1 murine macrophages, or growth inside these cells (data not show

1 murine macrophages, or growth inside these cells (data not shown). The bpaC mutants did not show defects in resistance to the bactericidal activity of normal human serum (data not shown), which is another biological function commonly associated with Oca autotransporters [2, 3, 19, 65, 66]. Virulence selleck products of B. https://www.selleckchem.com/products/cbl0137-cbl-0137.html mallei and B. pseudomallei mutant strains and BpaC expression

in vivo To determine whether BpaC contributes to virulence, we calculated the median lethal dose (LD50) of B. pseudomallei and B. mallei mutant strains in a mouse model of aerosol infection. The model entails the use of a Microsprayer® to deliver bacteria directly into the murine lungs [67]. The device generates aerosol particles from the tip of a bent, 23-gauge nebulizing tube attached to a high-pressure stainless Smad inhibitor steel syringe that contains bacteria. BALB/c mice were anesthetized and placed

in a custom-designed acrylic holder inside a Class II Biosafety cabinet. A modified pediatric otoscope equipped with a light source was then used to introduce the nebulizing tube portion of the Microsprayer® into the trachea of animals, and 50-μL of bacterial suspension was aerosolized into the lungs by pushing the plunger of the high-pressure syringe. Following infection, mice were observed daily for clinical signs of illness and morbidity. As shown in Table  2, the bpaC mutation did not have an impact on the LD50 values of B. mallei ATCC 23344 or B. pseudomallei DD503. Tissues (i.e. lungs, spleen, liver)

from mice that survived the acute phase of infection did not show differences in bacterial loads (data not shown). Based on these results, we conclude that the bpaC mutation does not affect the virulence of B. mallei ATCC 23344 or B. pseudomallei DD503 via the aerosol route of infection. Table 2 Median lethal dose determination Venetoclax of B. mallei and B. pseudomallei WT and mutant strains Organism Strain Inoculating dose (CFU) Group size % death LD50(CFU) B. mallei a ATCC 23344 (WT) 9,100 5 100       5,550 5 100       910 9 78 346     455 5 40       91 9 11   B. mallei a bpaC KO (mutant) 10,400 5 100       5,200 6 83       1,040 9 100 238     520 5 40       104 9 22   PBS (control) a   0 5 0   B. pseudomallei b DD503 (WT) 380,000 5 100       38,000 5 100 1,202     3,800 5 100       380 5 0   B. pseudomallei b bpaC KO (mutant) 350,000 5 100       35,000 5 100 1,107     3,500 5 100       350 5 0   PBS (control) b   0 5 0   a mice were monitored daily for clinical signs of illness/morbidity for 10 days post-inoculation. b mice were monitored daily for clinical signs of illness/morbidity for 6 days post-inoculation. To gain insight into the immune response to BpaC during infection, we tested sera from mice that survived aerosol challenge with B. mallei ATCC 23344 and B.


a V2-specific vasopressin receptor antagonist,


a V2-specific vasopressin receptor antagonist, slowed cyst Repotrectinib in vitro growth progression in ADPKD patients compared to historical controls [11]. In animal experiments, it was suggested that intervention with a V2-specific vasopressin receptor antagonist should be early in ADPKD [18]. It is not known how the declining rate differs between CKD stage 1 patients through to CKD stage 3 patients with ADPKD. It is important to delineate the characteristics of the natural course of disease progression in ADPKD when therapeutic intervention becomes feasible. Materials and methods Two hundred www.selleckchem.com/products/SB-525334.html and fifty-five patients with ADPKD participated in an observation study at Kyorin University, Teikyo University and Hokkaido University from 1995 to 2009. The patients fulfilled Ravine’s diagnostic criteria. The study was an observational case study

measuring serum creatinine at least once a year and monitoring blood pressure. Serum creatinine was measured enzymatically. The estimated glomerular filtration rate (eGFR, ml/min/1.73 m2) was calculated using the following formula: eGFR (male) = 194 × Cr−1.094 × Age−0.287, and eGFR (female) = eGFR (male) × 0.739. This equation is a Japanese coefficient for the modified Isotope Dilution Mass Spectrometry-Modification of Diet in Renal disease (IDMS-MDRD) selleck chemicals Study [12]. The slopes of the reciprocal of serum creatinine concentration (1/Cr) were also examined. The slopes of eGFR (ml/min/1.73 m2/year) and 1/Cr (dl/mg/year) were calculated when creatinine was measured for at least two points with an interval longer than 12 months. Slopes were calculated using linear regression analysis Rolziracetam in each patient. The staging of kidney function is based

on the K/DOQI Clinical Practice Guidelines on CKD [13]. Since 2006, total kidney volume (TKV) has been measured at Kyorin University Hospital in routine clinical practice by high-resolution magnetic resonance imaging using volumetric measurement of cross-sectional imaging, as described in the report from the Consortium for Radiologic Imaging Studies in Polycystic Kidney Disease (CRISP) [3, 14, 15]. Gadolinium enhancement was not used for safety concerns. The TKV slope is calculated using linear regression analysis and is expressed as the yearly change of TKV (ml/year). In the present study, hypertension is defined as high blood pressure requiring the use of anti-hypertensive agents. In the three hospitals where the study was conducted, blood pressure >130/85 was commonly treated by renin−antiotensin system blockers to achieve the target blood pressure. For evaluation of the relationship between eGFR and TKV, data were analyzed when eGFR and TKV were measured within 1 month. As eGFR and TKV were measured several times in one patient, initial measurement data were used to examine age-related changes of eGFR and TKV.

NDEA-treated samples exhibited allover higher oxidant/antioxidant

NDEA-treated samples exhibited allover higher oxidant/antioxidant status than control and NDEA+Q samples. Quercetin (NDEA+Q) succeeded in most cases to normalize the oxidant/antioxidant status of NDEA-treated samples. Moreover, histopathological Wnt tumor confirmation showed normal liver histology of the NDEA+Q samples. Our results are agreeable with Lijinsky [4] and Bogovski and Bogovski, [7] who reported that NDEA is known as precarcinogen capable of inducing tumors in different animal species and are suspected of being involved in some human tumors [7]. Confirming results reported that administration of NDEA to rats resulted in lipid peroxidation (represented

in higher MDA levels) and enhanced selleck chemical chemiluminescence in liver preneoplastic nodules, indicating the formation of activated oxygen species [27]. NDEA also produces 8-hydroxyguanine (8-OHG) [28], an indicator of oxidative damage to DNA (P 53 results) and the most abundant of more than 20 types of https://www.selleckchem.com/products/lcz696.html modifications produced under conditions of oxidative stress. This premutagenic DNA damage results in specific types of mutations and is likely to be involved in carcinogenesis. In contrast, Andrzejewski et al. [8] postulated that NDEA is an epigenetic

chemical compound. The antitumor effects of plant flavonoids have been reported to induce cell growth inhibition and apoptosis in a variety of cancer cells [9]. Quercetin, a ubiquitous bioactive flavonoid, Non-specific serine/threonine protein kinase can inhibit the proliferation of cancer cells [10, 11]. It has been shown that quercetin treatment caused cell cycle arrests such as G2/M arrest or G1 arrest in different cell types [10, 29]. Moreover, quercetin-mediated apoptosis may result from the induction of stress proteins, disruption of microtubules and mitochondrial, release of cytochrome

c, and activation of caspases [11, 30]. Granado-Serrano et al. [31] reported that quercetin may be a potential chemopreventive or therapeutic agent in hepatocarcinoma cells and further efforts to investigate these possibilities are needed. Specific P 53 gene PCR results may be contributed to the quercetin-mediated down regulation of mutant P 53 as reported by Avila et al. [32]. Contradictory results were reported by Chaumontet et al. [33] who reported the lack of tumor-promoting effects of the flavonoids. The oxidant/antioxidant status of liver samples illustrated that quercetin exerted its preventive effect through inhibition of lipid peroxidation to prevent oxidative DNA damage [28]. Consequently, the levels of GSH (a key player in reduction and detoxification processes) [17], GR (reduces GSSG to GSH which is an important cellular antioxidant) [18, 19] and GPX (whose main biological role is to protect the organism from oxidative damage) [18, 19] decreased significantly in NDEA+Q group.

When the substrate temperature reached approximately


When the substrate temperature reached approximately

room temperature, the chamber pressure was brought up to atmospheric pressure by the introduction of nitrogen gas. Finally, the substrate was removed from the chamber. A commercial MPCVD system (Model AX5200, ASTeX, Cornes Technologies Limited, Minato-ku, Japan) was used for the fabrication of CNFs. The Sn-filled CNFs grown on the Si substrate were GF120918 order characterized by ETEM (JEM-1000KRS, JEOL, Akishima-shi, Japan). They were collected from the substrate and deposited onto a metal grid thin foil with a carbon membrane using tweezers. The thin foil was then placed on a heated holder having a single-axis tilt mechanism (JEOL). The sample heating temperature was measured during the heating stage of the holder using a thermocouple placed directly in contact with the sample. The holder was inserted into the ETEM Selleckchem MAPK inhibitor chamber, in which structural characterization, elemental analysis, and in situ heating observation by ETEM with electron energy loss spectroscopy (EELS) were performed. The sample heating temperature during the in situ observations was 400°C. Results and discussion Figure 1 shows a scanning electron microscopy (SEM) image of Fludarabine manufacturer the as-grown Sn-filled CNFs on the Si substrate. The Sn-filled CNF yield

was very small compared with that of CNFs grown using Fe, Co, and Ni as the catalyst [10–15]. Thin, long contrasts indicate CNFs, and bright areas, indicated by the solid white arrows, these were confirmed around the central axis of the Sn-filled CNFs. The contrast in the SEM image originates from the emission of a second electron from a sample, and thus, bright contrasts indicate the existence of materials that differ from their surroundings. Further, these bright contrasts could be due to Sn, which is used as the

catalyst, and/or Si, which is used as the substrate. Elemental analysis by EELS (described below) revealed that this bright contrast is due to Sn. Under the CNFs, islands, 150 nm in average diameter, necessarily existed. These islands possibly formed as particles owing to the shrinking of the evaporated Sn layer on the Si substrate when the substrate was annealed. Smaller diameter islands, indicated by broken white arrows in Figure 1, also formed along with the large islands. However, CNFs did not grow on the small islands, demonstrating that large-diameter islands are necessary for CNF growth. This article focuses on the structure, elemental analysis, and in situ observations of the CNFs, so the small-diameter islands are not described in detail. The CNFs were approximately 400 nm long and 30 to 100 nm in diameter. Figure 1 SEM image of as-grown Sn-filled CNFs on Si substrate. Figure 2a shows a TEM image of a Sn-filled CNF collected from the Si substrate. The thin, long, rod-shaped contrast indicates the Sn-filled CNF, and the dark contrast seen at the central axis of the CNF confirms the existence of metal in its internal space.

Trevor Lawley (Sanger Institute) Standard culturing of C diffic

Trevor Lawley (Sanger Institute). Standard culturing of C. difficile isolates was carried out on blood agar plates at 37°C and anaerobic conditions. DNA Sequencing,

reference assembly and annotation DNA was isolated from one colony of the 31618 Vactosertib concentration strain by standard techniques [43]. The isolate was sequenced using the Illumina platform (Solexa) at the Leiden Genome Technology Center (LGTC) Smoothened Agonist at the LUMC, using the manufacturers’ protocols. Single end reads were generated and submitted to the NCBI sequence read archive (http://​www.​ncbi.​nlm.​nih.​gov/​sra) under accession number SRX030155. A reference assembly of the reads was carried out against strain C. difficile PCR ribotype 078 strain M120 (GenBank accession no. FN665653), using CLC genomics workbench (CLCbio, Aarhus, Denmark). Number of reads used was 5267302, of which 2968638 reads could be mapped to the M120 genome sequence. The unique 100 kb insert present in M120 was readily identified with the CLC genomics workbench. The ORFs present in the insert were identified by CLC genomics workbench and annotation was carried out manually, using BLAST and SMART. ORFs identified as “protein of unknown function” were further analyzed by profile-profile searches through HHpred RAD001 supplier (http://​toolkit. tuebingen.mpg.de/hhpred). Bioinformatic comparison of the mixed origin of Tn6164 The genome of strain M120 was compared to the genomes of C. difficile 630 (Genbank accession no.

AM180355), Thermoanaerobacter sp. (GenBank accession no. CP002210), S. pneumonia (Genbank accession no. CP002121) and C. fetus (Genbank accession no. FN594949) using the Artemis Comparison Tool [44]. Circularization of the transposon In order to investigate if the putative element could excise itself from the genome, PCR analysis was performed to amplify the joint region of a circular molecule using primers at the ends of the element, facing outward (primers 14 and 15 in Table 3). PCR amplifications were carried out using the NEB

Taq Polymerase kit (New England Biolabs, Herts, UK) according to the manufacturer’s instructions with 10 mM dNTPs (NEB). The primers that were used are listed in Table 3 (Sigma-Genosys, UK). Filter-matings assays Filter-matings were carried out as described previously [45]. C. difficile strains M120 and CD37 were cultured Histidine ammonia-lyase on Brain heart infusion (BHI) (Oxoid Ltd.) agar supplemented with 5% Horse blood (E&O laboratories). C. difficile strain CD37 was used as recipient. Transconjugants were selected for on BHI plates supplemented with 25 μg/ml rifampicin (Sigma Aldrich) and 10 μg/ml tetracycline (Sigma Aldrich). Transconjugants were examined using PCR with primer pair Lok1/Lok3 to confirm identity of the recipient strain and primer pairs Tn6164 accessory region Fw + Rev and Tn916 Fw + Rev to confirm the transfer of Tn6164 or Tn6190. Inverse PCR C. difficile genomic DNA was digested with PstI or EcoRI. After purification, the genomic DNA fragments were self-ligated to create circular DNAs.

In contrast, the pk2b2 allele was clearly expressed in all the fe

In contrast, the pk2b2 allele was clearly expressed in all the feminizing Wolbachia strains (Figure 2B). In hosts where both males and females are infected by CI-inducing or feminizing strains, no clear sex-specific differences were observed in pk1 and pk2 expression

(Figure 2A). We further examined the expression of pk2b2 and another prophage gene, orf7 which encodes the phage capsid, in several tissues of A. vulgare females harbouring the feminizing wVulC strain (Figure 2C). While orf7 was expressed MI-503 in vivo only in ovaries, the host tissue where the density of Wolbachia is higher, transcription of pk2b2 was revealed in all tissues tested (except the brain) (Figure 2C). Figure 2 Transcriptional analyses of pk1 and pk2 alleles. (A) Transcriptional results of the pk1 and pk2 click here alleles obtained from gonads of eight isopod species harbouring either feminizing (F) or CI-inducing (CI) Wolbachia strains. Plus or minus signals indicate expression, or not, of the copy(ies). Distinction is made between the two different pk2 alleles named pk2b1 and pk2b2 within the pk2b type. F: female; M: male. NA: no pk2a type alleles were amplified in these strains. (B) Transcriptional results of pk2b1 and pk2b2 alleles

are shown from ovaries or testes (when infected) of eight isopod species. Primers used are shown in ( Additional file 1: Table S1). The buy AZD1480 DNA template control (only wVulC presented) shows the intensity and specificity of the band detected with each pair of primers. RT + and RT- indicate, respectively, the presence or the absence of reverse transcriptase in the reactions. M: DNA size markers. (C) Transcriptional results of the 16S rDNA, pk2b2 and orf7 genes in seven different tissues of A. vulgare harbouring the wVulC Wolbachia strain. Ov: ovaries; Hae: haemocytes; HO: hematopoietic organ; Br: brain; N ch: nerve chain; gut; Ad: adipose tissue. Discussion In this

study, we found that a large copy number variation of pk1 and pk2 genes exists among Wolbachia strains, which is probably coupled to prophage dynamics and evolution. Copy number divergence in the ankyrin pk1 and pk2 Resveratrol is consistent with the results of previous Southern blotting analyses using the minor capsid orf7 phage gene [28]. Four different orf7 paralogs had already been identified in the wVulC strain through cloning and sequencing of heterogeneous PCR products [28]. Since multiple infections of Wolbachia in a single individual have never been observed in isopods, we can conclude that the phage WO is likely to be present in several copies in each Wolbachia strain. Our observations of Wolbachia strains of isopods suggest that dynamics of the prophage pk1 and pk2 genes is similar to that observed in the wRi and wPip-Pel genomes [8, 9].

As Professor Govindjee would say, Let There be Light… Let There b

As Professor DZNeP mouse Govindjee would say, Let There be Light… Let There be Greenness… Let There be Water… Let There be Carbon-di-oxide… And (by WAC1) Let There be Quantum Mechanical Rules for Electron and Proton Transfer, and, of course, Orderly Membrane Protein Assembly… And, More! And, you will have Oxygen to breathe with… And, of course, Food to eat! With Kind Regards, The Govindjee family (Submitted AZD5582 order by Anita, Govindjee’ s daughter; see Fig. 1 for pictures of the family.) Fig. 1 2013 photographs of Govindjee and his family. Top Left: A photograph of Govindjee with his wife Rajni; Top Right: Govindjee (in the middle) with his daughter Anita

Govindjee, and his son Sanjay Govindjee (http://​www.​ce.​berkeley.​edu/​~sanjay/​). Bottom: Left to right: Sanjay, Rajni, Marilyn Govindjee, Govindjee, Sunita Christiansen, Rajiv Govindjee, Arjun Govindjee, Anita Govindjee-Christiansen, and Morten Christiansen (http://​psych.​cornell.​edu/​people/​morten-christiansen). Sunita is Anita and Morten’s daughter; and Arjun and Rajiv are Sanjay and Marilyn’s sons Govindjee: Who is he? For those who don’t know Govindjee,

I provide here a brief biography. For details, see Eaton-Rye 2007a, b. Govindjee was born on October 24, 1932, at Allahabad, Uttar Pradesh, India, to Mr. Vishveshwar Prasad Asthana and Mrs. Savitri Devi Asthana. However, somehow, official records had listed his date of birth find more as October 24, 1933. Thus, we are celebrating his 80th birthday in 2013. Further, Govindjee, who uses one name only, did have a family name.

In fact, he was Govindji Asthana; not only his last name was dropped, he even changed the spelling of his first name to Govindjee, and, further, it is now used as his last name. Thus, what has happened now is that he is often listed as FNU Govindjee (where FNU stands for First Name Unknown) because computers need all fields filled! Since he uses one name only and computers need 2 names, he has been listed by various names including: Mister Govindjee, Illini Govindjee, and Govindjee Govindjee. His family has no problem: his wife is Rajni Govindjee (retired senior biophysicist from the mafosfamide University of Illinois at Urbana-Champaign); his daughter is Anita Govindjee (working for IBM; her husband Morten Christiansen is Professor of Psychology at Cornell University); and his son is Sanjay Govindjee (Professor at University of California Berkeley; his wife Marilyn Govindjee teaches Spanish in California). Govindjee has 3 grandchildren (Sunita Christiansen; Arjun Govindjee; and Rajiv Govindjee). Figure 1 shows a 2013 photograph of Govindjee and his immediate family during a 2013 family reunion in the Lake Tahoe area in California.

Agarwal et al [45] and Horvath et al [9] also observed that SA

Agarwal et al. [45] and Horvath et al. [9] also observed that SA application

can improve plant biomass and enhance the antioxidant response Adriamycin manufacturer against osmotic stress. The same is shown in our findings when we applied SA to pepper plants as compared to control plants. During endophytic-fungal association, it was observed that the SA application to EA plants significantly increased the growth and metabolism as compared to sole SA and control plants. Furthermore, the biomass loss was much pronounced in non-inoculated and sole SA plants as compared to EA and SA+EA plants. Previously, it was shown that exogenous SA to roots of fungal-inoculated rice does not inhibit the root colonization of fungi [12]. Ludwig-Müller et al.

[13] also reported that exogenous SA did not effected the root colonization by growth promoting fungi. However, our data shows the increased endophytic-colonization in SA treated host plants. This was also conformity to the results of Liu et al. [19], who indicated that exogenous SA application to fungal (Glomus mosseae) inoculated Avena nuda plants has increased the abiotic stress tolerance and had beneficial impacts on fungal colonization. The SA application Selonsertib to endophyte-inoculated plants not only increased endophytes abundance but also increased the host plant biomass, antioxidants and endogenous SA contents. It was shown that endogenous SA increased in endophyte-inoculated plants treated with SA as compared to sole SA and control plants under osmotic stress conditions. Increased endogenous SA and antioxidant activities play an important role in abiotic and biotic defense signaling [47, 48]. Under abiotic stress, high endogenous SA may

mitigate the negative effects of ROS accumulation. Such functions can counteract the adverse effects of stress under mutualistic relationship as SA initiates induced systemic resistance [51]. Enhanced SA levels are especially important to reduce the susceptibility of plants to biotic and abiotic stresses [51]. We assume Erastin order that the ISR stimulated through endophyte association activated the SA responses during osmotic stress. Mutualistic relationship initiates ISR and improves plant performance against biotic and abiotic stresses [43]. However, this concept is still overlooked in endophyte-induced ISR. Although Penicillium spp. have been known as potential inducers of ISR in various plants [11], our scientific understanding of the molecular mechanisms by which Penicillium sp. influence the outcome of plant abiotic stress tolerance is still marginal. Conclusion Fungal endophyte, P. resedanum not only improves plant growth but also extend greater benefits to the host-plants to mitigate the negative effects of gradual osmotic stress. Exogenous SA application to pepper plant JAK/stat pathway improved the stress tolerance of the plants while in combination with endophyte-inoculation it further regulated the stress impacts.

[25] The sequence comparison of this gene has been already used

[25]. The sequence comparison of this gene has been already used for species identification and phylogenetic analysis of other genera (e.g. Staphylococcus, Lactobacillus) and enteric pathogens [26–28]. A chaperonin database (cpnDB) is available on line, collecting bacterial and eukaryotic sequences (http://​www.​cpndb.​ca/​cpnDB/​home.​php)

[29]. The purpose of this study is the development of a rapid, reproducible and easy-to-handle molecular tool for the identification of Bifidobacterium species isolated from various environments. The protocol is based on the restriction endonuclease analysis of the PCR-amplified hsp60 partial gene sequence (hsp60 PCR-RFLP) with the use of a single restriction enzyme and has been tested on the 30 most widely distributed Bifidobacterium Captisol ic50 species and subspecies. RXDX-101 in vivo A diagnostic dichotomous key to speed up profile interpretation has also been proposed. Methods Bacterial RG7420 molecular weight strains and culture conditions The type strains used to develop the technique are listed in Table  1, whereas the strains used to validate the method are reported in Table  2. The strains, belonging to BUSCoB (Bologna University Scardovi Collection of Bifidobacteria) collection, were isolated from faeces

of human and animals and from sewage. Bacteria were maintained as frozen stocks at −80°C in the presence of skim milk as cryoprotective agent. Working cultures were prepared in TPY medium [1], grown anaerobically at 37°C and harvested at logarithmic phase. Table 1 Type-strains investigated Species International culture collection Bifidobacterium adolescentis ATCC 15703 Bifidobacterium angulatum ATCC 27535 Bifidobacterium animalis subsp. animalis ATCC 25527 Bifidobacterium animalis subsp. lactis DSM 10140 Bifidobacterium asteroides ATCC 25910 Bifidobacterium bifidum ATCC 29521 Bifidobacterium boum ATCC 27917 Bifidobacterium breve ATCC 15700 Bifidobacterium catenulatum ATCC 27539 Bifidobacterium choerinum ATCC 27686 Bifidobacterium

coryneforme ATCC 25911 Bifidobacterium cuniculi ATCC 27916 Bifidobacterium dentium ATCC Tau-protein kinase 27534 Bifidobacterium gallicum ATCC 49850 Bifidobacterium gallinarum ATCC 33777 Bifidobacterium indicum ATCC 25912 Bifidobacterium longum subsp. longum ATCC 15707 Bifidobacterium longum subsp. infantis ATCC 15697 Bifidobacterium longum subsp. suis ATCC 27533 Bifidobacterium minimum ATCC 27539 Bifidobacterium merycicum ATCC 49391 Bifidobacterium pseudolongum subsp pseudolongum ATCC 25526 Bifidobacterium pseudolongum subsp. globosum ATCC 25865 Bifidobacterium pseudocatenulatum ATCC 27919 Bifidobacterium pullorum ATCC 27685 Bifidobacterium ruminantium ATCC 49390 Bifidobacterium subtile ATCC 27537 Bifidobacterium thermacidophilum subsp. porcinum LMG 21689 Bifidobacterium thermacidophilum subsp.

​de/​transcriptomics/​transcriptomics-facility/​sm14koli ​html fo

​de/​transcriptomics/​transcriptomics-facility/​sm14koli.​html for details on content and layout of microarrays). Hybridization signals

to this website oligonucleotide probes corresponding to the intergenic regions were not analyzed further in this study. A total of 168 genes (2.7% of the 6206 ORFs predicted in the S. meliloti 1021 genome) displayed at least 2-fold changes in their mRNA levels (i.e. 1 ≤ M ≤ -1) and were catalogued as differentially expressed in both strains (see additional file 1: differentially accumulated transcripts in S. meliloti 1021 and 1021Δhfq derivative strain; the microarray data described in this work have been deposited AZD1152 in the ArrayExpress database under accession number A-MEXP-1760). Of these, 91 were found to

be down-regulated and 77 up-regulated in the 1021Δhfq mutant. Replicon distribution of the 168 Hfq-dependent genes revealed that 103 (61%) were chromosomal and 65 had plasmid location; 45 (27%) in pSymA and 20 (12%) in pSymB (Fig. 2, upper charts). Taking into account the gene content of S. meliloti 1021 with 54% genes annotated in the chromosome, 21% in pSymA and 24% located on pSymB, this distribution showed a replicon bias in Hfq activity with 1.3-fold more impact than expected on pSymA-encoded transcripts. The former observation is more evident when looking at the location of Compound C next genes scored as down-regulated in the 1021Δhfq mutant; as many as 34 (37%) of these 91 down-regulated genes were pSymA-borne which is almost 1.8-fold more than expected for the ORF content of this megaplasmid. Figure 2 Hfq-dependent alteration of the S. meliloti transcriptome and proteome. Differentially expressed transcripts (upper graphs) and proteins (lower graphs) in the S. meliloti hfq knock-out mutants.

Histograms show the number of differentially expressed genes and their distribution in the three S. meliloti replicons: chromosome (Chrom.), pSymA and pSymB. The distribution of annotated ORFs in the genome is indicated as reference. The adscription of these genes to functional categories according to the KEGG and S. meliloti databases is shown to the right in circle charts (see text for web pages of the referred databases). In brackets the number of genes belonging to each category. According to the S. meliloti 1021 genome sequence annotations (http://​iant.​toulouse.​inra.​fr/​bacteria/​annotation/​cgi/​rhime.​cgi)and the KEGG database (http://​www.​genome.​jp/​kegg/​) 137 (82%) out of the 168 genes with altered expression in 1021Δhfq could be assigned to particular functional categories, whereas 31 (18%) exhibited global or partial homology to database entries corresponding to putative genes with unknown function (Fig. 2, upper circle graph).