Visualizing Rare Watson-Crick-Like Tautomeric and Anionic Mismatches in DNA and RNA

The central dogma of molecular biology relies on the correct Watson-Crick (WC) geometry of canonical deoxyribonucleic acid (DNA) dG•dC and dA•dT base pairs to replicate and transcribe genetic information with speed and an astonishing level of fidelity. In addition, the Watson-Crick geometry of canonical ribonucleic acid (RNA) rG•rC and rA•rU base pairs is highly conserved to ensure that proteins are translated with high fidelity. However, numerous other potential nucleobase tautomeric and ionic configurations are possible that can give rise to entirely new pairing modes between the nucleotide bases. Very early on, James Watson and Francis Crick recognized their importance and in 1953 postulated that if bases adopted one of their less energetically disfavored tautomeric forms (and later ionic forms) during replication it could lead to the formation of a mismatch with a Watson-Crick-like geometry and could give rise to “natural mutations.”

Since this time numerous studies have provided evidence in support of this hypothesis and have expanded upon it; computational studies have addressed the energetic feasibilities of different nucleobases’ tautomeric and ionic forms in siico; crystallographic studies have trapped different mismatches with WC-like geometries in polymerase or ribosome active sites. However, no direct evidence has been given for (i) the direct existence of these WC-like mismatches in canonical DNA duplex, RNA duplexes, or non-coding RNAs; (ii) which, if any, tautomeric or ionic form stabilizes the WC-like geometry. This thesis utilizes nuclear magnetic resonance (NMR) spectroscopy and rotating frame relaxation dispersion (R1ρ RD) in combination with density functional theory (DFT), biochemical assays, and targeted chemical perturbations to show that (i) dG•dT mismatches in DNA duplexes, as well as rG•rU mismatches RNA duplexes and non-coding RNAs, transiently adopt a WC-like geometry that is stabilized by (ii) an interconnected network of rapidly interconverting rare tautomers and anionic bases. These results support Watson and Crick’s tautomer hypothesis, but additionally support subsequent hypotheses invoking anionic mismatches and ultimately tie them together. This dissertation shows that a common mismatch can adopt a Watson-Crick-like geometry globally, in both DNA and RNA, and whose geometry is stabilized by a kinetically linked network of rare tautomeric and anionic bases. The studies herein also provide compelling evidence for their involvement in spontaneous replication and translation errors.

Theranostic Fibers for Simultaneous Imaging and Drug Delivery

New methods for creating theranostic systems with simultaneous encapsulation of therapeutic, diagnostic, and targeting agents are much sought after. This work reports for the first time the use of coaxial electrospinning to prepare such systems in the form of core–shell fibers. Eudragit S100 was used to form the shell of the fibers, while the core comprised poly(ethylene oxide) loaded with the magnetic resonance contrast agent Gd(DTPA) (Gd(III) diethylenetriaminepentaacetate hydrate) and indomethacin as a model therapeutic agent. The fibers had linear cylindrical morphologies with clear core–shell structures, as demonstrated by electron microscopy. X-ray diffraction and differential scanning calorimetry proved that both indomethacin and Gd(DTPA) were present in the fibers in the amorphous physical form. This is thought to be a result of intermolecular interactions between the different components, the presence of which was suggested by infrared spectroscopy. In vitro dissolution tests indicated that the fibers could provide targeted release of the active ingredients through a combined mechanism of erosion and diffusion. The proton relaxivities for Gd(DTPA) released from the fibers into tris buffer increased (r1 = 4.79–9.75 s–1 mM–1; r2 = 7.98–14.22 s–1 mM–1) compared with fresh Gd(DTPA) (r1 = 4.13 s–1 mM–1 and r2 = 4.40 s–1 mM–1), which proved that electrospinning has not diminished the contrast properties of the complex. The new systems reported herein thus offer a new platform for delivering therapeutic and imaging agents simultaneously to the colon.

Proteomic analysis of coronary sinus serum reveals leucine-rich α2-glycoprotein as a novel biomarker of ventricular dysfunction and heart failure

BACKGROUND: Heart failure (HF) prevention strategies require biomarkers that identify disease manifestation. Increases in B-type natriuretic peptide (BNP) correlate with increased risk of cardiovascular events and HF development. We hypothesize that coronary sinus serum from a high BNP hypertensive population reflects an active pathological process and can be used for biomarker exploration. Our aim was to discover differentially expressed disease-associated proteins that identify patients with ventricular dysfunction and HF.

METHODS AND RESULTS: Coronary sinus serum from 11 asymptomatic, hypertensive patients underwent quantitative differential protein expression analysis by 2-dimensional difference gel electrophoresis. Proteins were identified using mass spectrometry and then studied by enzyme-linked immunosorbent assay in sera from 40 asymptomatic, hypertensive patients and 105 patients across the spectrum of ventricular dysfunction (32 asymptomatic left ventricular diastolic dysfunction, 26 diastolic HF, and 47 systolic HF patients). Leucine-rich α2-glycoprotein (LRG) was consistently overexpressed in high BNP serum. LRG levels correlate significantly with BNP in hypertensive, asymptomatic left ventricular diastolic dysfunction, diastolic HF, and systolic HF patient groups (P≤0.05). LRG levels were able to identify HF independent of BNP. LRG correlates with coronary sinus serum levels of tumor necrosis factor-α (P=0.009) and interleukin-6 (P=0.021). LRG is expressed in myocardial tissue and correlates with transforming growth factor-βR1 (P<0.001) and α-smooth muscle actin (P=0.025) expression.

CONCLUSIONS: LRG was identified as a serum biomarker that accurately identifies patients with HF. Multivariable modeling confirmed that LRG is a stronger identifier of HF than BNP and this is independent of age, sex, creatinine, ischemia, β-blocker therapy, and BNP.

LOTUS: A low cost, ultraviolet spectrograph

We describe the design, construction and commissioning of LOTUS; a simple, low-cost long-slit spectrograph for the Liverpool Telescope. The design is optimized for near-UV and visible wavelengths and uses all transmitting optics. It exploits the instrument focal plane field curvature to partially correct axial chromatic aberration. A stepped slit provides narrow (2.5x95 arcsec) and wide (5x25 arcsec) options that are optimized for spectral resolution and flux calibration respectively. On sky testing shows a wavelength range of 3200-6300 Angstroms with a peak system throughput (including detector quantum efficiency) of 15 per cent and wavelength dependant spectral resolution of R=225-430. By repeated observations of the symbiotic emission line star AG Peg we demonstrate the wavelength stability of the system is less than 2 Angstroms rms and is limited by the positioning of the object in the slit. The spectrograph is now in routine operation monitoring the activity of comet 67P/Churyumov-Gerasimenko during its current post-perihelion apparition.

Departure of high temperature iron lines from the equilibrium state in flaring solar plasmas

The aim of this study is to clarify if the assumption of ionization equilibrium and a Maxwellian electron energy distribution is valid in flaring solar plasmas. We analyze the 2014 December 20 X1.8 flare, in which the \ion{Fe}{xxi} 187~\AA, \ion{Fe}{xxii} 253~\AA, \ion{Fe}{xxiii} 263~\AA\ and \ion{Fe}{xxiv} 255~\AA\ emission lines were simultaneously observed by the EUV Imaging Spectrometer onboard the Hinode satellite. Intensity ratios among these high temperature Fe lines are compared and departures from isothermal conditions and ionization equilibrium examined. Temperatures derived from intensity ratios involving these four lines show significant discrepancies at the flare footpoints in the impulsive phase, and at the looptop in the gradual phase. Among these, the temperature derived from the \ion{Fe}{xxii}/\ion{Fe}{xxiv} intensity ratio is the lowest, which cannot be explained if we assume a Maxwellian electron distribution and ionization equilibrium, even in the case of a multi-thermal structure. This result suggests that the assumption of ionization equilibrium and/or a Maxwellian electron energy distribution can be violated in evaporating solar plasma around 10MK.

The perihelion activity of comet 67P/Churyumov-Gerasimenko as seen by robotic telescopes

Around the time of its perihelion passage the observability of 67P/Churyumov-Gerasimenko from Earth was limited to very short windows each morning from any given site, due to the low solar elongation of the comet. The peak in the comet's activity was therefore difficult to observe with conventionally scheduled telescopes, but was possible where service/queue scheduled mode was possible, and with robotic telescopes. We describe the robotic observations that allowed us to measure the total activity of the comet around perihelion, via photometry (dust) and spectroscopy (gas), and compare these results with the measurements at this time by Rosetta's instruments. The peak of activity occurred approximately two weeks after perihelion. The total brightness (dust) largely followed the predictions from Snodgrass et al. 2013, with no significant change in total activity levels from previous apparitions. The CN gas production rate matched previous orbits near perihelion, but appeared to be relatively low later in the year.

A Formal Approach to Support Interoperability in Scientific Meta-workflows

Scientific workflows orchestrate the execution of complex experiments frequently using distributed computing platforms. Meta-workflows represent an emerging type of such workflows which aim to reuse existing workflows from potentially different workflow systems to achieve more complex and experimentation minimizing workflow design and testing efforts. Workflow interoperability plays a profound role in achieving this objective. This paper is focused at fostering interoperability across meta-workflows that combine workflows of different workflow systems from diverse scientific domains. This is achieved by formalizing definitions of meta-workflow and its different types to standardize their data structures used to describe workflows to be published and shared via public repositories. The paper also includes thorough formalization of two workflow interoperability approaches based on this formal description: the coarse-grained and fine-grained workflow interoperability approach. The paper presents a case study from Astrophysics which successfully demonstrates the use of the concepts of meta-workflows and workflow interoperability within a scientific simulation platform.

Complejos de rutenio solubles en agua con fosfinas cuosolubles y bases púricas.

Complejos de rutenio solubles en agua con fosfinas acuosolubles y bases púricas. La presente invención trata sobre la obtención de complejos de rutenio solubles en agua con fosfinas acuosolubles y bases púricas, de fórmula general 1 en donde Ru representa un átomo de rutenio; Q representa un radical -R1, -R1-NH2, -R1-COOH, -R1-COO-, -R1-OH, -R1-COONCH3, -R1-COONCH2CH3, siendo R1 un grupo alquilo o arilo de hasta 18 carbonos; P representa una fosfina; wP representa una fosfina soluble en agua; Pur representa una base púrica o purina, citosina y timina.Dichos complejos se pueden obtener mediante tres procedimientos diferentes según los productos de partida que se utilicen y sean accesibles o más económicos. A través de la presente invención se pueden obtener una gran variedad de complejos de rutenio por la combinación de los compuestos que se unan al metal.

Equipo Autónomo para el encalado de cubiertas de invernaderos industriales

Equipo autónomo para el encalado de cubierta de invernaderos industriales. El equipo de encalado comprende un bastidor en V capaz de adaptar sus dimensiones a las diferentes luces que presentan los invernaderos industriales. El bastidor sienta en cada extremo sobre pareja de ruedas de rodadura (5). Asimismo, incorpora un sistema de pulverización constituido por: depósitos de abastecimiento (6), equipo de presión y las correspondientes barras de tratamiento (7). El sistema de barras de tratamiento (8) se encuentra suspendido sobre el bastidor de pórtico, siendo regulables en altura, pudiendo así adaptarse a las diferentes geometrías de invernadero industrial existentes.

Metodología para la implementación de un servicio de asesoría sobre formalización de predios en la Alcaldía de Itagüí

Siguiendo la metodología de Marco Lógico, durante el proceso de formulación del proyecto, se pudo identificar como un problema central la poca voluntad que existe en amplios sectores de la población en materia de legalización de predios, convirtiéndose este un problema central, tanto para las administraciones territoriales, como para la población. Para las administraciones territoriales y entidades encargadas de llevar el registro de predios y sus mutaciones, esto es un asunto importante, ya que es con base en los registros de predios legalizados que se establecen buena parte de los ingresos tributarios y se orientan varios de los programas sociales, incluidos los de vivienda. Mientras que para los sectores de la población que se han abstenido de iniciar procesos, la no legalización de predios redunda en pérdida de beneficios o en la dificultad para acceder a ellos. La metodología de Marco Lógico, permitió evidenciar que las principales causas del problema son la desconfianza y el desconocimiento en la población, por lo cual en el presente trabajo se definió como alternativa de solución la del diseño de un servicio de asesoría personalizado que contribuya en la solución del problema, sensibilizando e informando a la población simultáneamente.

Potencial fisiológico de sementes de soja enriquecidas com molibdênio no armazenamento e sua influência na atividade de enzimas do metabolismo do nitrogênio

Molybdenum is one of the essential micronutrients for soybeans, acting directly on nitrogen metabolism as enzyme cofactor of nitrogenase. Usually, this nutrient is supplied to the plants through seed treatment or foliar application. The aim of this study was to evaluate the molybdenum effects by foliar in the physiological potential of soybean seeds and verify its interference in the enzyme activities involved in nitrogen metabolism. Soybean seeds of BMX Turbo cultivar were used, produced in Erechim, RS, harvest 2013, from plants treated with the following Mo concentrations: 0; 25; 50 and 75 g ha-1, supplied through two commercial products (Biomol and Molybdate) and stored during 0 and 6 months in uncontrolled conditions. The first experiment was conducted in Seedtes Seed Analysis Laboratory in Pato Branco, PR. The used design was completely randomized in a factorial analysis 4 x 2 x 2 with four replications each. The physiological potential of the seeds was evaluated by the germination test, seedling growth, accelerated aging and emergence on the soil. The second experiment was conducted in a greenhouse, where the seeds derived from treatments with different concentrations of Mo: 0; 25; 50 and 75 g ha-1 supplied through two commercial products (Biomol and Molybdate) were grown in vases. The used design was completely randomized in a factorial analysis 4 x 2 with four replications. Evaluations were performed when the plants reached the R1 phenological stage concerning the nodulation, dry matter of root and shoot of the plants and the determination of the activity of the enzymes glutamine synthetase and glutamate synthetase and the content of total soluble proteins. The data were submitted to variance analysis and when significant they were assessed by Tukey’s test for comparison of products and seed storage and with regression study to the concentrations at 5% probability. Analyses were performed using SISVAR statistical software. The soybean seed storage under uncontrolled conditions affected the seed vigour produced with Mo, regardless of the commercial product used during production. The application of Mo through foliar positively influences the production of soya beans which presented increasing responses in the germination and vigour with the application of Mo above 25 g ha-1 . The enrichment of Mo through foliar did not affect the nodulation of plants of the next generation, however, the use of Mo above 25 g ha-1 provided an increase in the activity of enzymes involved in nitrogen metabolism as well as on the total protein content.

Desempenho de fosfitos de potássio no manejo de mofo branco em soja

Soybean plays an important role in the Brazilian agriculture being one of the products most exported by the country. Its yield may be affected by diseases such as white mold, caused by the fungus Sclerotinia sclerotiorum Lib. de Bary, which, under favorable field conditions prevents the crop of expressing all its productive potential. The fungus is cosmopolitan and infects more than 400 species of plants. This disease is difficult to control, and the use of chemicals has not been sufficient to avoid significant losses, thus, this products are expensive and may cause environmental damage. Alternative methods, such as foliar fertilizers based on potassium phosphite, can also be used in the management of this disease. In this context, this work aimed to study different sources of potassium phosphite and its effects in the control of white mold in soybeans, as well as the time of application in culture, its action in inducing plants defense responses and/or its influence over the seeds quality. The effect of phosphites, over the pathogen, was evaluated in vitro, on mycelial inhibition, the mass of dry mycelium and germination of sclerotia. In all tests, the following phosphites were utilized: Phosphite A (P2O5-40%; K2O-20% - 1 L/ha); Phosphite B (P2O5-40%; K2O-28% - 1 L/ha); Phosphite C (P2O5-40%; K2O-20% - 1 L/ha) e Phosphite D (P2O5-30%; K2O-20% - 2,4 L/ha). At the induction of resistance tests were evaluated the synthesis of phytoalexin in soybean cotyledons and the enzymes FAL and POX evaluated in seedlings in growing chamber, sprayed with phosphites and the fungicide fluazinam. Field experiment was carried out at Coronel Domingos Soares-PR, in the 2012/2013 season, in an area with natural infestation of the pathogen. Soybean cultivar BMX Active was no-till seeded with 0,5m between rows. The experimental was laid out as a factorial 5 x 4 scheme (treatment x application time). Phosphites sources were used, as described above, and water was sprayed in the control treatment. Treatments were applied at four different growth stages: V4, V4 + R1, R1 and R2 at the rates recommended by the manufacturer. Soybean yield components and seeds and health and physiological quality were evaluated after harvesting. None of the tested phosphites affected mycelial growth and sclerotia germination or influenced phytoalexin synthesis. Phosphites C and D stood out due to an increasing in the phenylalanine ammonia-lyase activity 48 hours after its inoculation. These same products also induced the synthesis and peroxidases and phosphite C kept the levels of this enzyme elevated up to 72 hours after inoculation. At the field trials, phosphites C and D stood out in the control of white mold. There was no significant interaction of potassium phosphite on physiological and sanitary quality of the seeds.

Reproductive competition triggers mass eviction in cooperative banded mongooses.

In many vertebrate societies, forced eviction of group members is an important determinant of population structure, but little is known about what triggers eviction. Three main explanations are: (i) the reproductive competition hypothesis, (ii) the coercion of cooperation hypothesis, and (iii) the adaptive forced dispersal hypothesis. The last hypothesis proposes that dominant individuals use eviction as an adaptive strategy to propagate copies of their alleles through a highly structured population. We tested these hypotheses as explanations for eviction in cooperatively breeding banded mongooses (Mungos mungo), using a 16-year dataset on life history, behaviour and relatedness. In this species, groups of females, or mixed-sex groups, are periodically evicted en masse. Our evidence suggests that reproductive competition is the main ultimate trigger for eviction for both sexes. We find little evidence that mass eviction is used to coerce helping, or as a mechanism to force dispersal of relatives into the population. Eviction of females changes the landscape of reproductive competition for remaining males, which may explain why males are evicted alongside females. Our results show that the consequences of resolving within-group conflict resonate through groups and populations to affect population structure, with important implications for social evolution.