A conformational analysis of walker motif A [GXXXXGKT (S)] in nucleotide-binding and other proteins

The sequence GXXXXGKT/S, popularly known as Walker motif A, is widely believed to be the site for binding nucleotides in many proteins. Examination of the crystal structures in the Protein Data Bank showed that about half of the examples having these sequences do not bind or use nucleotides. Data analyses showed 92 different Walker sequences of the variable quartet (XXXX). Ramachandran angles in this segment revealed conformational similarity in the group of 45 proteins, known to bind or utilize nucleotides. The conformations of this segment in other proteins differ widely and it is not known whether they play any role in their functions. A flip of a peptide unit at different locations, with little change in the backbone conformation was noted in nine pairs of these proteins having same Walker sequence. An examination of the immediate neighborhood of the Walker sequence indicates that this region is preceded by a β -strand and followed by an α-helix, resulting in the motif β–W–α, an invariant feature amongst nucleotide-binding proteins

Click-based porous cationic polymers for enhanced carbon dioxide capture

Imidazolium based porous cationic polymers were synthesized using an innovative and facile approach, which takes advantage of the Debus Radziszewski reaction to obtain meso- and microporous polymers following click chemistry principles. In the obtained set of materials, click based porous cationic polymers have the same cationic backbone, whereas they bear the commonly used anions of imidazolium poly(ionic liquid)s. These materials show hierarchical porosity and a good specific surface area. Furthermore, their chemical structure was extensively characterized using ATR FTIR and SS NMR spectroscopies, and HR MS. These polymers show good performance towards carbon dioxide sorption, especially those possessing the acetate anion. This polymer has an uptake of 2 mmol per g of CO2 at 1 bar and 273 K, a value which is among the highest recorded for imidazolium poly(ionic liquid)s. These polymers were also modified in order to introduce N-heterocyclic carbenes along the backbone. Carbon dioxide loading in the carbene-containing polymer is in the same range as that of the non-modified versions, but the nature of the interaction is substantially different. The combined use of in situ FTIR spectroscopy and microcalorimetry evidenced a chemisorption phenomenon that brings about the formation of an imidazolium carboxylate zwitterion.Comment: 29 page, 33 figure

A visit to the present: potential benefits of inclusion of mindfulness in study abroad programs

In this Thursday Forum, we explore benefits of inclusion of mindfulness in the study abroad setting. We describe some of the theory behind contemplative pedagogy, and offer examples of how mindfulness strategies were employed successfully in two of CSBSJU\u27s recent study abroad programs

Pembuatan Bilayer Anode (Nio-csz) - Elektrolit Csz Dengan Metode Electrophoretic Deposition

PEMBUATAN BILAYER ANODE (NiO-CSZ) - ELEKTROLIT CSZ DENGAN METODE ELECTROPHORETIC DEPOSITION. Telah dilakukan pembuatan bilayer anode NiO-CSZ - elektrolit CSZ dengan metode Electrophoretic Deposition (EPD). Substrat (anode) NiO-CSZ dibuat dengan metode pressing dan elektrolit CSZ ditumbuhkan di atas substrat NiO-CSZ dengan metode EPD. Elektrolit CSZ ditumbuhkan di atas substrat NiO-CSZ dengan variasi waktu deposisi masing-masing 10 menit, 20 menit, dan 30 menit dan disinter pada suhu 1250oC. Dari analisis yang dilakukan menggunakan X-Ray Diffractometer (XRD), diketahui terdapat 3 fasa yakni CSZ, Ni, dan NiO pada bilayer NiO-CSZ/CSZ untukwaktu deposisi 30menit. Pemeriksaan ketebalan lapisan CSZ dilakukan menggunakan mikroskop optik. Data foto memperlihatkan bahwa ketebalan lapisan CSZ di atas substrat NiO-CSZ meningkat dengan meningkatnya waktu deposisi. Berdasarkan hasil karakterisasi sifat listrik lapisan CSZ menggunakan LCR meter diketahui bahwa peningkatan waktu deposisi menurunkan nilai konduktivitas ionik lapisan CSZ untuk masing-masing waktu deposisi 10 menit, 20 menit, dan 30 menit sebesar 0,078 mS/cm, 0,062 mS/cm, dan 0,004 mS/cm pada suhu 300 oC

The Computational Power of Optimization in Online Learning

We consider the fundamental problem of prediction with expert advice where the experts are "optimizable": there is a black-box optimization oracle that can be used to compute, in constant time, the leading expert in retrospect at any point in time. In this setting, we give a novel online algorithm that attains vanishing regret with respect to $N$ experts in total $\widetilde{O}(\sqrt{N})$ computation time. We also give a lower bound showing that this running time cannot be improved (up to log factors) in the oracle model, thereby exhibiting a quadratic speedup as compared to the standard, oracle-free setting where the required time for vanishing regret is $\widetilde{\Theta}(N)$. These results demonstrate an exponential gap between the power of optimization in online learning and its power in statistical learning: in the latter, an optimization oracle---i.e., an efficient empirical risk minimizer---allows to learn a finite hypothesis class of size $N$ in time $O(\log{N})$. We also study the implications of our results to learning in repeated zero-sum games, in a setting where the players have access to oracles that compute, in constant time, their best-response to any mixed strategy of their opponent. We show that the runtime required for approximating the minimax value of the game in this setting is $\widetilde{\Theta}(\sqrt{N})$, yielding again a quadratic improvement upon the oracle-free setting, where $\widetilde{\Theta}(N)$ is known to be tight

Superrigid subgroups and syndetic hulls in solvable Lie groups

This is an expository paper. It is not difficult to see that every group homomorphism from the additive group Z of integers to the additive group R of real numbers extends to a homomorphism from R to R. We discuss other examples of discrete subgroups D of connected Lie groups G, such that the homomorphisms defined on D can ("virtually") be extended to homomorphisms defined on all of G. For the case where G is solvable, we give a simple proof that D has this property if it is Zariski dense. The key ingredient is a result on the existence of syndetic hulls.Comment: 17 pages. This is the final version that will appear in the volume "Rigidity in Dynamics and Geometry," edited by M. Burger and A. Iozzi (Springer, 2002

Floral bud distortion in soybean and incidence in Central India

We describe a peculiar and often harmful budding disorder in soybean, leading to huge yield loss in India. To determine the prevalence of floral distortion in soybean, an extensive random roving survey was undertaken in the soybean-growing regions of Madhya Pradesh, Maharashtra and the adjoining part of Karnataka states during two successive seasons of kharif (monsoon-planted) crops – Oct 2010 and Sept 2011. The average rate of the disorder ranged from 8.0% to 14.6% and severity from 2.0 to 90.0% during 2010 and 2011, respectively. Affected plants were found to have either no or deformed pods and distorted flowers, and they remained green after maturity. All the soybean varieties grown in the surveyed region (i.e. JS 335, JS 93-05, JS 73-23, JS 95-60, AMS-MB-5-19, CO-2, Bragg, JS 10-44, Samrat) were affected by the disorder. The PCR-based diagnosis revealed the absence of phytoplasma in symptomatic soybean samples.Keywords: Glycine max, chlorosis, green stem, thickening and twisting stem, yield loss

The DNA relaxation activity and covalent complex accumulation of Mycobacterium tuberculosis topoisomerase I can be assayed in Escherichia coli: application for identification of potential FRET-dye labeling sites

<p>Abstract</p> <p>Background</p> <p><it>Mycobacterium tuberculosis </it>topoisomerase I (MtTOP1) and <it>Escherichia coli </it>topoisomerase I have highly homologous transesterification domains, but the two enzymes have distinctly different C-terminal domains. To investigate the structure-function of MtTOP1 and to target its activity for development of new TB therapy, it is desirable to have a rapid genetic assay for its catalytic activity, and potential bactericidal consequence from accumulation of its covalent complex.</p> <p>Results</p> <p>We show that plasmid-encoded recombinant MtTOP1 can complement the temperature sensitive <it>topA </it>function of <it>E. coli </it>strain AS17. Moreover, expression of MtTOP1-G116 S enzyme with the TOPRIM mutation that inhibits DNA religation results in SOS induction and loss of viability in <it>E. coli</it>. The absence of cysteine residues in the MtTOP1 enzyme makes it an attractive system for introduction of potentially informative chemical or spectroscopic probes at specific positions via cysteine mutagenesis. Such probes could be useful for development of high throughput screening (HTS) assays. We employed the AS17 complementation system to screen for sites in MtTOP1 that can tolerate cysteine substitution without loss of complementation function. These cysteine substitution mutants were confirmed to have retained the relaxation activity. One such mutant of MtTOP1 was utilized for fluorescence probe incorporation and fluorescence resonance energy transfer measurement with fluorophore-labeled oligonucleotide substrate.</p> <p>Conclusions</p> <p>The DNA relaxation and cleavage complex accumulation of <it>M. tuberculosis </it>topoisomerase I can be measured with genetic assays in <it>E. coli</it>, facilitating rapid analysis of its activities, and discovery of new TB therapy targeting this essential enzyme.</p