Methods and Applications of In Silico Aptamer Design and Modeling

Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design. In this study, we review theoretical and joint theoretical-experimental studies dedicated to aptamer design and modeling. We consider aptamers with different targets, such as proteins, antibiotics, organophosphates, nucleobases, amino acids, and drugs. During nucleic acid modeling and in silico design, a full set of in silico methods can be applied, such as docking, molecular dynamics (MD), and statistical analysis. The typical modeling workflow starts with structure prediction. Then, docking of target and aptamer is performed. Next, MD simulations are performed, which allows for an evaluation of the stability of aptamer/ligand complexes and determination of the binding energies with higher accuracy. Then, aptamer/ligand interactions are analyzed, and mutations of studied aptamers made. Subsequently, the whole procedure of molecular modeling can be reiterated. Thus, the interactions between aptamers and their ligands are complex and difficult to understand using only experimental approaches. Docking and MD are irreplaceable when aptamers are studied in silico.     

Proton-Detected Solid-State NMR of the Cell-Free Synthesized α-Helical Transmembrane Protein NS4B from Hepatitis C Virus

Proton-detected 100 kHz magic-angle-spinning (MAS) solid-state NMR is an emerging analysis method for proteins with only hundreds of microgram quantities, and thus allows structural investigation of eukaryotic membrane proteins. This is the case for the cell-free synthesized hepatitis C virus (HCV) nonstructural membrane protein 4B (NS4B). We demonstrate NS4B sample optimization using fast reconstitution schemes that enable lipid-environment screening directly by NMR. 2D spectra and relaxation properties guide the choice of the best sample preparation to record 2D ¹H-detected ¹H,¹⁵N and 3D ¹H,¹³C,¹⁵N correlation experiments with linewidths and sensitivity suitable to initiate sequential assignments. Amino-acid-selectively labeled NS4B can be readily obtained using cell-free synthesis, opening the door to combinatorial labeling approaches which should enable structural studies.     

Thermal Stability of Polymer Additives: Comparison of Decomposition Models Including Oxidative Pyrolysis

The thermo‐oxidative stability of widely used polymer additives has been investigated. A comparative analytical approach with classic and innovative decomposition models for polymer additives was conducted and the results supported using quantum‐chemical calculations. Unique pyrolysis products of the analytes were compiled utilizing pyrolysis online coupled to gas chromatography followed by mass spectrometric detection (Pyr‐GC–MS). The pyrolysis was either performed under inert conditions or in an oxygen‐containing atmosphere. Squalane was applied as polymer‐mimicking liquid next to low density polyethylene (LDPE) and polyamide 6 (PA 6) as matrices for 10 selected additives. The additives included in this study range from antioxidants and plasticizers to processing aids. These were selected to address a range of application in consumer products and to cover different chemical classes. The toxicological relevance of additives and potential breakdown products was considered. Consequently, degradation of sterically hindered antioxidants, diarylamines, and a trimellitic acid derivative was investigated. The findings were used to predict the behavior of consumer products made of polymeric materials entailing additives. The level of Antioxidant 2246 [2‐tert‐butyl‐6‐[(3‐tert‐butyl‐2‐hydroxy‐5‐methylphenyl)methyl]‐4‐methylphenol] and one of its predicted decomposition products was determined in baby bottle nipples made of natural rubber [2‐tert‐butyl‐4‐methylphenol] utilizing the complementary technique of gas chromatography coupled to tandem mass spectrometry (GC–MS/MS). This study provides a comprehensive characterization of important polymer additives and enables the prioritization of degradation products for further risk assessment. J. VINYL ADDIT. TECHNOL., 25:E12–E27, 2019. © 2018 The Authors. Journal of Vinyl and Additive Technology published by Wiley Periodicals, Inc. on behalf of Society of Plastics Engineers     

An optimization method based on the evolutionary and topology approaches to reduce the mass of composite wind turbine blades

In optimization of transient problems, a robust, stable, and efficient numerical scheme for time integration is of much importance. Recently, the mixed Lag     

Macrophage Immunomodulation Through New Polymers that Recapitulate Functional Effects of Itaconate as a Power House of Innate Immunity

Itaconate (ITA) is an emerging powerhouse of innate immunity with therapeutic potential that is limited in its ability to be administered in a soluble form. A library of polyester materials that incorporate ITA into polymer backbones resulting in materials with inherent immunoregulatory behavior is developed. Harnessing hydrolytic degradation release from polyester backbones, ITA polymers result in the mechanism specific immunoregulatory properties on macrophage polarization in vitro. In a functional assay, the polymer-released ITA inhibits bacterial growth on acetate. Translation to an in vivo model of biomaterial associated inflammation, intraperitoneal injection of ITA polymers demonstrate a rapid resolution of inflammation in comparison to a control polymer silicone, demonstrating the value of sustained biomimetic presentation of ITA.     

A study of the local site effects on the ground response for the city of Eskişehir,Turkey

Bulletin of Engineering Geology and the Environment - Local soil characteristics play a key role in determining soil-structure interaction and reliability of the superstructure behavior under...     

Shaping the Toroidal Section of End Mills

The shaping of the toroidal cutting section of end mills is considered. Methods are devised for selecting the positional parameters in shaping the helical rake surface on the toroidal section. Relations are established between the geometric parameters of the end mill in the toroidal section.     

PETROLEUM POTENTIAL, THERMAL MATURITY AND THE OIL WINDOW OF OIL SHALES AND COALS IN CENOZOIC RIFT BASINS, CENTRAL AND NORTHERN THAILAND

Oil shales and coals occur in Cenozoic rift basins in central and northern Thailand. Thermally immature outcrops of these rocks may constitute analogues for source rocks which have generated oil in several of these rift basins. A total of 56 oil shale and coal samples were collected from eight different basins and analysed in detail in this study. The samples were analysed for their content of total organic carbon (TOC) and elemental composition. Source rock quality was determined by Rock‐Eval pyrolysis. Reflected light microscopy was used to analyse the organic matter (maceral) composition of the rocks, and the thermal maturity was determined by vitrinite reflectance (VR) measurements. In addition to the 56 samples, VR measurements were carried out in three wells from two oil‐producing basins and VR gradients were constructed. Rock‐Eval screening data from one of the wells is also presented. The oil shales were deposited in freshwater (to brackish) lakes with a high preservation potential (TOC contents up to 44.18 wt%). They contain abundant lamalginite and principally algal‐derived fluorescing amorphous organic matter followed by liptodetrinite and telalginite (Botryococcus‐type). Huminite may be present in subordinate amounts. The coals are completely dominated by huminite and were formed in freshwater mires. VR values from 0.38 to 0.47%R_o show that the exposed coals are thermally immature. VR values from the associated oil shales are suppressed by 0.11 to 0.28%R_o. The oil shales have H/C ratios >1.43, and Hydrogen Index (HI) values are generally >400 mg HC/g TOC and may reach 704 mg HC/ gTOC. In general, the coals have H/C ratios between about 0.80 and 0.90, and the HI values vary considerably from approximately 50 to 300 mg HC/gTOC. The HI_max of the coals, which represent the true source rock potential, range from ～160 to 310 mg HC/g TOC indicating a potential for oil/gas and oil generation. The steep VR curves from the oil‐producing basins reflect high geothermal gradients of ～62°C/km and ～92°C/km. The depth to the top oil window for the oil shales at a VR of ～0.70%R_o is determined to be between ～1100 m and 1800 m depending on the geothermal gradient. The kerogen composition of the oil shales and the high geothermal gradients result in narrow oil windows, possibly spanning only ～300 to 400 m in the warmest basins. The effective oil window of the coals is estimated to start from ～0.82 to 0.98%R_o and burial depths of ～1300 to 1400 m (～92°C/km) and ～2100 to 2300 m (～62°C/km) are necessary for efficient oil expulsion to occur.     

Theoretical and practical implications of creep curve shape analyses for 7010 and 7075

Over tensile stress ranges giving creep lives up to 2000 hours at 373 to 463 K, the creep and creep fracture properties of 7010 are compared with results recorded for 7075 and other precipitation-hardened aluminum alloys. Using the ϕ methodology to quantify the systematic variations in creep curve shape with changing test conditions, the behavior patterns displayed by the different alloys are shown to depend on the extent to which precipitate coarsening causes a progressive loss of creep strength with increasing test duration and temperature. The ϕ relationships also introduce new approaches for rationalization and interpretation of creep data sets, based on the activation energy for lattice diffusion in the alloy matrices and the yield stress or UTS at the creep temperatures.