D1 protein variants in Photosystem II from Thermosynechococcus elongatus studied by low temperature optical spectroscopy

In Photosystem II (PSII) from Thermosynechococcus elongatus, high-light intensity growth conditions induce the preferential expression of the psbA₃ gene over the psbA₁ gene. These genes encode for the D1 protein variants labeled D1:3 and D1:1, respectively. We have compared steady state absorption and photo-induced difference spectra at < 10 K of PSII containing either D1:1 or D1:3. The following differences were observed. (i) The pheophytin Q_x band was red-shifted in D1:3 (547.3 nm) compared to D1:1 (544.3 nm). (ii) The electrochromism on the Pheo_D1 Q_x band induced by Q_A⁻ (the C550 shift) was more asymmetric in D1:3. (iii) The two variants differed in their responses to excitation with far red (704 nm) light. When green light was used there was little difference between the two variants. With far red light the stable (t_1/2 > 50 ms) Q_A⁻ yield was ∼ 95% in D1:3, and ∼ 60% in D1:1, relative to green light excitation. (iv) For the D1:1 variant, the quantum efficiency of photo-induced oxidation of side-pathway donors was lower. These effects can be correlated with amino acid changes between the two D1 variants. The effects on the pheophytin Q_x band can be attributed to the hydrogen bond from Glu130 in D1:3 to the 13¹-keto of Pheo_D1, which is absent for Gln130 in D1:1. The reduced yield with red light in the D1:1 variant could be associated with either the Glu130Gln change, and/or the four changes near the binding site of P_D1, in particular Ser153Ala. Photo-induced Q_A⁻ formation with far red light is assigned to the direct optical excitation of a weakly absorbing charge transfer state of the reaction centre. We suggest that this state is blue-shifted in the D1:1 variant. A reduced efficiency for the oxidation of side-pathway donors in the D1:1 variant could be explained by a variation in the location and/or redox potential of P⁺.     

Population-based and family-based studies on the protein tyrosine phosphatase non-receptor 22 gene polymorphism and type 1 diabetes: A meta-analysis

Purpose

Studies investigating the association between PTPN22 gene C1858T polymorphism and type 1 diabetes (T1D) susceptibility among Caucasian population have reported conflicting results. To investigate this inconsistency, we performed a meta-analysis of all available studies dealing with the relationship between the PTPN22 C1858T polymorphism and T1D.

Methods

Databases including PubMed, Web of Science, and EMBASE were searched to find relevant studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of association.

Results

In total, 33 population-based studies with 22, 485 cases and 35, 292 controls, 9 family-based studies involving 7276 families were included. Under the random-effects model, the per-allele overall OR of the C1858T polymorphism for T1D was 1.89 (95% CI: 1.76–2.02, P < 10^− 5) by pooling all available case–control studies. In addition, we found significant evidence for overtransmission of the risk T allele in family-based studies (overall OR _TDT = 1.58, 95% CI: 1.43–1.74; P < 10^− 5). The summary OR from case–control and family-based association studies was 1.81 (95% CI: 1.70–1.93, P < 10^− 5).

Conclusions

In conclusion, this meta-analysis suggests that C1858T polymorphism in PTPN22 is associated with elevated T1D risk among Caucasian population.     

Association of the interleukin-10 − 592A/C, − 1082G/A and − 819T/C gene polymorphisms with type 2 diabetes: A meta-analysis

There is more evidence that interleukin-10 (IL-10), as a multifunctional regulatory cytokine of inflammatory responses, may have an important role in type 2 diabetes (T2D). However, genetic association studies that evaluated the relationship between IL-10 gene variants and T2D have produced conflicting results. The aim of this study was to determine whether the IL-10 gene polymorphisms (− 592A/C, − 1082G/A, − 819T/C) conferred susceptibility to T2D through a meta-analysis. A comprehensive search was conducted to examine all the eligible studies. A total of 9 studies involving 2838 T2D patients and 2773 controls were considered in the meta-analysis. Overall, there was no significant association between IL-10 − 592A/C and T2D (A vs C: OR = 0.93, P = 0.625; AA + AC vs CC: OR = 0.89, P = 0.511; AA vs AC + CC: OR = 0.93, P = 0.821). We failed to find the association between the IL-10 − 1082G allele and T2D (OR = 1.04, P = 0.430), but the genotypes of the IL-10 − 1082G/A polymorphism conferred a risk for the development of T2D (GA vs AA: OR = 1.21, P = 0.027; GG + GA vs AA: OR = 1.17, P = 0.048). Analysis of the − 819T/C polymorphism revealed no significant association with T2D (T vs C: OR = 1.04, P = 0.853; TT + TC vs CC: OR = 1.07, P = 0.834; TT vs TC + CC: OR = 1.08, P = 0.824). In conclusion, the present meta-analysis suggests association between the IL-10 − 1082G/A polymorphism and T2D. However, additional well-designed and larger scale primary studies are required to further evaluate the IL-10 gene polymorphisms and T2D.     

Selective binding of imatinib to the genetic variants of human α1-acid glycoprotein

Imatinib is a selective tyrosine kinase inhibitor, successfully used for the treatment of chronic myelogenous leukaemia. Its strong plasma protein binding referred to α₁-acid glycoprotein (AGP) component was found to inhibit the pharmacological activity. AGP shows genetic polymorphism and the two main genetic variants have different drug binding properties. The binding characteristics of imatinib to AGP genetic variants and the possibility of its binding interactions were investigated by various methods. The results proved that binding of imatinib to the two main genetic variants is very different, the high affinity binding belongs dominantly to the F1-S variant. This interaction is accompanied with specific spectral changes (induced circular dichroism, UV change, intrinsic fluorescence quenching), suggesting that the bound ligand has chiral conformation that would largely overlap with other ligands inside the protein cavity. Binding parameters of K_a = 1.7(± 0.2) × 10⁶ M^− 1 and n = 0.94 could be determined for the binding on the F1-S variant at 37°. Imatinib binding on the A variant is weaker and less specific. The binding affinity of imatinib to human serum albumin (nK_a ≈ 3 × 10⁴ M^− 1) is low. Pharmacologically relevant binding interactions with other drugs can be expected on the F1-S variant of AGP.     

14-3-3ε Gene variants in a Japanese patient with left ventricular noncompaction and hypoplasia of the corpus callosum

Background

Left ventricular noncompaction (LVNC) is a cardiomyopathy characterized by a prominent trabecular meshwork and deep intertrabecular recesses, and is thought to be due to an arrest of normal endomyocardial morphogenesis. However, the genes contributing to this process remain poorly understood. 14-3-3ε, encoded by YWHAE, is an adapter protein belonging to the 14-3-3 protein family which plays important roles in neuronal development and is involved in Miller–Dieker syndrome. We recently showed that mice lacking this gene develop LVNC. Therefore, we hypothesized that variants in YWHAE may contribute to the pathophysiology of LVNC in humans.

Methods and results

In 77 Japanese patients with LVNC, including the probands of 29 families, mutation analysis of YWHAE by direct DNA sequencing identified 7 novel variants. One of them, c.− 458G > T, in the YWHAE promoter, was identified in a familial patient with LVNC and hypoplasia of the corpus callosum. The − 458G > T variant is located within a regulatory CCAAT/enhancer binding protein (C/EBP) response element of the YWHAE promoter, and it reduced promoter activity by approximately 50%. Increased binding of an inhibitory C/EBPβ isoform was implicated in decreasing YWHAE promoter activity. Interestingly, we had previously shown that C/EBPβ is a key regulator of YWHAE.

Conclusions

These data suggest that the − 458G > T YWHAE variant contributes to the abnormal myocardial morphogenesis characteristic of LVNC as well as abnormal brain development, and implicate YWHAE as a novel candidate gene in pediatric cardiomyopathies.     

Association between cytotoxic T lymphocyte antigen-4 polymorphism and type 1 diabetes: A meta-analysis

Cytotoxic T lymphocyte-associated protein 4 (CTLA-4) is an important mediators of T-cell activation in autoimmune diseases. The association of polymorphisms of CTLA gene with type 1 diabetes (T1D) has widely been reported; however, the results are inconsistent. To obtain further insight into this topic, we performed a meta-analysis of 52 studies involving a total of 11,017 cases and 14,191 controls for 49A/G (rs231775) polymorphism of the CTLA-4 gene to evaluate the effect of CTLA-4 on genetic susceptibility for T1D. An overall random effects odds ratio of 1.41 (95% CI: 1.31–1.53, p < 10^− 5) was found for G allele versus A allele. Significant results were also observed for heterozygous (OR = 1.29, 95% CI: 1.16–1.45, p < 10^− 5) and homozygous (OR = 1.96, 95% CI: 1.66–2.31, p < 10^− 5). When stratified by ethnicity, sample size, diagnostic criterion, HWE status, genotyping method, and onset types, significantly increased risks were found for the polymorphism in almost all genetic models. Subgroup analysis and meta-regression was used to identify potential source of heterogeneity. There was strong evidence of heterogeneity, which largely disappeared after stratification by ethnicity. This meta-analysis demonstrated that the G allele of rs231775 of CTLA-4 is a risk factor associated with increased T1D susceptibility.     

Oxidation of thiocyanate by iron(V) in alkaline medium

The oxidation of thiocyanate by iron(V) (Fe(V)) was studied as a function of pH in alkaline solutions by a premix pulse radiolysis technique. The rates decrease with an increase in pH. The rate law for the oxidation of SCN⁻ by Fe(V) was obtained as −d[Fe(V)]/dt = k₁₀{[H⁺]²/([H⁺]² + K₂[H⁺] + K₂K₃)}[Fe(V)][SCN⁻], where k₁₀ = 5.72 ± 0.19 × 10⁶ M⁻¹ s⁻¹, pK₂ = 7.2, and pK₃ = 10.1. The reaction precedes via a two-electron oxidation, which converts Fe(V) to Fe(III). Thiocyanate reacts approximately 10³× faster with iron(V) than does with iron(VI).     

Genetic association of ADIPOQ gene variants with type 2 diabetes,obesity and serum adiponectin levels in south Indian population

Objective

To investigate the genetic association of eight variants of the adiponectin gene with type 2 diabetes mellitus (T2DM), obesity and serum adiponectin level in the south Indian population.

Methods

The study comprised of 1100 normal glucose tolerant (NGT) and 1100 type 2 diabetic, unrelated subjects randomly selected from the Chennai Urban Rural Epidemiology Study (CURES), in southern India. Fasting serum adiponectin levels were measured by radioimmunoassay. The variants were screened by polymerase chain reaction-restriction fragment length polymorphism. Linkage disequilibrium was estimated from the estimates of haplotype frequencies.

Results

Of the 8 variants, four SNPs namely, + 276 G/T (rs1501299), − 4522 C/T (rs822393), − 11365 C/G (rs266729), and + 712 G/A (rs3774261) were significantly associated with T2DM in our study population. The −3971 A/G (rs822396) and − 11391 G/A (rs17300539) SNPs' association with T2DM diabetes was mediated through obesity (where the association with type 2 diabetes was lost after adjusting for BMI). There was an independent association of + 276 G/T (rs1501299) and − 3971 A/G (rs822396) SNPs with generalized obesity and + 349 A/G (rs2241767) with central obesity. Four SNPs, −3971 A/G (rs822396), + 276 G/T (rs1501299), − 4522 C/T (rs822393) and Y111H T/C (rs17366743) were significantly associated with hypoadiponectinemia. The haplotypes GCCATGAAT and AGCGTGGGT conferred lower risk of T2DM in this south Indian population.

Conclusion

The adiponectin gene variants and haplotype contribute to the genetic risk towards the development of type 2 diabetes, obesity and hypoadiponectinemia in the south Indian population.     

Association of functional FEN1 genetic variants and haplotypes and breast cancer risk

Aim

As a tumor suppressor, FEN1 plays an essential role in preventing tumorigenesis. Two functional germline variants (-69G > A and 4150G > T) in the FEN1 gene have been associated with DNA damage levels in coke-oven workers and multiple cancer risk in general populations. However, it is still unknown how these genetic variants are involved in breast cancer susceptibility.

Methods

We investigated the association between these polymorphisms and breast cancer risk in two independent case–control sets consisted of a total of 1100 breast cancer cases and 1400 controls. The influence of these variations on FEN1 expression was also examined using breast normal tissues.

Results

It was found that the FEN1-69GG genotypes were significantly correlated to increased risk for developing breast cancer compared with the -69AA genotype in both sets [Jinan set: odds ratios (OR) = 1.41, 95% confidence interval (CI) = 1.20–1.65, P = 1.9×10^− 5; Huaian set: OR = 1.51, 95% CI = 1.22–1.86, P = 1.7×10^− 4]. Similar results were observed for 4150G > T polymorphism. The genotype–phenotype correlation analyses demonstrated that the -69G or 4150G allele carriers had more than 2-fold decreased FEN1 expression in breast tissues compared with -69A or 4150T carriers, suggesting that lower FEN1 expression may lead to higher risk for malignant transformation of breast cells.

Conclusion

Our findings highlight FEN1 as an important gene in human breast carcinogenesis and genetic variants in FEN1 confer susceptibility to breast cancer.     

Aminocarboxylate complexes of vanadium(III): Electronic structure investigation by high-frequency and -field electron paramagnetic resonance spectroscopy

Aminocarboxylate complexes of vanadium(III) are of interest as models for biologically and medicinally relevant forms of this interesting and somewhat neglected ion. The V(III) ion is paramagnetic, but not readily suited to conventional EPR, due to its integer-spin ground state (S = 1) and associated large zero-field splitting (zfs). High-frequency and -field EPR (HFEPR), however, has the ability to study such systems effectively. Three complexes, all previously structurally characterized: Na[V(trdta)] · 3H₂O, Na[V(edta)(H₂O)] · 3H₂O, and [V(nta)(H₂O)₃] · 4H₂O (where trdta stands for trimethylenediamine-N,N,N′,N′-tetraacetate and nta stands for nitrilotriacetate) were studied by HFEPR. All the investigated complexes produced HFEPR responses both in the solid state, and in aqueous solution, but those of [V(nta)(H₂O)₃] · 4H₂O were poorly interpretable. Analysis of multi-frequency HFEPR spectra yielded a set of spin Hamiltonian parameters (including axial and rhombic zfs parameters: D and E, respectively) for these first two complexes as solids: Na[V(trdta)] · 3H₂O: D = 5.60 cm⁻¹, E = 0.85 cm⁻¹, g = 1.95; Na[V(edta)(H₂O)] · 3H₂O: D = 1.4 cm⁻¹, E = 0.14 cm⁻¹, g = 1.97. Spectra in frozen solution yielded similar parameters and showed multiple species in the case of the trdta complex, which are the consequence of the flexibility of this ligand. The EPR spectra obtained in frozen aqueous solution are the first, to our knowledge, of V(III) in solution in general and show the applicability of HFEPR to these systems. In combination with very insightful previous studies of the electronic absorption of these complexes which provided ligand-field parameters, it has been possible to describe the electronic structure of V(III) in [V(trdta)]⁻ and [V(edta)(H₂O)]⁻; the quality of data for [V(nta)(H₂O)₃] does not permit analysis. Qualitatively, six-coordinate V(III) complexes with O,N donor atoms show no electronic absorption band in the NIR region, and exhibit relatively large magnitude zfs (D ? 5 cm⁻¹), while analogous seven-coordinate complexes do have a NIR absorption band and show relatively small magnitude zfs (D < 2 cm⁻¹).     

The kinetics of the hydrogen/deuterium exchange of epidermal growth factor receptor ligands

Five highly homologous epidermal growth factor receptor ligands were studied by mass spectral analysis, hydrogen/deuterium (H/D) exchange via attenuated total reflectance Fourier transform-infrared spectroscopy, and two-dimensional correlation analysis. These studies were performed to determine the order of events during the exchange process, the extent of H/D exchange, and associated kinetics of exchange for a comparative analysis of these ligands. Furthermore, the secondary structure composition of amphiregulin (AR) and heparin-binding-epidermal growth factor (HB-EGF) was determined. All ligands were found to have similar contributions of 3₁₀-helix and random coil with varying contributions of β-sheets and β-turns. The extent of exchange was 40%, 65%, 55%, 65%, and 98% for EGF, transforming growth factor-α (TGF-α), AR, HB-EGF, and epiregulin (ER), respectively. The rate constants were determined and classified as fast, intermediate, and slow: for EGF the 0.20 min⁻¹ (Tyr), 0.09 min⁻¹ (Arg, β-turns), and 1.88 × 10⁻³ min⁻¹ (β-sheets and 3₁₀-helix); and for TGF-α 0.91 min⁻¹ (Tyr), 0.27 min⁻¹ (Arg, β-turns), and 1.41 × 10⁻⁴ min⁻¹ (β-sheets). The time constants for AR 0.47 min⁻¹ (Tyr), 0.04 min⁻¹ (Arg), and 1.00 × 10⁻⁴ min⁻¹ (buried 3₁₀-helix, β-turns, and β-sheets); for HB-EGF 0.89 min⁻¹ (Tyr), 0.14 min⁻¹ (Arg and 3₁₀-helix), and 1.00 × 10⁻³ min⁻¹ (buried 3₁₀-helix, β-sheets, and β-turns); and for epiregulin 0.16 min⁻¹ (Tyr), 0.03 min⁻¹ (Arg), and 1.00 × 10⁻⁴ min⁻¹ (3₁₀-helix and β-sheets). These results provide essential information toward understanding secondary structure, H/D exchange kinetics, and solvation of these epidermal growth factor receptor ligands in their unbound state.     

Association of POL1, MALT1, MC4R, PHLPP and DSEL single nucleotide polymorphisms in chromosome 18q region with type 2 diabetes in Tunisians

Previous studies and replication analyses have linked chromosome 18q21.1–23 with type 2 diabetes (T2DM) and its complications, including diabetic nephropathy (DN). Here we investigated the association of POL1-nearby variant rs488846, MALT1-nearby variant rs2874116, MC4R-nearby variant rs1942872, PHLPP rs9958800 and DSEL-nearby variant rs9966483 single nucleotide polymorphisms (SNPs) in the 18q region, previously linked with DN in African-Americans, with T2DM in (North African) Tunisian subjects, followed by their association with DN, which was performed subsequent to the analysis of the association with T2DM. Study subjects comprised 900 T2DM cases and 748 normoglycemic control, and genotyping was carried out by PCR–RFLP analysis. Of the 5 SNPs analyzed, POL1-nearby variant rs488846 [P = 0.044], and MC4R-nearby variant rs1942872 [P = 0.012] were associated with moderate risk of T2DM. However, there was a lack of consistency in the association of the 5 tested SNPs with DN. As such, it appears that the three chromosome 18q region variants appear to play a role in T2DM pathogenesis, but not with DN in North African Tunisian Arabs.     

The effects of point of substitution on the electrochemical behavior of new manganese phthalocyanines, tetra-substituted with diethylaminoethanethiol

The syntheses and comparative studies of the spectral, voltammetry and spectroelectrochemical properties of new manganese phthalocyanine complexes, tetra-substituted with diethylaminoethanethio at the peripheral (complex 3a) and non-peripheral positions (complex 3b) are reported. Solution electrochemistry of complex 3a showed quasi-reversible metal-based (Mn^IIIPc⁻²/Mn^IIPc⁻², E_1/2 = −0.07 V vs. Ag|AgCl) and ring-based (Mn^IIPc⁻²/Mn^IIPc⁻³, E_1/2 = −0.78 V vs. Ag|AgCl) reductions, but no ring-based oxidation. However, complex 3b showed weak irreversible ring-oxidation signal (E_p = +0.86 vs. Ag|AgCl). Reversible metal-based (Mn^IIIPc⁻²/Mn^IIPc⁻², E_1/2 = −0.04 V vs. Ag|AgCl) and ring-based (Mn^IIPc⁻²/Mn^IIPc⁻³, E_1/2 = −0.68 V vs. Ag|AgCl) reductions were also observed for complex 3b. Spectroelectrochemistry was used to confirm these processes. Reduction process involving the metal (Mn^IIIPc⁻²/Mn^IIPc⁻²) was associated with the formation of manganese μ-oxo complex in complex 3a.     

Effects of inorganic nitrogen forms on growth, morphology, nitrogen uptake capacity and nutrient allocation of four tropical aquatic macrophytes (Salvinia cucullata, Ipomoea aquatica, Cyperus involucratus and Vetiveria zizanioides)

This study assesses the growth and morphological responses, nitrogen uptake and nutrient allocation in four aquatic macrophytes when supplied with different inorganic nitrogen treatments (1) NH₄⁺, (2) NO₃⁻, or (3) both NH₄⁺ and NO₃⁻. Two free-floating species (Salvinia cucullata Roxb. ex Bory and Ipomoea aquatica Forssk.) and two emergent species (Cyperus involucratus Rottb. and Vetiveria zizanioides (L.) Nash ex Small) were grown with these N treatments at equimolar concentrations (500 μM). Overall, the plants responded well to NH₄⁺. Growth as RGR was highest in S. cucullata (0.12 ± 0.003 d⁻¹) followed by I. aquatica (0.035 ± 0.002 d⁻¹), C. involucratus (0.03 ± 0.002 d⁻¹) and V. zizanioides (0.02 ± 0.003 d⁻¹). The NH₄⁺ uptake rate was significantly higher than the NO₃⁻ uptake rate. The free-floating species had higher nitrogen uptake rates than the emergent species. The N-uptake rate differed between plant species and seemed to be correlated to growth rate. All species had a high NO₃⁻ uptake rate when supplied with only NO₃⁻. It seems that the NO₃⁻ transporters in the plasma membrane of the root cells and nitrate reductase activity were induced by external NO₃⁻. Tissue mineral contents varied with species and tissue, but differences between treatments were generally small. We conclude, that the free-floating S. cucullata and I. aquatica are good candidate species for use in constructed wetland systems to remove N from polluted water. The rooted emergent plants can be used in subsurface flow constructed wetland systems as they grow well on any form of nitrogen and as they can develop a deep and dense root system.     

Low-Frequency Coding Variants at 6p21.33 and 20q11.21 Are Associated with Lung Cancer Risk in Chinese Populations

Genome-wide association studies have successfully identified a subset of common variants associated with lung cancer risk. However, these variants explain only a fraction of lung cancer heritability. It has been proposed that low-frequency or rare variants might have strong effects and contribute to the missing heritability. To assess the role of low-frequency or rare variants in lung cancer development, we analyzed exome chips representing 1,348 lung cancer subjects and 1,998 control subjects during the discovery stage and subsequently evaluated promising associations in an additional 4,699 affected subjects and 4,915 control subjects during the replication stages. Single-variant and gene-based analyses were carried out for coding variants with a minor allele frequency less than 0.05. We identified three low-frequency missense variants in BAT2 (rs9469031, c.1544C>T [p.Pro515Leu]; odds ratio [OR] = 0.55, p = 1.28 × 10⁻¹⁰), FKBPL (rs200847762, c.410C>T [p.Pro137Leu]; OR = 0.25, p = 9.79 × 10⁻¹²), and BPIFB1 (rs6141383, c.850G>A [p.Val284Met]; OR = 1.72, p = 1.79 × 10⁻⁷); these variants were associated with lung cancer risk. rs9469031 in BAT2 and rs6141383 in BPIFB1 were also associated with the age of onset of lung cancer (p = 0.001 and 0.006, respectively). BAT2 and FKBPL at 6p21.33 and BPIFB1 at 20q11.21 were differentially expressed in lung tumors and paired normal tissues. Gene-based analysis revealed that FKBPL, in which two independent variants were identified, might account for the association with lung cancer risk at 6p21.33. Our results highlight the important role low-frequency variants play in lung cancer susceptibility and indicate that candidate genes at 6p21.33 and 20q11.21 are potentially biologically relevant to lung carcinogenesis.     

Interleukin-28B rs12979860C/T and rs8099917T/G contribute to spontaneous clearance of hepatitis C virus in Caucasians

Two single nucleotide polymorphisms rs12979860C/T and rs8099917T/G around interleukin-28B (IL28B) locus have been extensively investigated in their association with hepatitis C virus (HCV) spontaneous clearance. However, with the variable and even inconsistent results, it is necessary to conduct a meta-analysis. A literature search was conducted to seek articles about genetic variation of IL28B and spontaneous clearance of HCV. Odds ratio with 95% confidential interval were calculated to estimate their relationship. Furthermore, meta-regression analysis was performed to search for potential affective factors. A total of 8 studies including 2460 patients with chronic HCV infection and 1052 individuals with spontaneous HCV clearance met inclusion criteria, in which seven studies describing rs12979860 and three studies describing rs8099917. Analysis performed in Caucasian populations indicated that rs12979860CC and rs8099917TT contributed to HCV spontaneous clearance in both dominant model (CC vs. CT + TT, P < 1 × 10^− 4; TT vs. TG + GG, P < 10^− 4, respectively) and co-dominant model (CC vs. CT, P < 1 × 10^− 4, CC vs. TT, P < 1 × 10^− 4; TT vs. TG, P < 10^− 4, TT vs. GG, P = 0.012, respectively). Meta-regression analysis suggested that male proportion (P = 1 × 10^− 5) and mean age (P = 1 × 10^− 3) might weaken the effect of rs12979860CC, but HCV genotype 1/4 (P = 4 × 10^− 4) might contribute to it. IL28B rs12979860CC and rs8099917TT genotypes contribute to spontaneous HCV clearance in Caucasians.     

Imputation of Exome Sequence Variants into Population- Based Samples and Blood-Cell-Trait-Associated Loci in African Americans: NHLBI GO Exome Sequencing Project

Researchers have successfully applied exome sequencing to discover causal variants in selected individuals with familial, highly penetrant disorders. We demonstrate the utility of exome sequencing followed by imputation for discovering low-frequency variants associated with complex quantitative traits. We performed exome sequencing in a reference panel of 761 African Americans and then imputed newly discovered variants into a larger sample of more than 13,000 African Americans for association testing with the blood cell traits hemoglobin, hematocrit, white blood count, and platelet count. First, we illustrate the feasibility of our approach by demonstrating genome-wide-significant associations for variants that are not covered by conventional genotyping arrays; for example, one such association is that between higher platelet count and an MPL c.117G>T (p.Lys39Asn) variant encoding a p.Lys39Asn amino acid substitution of the thrombpoietin receptor gene (p = 1.5 × 10⁻¹¹). Second, we identified an association between missense variants of LCT and higher white blood count (p = 4 × 10⁻¹³). Third, we identified low-frequency coding variants that might account for allelic heterogeneity at several known blood cell-associated loci: MPL c.754T>C (p.Tyr252His) was associated with higher platelet count; CD36 c.975T>G (p.Tyr325^∗) was associated with lower platelet count; and several missense variants at the α-globin gene locus were associated with lower hemoglobin. By identifying low-frequency missense variants associated with blood cell traits not previously reported by genome-wide association studies, we establish that exome sequencing followed by imputation is a powerful approach to dissecting complex, genetically heterogeneous traits in large population-based studies.     

Electronic absorption and MCD spectra for octacyanometallate complexes M(CN)8, M=Mo(IV), W(IV), n=4 and Mo(V), W(V), n=3

Electronic absorption and 8.0 T magnetic circular dichroism (MCD) spectra are reported for M(CN)₈ ⁴⁻, M=Mo(IV) and W(IV), in aqueous solution and M(CN)₈ ³⁻, M=Mo(V) and W(V), in acetonitrile solutions. In addition some absorption and MCD spectra are reported for the M(CN)₈ ³⁻ ions embedded in thin poly methyl methacrylate (PMMA) plastic films at temperatures from 295 to 10 K. The temperature dependence of the MCD spectra confirms the presence of C terms. The solution and PMMA spectra for the both Mo and W complexes in either the IV or V oxidation states are remarkably similar to each other for the same oxidation state and are interpreted within a D_2d structural framework for the isotropic environment. The weak bands below 3.0 μm⁻¹ (1 μm⁻¹=10⁴ cm⁻¹) for the M(IV) complexes are assigned as metal-localized ligand field (LF) transitions. LF transitions are also suggested for weaker unresolved absorption between 3.0 and 3.6 μm⁻¹ for the M(V) ions. The intense bands above 3.6 μm⁻¹ for M(IV) and 4.6 μm⁻¹ for M(V) complexes are interpreted as metal to ligand charge transfer (MLCT) from the metal b₁(x²−y²) HOMO to CN⁻-based π * orbitals. The prominent intense bands observed below 4.5 μm⁻¹for the M(V) complexes are assigned as ligand to metal charge transfer (LMCT) from occupied non-bonding or weakly π bonding CN⁻ orbitals to the half-filled b₁(x²−y²) HOMO.     

Dissecting a bimolecular process of MgATP²- binding to the chaperonin GroEL

Although allosteric transitions of GroEL by MgATP²⁻ have been widely studied, the initial bimolecular step of MgATP²⁻ binding to GroEL remains unclear. Here, we studied the equilibrium and kinetics of MgATP²⁻ binding to a variant of GroEL, in which Tyr485 was replaced by tryptophan, via isothermal titration calorimetry (ITC) and stopped-flow fluorescence spectroscopy. In the absence of K⁺ at 4-5 °C, the allosteric transitions and the subsequent ATP hydrolysis by GroEL are halted, and hence, the stopped-flow fluorescence kinetics induced by rapid mixing of MgATP²⁻ and the GroEL variant solely reflected MgATP²⁻ binding, which was well represented by bimolecular noncooperative binding with a binding rate constant, k_on, of 9.14 × 10⁴ M^− 1 s^− 1 and a dissociation rate constant, k_off, of 14.2 s^− 1, yielding a binding constant, K_b (= k_on/k_off), of 6.4 × 10³ M^− 1. We also successfully performed ITC to measure binding isotherms of MgATP²⁻ to GroEL and obtained a K_b of 9.5 × 10³ M^− 1 and a binding stoichiometric number of 6.6. K_b was thus in good agreement with that obtained by stopped-flow fluorescence. In the presence of 10-50 mM KCl, the fluorescence kinetics consisted of three to four phases (the first fluorescence-increasing phase, followed by one or two exponential fluorescence-decreasing phases, and the final slow fluorescence-increasing phase), and comparison of the kinetics in the absence and presence of K⁺ clearly demonstrated that the first fluorescence-increasing phase corresponds to bimolecular MgATP²⁻ binding to GroEL. The temperature dependence of the kinetics indicated that MgATP²⁻ binding to GroEL was activation-controlled with an activation enthalpy as large as 14-16 kcal mol^− 1.