Colony counts were performed after incubation at 37°C in air for Selleckchem C59 24 h. The number of colonies on plates containing H2O2 was compared with that on control plates and presented as bacterial survival (%). The assay was performed for 4 independent experiments. Sensitivity to killing by hydrogen peroxide was further examined in LB broth. An overnight culture of B. pseudomallei on Ashdown

agar was suspended in PBS and adjusted to approximately 1 × 108 CFU/ml. Ten microlitres of bacterial suspension was added into 1 ml of LB broth containing two-fold decreasing concentrations of H2O2 ranging from 500 to 31.25 μM. The mixtures were statically incubated at 37°C in air for 24 h and then the viable count and colony morphotype were determined by serial dilution and plating on Ashdown agar. The experiment

was performed for 2 independent experiments. Susceptibility of B. pseudomallei to reactive nitrogen intermediates (RNI) B. pseudomallei from an overnight culture on Ashdown agar was suspended Angiogenesis inhibitor in PBS and the bacterial concentration adjusted using OD at 600 nm. Thirty microlitres of bacterial suspension was added into 3 ml of two-fold decreasing concentrations of sodium nitrite (ranging from 10 to 0.1 mM) in LB broth at pH 5.0. The mixture was incubated at 37°C in air with shaking at 200 rpm and viable bacteria were determined at 6 h by serial dilution and plating on Ashdown agar. The number of viable bacteria in the presence of NaNO2 was compared with the number of bacteria in the inoculum and presented as bacterial survival (%). The experiment was performed in duplicate for 2 independent experiments. Susceptibility of B. pseudomallei to lysozyme and lactoferrin B. pseudomallei cultured overnight on Ashdown agar was harvested and suspended in 10 mM Tris-HCl buffer pH 5.0 [23]. The bacterial suspension was adjusted to a concentration of 1 × 107 CFU/ml. Fifty microlitres of bacterial suspension was added to an equal volume of 400 μg/ml chicken

egg white lysozyme (48,000 U/mg protein) (Sigma) to obtain a final concentration of 200 μg/ml. The mixture was incubated at most 37°C in air for 24 h, after which 10 μl of 10-fold serial dilutions were dropped on Ashdown agar. Sensitivity to lysozyme was also Selleckchem LXH254 tested in the presence of 3 mg/ml lactoferrin (Sigma) in a separate experiment [23]. E. coli strain HB101 was tested in parallel as a control. Susceptibility to human α-defensin and β-defensin B. pseudomallei was tested for resistance to HNP-1 and HBD-2 (Peptide international) as described previously [24], with the exception that HNP-1 was used at twice the dose. E. coli strain HB101 was tested in parallel as a control. Briefly, B. pseudomallei or E. coli strain HB101 colonies were washed and suspended in 1 mM sodium phosphate buffer pH 7.4 containing 1% TSB [24]. The bacterial suspension was adjusted to a concentration of 1 × 107 CFU/ml.

Scale bars: a = 1 mm, b, c = 100 μm, d, h, i = 50 μm, f = 20 μm, g, e, j =10 μm One or two ascomata per stroma. Ascomata up to 0.8 mm diam., scattered or in small groups, developing beneath the host epidermis, crust-like, as circular spots, selleckchem wall brown, with a small central ostiole, in section 225–285 μm high × 510–750 μm diam., lenticular, ostiolar canal lacking periphyses (Fig. 19a and b). Peridium 35–45 μm wide at sides, pale brown, at sides composed of a thin layer of thin-walled elongate cells, fusing with the stromatic tissue and host cells, at the base composed of thick-walled cells, forming a textura epidermoidea and fusing with host cells. A wedge of pale brown hyphae forming

a textura porrecta is present at the rim (Fig. 19c). Hamathecium of dense, long filliform pseudoparaphyses 1–3 μm broad, embedded in mucilage, anastomosing YM155 datasheet between and above the asci, rarely septate. Asci 142–207 × 14.2–19.8 μm, 8-spored, bitunicate, fissitunicate, clavate to cylindrical, with a furcate pedicel, up to 40 μm long, apex with an ocular chamber and apical ring (to 2 μm wide × 3 μm high, J-), developing from ascogenous tissue at

the base of the ascocarp (Fig. 19d, e, f, g and h). Ascospores 42–66 × 7–10.6 μm, biseriate, narrowly fusoid with broadly to narrowly rounded ends, Saracatinib concentration somewhat curved, yellow to pale brown, yellow in mass, 7-8-septate, constricted at the septa, the two central cells being the largest, surrounded by a gelatinous sheath; the sheath has a central “spine” and curved polar extrusions (Fig. 19i and j). Anamorph: Fossariinae none reported. Material examined: BRUNEI DARUSSALAM, Tungit Api Api mangrove, from decaying intertidal fronds of Nypa fruticans Wurmb., 14 Apr. 1987, K.D. Hyde (BRIP 17106, holotype). Notes Morphology Carinispora is distinguished from Phaeosphaeria by its saprobic

life style and lenticular ascomata formed under the host epidermis, peridium structure and sheath surrounding the ascospores (Hyde 1992a, 1994b). Two species were reported, i.e. C. nypae and C. velatispora K.D. Hyde. Phylogenetic study Suetrong et al. (2009) could not resolve Carinispora nypae in a phylogeny based on four genes. Concluding remarks Both Carinispora nypae and C. velatispora are reported as marine fungi, which should be taken into consideration for their familial placement. Caryosporella Kohlm., Proc. Indian Acad. Sci., Pl. Sci. 94: 355 (1985). (?Melanommataceae) Generic description Habitat marine, saprobic. Ascomata densely scattered or gregarious, superficial, subglobose, black, papillate, ostiolate, periphysate, carbonaceous. Peridium carbonaceous. Hamathecium of dense, long trabeculate pseudoparaphyses, anastomosing and branching above the asci. Asci 8-spored, bitunicate, fissitunicate, cylindrical. Ascospores ellipsoidal to broadly fusoid with narrowly hyaline rounded ends, deep reddish brown, thick-walled, 1-septate with hyaline germ pore at each end. Anamorphs reported for genus: suspected spermatia (Kohlmeyer 1985).

Effects of α-amylase on cell growth in cells from F344 and Lewis rats It has not yet been described, if α-amylase has effects on mammary gland cell growth and, if, to what extent. Experiments with different α-amylase concentrations identified 5 and 50 U/ml as proper concentrations to reveal differences in α-amylase efficacy (not illustrated). In order to find the appropriate treatment duration, experiments

were performed with α-amylase (5 and 50 U/ml) for one day, two, check details and four days (n = 4-14; Figure 2a). Cell numbers were not altered in F344 and Lewis cells after 5 U/ml for all treatments. After 50 U/ml, a significant decrease in number of cells was observed for Lewis cells after 2 days and also for F344 cells after 2 and 4 days (Figure 2a). Figure 2 Change in cell number after treatment of F344 and Lewis cells with salivary α-amylase for different incubation times. The mean α-amylase effect is shown in percent as change compared to control cells treated with water for the total number of cells, exclusively viable, and for dead cells after 5 and 50 U/ml for 1 day, 2 days, and 4 days (n = 4-14 wells per group). For counting, cells

were detached with trypsin/EDTA, and viable and dead cells could be determined by trypan-blue-exclusion. Results for total cell number and viable cells were comparable: there were no obvious differences after 5 U/ml α-amylase, but for 50 U/ml, a significant decrease in cell number was apparent after 2 days and more prominent in Lewis cells (a & b). Number of dead cells from Lewis rats was not influenced by amylase treatment (c). In contrast to this, dead cells from click here of F344 rats markedly changed with duration of treatment

in a eFT508 similar way for 5 and 50 U/ml. After 1 day of α-amylase, the number was significantly increased, unchanged after 2 days, and significantly decreased after 4 days. Significant differences between controls and α-amylase are indicated by asterisk (p < 0.05); significant differences between treatment durations and F344 vs. Lewis are indicated by rhomb (p < 0.05). These results were evaluated from the total number of counted cells including viable as well as dead cells after detachment by trypsin. Comparable results were achieved when numbers of viable cells were evaluated (Figure 2b). In contrast, the number of dead F344 cells varied, depending on the duration of treatment but not on the α-amylase concentration (Figure 2c), whereas for Lewis, the amount of dead cells was not influenced by α-amylase (Figure 2c). Thus, prolonged α-amylase treatment reduced the number of non-viable cells in F344 cells, but not in Lewis cells. Based on these experiments, the cells were treated with 5 and 50 U/ml α-amylase for 2 days (Figure 3). α-Amylase treatment with 50 U/ml significantly reduced the total cell number in F344 and Lewis cells indicating an inhibited cell proliferation. No significant alterations were seen after 5 U/ml compared to water-treated control cells.

J Comput Theor Nanosci 2013, 10:1–5.CrossRef 28. Neamen DA: Semiconductor Physics and Devices. 3rd edition. New York: McGraw-Hill; 2003. 29. Kargar A, Lee C: Graphene nanoribbon schottky diodes using asymmetric contacts. In Proceedings of the IEEE-NANO2009: 9th Conference on Nanotechnology, 2009: July 26–30 2009; Genoa. Piscataway: IEEE; 2009:243–245. 30. Jimenez D: A current–voltage model for Schottky-barrier graphene based transistors. Nanotechnology 2008, 19:345204.CrossRef 31. Ahmadi MT, Rahmani M, Ghadiry MH, Ismail R: Monolayer graphene nanoribbon homojunction characteristics. Sci Adv Mater 2012, 4:753–756.CrossRef 32. Sadeghi H, Ahmadi MT, Mousavi M, Ismail R: Channel conductance of ABA stacking VX-661 trilayer graphene field

effect transistor. Mod Phys Lett B 2012, 26:1250047.CrossRef 33. Avetisyan AA, Partoens B, Peeters FM: Electric-field control of the band gap and Fermi energy in graphene multilayers by top and back gates. Phys Rev B 2009, 80:195401.CrossRef 34. McCann E, Koshino M: Spin-orbit coupling and

broken spin degeneracy in multilayer graphene. Phys Rev B 2010, 81:241409.CrossRef 35. Guinea F, Castro Neto AH, Peres NMR: Electronic states and Landau levels in graphene stacks. Phys Rev B 2006, 73:245426.CrossRef 36. Latil S, Meunier V, Henrard L: Massless fermions HKI-272 cost in multilayer graphitic systems with misoriented layers: ab initio calculations and experimental fingerprints. Phys Rev B 2007, 76:201402.CrossRef 37. Castro EV, Novoselov KS, Morozov SV, Peres NMR, Santos JMB L, Nilsson J, Guinea F, Geim AK, Castro AH: Electronic

properties of a biased graphene bilayer. J Phys Condens Matter 2010, 22:175503.CrossRef 38. Kato T: Perturbation Theory for Linear Operators. Berlin: Springer; 1995:132. 39. Rahmani M, Ahamdi MT, Ghadiry MH, Anwar S, Ismail R: The effect of applied voltage on the carrier IWP-2 datasheet effective mass in ABA trilayer graphene nanoribbon. Comput Theor Nanosci 2012, 9:1–4.CrossRef C59 mw 40. Guinea F, Castro Neto AH, Peres NMR: Interaction effects in single layer and multi-layer graphene. Eur Phys J Spec Top 2007, 148:117–125.CrossRef 41. Krompiewski S: Ab initio studies of Ni-Cu-Ni trilayers: layer-projected densities of states and spin-resolved photoemission spectra. J Phys Condens Matter 1998, 10:9663.CrossRef 42. Arora VK: Failure of Ohm’s law: its implications on the design of nanoelectronic devices and circuits. In Proceedings of the 2006 25th IEEE International Conference on Microelectronics: May 14–17 2006; Belgrade. Piscataway: IEEE; 2006:15–22. 43. Rahmani M, Ahmadi MT, Ismail R, Ghadiry MH: Quantum confinement effect on trilayer graphene nanoribbon carrier concentration. J Exp Nanosci in press 44. Kumar SB, Guoa J: Chiral tunneling in trilayer graphene. Appl Phys Lett 2012, 100:163102.CrossRef 45. Datta S: Electronic Transport in Mesoscopic Systems. Cambridge: Cambridge University Press; 2012. 46. Polyanin AD: Cubic equation. [http://​eqworld.​ipmnet.​ru/​en/​solutions/​ae/​ae0103.​pdf] 47.

In those primitive self-encoding systems, the two reactions can compete for the genetic information molecule because both reactions use the same information molecule as a template. Therefore, it is important to find the condition under which the primitive self-encoding system works efficiently for understanding of how the present-day sophisticated Repotrectinib cost replication systems evolved. Recently, we reconstructed a self-encoding system for replication of genetic information (Kita

et al. submitting), in which the catalytic subunit of Q β replicase, an RNA-dependent RNA polymerase originated from coliphage Q β, was translated from the sense strand RNA by a reconstituted translation system, resulting in synthesis of complementary strands of sense selleck kinase inhibitor RNA to replicate the genetic information. The

characteristic features of this system are non-linear dynamics of RNA replication and competition for the template RNA between translation and replication. Using this reaction system as an experimental model, we try to understand the dynamic behavior of the system quantitatively. We constructed a kinetic model which could Saracatinib in vivo describe the whole dynamic behavior of the self-encoding replication system. The results of this quantitative study indicated that the balance between translation and replication was critical for efficient self-encoding replication because of the inhibitory effects of translation on RNA replication. These results would deepen our understanding of how living systems evolve to be a sophisticatedly coordinated replication systems. E-mail: ichihashi@ist.​osaka-u.​ac.​jp A Comparative Analyses of Different Methodologies Employed for the Reconstruction of the Gene Complement of the Last Common Ancestor Sara E. Islas, Arturo Becerra, Luis Delaye, Antonio Lazcano* Facultad de Ciencias UNAM, 04510, Mexico, D.F. Although it is generally accepted

that the last common ancestor (LCA, also referred to as LUCA) was a complex Fossariinae organism perhaps not so different from extant prokaryotes, there are different estimates of its gene complement. Here we report the outcome of a comparative analysis of the different methodologies that have been developed based on comparative genomics and phylogenetic analyses. The different estimates of the gene content of the LCA show an impressive overlap for a significant number of highly conserved sequences involved in basic biological processes. The core of highly conserved RNA-related sequences supports the hypothesis that the LCA was preceded by earlier entities E-mail: saraernes@yahoo.​com Random Sequence Polypeptides: A Model for Understanding the Origins of Natural Proteins A. Marcozzi1, C. Chiarabelli1,2, A. Quintarelli1, D. De Lucrezia2,1, P. L.

The key role of the BBB is protecting the brain from toxic selleck products substances. On the other hand, the blocking role of the BBB is problematic because drugs used to treat many diseases of the central nervous system are unable to cross this highly specific barrier [30]. Application of NP-Pt at the beginning of embryogenesis makes it possible for NP-Pt to penetrate different tissues, including brain precursor cells and structures. Moreover, enclosed and separated from the

mother and environment, the organism has no possibilities to remove the nanoparticles from the egg, and consequently, the embryos were permanently exposed to PN-Pt during 20 days of embryogenesis (before and after BBB occurrence). The present results demonstrated that PN-Pt did not cause any difference in brain weight evaluated at the end of embryogenesis. Histological assessment of the brain structure revealed some minor pathological changes, but the number of brain cortex Emricasan mouse eFT508 in vitro cells was not affected. However, more detailed examination of

the brain tissue ultrastructure indicated some neurotoxic symptoms from NP-Pt treatment, including deformation and degradation of the mitochondria. Similar results were obtained for cisplatin, showing mitochondrial and nuclear DNA damage in the dorsal root ganglia [31]. Thus, not only platinum salts but also NP-Pt, via mitochondrial disruption, may lead to mitochondria-dependent apoptosis. Although almost half the neuronal cells die by apoptosis during normal brain development, this physiological process may be enhanced under toxic conditions [32]. However, the stimulation of mechanism of apoptosis within tumor cells is considered a highly advanced cancer therapy [33] and, in this respect, NP-Pt can enhance the apoptosis of cancer cells. Cytochrome c released from the mitochondria into the cytosol is one of the first steps in the mitochondrial apoptotic pathway. Cytochrome c and ATP are bound to the apoptotic protease-activating factor-1 [34]. The merger of these two structures creates an apoptosome and

activates caspase-9. Active Arachidonate 15-lipoxygenase caspase-9 is responsible for the activation of the executioners, caspase-3 and caspase-7 [32, 35]. We examined the activity of caspase-3 to detect apoptosis. Our results showed an increasing level of caspase-3-positive cells in chicken brain samples from groups treated with NP-Pt. These results agree with studies suggesting that platinum-based drugs trigger DNA damage, which induces apoptosis with the activation of caspase-3 [36, 37]. Opposing apoptosis is the process of cell proliferation, and thus, the interaction between apoptosis and proliferation, observed after platinum-based drug treatment, is a key factor in cancer therapy [38]. To examine the status of proliferation after NP-Pt treatment, we also identified the level of PCNA-positive nuclei in the brain tissue.

By choosing the wavelengths at 274 to 278 nm, the first new products (products 1, 3, 5, and CCI-779 6) were observed

with the retention time of 6.658 min (Figure 1A), 4.367 min (Figure 1C), 3.705 min (Figure 1E), and 7.152 min (Figure 1F). The second new products (products 2 and 4) displayed simultaneous ultraviolet absorbance at 231 to 236 nm, 262 to 263 nm, and 391 to 394 nm with the retention time of 12.351 min (Figure 1B) and 8.519 min (Figure 1D). The first new product did not show any fluorescence, while the second new product showed a stable lipofuscin-like blue (excitation wavelength (Ex) 392 to 395 nm/emission wavelength (Em) 456 to 460 nm) fluorescence. The UV absorption maxima and fluorescence Ex/Em values of MDA, amino acids, and different products are shown in Table 1. These observations suggest that taurine or GABA reacts rapidly with MDA; in comparison, the reaction of Glu or Asp with MDA is difficult under supraphysiological conditions. Figure 1 LY2606368 chemical structure Principal reaction products. Taurine + MDA, GABA + MDA, Glu + MDA, and Asp + learn more MDA separated by HPLC analysis. Taurine, GABA, Glu, and Asp (5.0 mM) were incubated with MDA (5.0 mM) in 0.2 mM PBS (pH 7.4) at 37°C for 24 h. The principal reaction products of taurine + MDA separated by HPLC analysis were observed at 278 (A) and 391 nm (B). The principal reaction products of GABA + MDA separated by HPLC analysis were observed at 278 (C)

and 391 nm (D). The principal reaction products of Glu + MDA and Asp + MDA separated by HPLC analysis were observed at 278 (E) and 278 nm (F). Table 1 UV absorption maxima and fluorescence Ex/Em values Compound UV absorption maxima (nm) Fluorescence

Ex/Em (nm) MDA 245 No Taurine No No GABA No No Glu No No Asp No No Product 1 278 No Product 2 236, 263, 391 392/456 Product 3 274 No Product 4 231, 262, 394 395/458 Product 5 276 No Product 6 276 No Values of the starting materials and products observed by incubation of taurine + MDA, GABA + MDA, Glu + MDA, and Asp + Interleukin-3 receptor MDA for 48 h. Identification of reaction products by LC/MS The reaction products were identified using LC/MS after the mixtures of amino acids and MDA were incubated for about 48 h. The mixture of taurine + MDA was analyzed that a total ion current chromatogram in comparison with a DAD chromatogram and the mass spectrum corresponding to the retention time of product 1 was m/z 180.0 [MP1 + H]+ (Figure 2A). Similarly, the mass spectrum corresponding to product 2 was m/z 260.0 [MP2 + H]+ (Figure 2B). After the mixture of GABA and MDA was incubated, the mass spectrum corresponding to the retention time of product 3 was m/z 158.2 [MP3 + H]+ (Figure 2C). Similarly, the mass spectrum corresponding to product 4 was m/z 238.2 [MP4 + H]+ (Figure 2D). The mixture of Glu + MDA and Asp + MDA was analyzed. The mass spectrum corresponding to the retention time of product 5 was m/z 202.

We describe the establishment and characterization of a new human OS cell line, designated HM781-36B purchase as UTOS-1, derived from a conventional osteoblastic OS. In addition, we analyze chromosomal aberrations and DNA copy number changes in UTOS-1 by

array comparative genomic hybridization (aCGH). Methods Source of Tumor Cells An 18-year-old Japanese man noticed swelling and pain of the left shoulder for 2 months. Radiographs showed a periosteal reaction and an osteosclerotic change in the proximal metaphysis of the left humerus. An open biopsy of this humeral tumor confirmed that it was conventional osteoblastic OS (Figure 1). Immunohistochemically, most of the tumor cells were strongly positive for vimentin, alkaline phosphatase (ALP), osteopontin (OP), and osteocalcin (OC). Despite intensive chemotherapy, the patient died of lung metastasis 2 months after open biopsy. The present study was conducted after a human experimentation review by our ethics committee. Figure 1 Histologic appearance of the original tumor. Spindle-shaped tumor cells with atypical nuclei have proliferated with formation AICAR research buy of osteoid or immature bone matrix (H&E stain). Sclae bar: 100 μm. Tumorigenicity in severe combined immunodeficiency (SCID) mice To determine

the tumorigenicity of the UTOS-1 cell line in vivo, 1 × 108 cells were washed, check details suspended in phosphate-buffered saline (PBS), and injected subcutaneously into the leg of 4-week-old male SCID mice (CB-17/Icrscid; Clea Japan Incorporation, Megestrol Acetate Osaka, Japan). Also, tumor growth in vivo was measured by calculating tumor volume based on the measurement of 2 perpendicular diameters using a caliper [10]. The volume was estimated using the following formula: 0.5 × L × (S)2, where L and S are the largest and smallest perpendicular tumor diameters, respectively.

Establishment of the tumor cell line Tumor cells were seeded in a 25 cm2 plastic flask (35–3109; Falcon, Franklin Lakes, NJ, USA) [11]. These cells were cultured in RPMI 1640 (MP Biomedicals, Solon, OH, USA), supplemented with 100 mg/ml streptomycin (Meiji Seika, Tokyo, Japan), 100 U/ml penicillin (Meiji Seika) and 10% fetal bovine serum (FBS; Funakoshi, Tokyo, Japan), at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The medium was replaced once per week. When semiconfluent layers were obtained, the cells were dispersed with Ca2+- and Mg2+-free PBS containing 0.1% trypsin and 0.02% EDTA solution, and were then seeded in new flasks for passage. The configuration of tumor cells was almost equalized after the 3rd generation. These procedures were serially performed until the UTOS-1 cell line was established. Cell growth in vitro To determine the doubling time, UTOS-1 cells were seeded in each well of 96-well dishes (Corning Costar, Tokyo, Japan) with fresh medium containing 100 μl of RPMI 1640 with 10% FBS.

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Table 5 Nucleotide substitution rates among different epitope and non-epitope regions.   dN SE# dS SE P-value* Associated epitopes 0.01062 0.00952 0.20969 0.07091 < 0.001 Non-associated epitopes 0.02387 0.02537 0.24220 0.12666 < 0.001 Not included epitopes 0.10532 0.01277 0.29085 0.04305 < 0.001

ISRIB Non-epitopes 0.09793 0.01653 0.27329 0.04665 < 0.001 Average pairwise number of nonsynonymous (d N ) and synonymous (d S ) substitutions per nonsynonymous and synonymous site, respectively, estimated at different categories of epitope and non-epitope regions among reference www.selleckchem.com/products/tpca-1.html sequences of M group are given. # Standard errors were estimated with 100 bootstrap replications in MEGA4. * In pairwise t-tests, the null hypothesis of dS = dN was rejected in all four comparisons. The average dN and dS values for each category of sites obtained from the pairwise comparisons of the reference sequences from the M group are shown in Table 5. Notably, associated epitopes have significantly smaller dN

and dS values than respective dN and dS values at other categories of sites, including non-epitopes (one-way ANOVA and nonparametric Kruskal-Wallis tests, p < 0.001) (see also Additional file 8). While significantly lower dN values at associated epitopes can be attributed to SAHA strong purifying selection operating to reduce amino acid diversity at these highly conserved epitope regions, in agreement with our previous results [44, 78], the significantly

lower dS values indicate that the high degree Casein kinase 1 of sequence conservation exist not only at the amino acid level, but also at the nucleotide level in these associated regions. Notably, when we consider correlations between the levels of synonymous and nonsynonymous sequence divergence from different site categories for the same pair of sequences, relatively strong and statistically significant positive correlations (Pearson correlation coefficient values between 0.67 and 0.77, p < 0.01) exist between dN and dS values for both non-epitope and epitope regions that were not included in the association rule mining, including variable epitopes, but not for associated epitopes. Similar trends are detected using non-parametric correlation (Kendall’s tau values between 0.34 and 0.45, p < 0.001). This may be attributed to common factors (such as functional and structural constraints and mutation rate) influencing evolution of these regions, so that the regions with higher dS values are also likely to have higher dN values. On the other hand, the levels of synonymous and nonsynonymous sequence divergence at the associated epitopes have only weak or non-significant correlation both with each other (r = -0.14, p < 0.01), as well as with dN and dS values at other regions within the same genomes (see Additional file 9).