Epigenetic regulation in metabolic diseases: mechanisms and advances in clinical study

Epigenetics regulates gene expression and has been confirmed to play a critical role in a variety of metabolic diseases, such as diabetes, obesity, non-alcoholic fatty liver disease (NAFLD), osteoporosis, gout, hyperthyroidism, hypothyroidism and others. The term 'epigenetics' was firstly proposed in 1942 and with the development of technologies, the exploration of epigenetics has made great progresses. There are four main epigenetic mechanisms, including DNA methylation, histone modification, chromatin remodelling, and noncoding RNA (ncRNA), which exert different effects on metabolic diseases. Genetic and non-genetic factors, including ageing, diet, and exercise, interact with epigenetics and jointly affect the formation of a phenotype. Understanding epigenetics could be applied to diagnosing and treating metabolic diseases in the clinic, including epigenetic biomarkers, epigenetic drugs, and epigenetic editing. In this review, we introduce the brief history of epigenetics as well as the milestone events since the proposal of the term 'epigenetics'. Moreover, we summarise the research methods of epigenetics and introduce four main general mechanisms of epigenetic modulation. Furthermore, we summarise epigenetic mechanisms in metabolic diseases and introduce the interaction between epigenetics and genetic or non-genetic factors. Finally, we introduce the clinical trials and applications of epigenetics in metabolic diseases.

Stability and strength of transition-metal tetraborides and triborides

Using density functional theory, we show that the long-believed transition-metal tetraborides (TB(4)) of tungsten and molybdenum are in fact triborides (TB(3)). This finding is supported by thermodynamic, mechanical, and phonon instabilities of TB(4), and it challenges the previously proposed origin of superhardness of these compounds and the predictability of the generally used hardness model. Theoretical calculations for the newly identified stable TB(3) structure correctly reproduce their structural and mechanical properties, as well as the experimental x-ray diffraction pattern. However, the relatively low shear moduli and strengths suggest that TB(3) cannot be intrinsically stronger than c-BN. The origin of the lattice instability of TB(3) under large shear strain that occurs at the atomic level during plastic deformation can be attributed to valence charge depletion between boron and metal atoms, which enables easy sliding of boron layers between the metal ones.

Structure of human muscle creatine kinase

The crystal structure of human muscle creatine kinase has been determined by the molecular-replacement method and refined at 3.5A resolution. The structures of both the monomer and the dimer closely resemble those of the other known structures in the creatine kinase family. Two types of dimers, one with a non-crystallographic twofold symmetry axis and the other with a crystallographic twofold symmetry axis, were found to exist simultaneously in the crystal. These dimers form an infinite "double-helix"-like structure along an unusual long crystallographic 3(1) axis.

A case-control study on the environmental risk factors of Parkinson's disease in Tianjin, China

Using a case-control method, we studied the role of environmental risk factors and viral infection in the development of Parkinson's disease (PD) in China. Ninety-three PD patients and 186 controls were investigated with a questionnaire and from most of them, blood was taken to test the antibody levels of four virus (measles, rubella, HSV-1, CMV) IgG. The study result showed that positive family history, living near rubber plants, drinking river-water were associated with an increased risk of developing PD. In contrast, living in small cities, drinking well-water, drinking hard-liquor frequently, were associated with a decreased risk for PD. PD cases and controls did not differ with respect to other factors investigated including smoking and viral infection. These findings suggest that some environmental factors may be related to the development of PD, but further standardized studies will be required to confirm our results.

Crystal structure of an acidic phospholipase A2 from the venom of Agkistrodon halys pallas at 2.0 A resolution

The crystal structure of acidic phospholipase A2 from the venom of Agkistrodon halys pallas has been determined by molecular replacement at 2.0 A resolution to a crystallographic R-factor of 0.157. The overall structure of the molecule is very similar to those of other phospholipase A2 species of known structure. The catalytic site, the hydrophobic channel and the N-terminal region show greatest structural conservation. The Ca(2+)-binding region has a conformation that resembles closely that of bovine PLA2 rather than Crotalus atrox PLA2. Compared with other PLA2 species, the conformation of the C-terminal ridge shows significant difference due to the insertion of two residues. A unique aromatic patch appears on one face of the molecules, surrounded by two acidic residues, the relevant features of this structure and their possible biological implications are discussed.

Crystal structure of agkistrodotoxin, a phospholipase A2-type presynaptic neurotoxin from agkistrodon halys pallas

The crystal structure of agkistrodotoxin containing eight copies of molecules in the asymmetric unit has been determined at 2.8 A resolution to a crystallographic R factor of 0.207 by the molecular replacement technique. Two spatially adjacent regions of agkistrodotoxin molecule, turn 55-61 and stretch 85-91, are remarkably different from those of non-neurotoxic isoforms in conformation and electrostatic characteristics. These regions are likely to be involved in the recognition of agkistrodotoxin towards the specific receptor at the presynaptic membrane. The structural comparison of the interfacial recognition site with non-neurotoxic isoforms reveals a decreased hydrophobicity and lack of residues with bulky hydrophobic side-chains (i.e. Trp) to serve as membrane anchors. This structural feature of agkistrodotoxin may be related to the reduced non-specific binding of the toxin to non-targeted membrane before it arrives at the presynaptic membrane and recognizes the putative receptor. A unique hydrophobic patch including residues I19, P20, F21, A23, F24, M118 and F119 is found on the surface of the molecule near the entrance of the hydrophobic channel which plays an important role in crystal packing. The interaction mode between the patches might give a clue to the binding of the neurotoxin on the membrane. The agkistrodotoxin molecules in the asymmetric unit form two tetramers and each tetramer exhibits a novel "dimer of dimers"-like structure. A molecule-spanning four-stranded antiparallel beta-sheet is formed by the beta-wings of two molecules within a tetramer.

Structure of D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor carrying the fluorescent NAD derivatives at 2.7 A resolution

Ultraviolet irradiation of carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase leads to the formation of a fluorescent NAD derivative. The structure of the enzyme from Palinurus versicolor carrying this derivative has been determined by molecular replacement and refined using the restrained least-squares method to 2.7 A with a final crystallographic R-factor of 0.205. The polypeptide chain folding and subunit arrangement closely resemble the known structure of Homarus americanus GAPDH. The structure at the modified active site confirms that the photochemical reaction is a half-of-the-sites reaction and occurs in the red and yellow subunit pair. The stereochemical relationship between the Trp residues at the active site shows that Trp 310 is most probably involved in a radiationless energy transfer to the fluorophore. A large solvent channel connecting the catalytic and NAD(+)-binding sites was found parallel to the crystallographic axis alpha from packing analysis, suggesting that this crystal form may be suitable for a kinetic crystallographic study of the apoenzyme.

Structure of apo-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor

d-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) shows cooperative properties for binding coenzymes. The structure of apo-GAPDH from Palinurus versicolor has been solved at 2.0 A resolution by X-ray crystallography. The final model gives a crystallographic R factor of 0.178 in the resolution range 8 to 2 A. The structural comparison with holo-GAPDH from the same species reveals a conformational change induced by coenzyme binding similar to that observed in Bacillus stearothermophilus GAPDH but to a lesser extent. The differences in magnitude during the apo-holo transition between these two enzymes were analyzed with respect to the change of the amino acid composition in the coenzyme binding pocket. In the crystalline state of apo-GAPDH, the overall structures of the subunits are similar to each other; however, significant differences in temperature factors and minor differences in domain rotation upon coenzyme binding were observed for different subunits. These structural features are discussed in relation to the environmental asymmetry of crystallographically independent subunits.

Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor

The structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor was determined in the presence of coenzyme NAD+ at 1.88 A resolution with a final R-factor of 0.175. The structure refinement was carried out on the basis of the structure of holo-GAPDH at 2.0 A resolution using the program XPLOR. The carboxymethyl group connected to Cys149 is stabilized by a hydrogen bond between its OZ1 and Cys149N, and charge interaction between the carboxyl group and the nicotinamide moiety. The modification of Cys149 induced conformational changes in the active site, in particular, the site of sulphate ion 501 (the proposed attacking inorganic phosphate ion in catalysis), and segment 208-218 nearby. Extensive hydrogen-bonding interactions occur in the active site, which contribute to the higher stability of the modified enzyme. The modification of the active site did not affect the conformation of GAPDH elsewhere, including the subunit interfaces. The structures of the green and red subunits in the asymmetric unit are nearly identical, suggesting that the half-site reactivity of this enzyme is from ligand-induced rather than pre-existing asymmetry. It is proposed that the carboxymethyl group takes the place of the acyl group of the reaction intermediate, and the catalytic mechanism of this enzyme is discussed in the light of a comparison of the structures of the native and the carboxymethylated GAPDH.

Structure of agkistrodotoxin in an orthorhombic crystal form with six molecules per asymmetric unit

The structure of agkistrodotoxin crystallized under basic conditions has been determined at 2.8 A resolution by the molecular-replacement technique and refined to a crystallographic R factor of 0.194 and a free R factor of 0.260 with good stereochemistry. The molecular packing in the crystal differs from other PLA(2)s. The six molecules in the asymmetric unit form three dimers linked by Ca(2+) ions in a near-perfect six-ligand octahedral coordinating system. Extensive intermolecular hydrophobic interactions occur at the interfacial recognition site of each neurotoxin molecule, which provides an insight into phospholipase A(2)-membrane interactions. This hydrophobic interaction-induced molecular association along the interfacial recognition site suggests a self-protection mechanism of agkistrodotoxin.

[Meta analysis of parallel versus perpendicular double plating for distal humerus fracture of type C in adults]

Objective: To evaluate the effects of parallel versus perpendicular double plating for distal humerus fracture of type C. Methods: A standardized comprehensive literature search was performed by PubMed, Embase, Cochrane library, CMB, CNKI and Medline datebase.Randomized controlled studies on comparison between parallel versus perpendicular double plating for distal humerus fracture of type C before December 2015 were enrolled in the study.All date were analyzed by the RevMan 5.2 software. Results: Six studies, including 284 patients, met the inclusion criteria.There were 155 patients in perpendicular double plating group, 129 patients in parallel double plating group.The results of Meta-analysis indicated that there were statistically significant difference between the two groups in complications (OR=2.59, 95%CI: 1.03 to 6.53, P=0.04). There was no significant difference between the two groups in surgical duration (MD=-1.84, 95% CI: -9.06 to 5.39, P=0.62), bone union time (MD=0.09, 95%CI: -0.06 to 0.24, P=0.22), Mayo Elbow Performance Score (MD=0.09, 95%CI: -0.06 to 0.24, P=0.22), Range of Motions (MD=-0.92, 95%CI: -4.65 to 2.81, P=0.63) and the rate of excellent and good results (OR=0.64, 95%CI: 0.27 to 1.52, P=0.31). Conclusion: Both perpendicular and parallel double plating are effective in distal humerus fracture of type C, parallel double plating has less complications.

Crystallization and preliminary X-ray analysis of human muscle creatine kinase

Creatine kinase is a key enzyme in the energy homeostasis of cells and tissues with high and fluctuating energy demands. Human muscle MM creatine kinase is a dimeric protein with a molecular weight of approximately 43 kDa for each subunit. It has been crystallized by the hanging-drop vapor-diffusion method using 2-methyl-2, 4-pentanediol as precipitant. The crystals belong to the enantiomorphous space group P6222 or P6422 with cell parameters of a = b = 89.11 and c = 403.97 A. The asymmetric unit of the crystal contains two subunits. A data set at 3.3 A resolution has been collected using synchrotron radiation.

Cold exposure-induced plasma exosomes impair bone mass by inhibiting autophagy

Recently, environmental temperature has been shown to regulate bone homeostasis. However, the mechanisms by which cold exposure affects bone mass remain unclear. In our present study, we observed that exposure to cold temperature (CT) decreased bone mass and quality in mice. Furthermore, a transplant of exosomes derived from the plasma of mice exposed to cold temperature (CT-EXO) can also impair the osteogenic differentiation of BMSCs and decrease bone mass by inhibiting autophagic activity. Rapamycin, a potent inducer of autophagy, can reverse cold exposure or CT-EXO-induced bone loss. Microarray sequencing revealed that cold exposure increases the miR-25-3p level in CT-EXO. Mechanistic studies showed that miR-25-3p can inhibit the osteogenic differentiation and autophagic activity of BMSCs. It is shown that inhibition of exosomes release or downregulation of miR-25-3p level can suppress CT-induced bone loss. This study identifies that CT-EXO mediates CT-induced osteoporotic effects through miR-25-3p by inhibiting autophagy via targeting SATB2, presenting a novel mechanism underlying the effect of cold temperature on bone mass.

Effects of kappa-selenocarrageenan on membrane fluidity and ghost reseal ability of rat erythrocyte

Effects of kappa-selenocarrageenan (kappa-SeC) on membrane fluidity and ghost reseal ability of rat erythrocyte were studied by measuring the fluorescence polarization and the NADH-cytochrome C oxido-reductase, respectively. After rats were given ig kappa-SeC 140 mg.kg-1.d-1 x 30 d, the fluorescence polarization was decreased in comparison with saline control group (P < 0.05). It suggested that kappa-SeC increased the membrane fluidity. The reseal ability of erythrocyte membrane (ghost) was also elevated after ig kappa-SeC 140 and 70 mg.kg-1.d-1 x 30 d (P < 0.05).

The frequencies of disease names with the natural language used in the hospital information system

The statistical behavior of disease names referred by physicians with the natural language in a large hospital information system is little known despite the theoretical and practical interest. To address this issue, we reviewed and investigated the usage-frequencies of 18,274 disease names, 10,288 for outpatient care and 7986 for inpatient care, referred from October 1983 to June 1992 with the notation of the natural language in Japanese by the use of the registration-retrieval system of disease names at Fukui Medical School, Japan. Consequently, we found that the investigated distributions did not conform to the Poisson distribution, but conformed well to the Polya-Eggenberger distribution in both cases of outpatient and inpatient care. It implies that the disease names with the natural language are possibly referred by physicians with some interrelations.

Preliminary crystallographic studies on bacterioferritin from Azotobacter vinelandii

Bacterioferritin-cytochrome from Azotobacter vinelandii is an unusual protein containing haem groups as well as iron core like other ferritin. This paper reports the purification of bacterioferritin by affinity chromatography and the formation of brick-red crystals from a solution containing MgCl2. The crystals are optical isotropic with maximum dimensions of 0.4 X 0.4 X 0.1 mm3. The preliminary X-ray crystallographic studies have been performed. 1.5 degrees unscreened precession photographs show that the crystals of bacterioferritin belong to the cubic system, space group I432, with cell dimension 230 A. There are probably 8 molecules in one cubic unit cell and the molecule might have 32 symmetry. A molecular diameter of 115 A is derived from the packing of the molecules and a molecular weight of 826,000 is estimated for bacterioferritin.

Adipose exosomal noncoding RNAs: Roles and mechanisms in metabolic diseases

Exosomes are extracellular vesicles, measuring 40-160 nm in diameter, that are released by many cell types and tissues, including adipose tissue. Exosomes are critical mediators of intercellular communication and their contents are complex and diverse. In recent years, accumulating evidence has proved that multiple adipose tissue-derived exosomal noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), play pivotal roles in the pathogenesis of diverse metabolic diseases, such as obesity. In this narrative review, we focus on the adipose tissue-derived exosomal ncRNAs, especially exosomal miRNAs, and their dysregulation in multiple types of metabolic diseases. A deeper understanding of the role of adipose tissue-derived exosomal ncRNAs may help provide new diagnostic and treatment methods for metabolic diseases.