Equilibrium distributions of topological states in circular DNA: Interplay of supercoiling and knotting

Two variables define the topological state of closed double-stranded DNA: the knot type, K, and ΔLk, the linking number difference from relaxed DNA. The equilibrium distribution of probabilities of these states, P(ΔLk, K), is related to two conditional distributions: P(ΔLk|K), the distribution of ΔLk for a particular K, and P(K|ΔLk) and also to two simple distributions: P(ΔLk), the distribution of ΔLk irrespective of K, and P(K). We explored the relationships between these distributions. P(ΔLk, K), P(ΔLk), and P(K|ΔLk) were calculated from the simulated distributions of P(ΔLk|K) and of P(K). The calculated distributions agreed with previous experimental and theoretical results and greatly advanced on them. Our major focus was on P(K|ΔLk), the distribution of knot types for a particular value of ΔLk, which had not been evaluated previously. We found that unknotted circular DNA is not the most probable state beyond small values of ΔLk. Highly chiral knotted DNA has a lower free energy because it has less torsional deformation. Surprisingly, even at |ΔLk| > 12, only one or two knot types dominate the P(K|ΔLk) distribution despite the huge number of knots of comparable complexity. A large fraction of the knots found belong to the small family of torus knots. The relationship between supercoiling and knotting in vivo is discussed.

Molecular cloning of a high-affinity receptor for the growth factor-like lipid mediator lysophosphatidic acid from Xenopus oocytes

Lysophosphatidic acid (1-acyl-2-lyso-sn-glycero-3-phosphate, LPA) is a multifunctional lipid mediator found in a variety of organisms that span the phylogenetic tree from humans to plants. Although its physiological function is not clearly understood, LPA is a potent regulator of mammalian cell proliferation; it is one of the major mitogens found in blood serum. In Xenopus laevis oocytes, LPA elicits oscillatory Cl− currents. This current, like other effects of LPA, is consistent with a plasma membrane receptor-mediated activation of G protein-linked signal transduction pathways. Herein we report the identification of a complementary DNA from Xenopus that encodes a functional high-affinity LPA receptor. The predicted structure of this protein of 372 amino acids contains features common to members of the seven transmembrane receptor superfamily with a predicted extracellular amino and intracellular carboxyl terminus. An antisense oligonucleotide derived from the first 5–11 predicted amino acids, selectively inhibited the expression of the endogenous high-affinity LPA receptors in Xenopus oocytes, whereas the same oligonucleotide did not affect the low-affinity LPA receptor. Expression of the full-length cRNA in oocytes led to an increase in maximal Cl− current due to increased expression of the high-affinity LPA receptor, but activation of the low-affinity receptor was, again, unaffected. Oocytes expressing cRNA prepared from this clone showed no response to other lipid mediators including prostaglandins, leukotrienes, sphingosine 1-phosphate, sphingosylphosphorylcholine, and platelet-activating factor, suggesting that the receptor is highly selective for LPA.

The decomposition of peroxynitrite does not yield nitroxyl anion and singlet oxygen

In a recent article [Khan, A. U., Kovacic, D., Kolbanovsky, A., Desai, M., Frenkel, K. & Geacintov, N. E. (2000) Proc. Natl. Acad. Sci. USA 97, 2984–2989], the authors claimed that ONOO−, after protonation to ONOOH, decomposes into 1HNO and 1O2 according to a spin-conserved unimolecular mechanism. This claim was based partially on their observation that nitrosylhemoglobin is formed via the reaction of peroxynitrite with methemoglobin at neutral pH. However, thermochemical considerations show that the yields of 1O2 and 1HNO are about 23 orders of magnitude lower than those of ⋅NO2 and ⋅OH, which are formed via the homolysis of ONOOH. We also show that methemoglobin does not form with peroxynitrite any spectrally detectable product, but with contaminations of nitrite and H2O2 present in the peroxynitrite sample. Thus, there is no need to modify the present view of the mechanism of ONOOH decomposition, according to which initial homolysis into a radical pair, [ONO⋅ ⋅OH]cage, is followed by the diffusion of about 30% of the radicals out of the cage, while the rest recombines to nitric acid in the solvent cage.

Temporal distribution of the ganglion cell volleys in the normal rat optic nerve

We describe experiments on behaving rats with electrodes implanted on the cornea, in the optic chiasm, and on the visual cortex; in addition, two red light-emitting diodes (LED) are permanently attached to the skull over the left eye. Recordings timelocked to the LED flashes reveal both the local events at each electrode site and the orderly transfer of visual information from retina to cortex. The major finding is that every stimulus, regardless of its luminance, duration, or the state of retinal light adaptation, elicits an optic nerve volley with a latency of about 10 ms and a duration of about 300 ms. This phenomenon has not been reported previously, so far as we are aware. We conclude that the retina, which originates from the forebrain of the developing embryo, behaves like a typical brain structure: it translates, within a few hundred milliseconds, the chemical information in each pattern of bleached photoreceptors into a corresponding pattern of ganglion cell neuronal information that leaves via the optic nerve. The attributes of each rat ganglion cell appear to include whether the retinal neuropile calls on it to leave after a stimulus and, if so when, within a 300-ms poststimulus epoch. The resulting retinal analysis of the scene, on arrival at the cortical level, is presumed to participate importantly in the creation of visual perceptual experiences.

Sleep modifies retinal ganglion cell responses in the normal rat

Recordings were obtained from the visual system of rats as they cycled normally between waking (W), slow-wave sleep (SWS), and rapid eye movement (REM) sleep. Responses to flashes delivered by a light-emitting diode attached permanently to the skull were recorded through electrodes implanted on the cornea, in the chiasm, and on the cortex. The chiasm response reveals the temporal order in which the activated ganglion cell population exits the eyeball; as reported, this triphasic event is invariably short in latency (5–10 ms) and around 300 ms in duration, called the histogram. Here we describe the differences in the histograms recorded during W, SWS, and REM. SWS histograms are always larger than W histograms, and an REM histogram can resemble either. In other words, the optic nerve response to a given stimulus is labile; its configuration depends on whether the rat is asleep or awake. We link this physiological information with the anatomical fact that the brain dorsal raphe region, which is known to have a sleep regulatory role, sends fibers to the rat retina and receives fibers from it. At the cortical electrode, the visual cortical response amplitudes also vary, being largest during SWS. This well known phenomenon often is explained by changes taking place at the thalamic level. However, in the rat, the labile cortical response covaries with the labile optic nerve response, which suggests the cortical response enhancement during SWS is determined more by what happens in the retina than by what happens in the thalamus.

Synechocystis HSP17 is an amphitropic protein that stabilizes heat-stressed membranes and binds denatured proteins for subsequent chaperone-mediated refolding

The small heat shock proteins (sHSPs) are ubiquitous stress proteins proposed to act as molecular chaperones to prevent irreversible protein denaturation. We characterized the chaperone activity of Synechocystis HSP17 and found that it has not only protein-protective activity, but also a previously unrecognized ability to stabilize lipid membranes. Like other sHSPs, recombinant Synechocystis HSP17 formed stable complexes with denatured malate dehydrogenase and served as a reservoir for the unfolded substrate, transferring it to the DnaK/DnaJ/GrpE and GroEL/ES chaperone network for subsequent refolding. Large unilamellar vesicles made of synthetic and cyanobacterial lipids were found to modulate this refolding process. Investigation of HSP17-lipid interactions revealed a preference for the liquid crystalline phase and resulted in an elevated physical order in model lipid membranes. Direct evidence for the participation of HSP17 in the control of thylakoid membrane physical state in vivo was gained by examining an hsp17− deletion mutant compared with the isogenic wild-type hsp17+ revertant Synechocystis cells. We suggest that, together with GroEL, HSP17 behaves as an amphitropic protein and plays a dual role. Depending on its membrane or cytosolic location, it may function as a “membrane stabilizing factor” as well as a member of a multichaperone protein-folding network. Membrane association of sHSPs could antagonize the heat-induced hyperfluidization of specific membrane domains and thereby serve to preserve structural and functional integrity of biomembranes.

Otimização do método lignina brometo de acetila na determinação do teor de lignina em plantas forrageiras e comparação com os métodos lignina detergente ácido e lignina Klason

Técnicas analíticas empregadas para a quantificação do teor de lignina em plantas forrageiras, atualmente em uso, são questionáveis quanto às suas acurácias. O método lignina detergente ácido (LDA), que é um dos métodos mais utilizado em Ciência Animal e Agronomia, apresenta algumas falhas, particularmente devido à parcial solubilização da lignina durante a preparação da fibra em detergente ácido (FDA). A lignina Klason (LK), outro método muito usado, apresenta o inconveniente de mensurar a proteína da parede celular como sendo lignina. Em ambos os procedimentos recomenda-se também mensurar cinzas nos resíduos de lignina. A quantificação da concentração de lignina pelo método espectrofotométrico lignina brometo de acetila (LBA) vem ganhando interesse de pesquisadores no Brasil e no exterior. Nesta metodologia, a lignina da planta contida na preparação parede celular (PC) é solubilizada numa solução a 25% de brometo de acetila em ácido acético e a absorbância mensurada é com luz UV a 280 nm. O valor da absorbância é inserido numa equação de regressão e a concentração de lignina é obtida. Para que esta técnica analítica seja mais aceita pelos pesquisadores, ela deve ser, obviamente, convincente e atrativa. O presente trabalho analisou alguns parâmetros relacionados à LBA em 7 gramíneas e 6 leguminosas, em dois estádios de maturidade. Dentre as diferentes temperaturas de pré-secagem, os resultados indicaram que os procedimentos de 55°C com ventilação e liofilização podem ser utilizados com a mesma eficácia. As temperaturas de 55°C sem ventilação e 80°C sem ventilação não são recomendadas, pois aumentaram os valores de FDA e LDA, possivelmente devido ao surgimento de artefatos de técnica como os compostos de Maillard. No método LBA os valores menores das amostras de leguminosas chamaram a atenção e colocaram em questão se a lignina destas plantas seria menos solúvel no reagente brometo de acetila. Dentre algumas alterações na metodologia da técnica LBA, a utilização do moinho de bolas (para diminuir o tamanho particular) nas amostras de PC não mostrou efeito; a hipótese era melhorar a solubilização da lignina usando partículas menores. O uso de um ultrasonicador, que aumenta a vibração das moléculas e assim, facilitaria a solubilização da lignina no reagente brometo de acetila, melhorou a solubilização da lignina em cerca de 10%, tanto nas gramíneas como nas leguminosas. Foi acoplado um ensaio biológico como referência, a degradabilidade in vitro da matéria seca (DIVMS); e como a lignina está intimamente associada à estrutura fibrosa da parede celular, também foi feito um ensaio de degradabilidade in vitro da fibra em detergente neutro (DIVFDN). Os resultados confirmaram o efeito da maturidade, reduzindo a degradabilidade nas plantas mais maduras, e que o teor de lignina de leguminosas é realmente inferior ao de gramíneas. Os resultados de degradabilidade apresentaram coeficientes de correlação mais elevados com o método LBA, quando foi empregada a técnica do ultrasom; o método LK mostrou os menores coeficientes. Também testou-se, com sucesso, a utilização da FDN, como preparação fibrosa, ao invés de PC. A razão é simples: enquanto que a FDN é amplamente conhecida, a preparação PC não o é. Inquestionável que esta manobra facilitará substancialmente a divulgação desse método, tornando-a mais aceitável pela comunidade científica

al- Taṣrīḥ bi-ghawāmiḍ al-Talwīḥ : manuscript, undated

Title from f. 1r.

Forecasting migration between the EU, V4 and Eastern Europe. Impact of visa abolition. OSW Report, July 2014

This book is the result of one year of solid work among a multinational research team assembled from seven states (Poland, Czechia, Hungary, Slovakia, Ukraine, Belarus and Moldova). It aims at a detailed analysis of migration patterns and migration forecasts from Ukraine, Belarus and Moldova to the EU/V4. In particular, the nexus between EU visa policy and migration dynamics as well as the impact of economic, political and institutional factors on migration from Eastern Europe have been investigated. The importance of migration policy must be stressed here. Together with demand for the foreign labour force (labour market needs, level of wages, existing work opportunities) and migration networks (including ethnic links), migration policy has a powerful influence on the scale, directions and characteristics of human flows.

Measuring competitiveness in Europe: resource allocation, granularity and trade. Bruegel Blueprint Series Volume XVIV, January 2016

One of the most important lessons learned during the 2008-09 financial crisis was that the informational toolbox on which policymakers base their decisions about competitiveness became outdated in terms of both data sources and data analysis. The toolbox is particularly outdated when it comes to tapping the potential of micro data for the analysis of competitiveness – a serious problem given that it is firms, rather than countries that compete on global markets.

New insights into basophil heterogeneity.

Basophils have become increasingly recognized as important innate immune cells that mediate antihelminth immunity and barrier inflammation. Recent discoveries have uncovered previously unrecognized heterogeneity in basophil populations. However, how diversity in basophil regulation and function impacts human disease remains poorly defined. The goal of the present review is to highlight how new insights into basophil heterogeneity can help us to better understand disease pathogenesis and inform the development of new therapeutics.

Observation of manganese deposits made during the 1936 transect of C/S Lord Kelvin through the Northern Atlantic Ocean

In May and June 1936 Dr. C. S. Piggot of the Geophysical Laboratory, Carnegie Institution of Washington, took a series of 11 deep-sea cores in the North Atlantic Ocean between the Newfoundland banks and the banks off the Irish coast. These cores were taken from the Western Union Telegraph Co.'s cable ship Lord Kelvin with the explosive type of sounding device which Dr. Piggot designed. All but two of these cores (Nos. 8 and 11) are more than 2.43 meters (8 feet) long, and all contain ample material for study. Of the two short cores, No. 8 was taken from the top of the Faraday Hills, as that part of the mid-Atlantic ridge is known, where the material is closely packed and more sandy and consequently more resistant; No. 11 came from a locality where the apparatus apparently landed on volcanic rock that may be part of a submarine lava flow.

Cleveland neighborhood elderly transportation demonstration project. Final report.

Transportation Systems Center, Cambridge, Mass.

Peccati exterminium maximè ad quod natura vel consuetudo magis inclinat Dominis sodalibus congregationis Majoris Academicae Dilinganae in Xenium oblatum.

Mode of access: Internet.

Abdülhakim Siyalkuti hazretlerinin Şerh-i akaid Hayalisi ... [microform]

Lithograph.