Computational prediction of nucleic acid secondary structure: Methods,applications, and challenges

RNA molecules are crucial in different levels of cellular function, ranging from translation and regulating genes to coding for proteins. Additionally, nucleic acids (RNA and DNA molecules) are designed for novel applications in biotechnology. Understanding the structure of a molecule is important in inferring its function, and computational methods for structure prediction have captured the interest of many researchers.Some functions of RNA molecules in cells, such as gene regulation, result from the binding of one RNA molecule to another, so-called target RNA molecule. This has led to recent interest in prediction of the secondary structure formed from interacting molecules. In this paper, we provide a brief overview of methods, applications, and challenges in computational prediction of nucleic acid secondary structure, both for single strands and for interacting strands.     

Structure of the Flight Muscle Thick Filament from the Bumble Bee,Bombus ignitus,at 6 Å Resolution

Four insect orders have flight muscles that are both asynchronous and indirect; they are asynchronous in that the wingbeat frequency is decoupled from the frequency of nervous stimulation and indirect in that the muscles attach to the thoracic exoskeleton instead of directly to the wing. Flight muscle thick filaments from two orders, Hemiptera and Diptera, have been imaged at a subnanometer resolution, both of which revealed a myosin tail arrangement referred to as “curved molecular crystalline layers”. Here, we report a thick filament structure from the indirect flight muscles of a third insect order, Hymenoptera, the Asian bumble bee Bombus ignitus. The myosin tails are in general agreement with previous determinations from Lethocerus indicus and Drosophila melanogaster. The Skip 2 region has the same unusual structure as found in Lethocerus indicus thick filaments, an α-helix discontinuity is also seen at Skip 4, but the orientation of the Skip 1 region on the surface of the backbone is less angled with respect to the filament axis than in the other two species. The heads are disordered as in Drosophila, but we observe no non-myosin proteins on the backbone surface that might prohibit the ordering of myosin heads onto the thick filament backbone. There are strong structural similarities among the three species in their non-myosin proteins within the backbone that suggest how one previously unassigned density in Lethocerus might be assigned. Overall, the structure conforms to the previously observed pattern of high similarity in the myosin tail arrangement, but differences in the non-myosin proteins.     

Designs and concept reliance of a fully automated high-content screening platform

High-content screening (HCS) is becoming an accepted platform in academic and industry screening labs and does require slightly different logistics for execution. To automate our stand-alone HCS microscopes, namely, an alpha IN Cell Analyzer 3000 (INCA3000), originally a Praelux unit hooked to a Hudson Plate Crane with a maximum capacity of 50 plates per run, and the IN Cell Analyzer 2000 (INCA2000), in which up to 320 plates could be fed per run using the Thermo Fisher Scientific Orbitor, we opted for a 4 m linear track system harboring both microscopes, plate washer, bulk dispensers, and a high-capacity incubator allowing us to perform both live and fixed cell-based assays while accessing both microscopes on deck. Considerations in design were given to the integration of the alpha INCA3000, a new gripper concept to access the onboard nest, and peripheral locations on deck to ensure a self-reliant system capable of achieving higher throughput. The resulting system, referred to as Hestia, has been fully operational since the new year, has an onboard capacity of 504 plates, and harbors the only fully automated alpha INCA3000 unit in the world.     

Preparation and characterization of a novel positively charged nanofiltration membrane based on polysulfone

The goal of this study was to prepare positively charged nanofiltration (NF) membranes to remove cations from aqueous solutions. A composite NF membrane was fabricated by the modification of a polysulfone ultrafiltration support. The active top layer was formed by the interfacial crosslinking polymerization of poly(ethylene imine) (PEI) with p‐xylene dichloride (XDC). Then, it was quaternized by methyl iodide (MI) to form a perpetually positively charged layer. The chemical and morphological changes of the membrane surfaces were studied by Fourier transform infrared spectroscopy, scanning electron microscopy (SEM), and atomic force microscopy. To optimize the membrane operation, the PEI solution concentration, PEI coating time, XDC concentration, crosslinking time, and MI concentration were optimized. Consequently, high water flux (5.4 L m^?2 h^?1 bar^?1) and CaCl₂ rejection (94%) values were obtained for the composite membranes at 4 bars and 30°C. The rejections of the NF membrane for different salt solutions, obtained from pH testing, followed the order Na₂SO₄ < MgSO₄ < NaCl < CaCl₂. The molecular weight cutoff was calculated by the retention of poly(ethylene glycol) solutions with different molecular weights, and finally, the stoke radius was calculated as 1.47 nm. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132, 41988.