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.

A novel set of DIP-STR markers for improved analysis of challenging DNA mixtures.

Currently available molecular biology tools allow forensic scientists to characterize DNA evidence found at crime scenes for a large variety of samples, including those of limited quantity and quality, and achieve high levels of individualization. Yet, standard forensic markers provide limited or no results when applied to mixed DNA samples where the contributors are present in very different proportions (unbalanced DNA mixtures). This becomes an issue mostly for the analysis of trace samples collected on the victim or from touched objects. To this end, we recently proposed an innovative type of genetic marker, named DIP-STR that relies on pairing deletion/insertion polymorphisms (DIP) with standard short tandem repeats (STR). This novel compound marker allows detection of the minor DNA contributor in a DNA mixture of any gender and cellular origin with unprecedented resolution (beyond a DNA ratio of 1:1000). To provide a novel analytical tool useful in practice to common forensic laboratories, this article describes the first set of 10 DIP-STR markers selected according to forensic technical standards. The novel DIP-STR regions are short (between 146 and 271 bp), include only highly polymorphic tri-, tetra- and pentanucleotide tandem repeats and are located on different chromosomes or chromosomal arms to provide statistically independent results. This novel set of DIP-STR can target the amplification of 0.03-0.1 ng of DNA when mixed with a 1000-fold excess of major DNA. DIP-STR relative allele frequencies are estimated based on a survey of 103 Swiss individuals. Finally, this study provides an estimate of the occurrence of informative alleles and a calculation of the corresponding random match probability of the detected minor DIP-STR genotype assessed across 10,506 pairwise conceptual mixtures.

Synthesis of Janus compounds for the recognition of G-U mismatched nucleobase pairs

The design and synthesis of two Janus-type heterocycles with the capacity to simultaneously recognize guanine and uracyl in G-U mismatched pairs through complementary hydrogen bond pairing is described. Both compounds were conveniently functionalized with a carboxylic function and efficiently attached to a tripeptide sequence by using solid-phase methodologies. Ligands based on the derivatization of such Janus compounds with a small aminoglycoside, neamine, and its guanidinylated analogue have been synthesized, and their interaction with Tau RNA has been investigated by using several biophysical techniques, including UV-monitored melting curves, fluorescence titration experiments, and 1H NMR. The overall results indicated that Janus-neamine/guanidinoneamine showed some preference for the +3 mutated RNA sequence associated with the development of some tauopathies, although preliminary NMR studies have not confirmed binding to G-U pairs. Moreover, a good correlation has been found between the RNA binding affinity of such Janus-containing ligands and their ability to stabilize this secondary structure upon complexation.

Design and Validation of a Novel Generic Platform for the Production of Tetravalent IgG1-like Bispecific Antibodies.

We have designed and validated a novel generic platform for production of tetravalent IgG1-like chimeric bispecific Abs. The VH-CH1-hinge domains of mAb2 are fused through a peptidic linker to the N terminus of mAb1 H chain, and paired mutations at the CH1-CL interface mAb1 are introduced that force the correct pairing of the two different free L chains. Two different sets of these CH1-CL interface mutations, called CR3 and MUT4, were designed and tested, and prototypic bispecific Abs directed against CD5 and HLA-DR were produced (CD5xDR). Two different hinge sequences between mAb1 and mAb2 were also tested in the CD5xDR-CR3 or -MUT4 background, leading to bispecific Ab (BsAbs) with a more rigid or flexible structure. All four Abs produced bound with good specificity and affinity to CD5 and HLA-DR present either on the same target or on different cells. Indeed, the BsAbs were able to efficiently redirect killing of HLA-DR(+) leukemic cells by human CD5(+) cytokine-induced killer T cells. Finally, all BsAbs had a functional Fc, as shown by their capacity to activate human complement and NK cells and to mediate phagocytosis. CD5xDR-CR3 was chosen as the best format because it had overall the highest functional activity and was very stable in vitro in both neutral buffer and in serum. In vivo, CD5xDR-CR3 was shown to have significant therapeutic activity in a xenograft model of human leukemia.

Preconcentration of copper from natural water samples using ligand-less in situ surfactant-based solid phase extraction prior to FAAS determination

In the present work, a simple and rapid ligand-less, in situ, surfactant-based solid phase extraction for the preconcentration of copper in water samples was developed. In this method, a cationic surfactant (n-dodecyltrimethylammonium bromide) was dissolved in an aqueous sample followed by the addition of an appropriate ion-pairing agent (ClO4-). Due to the interaction between the surfactant and ion-pairing agent, solid particles were formed and subsequently used for the adsorption of Cu(OH)2 and CuI. After centrifugation, the sediment was dissolved in 1.0 mL of 1 mol L-1 HNO3 in ethanol and aspirated directly into the flame atomic absorption spectrometer. In order to obtain the optimum conditions, several parameters affecting the performance of the LL-ISS-SPE, including the volumes of DTAB, KClO4, and KI, pH, and potentially interfering ions, were optimized. It was found that KI and phosphate buffer solution (pH = 9) could extract more than 95% of copper ions. The amount of copper ions in the water samples varied from 3.2 to 4.8 ng mL-1, with relative standard deviations of 98.5%-103%. The determination of copper in water samples was linear over a concentration range of 0.5-200.0 ng mL-1. The limit of detection (3Sb/m) was 0.1 ng mL-1 with an enrichment factor of 38.7. The accuracy of the developed method was verified by the determination of copper in two certified reference materials, producing satisfactory results.

Effects of interband and intraband impurity scattering on coherence length in the pnictide superconductors

After discovery of cuprates, a search for new high temperature superconducting families began and it led to the discovery of layered pnictide compounds with critical temperatures limited up to ∼56 K. Pnictides consist elements from Group V of Periodic Table (nitrogen, phosphorus, arsenic, antimony and bismuth). In this work coherence length h in mixed state of pnictide superconductors is calculated numerically. In calculation is taken into account interband and intraband impurity scattering in framework of quasiclassical Eilenberger theory for s± pairing symmetry. Differences between Ginzburg-Landau and Eilenberger theories is shown and the comparison with existing models is done.

Effects of interband and intraband impurity scattering on coherence length in the pnictide superconductors

After discovery of cuprates, a search for new high temperature superconducting families began and it led to the discovery of layered pnictide compounds with critical temperatures limited up to ~56 K. Pnictides consist elements from Group V of Periodic Table (nitrogen, phosphorus, arsenic, antimony and bismuth). In this work coherence length ξh in mixed state of pnictide superconductors is calculated numerically. In calculation is taken into account interband and intraband impurity scattering in framework of quasiclassical Eilenberger theory for s± pairing symmetry. Differences between Ginzburg-Landau and Eilenberger theories is shown and the comparison with existing models is done.

Determination of Alkalinity and dissociation constants of high salinity waters: use of F5BC titration function

Measurements of parameters expressed in terms of carbonic species such as Alkalinity and Acidity of saline waters do not analyze the influence of external parameters to the titration such as Total free and associated Carbonic Species Concentration, activity coefficient, ion pairing formation and Residual Liquid Junction Potential in pH measurements. This paper shows the development of F5BC titration function based on the titrations developed by Gran (1952) for the carbonate system of natural waters. For practical use, samples of saline waters from Pocinhos reservoir in Paraiba were submitted to titration and linear regression analysis. Results showed that F5BC involves F1x and F2x Gran functions determination, respectively, for Alkalinity and Acidity calculations without knowing "a priori" the endpoint of the titration. F5BC also allows the determination of the First and Second Apparent Dissociation Constant of the carbonate system of saline and high ionic strength waters.

Quasiclassical Approach to the Vortex State in Iron-based Superconductors

The quasiclassical approach was applied to the investigation of the vortex properties in the ironbased superconductors. The special attention was paid to manifestation of the nonlocal effects of the vortex core structure. The main results are as follows: (i) The effects of the pairing symmetries (s+ and s₊₊) on the cutoff parameter of field distribution, ξh, in stoichiometric (like LiFeAs) and nonstoichiometric (like doped BaFe₂As₂) iron pnictides have been investigated using Eilenberger quasiclassical equations. Magnetic field, temperature and impurity scattering dependences of ξh have been calculated. Two opposite behavior have been discovered. The ξh /ξc2 ratio is less in s+ symmetry when intraband impurity scattering (Γ₀) is much larger than one and much larger than interband impurity scattering (Γπ), i.e. in nonstoichiometric iron pnictides. Opposite, the value ξh /ξc2 is higher in s+ case and the field dependent curve is shifted upward from the "clean" case (Γ₀ = Γπ = 0) for stoichiometric iron pnictides (Γ₀ = Γπ ≪ 1). (ii) Eilenberger approach to the cutoff parameter, ξh, of the field distribution in the mixed state of high

Gravidez e Diabetes Gestacional: uma combinação prejudicial à função sexual feminina?

OBJETIVO: Comparar a funcao sexual de gravidas adultas saudaveis a de mulheres com Diabetes Mellitus Gestacional (DMG) no terceiro trimestre da gravidez. MÉTODOS: Estudo transversal com dois grupos de gestantes em acompanhamento pre-natal. Foram criterios de inclusao: idade materna .20 anos, idade gestacional .28 semanas, relacionamento heterossexual com o mesmo parceiro ha pelo menos 6 meses e ser alfabetizada. Os criterios de exclusao foram: presenca de intercorrencias clinicas e/ou obstetricas que contraindicassem atividade sexual; hipertensao arterial controlada por medicamentos; gravidez resultante de estupro; parceiro sexualmente indisponivel ou ausente no ultimo mes; internacao hospitalar no ultimo mes; uso de cremes vaginais nos ultimos 30 dias; gestacao gemelar; uso regular de alcool e/ou drogas ilicitas; uso de medicamentos que interferissem na funcao sexual. Oitenta e sete pacientes preencheram os criterios de selecao e participaram do estudo. Para avaliacao da funcao sexual destes grupos utilizou-se o questionario Quociente Sexual . Versao Feminina (QS-F). Testes X² e t de Student foram utilizados para comparar diferencas entre os grupos, com valores p<0,05 considerados estatisticamente significantes. A analise estatistica foi realizada com o software Instat 3. RESULTADOS: A idade gestacional media nos dois grupos era de 34 semanas. Nao foram detectadas diferencas significantes nos escores medios totais do QS-F nos dois grupos (62,5 saudaveis vs 62,8 DMG, p=0,9). Aproximadamente metade das participantes (47 e 47,5% das saudaveis e DMG, respectivamente, p=0,9) teve escores totais de ate 60 na escala do QS-F, o que indica comprometimento em algum dos dominios avaliados (desejo e satisfacao sexual, excitacao, orgasmo, dispareunia e vaginismo). CONCLUSÕES: A prevalencia de comprometimento do desempenho sexual foi alta em gestantes no terceiro trimestre, nao diferindo significativamente entre mulheres saudaveis e aquelas com DMG.

Individual dietary counselling during and after pregnancy: Impact on diet and body weight

In Finland, maternity and child health clinics play a key role in promoting health in young families. Currently, obesity causes the greatest challenges to clinics. In obese pregnant women, an increased risk for metabolic diseases exist which can affect both the mother and child. The purpose of this thesis was to explore the role of dietary counselling: in Finnish health clinics; in the regulation of dietary intake; and in affecting the body weight of women. The main aim was to test the effect of dietary counselling and probiotic intervention on dietary intake and maternal body weight during and after pregnancy. In addition to dietary counselling, the effect of other factors, such as eating behaviour on dietary intake and body weight control after pregnancy was assessed. Another aim was also to evaluate dietary counselling practices by nurses (n = 327) in Finnish health clinics assessed by a questionnaire. At the beginning of the pregnancy, women (n = 256) enrolled in a dietary intervention study, were randomised into three groups. One group received dietary counselling with probiotics, one had counselling with placebo and the third group was the control group. The control group consisted of women whom did not receive counselling and took placebo. Probiotics and placebo supplements were used until the end of exclusive breastfeeding or six months after pregnancy. Women were followed from early pregnancy up to four years after pregnancy. Follow-up visits took place three times during pregnancy, at one and six months, and one, two and four years after pregnancy. Dietary counselling, provided by a nutritionist, aimed to influence the quality of dietary fat intake. Dietary counselling is important to provide in clinics, as determined by the nurses, and these nurses expressed a want to improve their own nutritional knowledge through education. The nurses had varying knowledge of current dietary recommendations. Dietary counselling for women during and after pregnancy resulted in beneficial changes in dietary intake up to one year after pregnancy and body weight and waist circumference up to four years after pregnancy. Probiotics had a beneficial effect together with dietary counselling on waist circumference until one year after pregnancy, but not throughout the long term, four years after pregnancy. Other factors, such as eating behaviour, associated with dietary intake and body weight control after pregnancy. Specifically, dietary recommendations are reached amongst women whom had high cognitive restraint in their eating behaviour and did not demonstrate uncontrolled eating. Overweight women more frequently emotionally ate compared to normal weight women and women with central adiposity related more frequently to having an uncontrolled eating behaviour than women with normal waist circumference. In addition, being overweight prior to pregnancy and excessive weight gain during pregnancy associated with increased body weight retention after pregnancy. This study showed that individual dietary counselling is useful in influencing dietary intake which adheres to dietary recommendations and this counselling influences, favourably, body weight after pregnancy. Especially, women with the risk for weight retention, such as women who have emotional and uncontrolled eating behaviours, who were overweight prior to pregnancy or those who had excessive weight gain during pregnancy, may benefit from individual dietary counselling. This study underscores the need to develop dietary counselling practices for pregnant women and their follow-up after pregnancy in Finnish health clinics. These practices include increasing the efficacy of the counselling such as collaboration with families, having knowledgable health professionals and having sufficient resources.

Conditioned food aversion to Ipomoea carnea var. fistulosa induced by Baccharis coridifolia in goats

Baccharis coridifolia is a plant that induces strong conditioned food aversion in ruminants. This research aimed to induce a conditioned food aversion to Ipomoea carnea var. fistulosa in goats, using B. coridifolia as an aversive agent, and to compare the aversion induced by this plant with the aversion induced by lithium chloride (LiCl). Thirteen goats were allotted into two groups: Group 1 with six goats was averted with 175mg/kg of body weight of LiCl and Group 2 with seven goats was averted with 0,25g/kg of bw of dried B. coridifolia. All goats were averted on day 1 after the ingestion of I. carnea. The aversion procedure with LiCl or B. coridifolia in goats from Groups 1 and 2, respectively, was repeated in those goats that again consumed the plant during tests on days 2, 3, and 7. The goats of both groups were challenged in pens on 23 and 38 days after the last day of aversion and challenged in the pasture on days 11, 15, 18, 20, 22, 25, 27 and 29 after the last day of aversion. After this period goats were challenged every 15 days on pasture until the 330º day after the last day of aversion (7th day). Two goats from Group 1 ingested I. carnea on the first day of the pasture challenge, 4 days after the last day of aversive conditioning in the pen. In addition, another goat in Group 1 started to consume the plant on day 18, and other two goats ate it on day 20. One goat in Group 1 that had never eaten I. carnea died on day 155. One goat from Group 2 started to ingest I. carnea on the first day of the pasture challenge, and a second goat started to consume this plant on day 182. At the end of the experiment, on day 330, the other five goats averted with B. coridifolia remained averted. These results suggest that B. coridifolia or an active compound from the plant could be used to induce aversion to toxic plants. Using B. coridifolia would be cheaper and, particularly in flocks with large number of animals, possibly easier than using LiCl, which requires the use of oral gavage and qualified personnel for its implementation.

Dynamics of coherent vortices in mixing layers using direct numerical and large-eddy simulations

Coherent vortices in turbulent mixing layers are investigated by means of Direct Numerical Simulation (DNS) and Large-Eddy Simulation (LES). Subgrid-scale models defined in spectral and physical spaces are reviewed. The new "spectral-dynamic viscosity model", that allows to account for non-developed turbulence in the subgrid-scales, is discussed. Pseudo-spectral methods, combined with sixth-order compact finite differences schemes (when periodic boundary conditions cannot be established), are used to solve the Navier- Stokes equations. Simulations in temporal and spatial mixing layers show two types of pairing of primary Kelvin-Helmholtz (KH) vortices depending on initial conditions (or upstream conditions): quasi-2D and helical pairings. In both cases, secondary streamwise vortices are stretched in between the KH vortices at an angle of 45° with the horizontal plane. These streamwise vortices are not only identified in the early transitional stage of the mixing layer but also in self-similar turbulence conditions. The Re dependence of the "diameter" of these vortices is analyzed. Results obtained in spatial growing mixing layers show some evidences of pairing of secondary vortices; after a pairing of the primary Kelvin-Helmholtz (KH) vortices, the streamwise vortices are less numerous and their diameter has increased than before the pairing of KH vortices.

Controle de plantas daninhas com cyanazine aplicado em mistura com outros herbicidas, na cultura do algodão (Gossypium hirsutum L.)

Com a finalidade de estudar a mistura de tanque mais eficiente com cyanazine em aplicação de pré-emergência na cultura algodoeira (Gossypium hirsutum L.) , foram estudados os seguintes tratamentos: cyanazine + diuron nas doses de 0,8 + 0,8 kg i.a/ha e 1,0 + 1,0 kg i.a/ha; cyanazine+ oryzalin , nas do sés de 1,2 + 0,8 kg i.a/ha e 1,6 + 1,2 kg i.a/h a; cyanazyne + metol a chlor, nas doses de 1,4 + 2,0 kg i.a/ha e 1,75 + 2,52 kg i.a/ ha;cianazine na dose de 1,75 kg i.a /ha; oryzalin na dose de 1,12 kg i.a/ha; metol achlor na dose de 2,52 kg i.a /ha e diuron na dose de 1,6 kg i.a /ha. Para efeito de comparação, utilizou-se uma testemunha sem capina e outra com capina manual. Nenhum tratamento apresentou injúria para as plantas de algodão e não houve diferenças significativas para o "stand" inicial. Já no "stand" final, a testemunha sem capina apresentou o menor número de plantas, sendo que não houve diferenças significativas dos outros tratamentos com a testemunha capinada. Para o rendimento, a mistura cyanazine + metolachior em ambas as doses estudadas, não apresentaram diferenças significativas da testemunha capinada. Quanto à altura da planta, peso de 100 sementes, porcentagem e índice de fibras não houve diferenças significativas entre os tratamentos estudados, somente o peso do capulho foi afetado pelo oryzalin. Pela avaliação visual (EWRC 1 a 9)*, os herbicidas apres entaram um controle satisfatório somente até os 30 dias após aplicação, sendo que a mistura cyanazine + metolachlor foi efici ente quanto a testemunha capinada. No controle da Portulaca oleracea , a mistura cyanazine + oryzalin na maior dose e oryzalin apresentaram 71,4% de controle ate os 30 dias e 79,4% e 82,4%, respectivamente, até 45 dias da aplicação. Para Amaranthus sp., à exceção da cyanazine e cyanazine + diuron nas doses menores, não apresentaram nenhum controle, sendo que os outros herbicidas controlaram com eficiência superior a 70%. Para Centratherium punctatum, o cyanazine apresentou 78,2% e 73,4%, respectivamente, após 50 e 45 dias da aplicação. Para Cyperus sp e & Brachiaria plantaginea, o metolachlor sozinho ou em mistura com cyanazine, apresentou uma eficiência de 90% para Cyperus sp. e de 70% para B. plantaginea até 45 dias da aplicação. Para as espécies não dominantes (maioria dicotiledôneas), o melhor controle foi de cyanazine + metol achlor na dose maior, com 70,5% e 60,2%, respectivamente, após 30 e 45 dias da aplicação. Para o total das espécies, cyanazine + metolachlor, em ambas doses estudadas, apresentaram controle de 66,2% e 67,3%, respectivamente, após 30 dias e 63,3% e 64,3%, respectivamente, após 45 dias da aplicação. Para as análises tecnológicas da fibra, não houve diferenças significativas na maturação da fibra, uniformidade de comprimento, índice Macronaire e índice Pressley. No comprimento da fibra, a mistura de cyanazine + diuron(0,8+ 0,8 kg ia/h a), apresentou o maior comprimento (26,1 mm) e cyanazine+ metol achlor (1,75 + 2,52 kg i.a / ha),o menor comprimento (24,9 mm), sem diferenças significativas com as testemunhas.

Persistent attenuation and enhancement of the earthworm main muscle contraction generator response induced by repeated stimulation of a peripheral neuron

Responses evoked in the earthworm, Amynthas hawayanus, main muscle contraction generator M-2 (postsynaptic mechanical-stimulus-sensitive) neuron by threshold mechanical stimuli in 2-s intertrial intervals (ITI) were used as the control or unconditioned responses (UR). Their attenuation induced by decreasing these intervals in non-associative conditioning and their enhancement induced by associating the unconditioned stimuli (US) to a train of short (0.1 s) hyperpolarizing electrical substitutive conditioning stimuli (SCS) in the Peri-Kästchen (PK) neuron were measured in four parameters, i.e., peak numbers (N) and amplitude ()averaged from 120 responses, sum of these amplitudes (SAMP) and the highest peak amplitude (V) over a period of 4 min. Persistent attenuation similar to habituation was induced by decreasing the control ITI to 0.5 s and 2.0 s in non-associative conditioning within less than 4 min. Dishabituation was induced by randomly pairing one of these habituated US to an electrical stimulus in the PK neuron. All four parameters of the UR were enhanced by forward (SCS-US), but not backward (US-SCS), association of the US with 25, 100 and 250-Hz trains of SCS with 40-ms interstimulus intervals (ISI) for 4 min and persisted for another 4 min after turning off the SCS. The enhancement of these parameters was proportional to the SCS frequencies in the train. No UR was evoked by the SCS when the US was turned off after 4 min of classical conditioning.