Finding finer functions for partially characterized proteins by protein-protein interaction networks

Based on high-throughput data, numerous algorithms have been designed to find functions of novel proteins. However, the effectiveness of such algorithms is currently limited by some fundamental factors, including (1) the low a-priori probability of novel proteins participating in a detailed function; (2) the huge false data present in high-throughput datasets; (3) the incomplete data coverage of functional classes; (4) the abundant but heterogeneous negative samples for training the algorithms; and (5) the lack of detailed functional knowledge for training algorithms. Here, for partially characterized proteins, we suggest an approach to finding their finer functions based on protein interaction sub-networks or gene expression patterns, defined in function-specific subspaces. The proposed approach can lessen the above-mentioned problems by properly defining the prediction range and functionally filtering the noisy data, and thus can efficiently find proteins’ novel functions. For thousands of yeast and human proteins partially characterized, it is able to reliably find their finer functions (e.g., the translational functions) with more than 90% precision. The predicted finer functions are highly valuable both for guiding the follow-up wet-lab validation and for providing the necessary data for training algorithms to learn other proteins.     

Liquid-Liquid Equilibrium for 1-Butanol-Water-KF and 1-Butanol-Water-K2CO3 Systems

KF or K2CO3 was added into the 1-butanol-water system and two phases were formed： water-rich phase （water phase） and 1-butanol-rich phase （1-butanol phase）. The liquid liquid equilibrium （LLE） data for 1-butanol-water-KF and 1-butanol-water-K2CO3 systems were measured at 25℃ and showed that 1-butanol phase contained negligible salt and water phase contained negligible 1-butanol when the concentrations of KF and K2CO3 in the water phase were equal to or higher than 27.11% and 31.68% , respectively. Thus water could be separated efficiently from 1-butanol-water by adding KF or K2CO3 into the system. A theoretical calculation of LLE data was calculated by using the Pitzer theory to get water activity in the water phase, and by the models, such as the Wilson, NRTL or the UNIQUAC for the 1-butanol phase. For 1-hutanol-water-KF system, the experimental data were found in good agreement with the calculated results by using Pitzer theory and Wilson equa tion, while for 1-butanol-water-K2CO3 system, the experimental data were found in good agreement with the calculated results by using Pitzer theory and UNIQUAC eauation.     

Intelligent Integrated Control of Underactuated Mechanical Systems with Second-order Nonholonomic Constraints

This paper describes an intelligent integrated control of an acrobot, which is an underactuated mechanical system with second-order nonholonomic constraints. The control combines a model-free fuzzy control, a fuzzy sliding-mode control and a modelbased fuzzy control. The model-free fuzzy controller designed for the upswing ensures that the energy of the acrobot increases with each swing. Then the fuzzy sliding-mode controller is employed to control the movement that the acrobot enters the balance area from the swing-up area. The model-based fuzzy controller, which is based on a Takagi-Sugeno fuzzy model, is used to balance the acrobot. The stability of the fuzzy control system for balance control is guaranteed by a common symmetric positive matrix, which satisfies linear matrix inequalities.     

Inducing dopaminergic differentiation of expanded rat mesencephalic neural stem cells by ascorbic acid in vitro

Ascorbic acid (AA) induced differentiation of neural stem cells (NSCs) into dopaminergic (DAergic) neurons is reported.NSCs derived from rat mesencephalon were maintained and expanded in a defined medium containing mitogens of basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF).Compared with the control, ascorbic acid treatment led to more DAergic neuronal differentiation as indicated by the expression of tyrosine hydroxylase (TH) and dopamine transporter (DAT), which are specific markers of dopamine neurons.AA induction also enhanced expression of Nurr1 and Shh.PD98059, an inhibitor of mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) pathway, could block AA-induced Nurr1, TH and DAT mRNA expression.The results might suggest a new strategy to provide enough dopaminergic cells for the therapy of Parkinson's disease (PD), and Nurr1 and ERK signaling pathway might participate in the AA-induced DAergic differentiation.     

Teeming stream protection using an argon shroud during casting of steel ingots

Two kinds of argon shroud protection devices with two different basic structures were designed and investigated. Industrial experiments and numerical simulations were used to examine the protection effect, and the mechanism of air entrapment during the casting of steel ingots was analyzed. The influence of the structure of the argon shroud protection device on the protection effect was investigated. An argon shroud protection device mounted to the nozzle holder on the bottom of the ladle does not provide a good protection effect because air can easily flow into the teeming system and cause reoxidation of molten steel during teeming. By contrast, an argon shroud protection device seated on the top of the central trumpet provides an excellent protection effect, where air has little chance of flowing into the teeming system during casting. The feasibilities of the argon shroud protection devices are discussed.     

Recognition of DNA damage by the Rad4 nucleotide excision repair protein

Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognizing the lesion and recruiting downstream factors. Here we present the crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer (CPD) lesion. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognized by Rad4, whereas the two CPD-linked nucleotides become disordered. These findings indicate that the lesions recognized by Rad4/XPC thermodynamically destabilize the Watson-Crick double helix in a manner that facilitates the flipping-out of two base pairs.     

A terahertz metamaterial with unnaturally high refractive index

Controlling the electromagnetic properties of materials, going beyond the limit that is attainable with naturally existing substances, has become a reality with the advent of metamaterials. The range of various structured artificial 'atoms' has promised a vast variety of otherwise unexpected physical phenomena, among which the experimental realization of a negative refractive index has been one of the main foci thus far. Expanding the refractive index into a high positive regime will complete the spectrum of achievable refractive index and provide more design flexibility for transformation optics. Naturally existing transparent materials possess small positive indices of refraction, except for a few semiconductors and insulators, such as lead sulphide or strontium titanate, that exhibit a rather high peak refractive index at mid- and far-infrared frequencies. Previous approaches using metamaterials were not successful in realizing broadband high refractive indices. A broadband high-refractive-index metamaterial structure was theoretically investigated only recently, but the proposed structure does not lend itself to easy implementation. Here we demonstrate that a broadband, extremely high index of refraction can be realized from large-area, free-standing, flexible terahertz metamaterials composed of strongly coupled unit cells. By drastically increasing the effective permittivity through strong capacitive coupling and decreasing the diamagnetic response with a thin metallic structure in the unit cell, a peak refractive index of 38.6 along with a low-frequency quasi-static value of over 20 were experimentally realized for a single-layer terahertz metamaterial, while maintaining low losses. As a natural extension of these single-layer metamaterials, we fabricated quasi-three-dimensional high-refractive-index metamaterials, and obtained a maximum bulk refractive index of 33.2 along with a value of around 8 at the quasi-static limit.     

Functional identification of gene cluster for the aniline metabolic pathway mediated by transposable element

A convenient and widely applicable method has been developed to clone aniline metabolic gene cluster in this study. Three positive recombinant plasmids pDA1, pDB2 and pDB11 were cloned from genomic library of aniline degradation strain AD9. The result of aniline dioxygenase （AD） activity and catechol 2,3-oxygenase （C230） activity assay showed that pDA1 and pDB11 contain aniline dioxygenase genes and catechol 2,3-dioxygenase genes, respectively. The sequence analysis of the total 24.7-kb region revealed that this region contains 25 ORFs, of which 17 genes involve metabolism of aniline. In the gene cluster, the first five genes （tadQTA1A2B） and the subsequent gene （tadR1） were predicted to encode a multi-component aniline dioxygenase and a LysR-type regulator, respectively, while the others （tadD1C1D2C2EFGIJKL） were expected to encode metacleavage pathway enzymes for catechol degradation. The gene cluster was surrounded by two IS1071 sequences.     

A new type of triploid crucian crap?red crucian carp (♀)×allotetraploid (♂)

A new type of triploid hybrids (TC) was produced by crossing red crucian carp (♀) with allotetraploid hybrids (♂). This type of triploids with no barbel was spindle-shaped and gray in color. Compared with their parents, some data of the morphological traits in the triploid hybrids were intermediate to those of their parents, and some were beyond their parents with heterozygous traits. Under the same culture conditions, the growth rate of the new type triploids was faster than their maternal red crucian carp (RC). The gonadal development of triploids was obviously slower than that of diploids, and the germ cells in them were degenerated. Compared with another type of triploids produced by Japanese crucian carp (♀) with allotetraploid hybrids (♂), the new type triploids not only kept faster growth rate and sterility, but also had no barbel that was similar to the common carp. The absence of the barbel in the new type of triploids has the important significance in both the inheritance and fish breeding.