Genetic Variants Associated with Serum Thyroid Stimulating Hormone (TSH) Levels in European Americans and African Americans from the eMERGE Network

Thyroid stimulating hormone (TSH) hormone levels are normally tightly regulated within an individual; thus, relatively small variations may indicate thyroid disease. Genome-wide association studies (GWAS) have identified variants in PDE8B and FOXE1 that are associated with TSH levels. However, prior studies lacked racial/ethnic diversity, limiting the generalization of these findings to individuals of non-European ethnicities. The Electronic Medical Records and Genomics (eMERGE) Network is a collaboration across institutions with biobanks linked to electronic medical records (EMRs). The eMERGE Network uses EMR-derived phenotypes to perform GWAS in diverse populations for a variety of phenotypes. In this report, we identified serum TSH levels from 4,501 European American and 351 African American euthyroid individuals in the eMERGE Network with existing GWAS data. Tests of association were performed using linear regression and adjusted for age, sex, body mass index (BMI), and principal components, assuming an additive genetic model. Our results replicate the known association of PDE8B with serum TSH levels in European Americans (rs2046045 p = 1.85×10⁻¹⁷, β = 0.09). FOXE1 variants, associated with hypothyroidism, were not genome-wide significant (rs10759944: p = 1.08×10⁻⁶, β = −0.05). No SNPs reached genome-wide significance in African Americans. However, multiple known associations with TSH levels in European ancestry were nominally significant in African Americans, including PDE8B (rs2046045 p = 0.03, β = −0.09), VEGFA (rs11755845 p = 0.01, β = −0.13), and NFIA (rs334699 p = 1.50×10⁻³, β = −0.17). We found little evidence that SNPs previously associated with other thyroid-related disorders were associated with serum TSH levels in this study. These results support the previously reported association between PDE8B and serum TSH levels in European Americans and emphasize the need for additional genetic studies in more diverse populations.     

Latexin sensitizes leukemogenic cells to gamma-irradiation-induced cell-cycle arrest and cell death through Rps3 pathway

Leukemia is a leading cause of cancer death. Recently, the latexin (Lxn) gene was identified as a potential tumor suppressor in several types of solid tumors and lymphoma, and Lxn expression was found to be absent or downregulated in leukemic cells. Whether Lxn functions as a tumor suppressor in leukemia and what molecular and cellular mechanisms are involved are unknown. In this study, the myeloid leukemogenic FDC-P1 cell line was used as a model system and Lxn was ectopically expressed in these cells. Using the protein pull-down assay and mass spectrometry, ribosomal protein subunit 3 (Rps3) was identified as a novel Lxn binding protein. Ectopic expression of Lxn inhibited FDC-P1 growth in vitro. More surprisingly, Lxn enhanced gamma irradiation-induced DNA damages and induced cell-cycle arrest and massive necrosis, leading to depletion of FDC-P1 cells. Mechanistically, Lxn inhibited the nuclear translocation of Rps3 upon radiation, resulting in abnormal mitotic spindle formation and chromosome instability. Rps3 knockdown increased the radiation sensitivity of FDC-P1, confirming that the mechanism of action of Lxn is mediated by Rps3 pathway. Moreover, Lxn enhanced the cytotoxicity of chemotherapeutic agent, VP-16, on FDC-P1 cells. Our study suggests that Lxn itself not only suppresses leukemic cell growth but also potentiates the cytotoxic effect of radio- and chemotherapy on cancer cells. Lxn could be a novel molecular target that improves the efficacy of anti-cancer therapy.Leukemia is one of the most common cancers and one of the leading causes of cancer death. In the United States, an estimated 52 380 new cases of leukemia will be diagnosed in 2014, and approximately 24 090 patients will die of this disease (NCI Stat Fact Sheets: http://seer.cancer.gov/statfacts/html/leuks.html). Leukemia can be treated by chemotherapy, radiation therapy and bone marrow transplantation. Radiation and most chemotherapeutic reagents induce apoptosis in tumor cells, resulting in tumor regression. However, some cancer cells are resistant to therapy-induced apoptosis, leading to treatment failure and cancer relapse.^1,2 There is an urgent need for discovery of novel molecular targets that can abrogate death resistance in leukemic cells and enhance the cytotoxic efficacy of anti-cancer therapies.Latexin (Lxn) could be an interesting candidate for this purpose. Lxn is a novel regulator of hematopoietic stem cell function and homeostatic hematopoiesis.³ It is downregulated in several types of solid and liquid tumors, and overexpression of Lxn inhibits tumor cell growth.^{4, 5, 6, 7, 8} In lymphoma, the tumor suppressor function of Lxn is mediated through Bcl-2-induced apoptosis.⁵ Moreover, Lxn was reported to be a TNF-responsive gene in human papillovirus-infected keratinocytes, suggesting that it may contribute to TNF-induced suppression of cervical cancer.⁹ Lxn is also implicated in inflammation because it is highly enriched in mast cells and can be upregulated by lipopolysaccharide.^10,11 In addition, Lxn regulates the interaction of hematopoietic stem/progenitor cells to stroma through altering the abundance of cell adhesion molecules.¹² The only known Lxn binding protein is carboxypeptidase A (CPA), and it inhibits CPA activity, indicating that Lxn might be involved in protein degradation and metabolism.^{10,13, 14, 15} However, we have already shown that the tumor suppressor function of Lxn is not through the canonical CPA pathway in lymphoma cells.⁵Currently, the mechanism of action of Lxn in normal and malignant conditions remains unknown, and no reports have been made as to other proteins that could bind to Lxn. In this study, we aimed to discover novel Lxn binding proteins, and evaluate whether Lxn could enhance the cytotoxic effect of radiation and chemotherapeutic agent on leukemic cells. We used myeloid leukemogenic progenitor cell line FDC-P1 as a model system and ectopically expressed Lxn in these cells.^{16, 17, 18} Using a protein pull-down assay and mass spectrometry (MS), we identified ribosomal protein subunit 3 (Rps3) as a novel Lxn binding protein. We then examined the response of Lxn-overexpressing FDC-P1 cells to gamma-irradiation and found that Lxn sensitizes these cells to radiation-induced cell death and inhibits tumor cell growth. FDC-P1 cells with ectopic Lxn expression demonstrate more DNA double-strand breaks (DSBs) upon irradiation, which triggers a dramatic G2/M arrest and blocks G1- and S-phase entry. The abnormal cell-cycle progression results in massive necrosis and depletion of Lxn-overexpressing cells. Mechanistically, the increased level of Lxn reduces nuclear translocation of Rps3 upon radiation, which causes abnormal mitotic spindle formation and chromosome instability. Moreover, Rps3 knockdown increases the radiation sensitivity of FDC-P1 cells, confirming that Rps3 is involved in Lxn-mediated radiation response. In addition, Lxn enhances cytotoxicity of chemotherapeutic agent, VP-16, on FDC-P1 cells. This study, for the first time, unravels a mechanistic role of Lxn as a tumor suppressor via a previously unknown Rps3 pathway. Lxn could be a novel molecular target that improves the efficacy of anti-cancer therapy.     

Homology Modeling and Comparative Profiling of Superoxide Dismutase Among Extremophiles: Exiguobacterium as a Model Organism

Superoxide dismutase (SOD), a well known antioxidant enzyme, is known to exert its presence across bacteria to humans. Apart from their well-known antioxidant defense mechanisms, their association with various extremophiles in response to various stress conditions is poorly understood. Here, we have discussed the conservation and the prevalence of SODs among 21 representative extremophiles. A systematic investigation of aligned amino acid sequences of SOD from all the selected extremophiles revealed a consensus motif D-[VLE]-[FW]-E-H-[AS]-Y-[YM]. To computationally predict the correlation of SOD with the various stress conditions encountered by these extremophiles, Exiguobacterium was selected as a model organism which is known to survive under various adverse extremophilic conditions. Interestingly, our phylogenetic study based on SOD homology revealed that Exiguobacterium sibiricum was one of the closest neighbors of Deinococcus radiodurans and Thermus thermophilus. Next, we sought to predict 3-D model structure of SOD for E. sibiricum (PMDB ID: 0078260), which showed >95 % similarity with D. radiodurans R1 SOD. The reliability of the predicted SOD model was checked by using various validation metrics, including Ramachandran plot, Z-score and normalized qualitative model energy analysis score. Further, various physicochemical properties of E. sibiricum SOD were calculated using different prominent resources.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-014-0482-8) contains supplementary material, which is available to authorized users.     

Potential Use of Rice Field Cyanobacterium Nostoc muscorum in the Evaluation of Butachlor Induced Toxicity and their Degradation

In the present study, butachlor (5, 10, 20, 40 and 80 ppm) induced toxicity in Nostoc muscorum and their degradation was evaluated. The dose of butachlor dependent decreased in the cell survival and growth of N. muscorum was noticed. Scanning electron microscopy revealed the adverse impact on the cell size and shapes. Low concentrations of butachlor (10 and 20 ppm) induced the over expression of a polypeptides of 31.0 K Da and 42.7 K Da, respectively which could be responsible for developing resistance in the organism up to certain level. Further, the degradation product of butachlor as a result of metabolic activities of N. muscorum, identified by GC-MS analysis includes phenols and benzene dicarboxylic acid indicating the utilization of herbicide during active growth.     

Explaining the Non-Newtonian Character of Aggregating Monoclonal Antibody Solutions Using Small-Angle Neutron Scattering

A monoclonal antibody solution displays an increase in low shear rate viscosity upon aggregation after prolonged incubation at 40°C. The morphology and interactions leading to the formation of the aggregates responsible for this non-Newtonian character are resolved using small-angle neutron scattering. Our data show a weak repulsive barrier before proteins aggregate reversibly, unless a favorable contact with high binding energy occurs. Two types of aggregates were identified after incubation at 40°C: oligomers with radius of gyration ∼10 nm and fractal submicrometer particles formed by a slow reaction-limited aggregation process, consistent with monomers colliding many times before finding a favorable strong interaction site. Before incubation, these antibody solutions are Newtonian liquids with no increase in low shear rate viscosity and no upturn in scattering at low wavevector, whereas aggregated solutions under the same conditions have both of these features. These results demonstrate that fractal submicrometer particles are responsible for the increase in low shear rate viscosity and low wavevector upturn in scattered intensity of aggregated antibody solutions; both are removed from aggregated samples by filtering.     

Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.)

Comparative proteomic analyses were performed to detail the evolutionary consequences of strong directional selection for enhanced fiber traits in modern upland cotton (Gossypium hirsutum L.). Using two complementary proteomic approaches, 2-DE and iTRAQ LC–MS/MS, fiber proteomes were examined for four representative stages of fiber development. Approximately 1,000 protein features were characterized using each strategy, collectively resulting in the identification and functional categorization of 1,223 proteins. Unequal contributions of homoeologous proteins were detected for over a third of the fiber proteome, but overall expression was balanced with respect to the genome-of-origin in the allopolyploid G. hirsutum. About 30 % of the proteins were differentially expressed during fiber development within wild and domesticated cotton. Notably, domestication was accompanied by a doubling of protein developmental dynamics for the period between 10 and 20 days following pollination. Expression levels of 240 iTRAQ proteins and 293 2-DE spots were altered by domestication, collectively representing multiple cellular and metabolic processes, including metabolism, energy, protein synthesis and destination, defense and stress response. Analyses of homoeolog-specific expression indicate that duplicated gene products in cotton fibers can be differently regulated in response to selection. These results demonstrate the power of proteomics for the analysis of crop domestication and phenotypic evolution.     

Effect of Auxiliary Substances on Complexation Efficiency and Intrinsic Dissolution Rate of Gemfibrozil–β-CD Complexes

The studies reported in this work are aimed to elucidate the ternary inclusion complex formation of gemfibrozil (GFZ), a poorly water-soluble drug, with β-cyclodextrin (β-CD) with the aid of auxiliary substances like different grades of povidone(s) (viz. PVP K-29/32, PVP K-40, Plasdone S-630, and Polyplasdone XL), organic base (viz. triethanolamine), and metal ion (viz. MgCl₂·6H₂O), by investigating their interactions in solution and solid state. Phase solubility studies were carried out to evaluate the solubilizing power of β-cyclodextrin, in association with various auxiliary substances, to determine the apparent stability constant (K _C) and complexation efficiency (CE) of complexes. Improvement in K _C values for ternary complexes clearly proves the benefit of the addition of auxiliary substances to promote CE. Of all the approaches used, the use of polymer Plasdone S-630 was found to be the most promising approach in terms of optimum CE and K _C. GFZ–β-CD (1:1) binary and ternary systems were prepared by kneading and lyophilization methods. The ternary systems clearly signified superiority over binary systems in terms of CE, solubility, K _C, and reduction in the formulation bulk. Optimized ternary system of GFZ–β-CD–Plasdone S-630 prepared by using lyophilization method indicated a significant improvement in intrinsic dissolution rate when compared with ternary kneaded system. Differential scanning calorimetry, X-ray diffraction, Fourier transform infrared, scanning electron microscopy, and proton nuclear magnetic resonance were carried out to characterize the binary and optimized ternary complex. The results suggested the formation of new solid phases, eliciting strong evidences of ternary inclusion complex formation between GFZ, β-CD, and Plasdone S-630, particularly for lyophilized products.     

Development and Statistical Optimization of Solid Lipid Nanoparticles of Simvastatin by Using 2<Superscript>3</Superscript> Full-Factorial Design

The objective of this study was to develop solid lipid nanoparticles (SLNs) of simvastatin and to optimize it for independent variables (amount of glycerol monostearate, concentration of poloxamer, and volume of isopropyl alcohol) in order to achieve desired particle size with maximum percent entrapment efficiency (% EE) and percent cumulative drug release (% CDR). To achieve our goal, eight formulations (F ₁–F ₈) of SLNs were prepared by solvent injection technique and optimized by 2³ full-factorial design. The design was validated by extra design checkpoint formulation (F ₉), and the possible interactions between independent variables were studied. The responses of the design were analyzed using Design Expert 7.1.6. (Stat-Ease, Inc, USA), and the analytical tools of software were used to draw Pareto charts and response surface plots. On the basis of software analysis, formulation F ₁₀ with a desirability factor of 0.611 was selected as optimized formulation and was evaluated for the independent parameters. Optimized formulation showed particle size of 258.5 nm, % EE of 75.81%, with of 82.67% CDR after 55 h. The release kinetics of the optimized formulation best fitted the Higuchi model, and the recrystallization index of optimized formulation was found to be 65.51%.     

High-affinity binding of seminal plasma PSP94 to human immunoglobulin is through the Fab domain

Prostate secretory protein of 94 amino acids (PSP94) is one of the major proteins present in human seminal plasma. We had earlier reported that PSP94 has the ability to bind to human IgG. The aims of the present study were to further delineate the PSP94–IgG interaction and to understand whether this could have any significance in sperm function. Direct binding of IgG fragments to PSP94 showed maximal binding with F(ab′)₂ followed by Fab, while Fc displayed least binding in ELISA. Binding kinetics of PSP94–IgG interaction using surface plasmon resonance (SPR) revealed high-affinity binding of IgG to PSP94 with a dissociation constant (K_D) of 8.8 × 10⁻¹¹ M. PSP94–IgG interaction was found to be through the Fab domains of IgG. Real-time interaction kinetics revealed association constants for binding of IgG, Fab, and F(ab′)₂ towards PSP94 to be of the same order but with altered dissociation constants. IgG and its F(ab′)₂ fragment once complexed to PSP94 demonstrated negligible dissociation, while dissociation rate of Fab fragment was 6.6 × 10⁻⁴. In silico molecular modeling of PSP94–IgG complex identified N- and C-terminal β-strands of PSP94 to be the most plausible region involved in IgG interaction. Immunofluorescence studies revealed that IgG bound to human spermatozoa predominantly in the tail region, which could be prevented when IgG was preincubated with PSP94. This study reports for the first time that IgG forms a high-affinity complex with PSP94 through its F(ab′)₂ domain and reveals the ability of PSP94 to prevent binding of IgG to spermatozoa.