Reliability of high-throughput genotyping of whole genome amplified DNA in SNP genotyping studies

Whole genome amplification (wga) of DNA is being widely implemented in many laboratories to extend the life of samples only available in limited quantities for genetic analysis. We determined the reliability of wgaDNA genotypes in three sets of replicates from the same individuals: (i) 23 pairs of genomic DNA (gDNA), (ii) 43 pairs gDNA versus wgaDNA, and (iii) 29 pairs of independently amplified wgaDNA. Amplification was performed using multiple displacement amplification (MDA). Genotyping was successful for both DNA types for 1268 out of 1534 SNPs from 164 cardiovascular candidate genes assayed in a single Illumina panel. Amplified DNA failed for 77 SNPs (6%) that were genotyped successfully with genomic material. Percent of successful SNP calls, and concordance between pairs and kappa statistics (kappa) were determined. A total of 54 110 genotypes from gDNA-wgaDNA pairs were available for concordance analysis. Mean kappa for gDNA-wgaDNA pairs was 0.99. Concordance between gDNA-wgaDNA pairs was higher than amongst wgaDNA pairs (mean kappa for the 29 independently amplified pairs of wgaDNA was 0.95; interquartile range: 0.93-1.00). A statistical analysis of those SNPs which failed to genotype from amplified DNA only revealed that those loci were more likely to be closer to the telomeres and in locally GC-rich sequences. In summary, the MDA method produces wgaDNA samples that can be genotyped using high-throughput technology with a very high reproducibility to the original DNA but with slightly lower call rates. DNA amplification methodologies provide a useful solution for current and future large-scale genetic analyses especially with limited quantities of samples and DNA.     

A zwitterion of 1,5‐bis­(2‐hydroxy­benzamido)‐3‐aza­pentane: a two‐dimensional hydrogen‐bonding network involving dimers

The title compound, 2‐{N‐[2‐(2‐hydroxy­benzamido)ethyl­ammonio­ethyl]amino­carbon­yl}phenolate, C₁₈H₂₁N₃O₄, crystallizes in a zwitterionic form as a result of inter­molecular proton transfer and possesses a negatively charged phenolate group and a protonated amino group. The 2‐hydroxy­benzamide and 2‐(amino­carbonyl)­phenolate moieties attached to the two ends of the C—C—N—C—C backbone adopt a cis conformation in relation to this backbone. All N‐ and O‐bound H atoms are involved in hydrogen‐bond formation; the zwitterions are first linked into head‐to‐tail dimers, which are further organized into a two‐dimensional network parallel to the crystallographic bc plane.     

Electronic spectroscopy of the E<--X transition of NO-Kr and shielding/penetration effects in Rydberg states of NO-Rg complexes

We report the results of a (2+1) resonance-enhanced multiphoton ionization (REMPI) study of the E2Sigma+(4ssigma) Rydberg state of NO-Kr. We present an assignment of the two-photon spectrum based on a simulation, and discuss it in the context of previously-reported spectra of NO-Ne and NO-Ar. In addition, we report on spectra in the region of the vNO=1 level of the E, F and H' 4s and 3d Rydberg states of NO-Rg (Rg=Ne-Kr). Since the NO vibrational frequency is affected by electron donation from the rare-gas (Rg) atom to the NO+ core, as well as by the penetration of the Rydberg electron, the fundamental NO-stretch frequency reflects the interactions in the complex. The results indicate that the 4s Rydberg state has a strong interaction between the NO+ core and the Kr atom, as was the case for NO-Ar and NO-Ne. For the 3d Rydberg states, although penetration is not as significant as for the 4s Rydberg states, it does play an important role, with subtle angular effects being notable.     

Compactification of a myelin mimetic Langmuir monolayer upon adsorption and unfolding of myelin basic protein

The surface shear viscosity of a myelin mimetic Langmuir monolayer is investigated upon adsorption of myelin basic protein (MBP). We measure an increase of the surface shear viscosity at picomolar concentrations of the protein, suggesting that the globular conformation of MBP changes upon adsorption at the monolayer. The conformational change enables hydrodynamic interactions of the proteins, with a typical separation of hundreds of nanometers. This unfolding is essential for the compactification of the myelin sheath, serving an enhanced saltatory signal transduction in vertebrates. The viscometry used extends the sensitivity of standard surface viscometers toward lower viscosities.     

Synthesis of functional magnetic porous SrFe<Subscript>12</Subscript>O<Subscript>19</Subscript>/P(St-DVB-MAA) microspheres by a novel suspension polymerization

In this study, a novel and effective suspension polymerization has been employed to prepare functional magnetic porous SrFe₁₂O₁₉/P(St-DVB-MAA) microspheres in the presence of bilayer surfactants (sodium dodecyl benzene sulfonate (SDBS) and oleic acid (OA)) coated on micro-size magnetic SrFe₁₂O₁₉. This was achieved by pre-polymerizing the organic phase, which contained co-monomers, porogens and treated magnetic particles, at 65°C for 0.5 h under ultrasound conditions. Aqueous solutions containing a dispersion agent were then added to effect suspension polymerization. Scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), thermogravimetric analysis (TGA) and magnetic property measurement system (MPMS) were used to characterize the functional magnetic porous microspheres. The results show that the microparticles are well shaped with a uniform size distribution of about 0.5 ∼ 0.7 mm and the surfaces of the microspheres have many micro-pores with an average diameter of 0.533 μm. There are carboxyl groups (−COOH) on the surface of the microspheres to the extent of 0.65 mmol g⁻¹, as determined by conductometric titration. According to the XRD spectra, iron oxide consists mainly of SrFe₁₂O₁₉ which reveals hexahedral structure. The content of magnetic SrFe₁₂O₁₉ reaches 17.81% (by mass), and the microspheres have good heat resistance. The magnetic porous microspheres are ferromagnetic with high residual magnetization and coercivity, 21.59 emu g⁻¹ and 4.13 kOe, respectively. The saturation magnetisation is around 42.85 emu g⁻¹.      

Immunosuppressive ent‐Kaurene Diterpenoids from Isodon serra

Three new enmein‐type ent‐kaurenoids, i.e., the two pairs 1 and 2 of 20‐epimers and the (20R)‐isomer 3 , besides the seven known diterpenoids 4 – 10 , were isolated from the aerial parts of Isodon serra. Their structures were elucidated by spectroscopic techniques and X‐ray diffraction. The immunosuppressive effect for T‐lymphocytes proliferation induced by Con A in BALB/c mouse was evaluated for the isolates 1 – 10 . They all displayed a remarkable inhibitory effect, with multi‐glycosides of Tripterygium wilfordii as positive reference substance (Table 3).     

Facile fabrication of recyclable and active nanobiocatalyst: purification and immobilization of enzyme in one pot with Ni-NTA functionalized magnetic nanoparticle

Ni-NTA functionalized iron oxide magnetic nanoparticle was synthesized and used to selectively immobilize a his-tagged enzyme from cell free extract as an active and recyclable nanobiocatalyst, where purification and immobilization of the target enzyme were accomplished in one pot.     

Optimisation of Hydrocortisone Production by Curvularia lunata

A new method for breeding the hydrocortisone overproducing strain Curvularia lunata by screening ketoconazole-resistance mutant was developed. A hydrocortisone overproducing mutant C. lunata KA-91 with ketoconazole-resistance marker was obtained from protoplasts treated with ultraviolet radiation. The hydrocortisone conversion rate of C. lunata KA-91 was increased by 42.1% compared to the original strain CL-114 at the substrate 17α-hydroxypregn-4-en-3, 20-dione-21-acetate addition concentration of 1.0 g/L. The by-products produced by KA-91 were fewer than those of the original strain. It was assumed that the higher cytochrome P450 content of ketoconazole-resistance mutant resulted in the increase of 11β-hydroxylation capacity. The culture conditions for biotransformation of 17α-hydroxypregn-4-en-3, 20-dione-21-acetate to hydrocortisone were optimized by response surface methodology. Plackett–Burman design was applied to elucidate the key factors affecting the hydrocortisone production, and the results indicated that glucose, initial pH, and glucose to total nitrogen sources ratio (ω) had significant effects on hydrocortisone production. Box–Behnken design was employed to search for the optimal parameters of those three key factors. According to the model, the trial checking at the optimal conditions showed a high hydrocortisone conversion rate of 82.67%.