Having established that Histone Methyltransferase inhibitor strain R2846 can utilize ferric

ferrichrome as a sole iron source we set out to determine if the fhu gene cluster was involved in the utilization of this iron source. An insertional mutation within the coding sequence of fhuD was successfully constructed as described in the methods section and a mutation derivative LGX818 clinical trial of strain R2846 was designated HI2128. Figure 2A shows that strain HI2128 was unable to grow when supplied with ferric ferrichrome as the sole iron source. The same mutation did not significantly impair the utilization of heme alone (Figure 2A) or either ferric citrate nor ferrous ammonium sulphate in the presence of PPIX (data not shown), indicating that the defect is specific for the ferrichrome molecule rather than impacting the acquisition of the iron moiety or of PPIX. In addition to strain R2846 the fhuD insertional mutation was introduced

into two strains that were positive for the presence of the fhu gene cluster as determined by PCR analyses (Table 2); the two additional strains into which the fhuD mutation was introduced were HI1380 and HI1390 and correctly constructed mutants of each were identified and designated HI2131 and HI2132 respectively. Both strains HI1380 and HI1390 were able to utilize ferric ferrichrome as an iron source while neither www.selleckchem.com/products/tucidinostat-chidamide.html of the corresponding fhuD insertion mutants, HI2131 and HI2132, were able to do so (Figures

2B and 2C). Similarly to the data reported for NTHi R2846 neither of the mutant strains were impacted in their ability to utilize other heme and iron sources (Figures 2B and 2C). These data demonstrate that H. influenzae strains containing the fhu operon are able to utilize at least one exogenously supplied siderophore, ferrichrome, as an iron source. Ferrichrome is synthesized by members of the fungal genera Aspergillus, Ustilago and Penicillium, Tangeritin and may not represent a readily available iron source in the human nasopharynx. Thus, ferrichrome may not represent the ideal substrate for the fhu locus of H. influenzae which would be utilized relatively inefficiently and this fact may be reflected in the long lag time observed for growth in ferrichrome. However, the fhuBCDA system may function more efficiently to transport other xenosiderophores produced by other microorganisms and further investigations will aim to address this issue. Iron/heme repression of transcription of the fhu genes Since the genes of the identified fhu gene cluster are involved in acquisition of iron the potential role of iron and heme (FeHm) in the regulation of transcription of the genes was determined; since fhuC and r2846.1777 are respectively the first and last genes in the putative operon transcriptional analysis within the operon was limited to these two genes.

5%). As with swabs, the 14 repetition version of the arp gene was also the most common in WB samples. The most common tpr profile in WB samples was ‘a’, found in 17 of 19 WB samples [18, 22]. Interestingly, none of the WB subtypes identified in our study (12d, 12e, 14e, 14j, 14k, 15d) were similar to the published WB subtypes. There Thiazovivin are several limitations to this study. One of these is the small number of available parallel PCR-typeable samples taken from the same patient. Therefore, observed

differences should be interpreted with caution and more parallel samples need to be tested in future. Another limitation is the small number of fully-typed samples, especially in the sequence-based typing system. The observed lower discriminatory power of sequence-based typing compared to CDC typing is likely a result of genetic variability of tpr and arp loci, however, this explanation needs to be verified. Taken together, parallel samples taken from the same patient, at the same time, revealed potential instability at the tpr and arp loci, which is often used in molecular typing of treponemes. These loci are likely to show treponemal intra-strain variability and the results of molecular typing should be interpreted with caution, especially in epidemiological www.selleckchem.com/products/AZD1152-HQPA.html studies. Differences in frequencies of genotypes in whole blood and swab samples suggest an antigenic/adherence character for proteins encoded by these loci and also immunological differences

between compartments (i.e. skin and whole blood).

Conclusions The CDC typing scheme revealed subtype differences in parallel samples taken from 11 of 18 tested patients (61.1%). The arp and tpr loci are likely to show treponemal intra-strain variability since the sequence-based typing system revealed identical sequences in the TP0136, TP0548, and 23S rRNA genes. Therefore, the results of CDC typing should be interpreted with caution, especially in epidemiological studies. Differences in treponemal genotypes detected in whole blood and swab samples suggest immunological differences between the skin and whole blood compartments Urocanase and/or differences in adherence of genetic variants of treponemes to human cells. Methods Collection of clinical samples Clinical samples were collected from 2006 – 2012 in several clinical departments in the Czech Republic (Department of Medical Microbiology and Department of Dermatology, Faculty of Medicine, St. Anne’s Hospital and Masaryk University Brno, Department of Dermatology, Faculty Hospital Brno, Department of Dermatology, 1st Faculty of Medicine, Rapamycin price Charles University in Prague, the National Reference Laboratory for Diagnostics of Syphilis, and the National Institute for Public Health, Prague). All clinical samples were collected after patients gave informed consent. Syphilis was diagnosed based on clinical symptoms and results of several serological tests (e.g. Rapid Plasma Reagin (RPR) test, Venereal Disease Research Laboratory (VDRL) test, T.

The MG1655 (wild-type K-12) strain and the CF5802 strain [25], deficient in polyphosphate kinase and exopolyphosphatase (MG1655 Δppk-ppx::km) were gifts from Dr. M. Cashel (Laboratory of Molecular Genetics, NICHD, National Institutes of Health, Bethesda, MD, USA). The heat-sensitive CV2 (CGSC # 4682, initially derived from E. coli strain K-10) [26] and the SpoT-deficient NF161 (CGSC # 5244 derived from K-12) [12] strains were obtained from the E. coli Genetic Resource Center (Yale

University, New Haven, CT, USA). A strain devoid of RelA (MFT702 ΔrelA derived from MG1655) [10] was a gift from Dr. T. Conway (Advanced Center for Genome Technology, University of Oklahoma, Norman, OK, check details USA). The BL21 strains overexpressing either human recombinant ThTPase as GST fusion protein (BL21-hThTPase) or E. coli adenylate kinase (BL21-AK) were produced as previously described [21, 27]. Growth and processing of the bacteria The bacteria were grown overnight (37°C, 250 rpm) in 50-100 mL Luria-Bertani (LB) medium (S3I-201 ic50 tryptone, 10 g/L; yeast extract, 5 g/L; NaCl, 10 g/L, pH 7.0). The bacteria were centrifuged (5 min; 5000 × g) and suspended in the initial volume of M9 minimal medium (Na2HPO4, 6 g/L; KH2PO4, 3 g/L; NaCl, 0.5 g/L; NH4Cl, 1 g/L; CaCl2, 3 mg/L; MgSO4, 1 mM, pH 7.0) containing various metabolic

substrates in sterile PS-tubes (18,0/95 mm, 14 mL, Greiner Bio-One BVBA/SPRL, Wemmel, Belgium). If not otherwise stated, the bacteria Celastrol were incubated at 37°C with shaking KU-60019 price (250 rpm). The density of the cultures was determined by reading the absorbance at 600 nm (A600). After incubation, the bacteria were sedimented as above, the pellets were suspended in 12% TCA, the precipitated proteins were spun down (15 min, 15,000 × g) and the pellet was dissolved in 0.8 N NaOH for protein determination by the method of Peterson [28]. The supernatant was treated with diethyl ether to remove TCA and analyzed by HPLC for thiamine compounds [29]. For the determination of adenine nucleotides by HPLC, TCA (12%) was added directly to the bacterial suspension. For growth in the absence of oxygen,

the bacteria were incubated in sterile tubes with screw caps (Greiner Bio-One BVBA/SPRL, Wemmel, Belgium). The culture was sparged with N2 for 1 min and the tubes were hermetically closed before incubation. Determination of thiamine compounds and adenine nucleotides Thiamine compounds were determined by HPLC as previously described, after conversion to fluorescent thiochromes [29] and ATP was determined by luciferin luminescence using the Bac-Titer-Glo kits (Promega Benelux b.v., Leiden, The Netherlands). For determination of the energy charge [20], ATP, ADP and AMP concentrations were determined by a HPLC method, using fluorescence detection after ethenylation with chloroacetaldehyde [30]. Intracellular concentrations were estimated assuming an intracellular volume of 3.2 μL per mg of protein [8].

Sodium 500 mg/d* An electrolyte that helps regulate fluid balance, nerve transmission, and acid-base balance. Excessive decreases in sodium may predispose athletes to cramping and hyponatremia. During the first several days of intense training in the heat, a greater amount of sodium is lost in sweat. Additionally, prolonged ultraendurance exercise may decrease sodium levels

leading to hyponatremia. Increasing salt availability during heavy training LY2835219 datasheet in the heat has been shown to help maintain fluid balance and prevent hyponatremia [64, 509]. Vanadyl sulfate (vanadium) None Vanadium may be https://www.selleckchem.com/products/GDC-0449.html involved in reactions in the body that produce insulin-like effects on protein and glucose metabolism. Due to the anabolic nature of insulin, this has brought attention to vanadium as a supplement to increase muscle mass, enhance strength and power. Limited research has shown that type 2 diabetics may improve their glucose control; however, there is no proof that vanadyl sulfate has any effect on muscle mass, strength, or power [248, 249]. Zinc Males 11 mg/d Females 8 mg/d Constituent of enzymes involved in digestion. Associated with immunity. Theorized to reduce incidence of upper respiratory tract infections in athletes involved in heavy training. Studies indicate that zinc supplementation (25 mg/d) during training minimized exercise-induced changes in immune

function [55, 473, 510, 511]. Recommended Dietary Allowances

(RDA) based on the 2002 BMN 673 Food & Nutrition Board, National Academy of Sciences-National Research Council recommendations. * Estimated minimum requirement Water The most important nutritional ergogenic aid for athletes is water. Exercise performance can be significantly impaired when 2% or more of body weight is lost through sweat. For example, when a 70-kg athlete loses more than 1.4 kg of body weight during exercise (2%), performance capacity is often significantly decreased. Further, weight loss of more than 4% of body weight during exercise may lead to heat illness, heat exhaustion, heat stroke, and possibly death [58]. For this reason, it is critical that athletes consume a sufficient amount of water and/or GES sports drinks during exercise in order to maintain hydration status. The normal sweat rate of athletes ranges from 0.5 to 2.0 Cediranib (AZD2171) L/h depending on temperature, humidity, exercise intensity, and their sweat response to exercise [58]. This means that in order to maintain fluid balance and prevent dehydration, athletes need to ingest 0.5 to 2 L/h of fluid in order to offset weight loss. This requires frequent ingestion of 6-8 oz of cold water or a GES sports drink every 5 to 15-min during exercise [58, 66–69]. Athletes and should not depend on thirst to prompt them to drink because people do not typically get thirsty until they have lost a significant amount of fluid through sweat.

We observed that protein oxidation led to the formation of a dimer and loss of DNA binding, these phenomena are reversed by DTT in vitro. Thus S. selleck chemicals llc meliloti OhrR oxidation mechanism is similar to that described for OhrR of X. campestris. The expression of ohr and ohrR was assayed at the transcriptional level.

Their expression was constant throughout growth and no induction during stationary growth phase was observed. Similarly, osmotic stress did not induce ohr or ohrR expression. These observations match with the expression of these genes in X. campestris, A. tumefasciens, B. subtilis, P. aeruginosa and S. coelicolor [20, 31, 32, 34, 44]. As previously observed in these bacteria, ohr and ohrR genes of S. meliloti were induced by tBOOH and CuOOH. H2O2 was a poor inducer of ohr gene in S. meliloti. Induction of ohr by H2O2 in other bacteria is contradictory. Western analysis Pritelivir datasheet and gene fusion assays showed that ohr is not induced by H2O2 in A. tumefasciens, B. subtilis, P. aeruginosa

and S. coelicolor [31, 33, 34, 36] and only X. campestris ohr is slightly induced by H2O2 [20]. Transcriptomic studies of H2O2 stress response in B. subtilis [32] and P. aeruginosa [44] showed in contrast an ohr induction. Induction of ohr requires the oxidation of OhrR. We observed that S. meliloti OhrR is oxidized by H2O2 in vitro and did not bind to the operator when incubated with H2O2. Nevertheless, H2O2 is a poor inducer of ohr in vivo and is not Megestrol Acetate an inducer of ohrR expression. H2O2 also causes a loss of B. subtilis OhrR binding AZD6244 research buy to ohrA promoter in vitro while in vivo derepression of ohrA upon exposure to H2O2 was not observed [28, 36]. The role of H2O2 in alfalfa during symbiosis is not restricted to plant defence against bacteria. It is also important

for symbiotic process [45]. H2O2 is necessary for cell wall formation and infection thread rigidity [4]. Production of H2O2 was detected in root hairs, infection threads, infection and senescence zones but not in fixing zone [46]. The expression of ohr and ohrR was detected only in nitrogen fixing zone, thus they are not expressed constitutively and they are not induced by H2O2 in planta. These data suggest that organic peroxides are produced in nodules so that Ohr protein plays a role during nitrogen fixation. Conclusions Resistance to organic hydroperoxides has not been previously analysed in S. meliloti. We have demonstrated that Ohr protein is essential for S. meliloti to survive organic peroxide stress. The expression of ohr and ohrR genes in nodules suggests that the Ohr protein participates in organic peroxides detoxification within the nodule. Methods Bacterial strains, plasmids, and culture conditions The bacterial strains used in this study are detailed in Table 1. S. meliloti strains were grown aerobically at 30°C in the complex medium LB [47] to an optical density at 570 nm (OD570) of 1.5 to 1.

Obviously, C-line and T-line emitted fluorescence. However, this photo was taken without a UV filter, containing a strong background caused by the excitation light source. As a comparison, Figure 5a presents a QD lateral flow strip picture with a UV filter, which PLX-4720 cell line accepted little Selleck GDC-973 influence of the excitation light source, demonstrating that the UV filter is essential. Though the effect of the excitation light source was eliminated, the fluorescent intensity was also weak in detecting

a low-concentration sample (Figure 7a). The proper image enhancement algorithm played a critical role. In order to display our method’s superiority, traditional HE and WTHE algorithms were compared with the proposed algorithm (Figure 7). Figure 7b,c shows test strip images after processing of the traditional

HE and WTHE algorithms, respectively. The test strip image processed by the proposed modified WTHE algorithm is shown in Figure 7d. By comparing this method with other image enhancement algorithms, the results indicated that the proposed algorithm could produce a satisfying effect with distinguishing C-line CFTRinh-172 solubility dmso and T-line from the background. Figure 7 Images of test strip. (a) Original test strip image.(b) Test strip image with traditional HE. (c) Test strip image with WTHE. (d) Test strip image with proposed algorithm. During processing, we set v = 0.1 and r = 0.4, with the least mean square error (MSE). After image processing, the distinct graph of T-line and C-line is displayed in Figure 8 to certify the effectiveness of this algorithm. Figure 8 Curve figure of the test strip image after processing of the proposed modified WTHE algorithm. Diagnosis of CagA samples In order to test the device, 50 positive and 50 negative CagA samples from a clinical hospital were collected for detection. The outcomes showed that the instrument could realize detection with a specificity of 98% and a sensitivity of 96%. The specificity and sensitivity are calculated according Clostridium perfringens alpha toxin to the following equations, respectively: Compared with naked eye detection, the device could recognize low-concentration samples by employing the proposed

image processing algorithm, thus greatly enhancing sensitivity. Additionally, in order to improve specificity, more samples could be detected to set a more exact threshold. To eliminate the error introduced by the differences between test strips and samples, we used HCG samples to set a threshold of T/C ratio to determine the specification. The more antigen targeting in the sample, the more QD conjugates would be captured on the test line, which leads to the increase of the T/C ratio. According to the principle described above, the T/C ratio would be proportional to the concentration of CagA in the samples. Compared to the bare detection of the test line, this quantitative approach is much more credible and applicable. Besides, seven CagA samples with different concentration were also prepared by our group.

: Oncoprotein Bmi-1 renders apoptotic resistance to glioma cells through activation of the IKK-nuclear

factor-kappaB Pathway. Am J Pathol 2010,176(2):699–709.PubMedCrossRef 14. Dupasquier S, Abdel-Samad R, Glazer RI, Bastide P, Jay P, Joubert D, Cavailles V, Blache P, Quittau-Prevostel C: A new mechanism of SOX9 action to regulate Foretinib purchase PKCalpha expression in the intestine epithelium. J Cell Sci 2009,122(Pt 13):2191–2196.PubMedCrossRef 15. Darido C, Buchert M, Pannequin J, Bastide P, Zalzali H, Mantamadiotis T, Bourgaux JF, Garambois V, Jay P, Blache P, et al.: Defective claudin-7 regulation by Tcf-4 and Sox-9 disrupts the polarity and increases the tumorigenicity of colorectal cancer cells. Cancer Res 2008,68(11):4258–4268.PubMedCrossRef 16. Okubo T, Knoepfler PS, Eisenman RN, Hogan BL: Nmyc plays

an essential role during lung development as a dosage-sensitive regulator of progenitor cell proliferation Selumetinib datasheet and differentiation. Development PD0325901 ic50 2005,132(6):1363–1374.PubMedCrossRef 17. Thomsen MK, Ambroisine L, Wynn S, Cheah KS, Foster CS, Fisher G, Berney DM, Moller H, Reuter VE, Scardino P, et al.: SOX9 elevation in the prostate promotes proliferation and cooperates with PTEN loss to drive tumor formation. Cancer Res 2010,70(3):979–987.PubMedCrossRef 18. Carbonnelle-Puscian A, Vidal V, Laurendeau I, Valeyrie-Allanore L, Vidaud D, Bieche I, Leroy K, Lantieri L, Wolkenstein P, Schedl A, et al.: SOX9 expression increases with malignant

potential Aprepitant in tumors from patients with neurofibromatosis 1 and is not correlated to desert hedgehog. Hum Pathol 2011,42(3):434–443.PubMedCrossRef 19. Ling S, Chang X, Schultz L, Lee TK, Chaux A, Marchionni L, Netto GJ, Sidransky D, Berman DM: An EGFR-ERK-SOX9 signaling cascade links urothelial development and regeneration to cancer. Cancer Res 2011,71(11):3812–3821.PubMedCrossRef Competing interests The authors declare that they have no competing interests. Authors’ contributions Chun-Hui Zhou and Li-Ping Ye participated in the data collection, performed the statistical analysis and drafted the manuscript. Shi-Xing Ye assisted with the data collection, Yan-Li, Xin-Yin Zhang, Xin-Yu Xu made substantial contributions to the analysis and interpretation of data, Dr. Li-Yun Gong conceived of the study, participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.”
“Background Immunoglobulin (Ig)D multiple myeloma (IgD MM) is a rare subtype of myeloma, accounts for less than 2% of all myelomas [1] and is accompanied with aggressive course, resistance to chemotherapy and poor outcome. It is often associated with relatively high frequencies of renal failure, extra osseous disease, hypercalcemia, amyloidosis and Bence-Jones proteinuria [2–5]. The survival of patients with IgD MM has been reported to be shorter than that of patients with other types of M-protein [2, 4, 6].

However, to the best of our knowledge, few reports are relevant to the kinked InP NWs, particularly the detailed microstructures related to the bending configuration. Generally, it is believed that the kinks in the NWs would influence their transport properties, electron, and hole collection efficiencies for technological applications [12, 13]. In this regard, a detailed study on the formation of these kinks is extremely important, which could provide valuable information to further design NW materials with different shapes, morphologies, and microstructures, expanding their application

domains [14]. In our experiment, kinked InP NWs frequently emerged in the growing process, which possess a crystal structure of face-centered cubic (zinc blende) [6]. In order to understand the growth mechanism of these bending InP NWs, the morphologies and microstructures of different InP NWs were studied utilizing JNJ-26481585 chemical structure scanning electron microscopy (SEM) and high-resolution transmission electronic microscopy (HRTEM), respectively. Through comprehensive statistical analysis and intensive structural characterization, it is revealed that the dominant bending angles of InP NWs are approximately 70°, 90°, 110°, and 170°. The formation of bending angles of approximately 70° and 110° is mainly attributed to the occurrence of nanotwins and

stacking faults (SFs), which could easily form by the glide of 111 planes. However, for approximately 90° bending, local amorphorization 4��8C is believed to be the main cause for this phenomenon while approximately 170° kinks are mostly induced by small-angle boundaries, Silmitasertib molecular weight where the insertion of extra atomic planes could make the NWs slightly bent. In addition, NWs

with multiple curves composed of different bending angles are also observed. Methods Synthesis of InP NWs InP NWs used in this study were prepared by a solid-source catalytic chemical vapor deposition method in a dual-zone 3-MA datasheet horizontal tube furnace as previously reported [6]. Briefly, the solid source (1 g, InP powder, 99.9999% purity) was placed in a boron nitride crucible and evaporated at the center of the upstream zone, while the growth substrate (0.5 nm Au film deposited on SiO2/Si) was placed in the middle of the downstream zone with a tilt angle of approximately 20° and a distance of 10 cm away from the source. Au films with a thickness of 0.5 nm were thermally evaporated under a vacuum of approximately 1 × 10−6 Torr onto the substrates. During the growth of NWs, the substrate was thermally annealed at 800°C for 10 min in a hydrogen environment (99.999% pure H2, 100 sccm, 1 Torr) to obtain Au nanoclusters which acted as the catalysts. When the substrate temperature was cooled to the preset growth temperature (460°C), the source was heated to the required source temperature (770°C) for 60 min. After the growth, the source and substrate heater were stopped and cooled down to the room temperature under the flow of H2 gas.

The diploid yeast-expressing proteins that interacted were finally selected in medium that contained

a chromogenic substrate (X-α-GAL) to observe the transcriptional activation of the reporter gene mel1, a GAL4-regulated gene coding for the α-galactosidase enzyme. A total of 24 clones showed the activation of the reporter gene mel1 by turning blue (data not shown), which confirmed that there was interaction between PbMLS and the gene products listed in the Additional file 4: Table S3. To identify gene products that interacted with PbMLS, the cDNAs of the clones were sequenced after PCR amplification. ESTs (Expressed Sequence Tags) were processed using the bioinformatics tool Blast2GO. The functional classification was based on the homology of each selleck EST against the GenBank database using the BLAST algorithm [17], with a significant homology cutoff of ≤ 1e-5 and functional annotation by MIPS [16]. Additionally, sequences were grouped into functional categories through the PEDANT 3 database [18]. The analysis indicated the presence of several find more functional categories of genes and cell functions related to cellular transport, buy BIBW2992 protein fate, protein synthesis, nucleotide metabolism, signal transduction, cell cycle and DNA processing, and hypothetical protein (Additional file 4: Table S3). Construction of

protein interaction maps A comprehensive genetic interaction dataset has Thymidine kinase been described for the model yeast S. cerevisiae[19]. Because genes that act in the same pathway display similar patterns of genetic interactions with other genes [19–22], we investigated whether Paracoccidioides Pb01 protein sequences that interacted with PbMLS and were tracked by the pull-down and two-hybrid assays (Additional file 3: Table S2 and

Additional file 4: Table S3, respectively) were found in the structural genome database of S. cerevisiae[23]. Those sequences and others from The GRID protein interaction database [24] of S. cerevisiae were used to construct protein interaction maps generated by the Osprey Network Visualization System [25] (Figure 1). Protein sequences from macrophage were not used because some of them were not found in the S. cerevisiae database. The blue lines indicate protein interactions with MLS from Paracoccidioides Pb01 experimental data. The green lines indicate protein interactions with MLS already described in The GRID interaction database [24] of S. cerevisiae. A pink line corresponds to both. The colored dots show the functional classification of proteins. Figure 1 Map of interactions between MLS and other proteins generated by the Osprey Network Visualization System [25]. (A) Protein interactions obtained by a two-hybrid assay. Protein interactions obtained by pull-down assays with protein extracts of Paracoccidioides mycelium (B), yeast (C) and yeast secretions (D).

coli K12: MG1655 and W3110 (both derived from W1485 approximately 40 years ago [98]), and DH10B which was constructed by

a series of genetic manipulations [99]. Each of these three substrains encode 89 lipoproteins found in both other substrains (Additional file 4). Four additional lipoproteins are detected in DH10B (BorD, CusC, RlpA and RzoD) and are second copies lipoprotein genes, present in the 113-kb tandemly repeated region of the chromosome (Figure 8B, coordinates 514341 to 627601, [99]), and strain DH10B contains one gene encoding the Rz1 proline-rich lipoprotein from bacteriophage lambda absent from the two other substrains. Lipoprotein YghJ, that shares 64% homology with V. cholerae virulence-associated accessory colonization factor AcfD [100], is absent from the DH10B genome annotation. However, comparative genomic analysis shows that a yghJ locus could be annotated in this strain but corresponds to a pseudogene NVP-HSP990 datasheet caused by a frameshift event (Figure 8C). YfbK was also overlooked in the DH10B annotation process but in this case, the gene is intact. Finally, differences between lipoprotein prediction NU7026 solubility dmso results concerning YafY, YfiM and YmbA are due to erroneous N-terminus predictions. YafY in DH10B was predicted to be a lipoprotein due to the N-terminal 17 aa-long type II signal peptide and was published as a new inner membrane lipoprotein [101]. In substrains MG1655 and WS3110, the original annotation

fused the yafY loci with its upstream pseudogene ykfK (137 N-terminal aa longer). The presumed VX-661 start codons of YfiM and YmbA in MG1655 were recently changed by adding 17 (lrilfvcsllllsgcsh) and 5 (mkkwl) N-terminal amino acids, respectively (PMC1325200). These modifications substantially affect the prediction of their subcellular localization. Inspection below of the genomic sequences of the two other substrains leads to equivalent changes such that YfiM and YmbA in all three substrains are now predicted to be lipoproteins.

In conclusion, using CoBaltDB to compare lipoproteomes between substrains, we were able to detect genomic events as well as “”annotation”" errors. After correction, we can conclude that the three E. coli K12 substrains have 93 lipoproteins in common; that one locus whose function is related to virulence has been transformed into a pseudogene in DH10B; and that DH10B contains five additional lipoproteins due to duplication events and to the presence of prophages absent from the other two substrains (Figure 8D). Figure 8 Using CoBaltDB in comparative proteomics. Example of E. coli K12 substrains lipoproteomes. 4-Using CoBaltDB to improve the classification of orthologous and paralogous proteins Protein function is generally related to its subcellular compartment, so orthologous proteins are expected, in most cases, to be in the same subcellular location. Consequently, inconsistencies of location predictions between orthologs potentially indicate distinct functional subclasses.