Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity.

The ability to generate RNA aptamers for synthetic biology using in vitro selection depends on the informational complexity (IC) needed to specify functional structures that bind target ligands with desired affinities in physiological concentrations of magnesium. We investigate how selection for high-affinity aptamers is constrained by chemical properties of the ligand and the need to bind in low magnesium. We select two sets of RNA aptamers that bind planar ligands with dissociation constants (K(d)s) ranging from 65 nM to 100 microM in physiological buffer conditions. Aptamers selected to bind the non-proteinogenic amino acid, p-amino phenylalanine (pAF), are larger and more informationally complex (i.e., rarer in a pool of random sequences) than aptamers selected to bind a larger fluorescent dye, tetramethylrhodamine (TMR). Interestingly, tighter binding aptamers show less dependence on magnesium than weaker-binding aptamers. Thus, selection for high-affinity binding may automatically lead to structures that are functional in physiological conditions (1-2.5 mM Mg(2+)). We hypothesize that selection for high-affinity binding in physiological conditions is primarily constrained by ligand characteristics such as molecular weight (MW) and the number of rotatable bonds. We suggest that it may be possible to estimate aptamer-ligand affinities and predict whether a particular aptamer-based design goal is achievable before performing the selection

The Band Gap in Silicon Nanocrystallites

The gap in semiconductor nanocrystallites has been extensively studied both theoretically and experimentally over the last two decades. We have compared a recent ``state-of-the-art'' theoretical calculation with a recent ``state-of-the-art'' experimental observation of the gap in Si nanocrystallite. We find that the two are in substantial disagreement, with the disagreement being more pronounced at smaller sizes. Theoretical calculations appear to over-estimate the gap. Recognizing that the experimental observations are for a distribution of crystallite sizes, we proffer a phenomenological model to reconcile the theory with the experiment. We suggest that similar considerations must dictate comparisons between the theory and experiment vis-a-vis other properties such as radiative rate, decay constant, absorption coefficient, etc.Comment: 5 pages, latex, 2 figures. (Submitted Physical Review B

Electron beam induced damage in PECVD Si3N4 and SiO2 films on InP

Phosphorus rich plasma enhanced chemical vapor deposition (PECVD) of silicon nitride and silicon dioxide films on n-type indium phosphide (InP) substrates were exposed to electron beam irradiation in the 5 to 40 keV range for the purpose of characterizing the damage induced in the dielectic. The electron beam exposure was on the range of 10(exp -7) to 10(exp -3) C/sq cm. The damage to the devices was characterized by capacitance-voltage (C-V) measurements of the metal insulator semiconductor (MIS) capacitors. These results were compared to results obtained for radiation damage of thermal silicon dioxide on silicon (Si) MOS capacitors with similar exposures. The radiation induced damage in the PECVD silicon nitride films on InP was successfully annealed out in an hydrogen/nitrogen (H2/N2) ambient at 400 C for 15 min. The PECVD silicon dioxide films on InP had the least radiation damage, while the thermal silicon dioxide films on Si had the most radiation damage

Submicron gate InP power MISFET's with improved output power density at 18 and 20 GHz

The microwave characteristics are presented at 18 and 20 GHz of submicron gate indium phosphide (InP) metal-insulator-semiconductor field-effect transistors (MISFET's) for high output power density applications. InP power MISFET's were fabricated and the output power density was investigated as a function of drain-source spacing. The best output power density and gain were obtained for drain-source spacing of 3 microns. The output power density is 2.7 times greater than was previously measured for InP MISFET's at 18 and 20 GHz, and the power-added efficiency also increased

Augmenting graphs to minimize the diameter

We study the problem of augmenting a weighted graph by inserting edges of bounded total cost while minimizing the diameter of the augmented graph. Our main result is an FPT 4-approximation algorithm for the problem.Comment: 15 pages, 3 figure

Setting a research agenda for progressive multiple sclerosis: The International Collaborative on Progressive MS

Despite significant progress in the development of therapies for relapsing MS, progressive MS remains comparatively disappointing. Our objective, in this paper, is to review the current challenges in developing therapies for progressive MS and identify key priority areas for research. A collaborative was convened by volunteer and staff leaders from several MS societies with the mission to expedite the development of effective disease-modifying and symptom management therapies for progressive forms of multiple sclerosis. Through a series of scientific and strategic planning meetings, the collaborative identified and developed new perspectives on five key priority areas for research: experimental models, identification and validation of targets and repurposing opportunities, proof-of-concept clinical trial strategies, clinical outcome measures, and symptom management and rehabilitation. Our conclusions, tackling the impediments in developing therapies for progressive MS will require an integrated, multi-disciplinary approach to enable effective translation of research into therapies for progressive MS. Engagement of the MS research community through an international effort is needed to address and fund these research priorities with the ultimate goal of expediting the development of disease-modifying and symptom-relief treatments for progressive MS

Ornamental Fishes of the Western Ghats of India

India is blessed with a rich diversity of freshwater fishes both in the Western Ghats and North Eastern Hills. The Western Ghats of India is one of the 34 - biodiversity ‘hotspot’ areas of the world. The rate of endemism is well reflected in the case of lower vertebrates especially with regard to fishes. Of the 300 species of freshwater fishes in the Western Ghats, 155 are considered ornamental fishes, of which 117 are endemic to the Western Ghats (Gopalakrishnan & Ponniah, 2000). At present, only a small fraction of the endemic fish diversity is utilized in ornamental fish trade. All the ornamental fishes marketed in India are exotic. Eventhough there are quite a lot of indigenous fishes, having high potential as ornamental fishes, they have not been properly exploited. The fish fauna of the Western Ghats include variety of barbs, rasboras, killifishes, glassfishes, catfishes, catopra, hill trouts, and danios, which are ideal candidates for ornamental fish industry. They are exceptionally beautiful with a wide variety of bands, blotches, spots, and colourful fins on their body. In spite of the fact that the Western Ghats of India is a gold mine of endemic freshwater fishes suitable for the ornamental fish trade, no concerted efforts have so far been undertaken for the development of sustainable market for these resources. Lack of scientific information on these native aquatic fauna is the main reason for the poor performance of this sector

Examining consumer acceptance of green innovations using innovation characteristics: A conceptual approach

In the wake of global warming and environmental preservation, all processes and actions are now being directed along the lines of creating a greener environment. Household solar equipments are one such initiative, whereby people around the world are being encouraged to adopt green innovations even within homes. Recent emphasis is particularly along the usage of solar energy for home lighting, heating and cooking. To achieve increased adoption of these green innovations, it is important to understand the behaviours of various factors that may influence consumers in forming favourable intentions towards such innovations. This article aims to develop a theory-based conceptual framework for examining user adoption of household solar innovations. Attributes from Rogers’ Diffusion of Innovations theory, Tornatzky and Klein’s Meta-Analysis, and Moore and Benbasat’s Perceived Characteristics of Innovating theory will be used to design the intended framework for examining the adoption of household solar and other green innovations