Competition between B-Z and B-L transitions in a single DNA molecule: Computational studies

Under negative torsion, DNA adopts left-handed helical forms, such as Z-DNA and L-DNA. Using the random copolymer model developed for a wormlike chain, we represent a single DNA molecule with structural heterogeneity as a helical chain consisting of monomers which can be characterized by different helical senses and pitches. By Monte Carlo simulation, where we take into account bending and twist fluctuations explicitly, we study sequence dependence of B-Z transitions under torsional stress and tension focusing on the interaction with B-L transitions. We consider core sequences, (GC)(n) repeats or (TG)(n) repeats, which can interconvert between the right-handed B form and the left-handed Z form, imbedded in a random sequence, which can convert to left-handed L form with different (tension dependent) helical pitch. We show that Z-DNA formation from the (GC)(n) sequence is always supported by unwinding torsional stress but Z-DNA formation from the (TG)(n) sequence, which are more costly to convert but numerous, can be strongly influenced by the quenched disorder in the surrounding random sequence.National Research Foundation NRF-2012 R1A1A3013044 NRF-2014R1A1A2055681NRF-2012R1A1A2021736IBS-R023-D1NRF-2015R1A2A2A01005916Chemistr

Helices at Interfaces

Helically coiled filaments are a frequent motif in nature. In situations commonly encountered in experiments coiled helices are squeezed flat onto two dimensional surfaces. Under such 2-D confinement helices form "squeelices" - peculiar squeezed conformations often resembling looped waves, spirals or circles. Using theory and Monte-Carlo simulations we illuminate here the mechanics and the unusual statistical mechanics of confined helices and show that their fluctuations can be understood in terms of moving and interacting discrete particle-like entities - the "twist-kinks". We show that confined filaments can thermally switch between discrete topological twist quantized states, with some of the states exhibiting dramatically enhanced circularization probability while others displaying surprising hyperflexibility

Efekti korišćenja astaksantina u ishrani na rast, pigmentaciju mišića i antioksidantne aktivnosti mlađi kalifornijske pastrmke (oncorhynchus mykiss)

This study was designed to test the effects of dietary astaxanthin on growth, muscle pigmentation, antioxidant activity and biochemical composition of juvenile rainbow trout (Oncorhynchus mykiss). Experimental diets were formulated to contain 50, 75 and 100 ppm astaxanthin (designed as AS50, AS75 and AS100). The diet without supplementation of astaxanthin was considered as the control diet. Each experimental diet was fed to three replicate groups of fish (18.5 g/fish) to visual satiation two times a day for 10 weeks. Growth performance and proximate composition of muscle of fish were not affected by dietary AS levels (P> 0.05). Total carotenoid concentration in the muscle of fish fed the AS50 diet was higher than that of fish fed the control diet, but no different to that of fish fed the AS75 and AS100 diets. The astaxanthin concentration in the muscle of fish fed AS50, AS75 and AS100 diets were higher than that of control diet. The redness (a*) of the muscle of fish fed AS50, AS75 and AS100 diets were higher than that of fish fed the control diet (P 0.05) nije uticao na performansu rasta i hemijski sastav mišića ribe. Ukupna koncentracija karotenoida u mišiću ribe koja je hranjena AS50 hranom bila je viša nego kod riba hranjenih kontrolnom hranom, ali nije bila drugačija od riba hranjenih AS75 i AS100 hranom. Koncentracija astaksantina u mišiću riba hranjenih AS50, AS75 i AS100 hranom bila je viša nego kod riba hranjenih kontrolnom hranom. Crvena boja (a*) mišića ribe koja je hranjena AS50, AS75 i AS100 hranom bila je jača nego kod ribe hranjene kontrolnom hranom (P< 0.05). Antioksidantna aktivnost DPPH, radikala hidroksila i alkila u plazmi i jetri riba nisu zavisili od nivoa astaksantina osim kod plazme koja je imala antioksidantnu aktivnost alkilnih radikala. Rezultati ove studije nagoveštavaju da se hrana koja sadrži 50 ppm astaksantina može koristiti da bi se poboljšala crvena boja mišične pigmentacije kod mlađi kalifornijske pastrmke

Science Walden: Exploring the Convergence of Environmental Technologies with Design and Art

Science Walden, which is inspired by two prominent literary works, namely, Walden by Henry David Thoreau (1817-1862) and Walden Two by Burrhus Frederic Skinner (1904-1990), is aimed at establishing a community that embodies humanistic values while embracing scientific advancement to produce renewable energy and water sources. This study attempts to capitalize on feces standard money (FSM) and artistic collaboration between scientists and artists as a means of achieving the forms of life depicted in Walden and Walden Two. On our campus, we designed and built a pavilion that serves as a laboratory where scientific advantages, design, and art are merged. In the pavilion, feces are processed in reactors and facilities for sustainable energy production, and rainwater is harvested and treated for use in daily life. Our application of design and art contributes to easing interaction between the general public and scientists because it visualizes an ambiguous theory and concretizes it into an understandable image.ope

Genome shotgun sequencing and development of microsatellite markers for gerbera (Gerbera hybrida H.) by 454 GS-FLX

The objective of this research was to develop and characterize microsatellite markers for gerbera. We used shotgun sequencing with Roche 454 GS-FLX Titanium technology to identify microsatellite loci in gerbera genomic DNA (Gerbera hybrida). The total length of non-redundant sequences obtained was 22,527,019 bp, which consisted of 3,085 contigs and 28,249 singletons. We assembled 61,958 reads into 3,085 contigs, of which 114 (3.70%) contained microsatellite repeats. The average G+C content was 39.3%. Functional annotation to known sequences yielded 14.7% unigenes in the ‘Raon’ cultivar. Analysis of the gerbera genome DNA (‘Raon’) general library showed that sequences of (AT), (AG), (AAG) and (AAT) repeats appeared most often, whereas (AC), (AAC) and (ACC) were the least frequent. Primer pairs were designed for 80 loci. Only eight primer pairs produced reproducible polymorphic bands in the 28 gerbera accessions analyzed. A total of 30 alleles were identified from the eight polymorphic SSR loci, with two to eight alleles per locus (average level of 3.75). These markers will be useful for investigating genetic diversity and differentiation in gerbera. Keywords: Genetic diversity, genomics, microsatellite isolation, pyrosequencing, SSRs. African Journal of Biotechnology Vol. 11(29), pp. 7388-7396, 10 April, 201

A childhood case of spinal tuberculosis misdiagnosed as muscular dystrophy

Tuberculosis is primarily a pulmonary disease, but extra-pulmonary manifestations are not uncommon, especially in children and adolescents. Ten percent of extra pulmonary tuberculosis localizes to the bones and joints, and 56% of such cases affect the spine. We treated a childhood case of spinal tuberculosis misdiagnosed as muscular dystrophy in a patient without specific constitutional symptoms. We report this case because the patient had an unusual presentation of spinal tuberculosis