Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.

First principles analysis of the stability and diffusion of oxygen vacancies in meetal oxides

Oxygen vacancies in metal oxides are known to determine their chemistry and physics. The properties of neutral oxygen vacancies in metal oxides of increasing complexity (MgO, CaO, alpha-Al2O3, and ZnO) have been studied using density functional theory. Vacancy formation energies, vacancy-vacancy interaction, and the barriers for vacancy migration are determined and rationalized in terms of the ionicity, the Madelung potential, and lattice relaxation. It is found that the Madelung potential controls the oxygen vacancy properties of highly ionic oxides whereas a more complex picture arises for covalent ZnO.

Oxygen vacancies as active sites for water dissociation on rutile TiO2(110)

Through an interplay between scanning tunneling microscopy experiments and density functional theory calculations, we determine unambiguously the active surface site responsible for the dissociation of water molecules adsorbed on rutile TiO2(110). Oxygen vacancies in the surface layer are shown to dissociate H2O through the transfer of one proton to a nearby oxygen atom, forming two hydroxyl groups for every vacancy. The amount of water dissociation is limited by the density of oxygen vacancies present on the clean surface exclusively. The dissociation process sets in as soon as molecular water is able to diffuse to the active site.

Bonding of gold nanoclusters to oxygen vacancies on rutile TiO2(110)

Through an interplay between scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, we show that bridging oxygen vacancies are the active nucleation sites for Au clusters on the rutile TiO2(110) surface. We find that a direct correlation exists between a decrease in density of vacancies and the amount of Au deposited. From the DFT calculations we find that the oxygen vacancy is indeed the strongest Au binding site. We show both experimentally and theoretically that a single oxygen vacancy can bind 3 Au atoms on average. In view of the presented results, a new growth model for the TiO2(110) system involving vacancy-cluster complex diffusion is presented.

The role of geography and ecology in shaping repeated patterns of morphological and genetic differentiation between European minnows (Phoxinus phoxinus) from the Pyrenees and the Alps

Neutral and selective processes c an drive repeated patterns of evolu tion in dif ferent groups of populationsexp eriencing similar ecol ogica l gradients. In this paper, we used a combinat ion of nucl ear and mitochondrialDNA markers, as well as geometric morphometrics, to investigate repeated patterns of morphological andgenetic divergence of E uropean minnows in two mountain ranges : the Pyrenees and the Al ps. Europeanminnows (Phoxinus phoxinus) are cyprinid fish i nha bitin g most freshwater bodies in Europe, including those indifferent mountain r anges that could act as major geographical barriers to gene flow. We explored patterns ofP. phoxinus phenotypic and genetic di versi fication along a gradi ent of alti tude common to the two mountainranges, and tested for isolation by distance (IBD), isolation by environment (IBE) and isolation by adaptation(IBA). The results indicated that populations from the Pyr enees a nd the Alps bel ong to two well differentiated,reciprocally monophyletic mt DNA lineages. Substantial genetic differentiation due to geographical isolationwithin and between populations from the Pyrenees and the Alps was also found using rapidly evolving AFLPsmarkers (isolation by distance or IBD), as well as morphological differences between mountain ranges. Als o,morphology varied strong ly with elevation and so did genetic differentiation to a lower extent. Despitemoderate evidence for IBE and IBA, and therefore of repeated evolution, substantial population heterogeneitywas found at the genetic level, suggesting that selection and population specific genetic drift act in concert toaffect genetic divergence.

Store-operated Ca2+ Entry Mediated by Orai1 and TRPC1 Participates to Insulin Secretion in Rat β-Cells.

Store-operated Ca(2+) channels (SOCs) are voltage-independent Ca(2+) channels activated upon depletion of the endoplasmic reticulum Ca(2+) stores. Early studies suggest the contribution of such channels to Ca(2+) homeostasis in insulin-secreting pancreatic β-cells. However, their composition and contribution to glucose-stimulated insulin secretion (GSIS) remains unclear. In this study, endoplasmic reticulum Ca(2+) depletion triggered by acetylcholine (ACh) or thapsigargin stimulated the formation of a ternary complex composed of Orai1, TRPC1, and STIM1, the key proteins involved in the formation of SOCs. Ca(2+) imaging further revealed that Orai1 and TRPC1 are required to form functional SOCs and that these channels are activated by STIM1 in response to thapsigargin or ACh. Pharmacological SOCs inhibition or dominant negative blockade of Orai1 or TRPC1 using the specific pore mutants Orai1-E106D and TRPC1-F562A impaired GSIS in rat β-cells and fully blocked the potentiating effect of ACh on secretion. In contrast, pharmacological or dominant negative blockade of TRPC3 had no effect on extracellular Ca(2+) entry and GSIS. Finally, we observed that prolonged exposure to supraphysiological glucose concentration impaired SOCs function without altering the expression levels of STIM1, Orai1, and TRPC1. We conclude that Orai1 and TRPC1, which form SOCs regulated by STIM1, play a key role in the effect of ACh on GSIS, a process that may be impaired in type 2 diabetes.

Prognostic Importance of the Cuse of Renal Failure in Patients With Cirrhosis

BACKGROUND & AIMS: The prognostic value of the different causes of renal failure in cirrhosis is not well established. This study investigated the predictive value of the cause of renal failure in cirrhosis. METHODS: Five hundred sixty-two consecutive patients with cirrhosis and renal failure (as defined by serum creatinine 1.5 mg/dL on 2 successive determinations within 48 hours) hospitalized over a 6-year period in a single institution were included in a prospective study. The cause of renal failure was classified into 4 groups: renal failure associated with bacterial infections, renal failure associated with volume depletion, hepatorenal syndrome (HRS), and parenchymal nephropathy. The primary end point was survival at 3 months. RESULTS: Four hundred sixty-three patients (82.4%) had renal failure that could be classified in 1 of 4 groups. The most frequent was renal failure associated with infections (213 cases; 46%), followed by hypovolemia-associated renal failure (149; 32%), HRS (60; 13%), and parenchymal nephropathy (41; 9%). The remaining patients had a combination of causes or miscellaneous conditions. Prognosis was markedly different according to cause of renal failure, 3-month probability of survival being 73% for parenchymal nephropathy, 46% for hypovolemia-associated renal failure, 31% for renal failure associated with infections, and 15% for HRS (P .0005). In a multivariate analysis adjusted for potentially confounding variables, cause of renal failure was independently associated with prognosis, together with MELD score, serum sodium, and hepatic encephalopathy at time of diagnosis of renal failure. CONCLUSIONS: A simple classification of patients with cirrhosis according to cause of renal failure is useful in assessment of prognosis and may help in decision making in liver transplantation.

Cicloadições [3+4] via cátions oxialílicos: aplicações em sínteses orgânicas

Several methodologies for the generation of oxyallyl cations from polybromoketones and other substrates are discussed. The mechanistic aspect of the [3+4] cycloaddition reaction between these cations and dienes leading to the formation of seven membered ring carbocyclic compounds is presented. Finally, some synthetic applications of the [3+4] cycloaddition are shown.

Caracterização química e física de vermicomposto e avaliação de sua capacidade em adsorver cobre e zinco

The physical and chemical characterization of vermicompost from bovine manure has been studied. It was examined the pH and cation exchangeable capacity (CEC), organic matter content, electric conductivity and elementary and XRD analyses, among other characteristics. The vermicompost was then applied to the retention and competition of metal micronutrients and pollutants (Cu and Zn) from metal nitrate solutions. The retention was affected by both the pH and adsorption time, while the competitive character of these metals for the substrate was relevant to each pH examined.

Adsorção de íons Cu2+ em latossolo vermelho-amarelo húmico

In environmental studies it is necessary to know the adsorption behavior of metals by soils, since the unfavorable effects of heavy metals and even the micronutrients at high concentrations in the environment are related to these adsorbents' ability to immobilize them. A sample of a humic yellow red oxisol from Araponga region in the State of Minas Gerais, Brazil, was used to verify the adsorption behavior of Cu2+ ions in this substrate. The mathematical model described by Langmuir's adsorption equation in its linearized form was applied and the values of the maximum capacity b and those of the constant related to the bonding energy a were obtained. Aliquots of copper nitrate solutions containing several concentrations of this metal were added to soil samples, the pH being predetermined for developing the adsorption experiments. The chemical and physical characterization of soil sample were performed by determining the organic carbon, nitrogen and phosphorus concentrations, cation exchange capacity (CEC), pH, concentration of metals (Al, Fe, K, Mg, Ca, Zn, Cu, Ni, Cr, Co, Pb, and Cd), granulometric analysis and X-ray diffraction. Langmuir isotherms presented two distinct adsorption regions at both pH 4 and pH 5, showing that the adsorptive phenomenon occurs in two distinct stages. The adsorption sites for the lower part presented greater bonding energy and low adsorption capacity compared with the adsorption sites of the part of the curve corresponding to higher Cu concentrations in the equilibrating solution.

Kromatografinen erotus bioetanolin valmistuksessa lignoselluloosasta

Bioetanolin tuotanto kiinnostaa monissa maissa johtuen kansainvälisissä sopimuksissa määritellyistä ilmastotavoitteista. Työssä tutkittiin laboratorio-oloissa ioninvaihtohartsien ominaisuuksien ja erotuksen olosuhteiden vaikutusta rikkihapon ja glukoosin kromatografiseen erotukseen. Tehokkaimmaksi hartsiksi osoittautui polysulfonoitu mesohuokoinen vahva kationinvaihtohartsi Finex CS100C. CS100C:lla voitiin erottaa rikkihappoa ja glukoosia tehokkaimmin korkeissa 25 p-% ja 36 p-% glukoosi- ja rikkihappo-pitoisuuksissa. Lisäksi sillä havaittiin suurin tuotto simuloidussa liikkuvassa pedissä. Yhdessä kolonnissa suoritetuissa erotuskokeissa tutkittiin hartsien erotuskykyä rikkihapolle ja glukoosille sekä virtausnopeuden vaikutusta erotukseen lämpötilassa 22 °C. Saatujen tulosten pohjalta valittiin CS11GC, CS16GC ja CS100C tarkempaan isotermin määritykseen ja simulointiin hyvän erotuskyvyn sekä keskinäisten erojen takia. Adsorptioisotermit määritettiin kolonnikokein sekä 22 °C:n että 50 °C:n lämpötilassa. Isotermeistä havaittiin, että tasapaino kiinto- ja liuosfaasien välille saavutetaan rikkihapolla alhaisella 1 cm3/min virtausnopeudella varmemmin kuin suuremmalla 2,5 cm3/min virtausnopeudella. 50 °C:n lämpötilassa hapon ja glukoosin isotermit olivat jyrkempiä kuin 22 °C:n lämpötilassa. Määritettyihin hapon ja sokerin isotermeihin sovitettiin mallit, joiden parametreja käytettiin yksittäisen kolonnin simulointiin. Simuloinnissa oli estimoitavia parametreja yhdellä kolonnilla aineensiirtokertoimet sekä läpäisykäyristä määritetyt isotermiparametrit glukoosille sekä rikkihapolle ja SMB–erotuksessa vyöhykkeiden 2 ja 3 suhteelliset virtausnopeudet. Siirryttäessä lämpötilojen 22 °C ja 50 °C välillä hartsien parametrit muuttuivat sokerille täysin ja hapolle vain aineensiirtokertoimen osalta. CS100C oli tehokkain SMB–erotuksessa korkeimmalla 0,11 cm3/min tuottavuudella 95 %:n saannon saavuttamiseksi 95 % tuotepuhtaudella raffinaatissa ja ekstraktissa.

Uso do violeta de alizarina N (AVN) como reagente espectrofotométrico na determinação de alumínio

The present work proposes the application of the 4-Hidroxy-3-(2-hydroxynaphtylazo)-benzenesulphonic acid (C.I. 15670), Alizarine Violet N (AVN), as a reagent for direct aluminium determination using molecular absorption spectrophotometry in the presence of tensoatives. Al(III) cation reacts with AVN in pH 9.4, forming a red complex, stable for at least 24 hours, with absorption minimum at 607nm and, against a reagent blank, (epsiloncomplex - epsilonreagent) = -2.71x10(4) L.mol-1.cm-1. The reaction occurs in the presence of a Triton-X100 and CTAB tensoatives mixture, in the presence of EDTA. Al(III) determination is possible in the linear range of 50 up to 400ng.mL-1, with a detection limit of 41 ng.mL-1.

Síntese e atividade fitotóxica de 2-fenil-6,7-exo-isopropilidenodioxi-8-oxabiciclo [3.2.1]oct-2-eno

The [3+4] cycloaddition between furan and the oxyallyl cation generated from 1-bromo-1-phenylpropan-2-one (4), resulted in the formation of 2-phenyl-8-oxabicyclo[3.2.1]oct-6-en-3-one (5) in 30% yield. This compound was further converted into 2-phenyl-6,7-exo-isopropylidenedioxi-8-oxabicyclo[3.2.1]oct-2-ene (13) in 35.4% yield. The selective effect of compound (13) and its isomer 3-phenyl-6,7-exo-isopropylidenedioxi-8-oxabicyclo[3.2.1]oct -2-ene (1a) on the radicle growth of Sorghum bicolor L. (sorghum) and Cucumis sativus L. (cucumber) were evaluated. For both plants, compound 13 showed to be more potent than its isomer 1a.

O uso de sílica gel organofuncionalizada como agente sequestrante para metais

An overview about the homogeneous and heterogeneous methods of synthesizing silylating agents and applications of the organofunctionalized silica-gel samples was explored. The pendant molecules attached covalently to the inorganic surface displayed important properties to act as sequestrating agents for metals in aqueous and non-aqueous solutions. The large variety of basic centres anchored on organic molecules improve the capacity in adsorbing cations. The increase in adsorption is dependent on the number of basic atoms disposed on the pendant molecules on the surface. The combination of acidic and basicity properties favours the selectivity, such is exemplified by the thiol modified silicas towards mercury (II) cations.

Sobre a aplicabilidade da termogravimetria para a estimativa de parâmetros termoquímicos de compostos de coordenação: os elementos lantanídicos

By using thermochemical data reported for a series of chelates of the type [Ln(thd)3], thd = 2, 2, 6, 6 ­ tetramethyl- 3,5-heptanedione and Ln = La, Pr, Nd, Sm, Gd, Tb, Ho, Er, Tm and Yb, empirical correlations were found involving thermochemical parameters (e.g. dissociation enthalpy) and the thermodynamic temperatures of the beginning of thermal degradation of the chelates, t i. It is shown that t i values are of capital importance in the study of this all class of coordination compounds. Among others, the empirical equation is obtained: r3+ = (-0,013.Z + 1,36)/0,005, that relates the lanthanide cation radius (pm) with the atomic number of the element. The remarkable fact is that this equation is achieved by using thermogravimetric and calorimetric parameters. Is also shown that t i values are related with the P(M) function values, which are very close related with the energy difference, deltaE, between the lowest electronic energy level of the f n s²d¹ configuration and the lowest energy level of the f n+1s² configuration in the neutral gaseous atoms.