PRMT5 enhances generation of induced pluripotent stem cells from dairy goat embryonic fibroblasts via down-regulation of p53

OBJECTIVES

Protein arginine methyltransferase 5 (PRMT5), is thought to play a role in epigenetic reprogramming of mouse germ cells. However, up to now there has been little information concerning its expression profile and effects on generation of induced pluripotent stem cells (iPSCs) from somatic cells, in livestock. Here, we have explored PRMT5 expression profiles in dairy goats and its consequences to derivation of iPSCs from dairy goat embryonic fibroblasts (GEFs).

MATERIALS AND METHODS

We investigated effects of PRMT5 on iPS-like cells production in vitro. alkaline phosphatase (AP) staining, QRT-PCR and western blotting analysis of expression of related markers were used to evaluate efficiency of generation of iPSCs derived from GEFs.

RESULTS

These showed PRMT5 to be a conservative gene widely expressed in various tissues and different-aged testes. PRMT5 overexpression in combination with OCT3/4, SOX2, KLF4 and C-MYC (POSKM) significantly increased number of AP positive iPS-like colony-derived GEFs compared to OSKM alone, in our dairy goats. Moreover, our results demonstrated that PRMT5 overexpression stimulated GEF proliferation and down-regulated p53, p21 (a target gene of p53) and the apoptotic marker caspase 3, to enhance somatic cell reprogramming.

CONCLUSION

This study provides an efficient model for future studies on mechanisms underlying goat somatic cell reprogramming and differentiation.

Folic acid supplementation and dietary folate intake, and risk of preeclampsia

BACKGROUND/OBJECTIVES

Folic acid supplementation has been suggested to reduce the risk of preeclampsia. However, results from few epidemiologic studies have been inconclusive. We investigated the hypothesis that folic acid supplementation and dietary folate intake before conception and during pregnancy reduce the risk of preeclampsia.

SUBJECTS/METHODS

A birth cohort study was conducted in 2010-2012 at the Gansu Provincial Maternity & Child Care Hospital in Lanzhou, China. A total of 10,041 pregnant women without chronic hypertension or gestational hypertension were enrolled.

RESULTS

Compared with nonusers, folic acid supplement users had a reduced risk of preeclampsia (OR=0.61, 95% CI: 0.43-0.87). A significant dose-response of duration of use was observed among women who used folic acid supplemention during pregnancy only (P-trend=0.007). The reduced risk associated with folic acid supplement was similar for mild or severe preeclampsia and for early- or late-onset preeclampsia, although the statistical significant associations were only observed for mild (OR=0.50, 95% CI: 0.30-0.81) and late-onset (OR=0.60, 95% CI: 0.42-0.86) preeclampsia. The reduced risk associated with dietary folate intake during pregnancy was only seen for severe preeclampsia (OR=0.52, 95% CI: 0.31-0.87, for the highest quartile of dietary folate intake compared with the lowest).

CONCLUSIONS

Our study results suggest that folic acid supplementation and higher dietary folate intake during pregnancy reduce the risk of preeclampsia. Future studies are needed to confirm the associations.

Copy number variation detection using SNP genotyping arrays in three Chinese pig breeds

We performed genome-wide CNV detection based on SNP genotyping data of 96 Chinese-native Tibetan, Dahe and Wuzhishan pigs. These pigs are particularly interesting because of their excellent adaptation to hypoxia or small body size, which facilitates the use of them as models of different human diseases in addition to valuable agricultural animals. A total of 105 CNV regions (CNVRs) were identified, encompassing 16.71 Mb of the pig genome. Seven of 10 (70%) CNVRs selected randomly were validated by quantitative real-time PCR. Comparison with previous studies revealed 25 (23.81%) novel CNVRs, indicating that CNV coverage of the pig genome is still incomplete and there exists large diversity between pig breeds. Functional analysis of genes located in these CNVRs confirmed the high representation of genes involved in sensory perception, neurological system processes and other basic metabolic processes. In addition, the majority of these CNVRs were detected to span reported pig QTL that affect various traits, which highlighted three biologically interesting genes with copy number changes (i.e., ANKRD34B, FAM110B and ABCG1). These genes may have economic importance in pig breeding and are worth being further investigated. We also obtained some CNVRs harboring genes that had human orthologs involved in human diseases such as cardiovascular disease and Alzheimer's disease. The findings of this study are a significant extension of the coverage of CNVRs in the pig genome and provide valuable resources for follow-up-associated studies of CNVs in pig complex traits as well as important implications of human diseases.

Calculation of protein–ligand binding affinities based on a fragment quantum mechanical method

An efficient fragment-based quantum mechanical method has been successfully applied for reliable prediction of protein–ligand binding affinities.

Correction: Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

Correction for ‘Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation’ by Tong Zhu et al., Phys. Chem. Chem. Phys., 2012, 14, 7837–7845.

Delayed diagnosis of ureteral injuries following gynecological laparoscopic surgery: three case reports and review

PURPOSE OF INVESTIGATION

The clinical manifestations, causes, and methods for the treatment and prevention of ureteral injuries presenting late after gynecological laparoscopic surgeries were investigated.

MATERIALS AND METHODS

The medical records of patients who experienced delayed recognition of ureteral injuries after gynecological laparoscopic surgeries in the present hospital between 2008 and 2012 were reviewed retrospectively.

RESULTS

There are three cases of ureteral injuries which are diagnose-delayed, The incidence of the malignant tumor groups was 0.99%, and for malignant patients undergoing laparoscopic lymphadenectomy it was 1.3%.

CONCLUSION

The main way to prevent delayed ureteral injuries is to avoid adhesion between the ureter and surrounding tissues as well as eliminate electrothermal trauma during laparoscopic operations. Surgical repair is effective for such patients.

Quantifying the total ionic release from nanoparticles after particle-cell contact

In order to assess the potential hazards of nanoparticles (NPs) releasing, better knowledge about their toxicity to microbes is required. However, it remains controversial whether NPs could exert particles pecifictoxicity. In this study, the toxic impacts of four kinds of rare earth oxides (REO) NPs (La(2)O(3),CeO(2), Gd(2)O(3), and Yb(2)O(3)) on gram-negative Escherichia coli (E. coli) pBR322 were examined. The results indicate that all the tested NPs possessed cytotoxicity against E. coli. To evaluate the ion-related toxicity of REO NPs, the NPs dissolution in the presence of test organisms was quantitatively measured using X-ray absorption fine structure (XAFS) spectroscopy. Our results suggest that NPs-cell contact could facilitate the dissolution of NPs, and the additional ionic release at the particle-cell interface might result in a substantial increase in the ion-related toxicities towards the test organisms. Therefore, the ion-related toxicity of NPs might be grossly underestimated if the additional dissolution of NPs caused by particle-cell contact was overlooked, further leading to a false interpretation of particle-specific toxicity. To the best of our knowledge, this is the first determination of the total NPs dissolution after particle-cell contact. These findings are helpful to advance mechanistic understanding of the toxicity exerted by dissolvable metal-based NPs.

Nonseparable exchange–correlation functional for molecules, including homogeneous catalysis involving transition metals

A gradient approximation, GAM, to the exchange–correlation functional of Kohn–Sham theory with broad performance for metal and nonmetal bond energies and weak interactions is reported.

Quantifying the distribution of ceria nanoparticles in cucumber roots: the influence of labeling

Study on the fluorescent-labeling-caused changes in the distribution and bio-effects of ceria nanoparticles.

Thermally controlled growth of carbon onions within porous graphitic carbon-detonation nanodiamond monolithic composites

The addition of detonation nanodiamond to carbon monolithic composites has improved graphitic nature, pore volume, surface area and thermal conductivity.

Clinical effects of preventive interventional therapy in gastrointestinal bleeding patients with negative digital subtraction angiography findings

AIM: To assess the clinical effects and value of preventive interventional treatment in gastrointestinal hemorrhage patients with negative digital subtraction angiography (DSA) findings.

METHODS: Seventy-eight gastrointestinal hemorrhage patients with negative DSA findings treated at our hospital from June 2010 to June 2014 were randomly divided into two groups to receive gastroduodenal artery embolization combined with superior mesenteric arterial hypophysin infusion (interventional therapy group, n = 39) and traditional internal medicine conservative treatment (control group n = 39), respectively. Therapeutic effects and the incidence of complications were compared between the two groups.

RESULTS: Short- and long-term success rates of hemostasis were significantly higher in the interventional treatment group than in the control group (92.31% vs 64.10%, 82.05% vs 58.97%, P < 0.05). The amount of blood transfusion (154.56 mL ± 10.37 mL vs 186.21 mL ± 11.34 mL, P < 0.05) was significantly less and hospitalization time (10.35 d ± 2.46 d vs 13.02 d ± 3.03 d, P < 0.05) was significantly shorter in the interventional treatment group than in the control group, while the incidence of adverse reactions showed no significant difference between the two groups (P > 0.05).

CONCLUSION: Preventive gastroduodenal artery embolization combined with superior mesenteric arterial hypophysin infusion has a good therapeutic effect in gastrointestinal bleeding patients with negative DSA findings.

Disparate results between proliferation rates of surgically excised prostate tumors and an in vitro bioassay using sera from a positive randomized controlled trial

In vitro bioassay has been used extensively to test the effects of culturing cancer cells in sera from humans participating in dietary interventions, i.e, studies of modified intake of nutrients for the purpose of reducing cancer risk or progression. It has been hypothesized that cell proliferation rates determined by the in vitro bioassay indicate whether modification of dietary intake could decrease cancer cell growth in vivo. It has been suggested, however, that the in vitro bioassay may not correlate with tumor cell proliferation rates in prostate cancer. We investigated the concordance of cell proliferation rates from surgically excised prostate tumor tissue with the in vitro bioassay using sera from matched patients. We used samples from an earlier randomized clinical trial that showed that supplementation with flaxseed significantly inhibited prostate cancer cell proliferation rates in vivo as indicated by Ki67 staining in tumor specimens. Proliferation rates of LNCaP, DU145 and PC3 cell lines cultured in 10% human sera from participants in the flaxseed trial were determined using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Spearman's Rho correlation coefficients (ρ) indicated no association between Ki67 staining in prostate tumors and the in vitro bioassay for the three cell lines. These disparate findings suggest that the in vitro bioassay may not provide an accurate assessment of the environment in vivo.

Lower free testosterone level is correlated with left ventricular diastolic dysfunction in asymptomatic middle-aged men with type 2 diabetes mellitus

AIMS

Low testosterone (T) level is associated with cardiovascular risk factors. However, the relationship between T level and heart function in asymptomatic men with type 2 diabetes mellitus (T2DM) is unknown.

METHODS

A total of 325 men were recruited who had no history, symptoms, or signs of heart disease.

RESULTS

T2DM had significantly lower free T (FT) levels than those with normal glucose metabolism (NGM) (428 ± 38 pmol/l vs. 444 ± 38 pmol/l, p = 0.0002), and had an increased risk of LVDD (66.1% vs. 31.8%). There was a significant difference in FT level between subjects with and without LVDD among those with T2DM (421 ± 37 pmol/l vs. 442 ± 40 pmol/l, p = 0.0007), but not among those with NGM (439 ± 37 pmol/l vs. 447 ± 39 pmol/l, p = 0.247) or in the group overall (426 ± 38 pmol/l vs. 445 ± 38 pmol/l, p = 0.156). Lower FT level was significantly associated with LVDD [univariate odds ratio (OR) = 0.63, p = 0.032; multivariate OR = 0.71, p = 0.039]. Receiver operating characteristic curve analysis of the usefulness of FT level for predicting LVDD showed an area under the curve (AUC) of 0.85 for T2DM (p < 0.001) and 0.66 for NGM (p < 0.05). FT level had a high predictive value for LVDD in T2DM (83% for FT < 414 pmol/l), but a low predictive value in NGM (61% for FT < 423 pmol/l). Comparison of the AUCs showed that FT level was more strongly correlated with LVDD in T2DM than in NGM.

CONCLUSIONS

Lower FT level is correlated with LVDD in asymptomatic middle-aged men with T2DM.

Synthesis, in Vitro Covalent Binding Evaluation, and Metabolism of (14)C-Labeled Inhibitors of 11β-HSD1

In this letter, we reported the design and synthesis of three potent, selective, and orally bioavailable 11β-HSD1 inhibitors labeled with (14)C: AMG 456 (1), AM-6949 (2), and AM-7715 (3). We evaluated the covalent protein binding of the labeled inhibitors in human liver microsomes in vitro and assessed their potential bioactivation risk in humans. We then studied the in vitro mechanism of 2 in human hepatocytes and the formation of reactive intermediates. Our study results suggest that 1 and 3 have low potential for metabolic bioactivation in humans, while 2 has relatively high risk.

Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine

A common problem with non-nucleoside reverse transcriptase inhibitors (NNRTIs) of HIV-1 is the emergence of mutations in the HIV-1 RT, in particular Lys103 → Asn (K103N) and Tyr181 → Cys (Y181C), which lead to resistance to this entire class of inhibitors. In this study, we theoretically designed two new non-nucleoside HIV-1 RT inhibitors, Mnev-1 and Mnev-2, derived from nevirapine, in order to reduce the resistance caused by those HIV-1 RT mutations. The binding modes of Mnev-1 and Mnev-2 with the wild-type HIV-1 RT and its mutants (K103N and Y181C) were suggested by molecular docking followed by 20-ns molecular dynamics (MD) simulations in explicit water of those binding complexes (HIV-1 RTs with the new inhibitors). A molecular mechanics/generalized Born surface area (MM/GBSA) calculation was carried out for multiple snapshots extracted from the MD trajectory to estimate the binding free energy. The results of the calculations show that each of the new inhibitors forms a stable hydrogen bond with His235 during the MD simulations, leading to tighter binding of the new inhibitors with their targets. In addition, the repulsive interaction with Cys181 in the Y181C-nevirapine complex is not present in the novel inhibitors. The binding affinities predicted using the MM/GBSA calculations indicate that the new inhibitors could be effective at bypassing the drug resistance of these HIV-1 RT mutants.

Fragment quantum mechanical calculation of proteins and its applications

Conspectus The desire to study molecular systems that are much larger than what the current state-of-the-art ab initio or density functional theory methods could handle has naturally led to the development of novel approximate methods, including semiempirical approaches, reduced-scaling methods, and fragmentation methods. The major computational limitation of ab initio methods is the scaling problem, because the cost of ab initio calculation scales nth power or worse with system size. In the past decade, the fragmentation approach based on chemical locality has opened a new door for developing linear-scaling quantum mechanical (QM) methods for large systems and for applications to large molecular systems such as biomolecules. The fragmentation approach is highly attractive from a computational standpoint. First, the ab initio calculation of individual fragments can be conducted almost independently, which makes it suitable for massively parallel computations. Second, the electron properties, such as density and energy, are typically combined in a linear fashion to reproduce those for the entire molecular system, which makes the overall computation scale linearly with the size of the system. In this Account, two fragmentation methods and their applications to macromolecules are described. They are the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method and the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. The EE-GMFCC method is developed from the MFCC approach, which was initially used to obtain accurate protein-ligand QM interaction energies. The main idea of the MFCC approach is that a pair of conjugate caps (concaps) is inserted at the location where the subsystem is divided by cutting the chemical bond. In addition, the pair of concaps is fused to form molecular species such that the overcounted effect from added concaps can be properly removed. By introducing the electrostatic embedding field in each fragment calculation and two-body interaction energy correction on top of the MFCC approach, the EE-GMFCC method is capable of accurately reproducing the QM molecular properties (such as the dipole moment, electron density, and electrostatic potential), the total energy, and the electrostatic solvation energy from full system calculations for proteins. On the other hand, the AF-QM/MM method was used for the efficient QM calculation of protein nuclear magnetic resonance (NMR) parameters, including the chemical shift, chemical shift anisotropy tensor, and spin-spin coupling constant. In the AF-QM/MM approach, each amino acid and all the residues in its vicinity are automatically assigned as the QM region through a distance cutoff for each residue-centric QM/MM calculation. Local chemical properties of the central residue can be obtained from individual QM/MM calculations. The AF-QM/MM approach precisely reproduces the NMR chemical shifts of proteins in the gas phase from full system QM calculations. Furthermore, via the incorporation of implicit and explicit solvent models, the protein NMR chemical shifts calculated by the AF-QM/MM method are in excellent agreement with experimental values. The applications of the AF-QM/MM method may also be extended to more general biological systems such as DNA/RNA and protein-ligand complexes.

Ab initio molecular crystal structures, spectra, and phase diagrams

Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling illustrations of their unprecedented power in addressing some of the outstanding problems of solid-state chemistry, high-pressure chemistry, or geochemistry. They are the structure and spectra of ice Ih, in particular, the origin of two peaks in the hydrogen-bond-stretching region of its inelastic neutron scattering spectra, a solid-solid phase transition from CO2-I to elusive, metastable CO2-III, pressure tuning of Fermi resonance in solid CO2, and the structure and spectra of solid formic acid, all at the level of second-order Møller-Plesset perturbation theory or higher.