolbachia phylogeny is not completely random with respect to host species. Some Wolbachia strains from B. kissophila cluster together, whilst others Thalidomide cluster with strains from B. spec I (BEL4_2) or B. rubrioculus (FR15). Two B. kissophila-derived strains (NL9 and FR13) are very divergent from all other B. kissophila strains. In the exceptional case of B. sarothamni, the same Wolbachia genotype was found in all five populations (from Belgium and France; except for a minor difference in trmD for BEL6; Figure 2, 4, and Table 2). This strain was not found in any of the other species, although it closely resembles the Wolbachia strain infecting B. berlesei at three of the four genes (wsp is highly divergent between the two strains). Bryobia sarothamni and B.

We can thus assume that iron absorption amounts to 1 mg/day and iron release from macrophages to 20 mg/day when the serum ferritin level is 100 ng/ml selleck products and maximal iron recycling in macrophages is 25 mg/day. Consequently, as shown in Fig. 3, the estimated relative amount of iron available for erythropoiesis decreases as serum ferritin increases. The concentration

of hepcidin, which can be estimated from the ferritin–hepcidin relationship, is somewhat lower than the half maximal inhibitory concentration of hepcidin observed in cell culture models but may be effective after long-term exposure as is the case under clinical conditions [45, 60]. Fig. 3 Estimated serum hepcidin levels, intestinal iron absorption, iron release from macrophages, and total available iron available for erythropoiesis. These parameters vary according to serum ferritin levels. Based on the relationship between serum ferritin and hepcidin levels, percent nonheme SB202190 order iron absorption, and percent early iron release from macrophages (see Fig. 2), we can estimate the total iron available for erythropoiesis. For these calculations, we assume that iron absorption is 1 mg/day and iron release by macrophages 20 mg/day for a serum ferritin level of 100 ng/ml, and a maximal amount of iron recycling by macrophages of 25 mg/day. Based on these calculations, the estimated amount of iron available for erythropoiesis decreases with increasing concentrations

of serum ferritin Iron usage in Japan and worldwide In the prospective study of the hemodialysis patient cohort of the Japan Dialysis Outcomes and Practice Patterns Study (DOPPS) in 2007, mean Hb and serum ferritin levels were 10.38 g/dl and 224 ng/ml, respectively,

and the percentage of patients with ferritin levels <100 ng/ml was 41.3 % [61]. Of note, the 47.2 % of patients with Hb ≥11 g/dl had ferritin levels <100 ng/ml, and only 40.6 % of them received IV iron. These observations suggested that a substantial percentage of patients could maintain Hb levels >11.0 g/dl without iron supplementation, owing to intestinal iron absorption. Therefore, L-gulonolactone oxidase the amount of iron absorbed from the intestine could compensate for that lost in the blood of these patients. From the 2010 DOPPS Annual Report (http://​www.​dopps.​org/​annualreport/​index.​htm), mean serum ferritin levels were >400 ng/ml in patients from all countries except Japan. In the United States, which represented the majority of patients included in the DOPPS, mean serum ferritin levels were >550 ng/ml, and 73.7 % of these patients were receiving IV iron. As the serum ferritin level is associated with hepcidin, in patients with serum ferritin levels >500 ng/ml iron absorption and iron recycling in macrophages could be minimal. In these situations, less intestinal iron absorption compelled physicians to use IV iron to maintain iron balance, which in turn led to a further increase in storage iron.

Adv Drug Deliv Rev 2003,55(3):329–347.CrossRef selleck 24. Danhier F, Ansorena E, Silva JM, Coco R, Le Breton A, Preat V: PLGA-based nanoparticles: an overview of biomedical applications. J Control Release 2012,161(2):505–522.CrossRef 25. Nitta SK, Numata K: Biopolymer-based nanoparticles for drug/gene delivery and tissue engineering. Int J Mol Sci 2013,14(1):1629–1654.CrossRef 26. Zhang S, Zhao B, Jiang H, Wang B, Ma B: Cationic lipids and polymers mediated vectors for delivery of siRNA. J Control Release 2007,123(1):1–10.CrossRef 27. Rudolph C, Schillinger U, Ortiz A, Tabatt K, Plank C, Muller

RH, Rosenecker J: Application of novel solid lipid nanoparticle (SLN)-gene vector formulations based on a dimeric HIV-1 TAT-peptide in vitro and in vivo. Pharm Res 2004,21(9):1662–1669.CrossRef 28. Bruniaux J, Sulpice E, Mittler F, Texier I, Gidrol X, Navarro F: Cationic lipid nanoemulsions for RNAi screening. In Proceedings of the Technical Proceedings of the 2013 NSTI Nanotechnology Conference and Expo, NSTI-Nanotech. Washington, DC United States; 2013. 12–16 May 2013, vol 3, pp. 323–326 29. Fishbein I, Chorny M, Levy RJ: Site-specific gene therapy for cardiovascular disease. Curr Opin Drug Discov Devel 2010,13(2):203–213. 30. Khan R, Khan MH: Use of collagen as a biomaterial: an update. J Indian Soc Periodontol 2013,17(4):539.CrossRef

31. Karimi M, selleckchem Avci P, Mobasseri R, Hamblin M, Naderi-Manesh H: The novel albumin–chitosan core–shell nanoparticles for gene delivery: preparation, Nitroxoline optimization and cell uptake investigation. J Nanopart Res 2013,15(5):1–14.CrossRef 32. Shi Q, Tiera MJ, Zhang X, Dai K, Benderdour M, Fernandes JC: Chitosan-DNA/siRNA

nanoparticles for gene therapy. Non-Viral Gene Ther 2011, 19:455–480. 33. Raftery R, O’Brien FJ, Cryan SA: Chitosan for gene delivery and orthopedic tissue engineering applications. Molecules (Basel, Switzerland) 2013,18(5):5611–5647.CrossRef 34. Strand SP, Lelu S, Reitan NK, de Lange DC, Artursson P, Vårum KM: Molecular design of chitosan gene delivery systems with an optimized balance between polyplex stability and polyplex unpacking. Biomaterials 2010,31(5):975–987.CrossRef 35. Mamo T, Moseman EA, Kolishetti N, Salvador-Morales C, Shi J, Kuritzkes DR, Langer R, von Andrian U, Farokhzad OC: Emerging nanotechnology approaches for HIV/AIDS treatment and prevention. Nanomedicine 2010,5(2):269–285.CrossRef 36. Thomas M, Lu JJ, Zhang C, Chen J, Klibanov AM: Identification of novel superior polycationic vectors for gene delivery by high-throughput synthesis and screening of a combinatorial library. Pharm Res 2007,24(8):1564–1571.CrossRef 37. Patnaik S, Gupta KC: Novel polyethylenimine-derived nanoparticles for in vivo gene delivery. Expert Opin Drug Deliv 2013,10(2):215–228.CrossRef 38. Morille M, Passirani C, Vonarbourg A, Clavreul A, Benoit J-P: Progress in developing cationic vectors for non-viral systemic gene therapy against cancer. Biomaterials 2008,29(24–25):3477–3496.CrossRef 39.

126. Further analysis was conducted based on an expanded version of Clusters-of-Orthologous groups (COGs) [12,56]. The new annotation of C. thermocellum lists the JGI categorizations which do not correspond directly to COG categories. ORNL computational biology group has also defined COG categories for 1928 genes in the new annotation of C. thermocellum. Both can be found here: http://​genome.​ornl.​gov/​microbial/​cthe/​ [55]. Additional categories were assigned for subcategories of COGs such as cellulosomal genes

and transport and secretion genes. Genes were initially VX-689 datasheet assigned to COGs during the annotation using RPS Blast and refined via manual curation as shown in (Additional file 1: Table S2). The full list of genes with category definition can be found buy AMN-107 in Additional file 5. To determine the significance of up or down regulation within a given category, an odds ratio of the number of up- or down-regulated genes in a category versus the total number of up- or down- regulated genes across the genome was used with a normally distributed 95% confidence interval (α = 0.05). Odds ratios of certain additional subsets of genes were conducted to further determine significance [57]. Quantitative-PCR (qPCR) analysis RNA-seq data were validated using real-time

qPCR, as described previously [7,8], except that the Bio-Rad MyiQ2 Two-Color Real-Time PCR Detection System (Bio-Red Laboratories, CA) and Roche FastStart SYBR Green Master (Roche Applied Science, IN) were used for this experiment. Six genes were analyzed using qPCR from cDNA derived from the mid-log time point samples for the WT and PM in standard media. Acknowledgements The authors thank Dawn M. Klingeman and Courtney M. Johnson for mafosfamide assistance with RNA purification; Dawn M. Klingeman and Charlotte M. Wilson for qPCR and PCR preparation and analysis and Qiang He and Chris Hemme for assistance with transcriptome analysis. RNA-Seq data was generated by the U.S. Department of Energy (DOE) Joint Genome Institute, which is supported by the Office of Science of the under contract no. DE-AC02-05CH11231. This

research was supported by the BioEnergy Science Center, a Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the Department of Energy Office of Science. Additional support was provided by the Institute for a Secure and Sustainable Environment at the University of Tennessee. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the DOE under Contract DE-AC05-00OR22725. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Additional files Additional file 1 Supplemental Information. Contains all supplementary tables and figures. Additional file 2 All statistically significant differentially expressed genes.