Effect of Base Sequence on G-Wire Formation in Solution

The formation and dimensions of G-wires by different short G-rich DNA sequences in solution were investigated by dynamic light scattering (DLS) and polyacrilamide gel electrophoresis (PAGE). To explore the basic principles of wire formation, we studied the effects of base sequence, method of preparation, temperature, and oligonucleotide concentration. Both DLS and PAGE show that thermal annealing induces much less macromolecular self-assembly than dialysis. The degree of assembly and consequently length of G-wires (5-6 nm) are well resolved by both methods for DNA sequences with intermediate length, while some discrepancies appear for the shortest and longest sequences. As expected, the longest DNA sequence gives the longest macromolecular aggregates with a length of about 11 nm as estimated by DLS. The quadruplex topologies show no concentration dependence in the investigated DNA concentration range (0.1 mM–0.4 mM) and no structural change upon heating

Determination of the multiple-scattering correction factor and its cross-sensitivity to scattering and wavelength dependence for different AE33 Aethalometer filter tapes: a multi-instrumental approach

Providing reliable observations of aerosol particles' absorption properties at spatial and temporal resolutions suited to climate models is of utter importance to better understand the effects that atmospheric particles have on climate. Nowadays, one of the instruments most widely used in international monitoring networks for in situ surface measurements of light absorption properties of atmospheric aerosol particles is the multi-wavelength dual-spot Aethalometer, AE33. The AE33 derives the absorption coefficients of aerosol particles at seven different wavelengths from the measurements of the optical attenuation of light through a filter where particles are continuously collected. An accurate determination of the absorption coefficients from the AE33 instrument relies on the quantification of the non-linear processes related to the sample collection on the filter. The multiple-scattering correction factor (C), which depends on the filter tape used and on the optical properties of the collected particles, is the parameter with both the greatest uncertainty and the greatest impact on the absorption coefficients derived from the AE33 measurements. Here we present an in-depth analysis of the AE33 multiple-scattering correction factor C and its wavelength dependence for two different and widely used filter tapes, namely the old, and most referenced, TFE-coated glass, or M8020, filter tape and the currently, and most widely used, M8060 filter tape. For performing this analysis, we compared the attenuation measurements from AE33 with the absorption coefficients measured with different filter-based techniques. On-line co-located multi-angle absorption photometer (MAAP) measurements and off-line PP_UniMI polar photometer measurements were employed as reference absorption measurements for this work. To this aim, we used data from three different measurement stations located in the north-east of Spain, namely an urban background station (Barcelona, BCN), a regional background station (Montseny, MSY) and a mountaintop station (Montsec d'Ares, MSA). The median C values (at 637 nm) measured at the three stations ranged between 2.29 (at BCN and MSY, lowest 5th percentile of 1.97 and highest 95th percentile of 2.68) and 2.51 (at MSA, lowest 5th percentile of 2.06 and highest 95th percentile of 3.06). The analysis of the cross-sensitivity to scattering, for the two filter tapes considered here, revealed a large increase in the C factor when the single-scattering albedo (SSA) of the collected particles was above a given threshold, up to a 3-fold increase above the average C values. The SSA threshold appeared to be site dependent and ranged between 0.90 to 0.95 for the stations considered in the study. The results of the cross-sensitivity to scattering displayed a fitted constant multiple-scattering parameter, Cf, of 2.21 and 1.96, and a cross-sensitivity factor, ms, of 1.8 % and 3.4 % for the MSY and MSA stations, respectively, for the TFE-coated glass filter tape. For the M8060 filter tape, Cf values of 2.50, 1.96 and 1.82 and ms values of 1.6 %, 3.0 % and 4.9 % for the BCN, MSY and MSA stations, respectively, were obtained. SSA variations also influenced the spectral dependence of C, which showed an increase with wavelength when SSA was above the site-dependent threshold. Below the SSA threshold, no statistically significant dependence of C on the wavelength was observed. For the measurement stations considered here, the wavelength dependence of C was to some extent driven by the presence of dust particles during Saharan dust outbreaks that had the potential to increase the SSA above the average values. At the mountaintop station, an omission of the wavelength dependence of the C factor led to an underestimation of the absorption Ångström exponent (AAE) by up to 12 %. Differences in the absorption coefficient determined from AE33 measurements at BCN, MSY and MSA of around 35 %–40 % can be expected when using the site-dependent experimentally obtained C value instead of the nominal C value. Due to the fundamental role that the SSA of the particles collected on the filter tape has in the multiple-scattering parameter C, we present a methodology that allows the recognition of the conditions upon which the use of a constant and wavelength-independent C is feasible.This research has been supported by the Ministerio de Economía, Industria y Competitividad, Gobierno de España (CAIAC project (grant no. PID2019-108990PB-100)); the European Cooperation in Science and Technology (Action CA16109 COLOSSAL); the Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR 2017 SGR41); and the European Commission, Horizon 2020 Framework Programme (ACTRIS IMP (grant no. 871115)).Peer reviewe

Towards a better understanding of fine PM sources: online and offline datasets combination in a single PMF

Co-located one-year measurements of non-refractory submicronic particulate matter (NR-PM1), black carbon (BC) and metals, obtained respectively, by a Q-ACSM (Aerodyne Research Inc.), an Aethalometer (Aerosol d.o.o.) and offline fine PM samples collected on quartz-fibre filters, were combined in a single PMF in two different resolutions (30 minutes for the NR-PM1 and BC, and 24h every 4 days for the offline samples). The multi-time resolution PMF (MTR-PMF) was run varying both the time resolution (averaging the dataset) and the uncertainty weightings of both datasets in order to assess the impact of these variations on the model output. The resolution assessment revealed that averaging the high-resolution data was disadvantageous in terms of model residuals and environmental feasibility. Regarding uncertainty weightings, overweighting the uncertainties of the 24-h dataset dividing them by two provided the most optimal scaled residuals adjustment. The MTR-PMF was run with the optimised time resolution and uncertainty weightings retrieving eight PM1 sources: ammonium sulphate (AS) + heavy oil combustion (24%), ammonium nitrate (AN) and ammonium chloride (15%), fresh SOA (15%), traffic (14%), biomass burning (11%), aged SOA + mineral dust (8%), urban mix (7%) and cooking-like organic aerosol + industry (6%). The MTR-PMF technique allowed the identification of two more sources respect a dataset containing the same species at a 24h time resolution (base case) and four more respect to the conventional offline and PMF, proving that the combination of both high and low time resolution data through MTR-PMF is significantly beneficial for SA. This is especially true for those sources which have been disentangled with respect to the conventional and base case PMFs.Peer reviewe

Double trouble at high density::Cross-level test of ressource-related adaptive plasticity and crowding-related fitness.

Population size is often regulated by negative feedback between population density and individual fitness. At high population densities, animals run into double trouble: they might concurrently suffer from overexploitation of resources and also from negative interference among individuals regardless of resource availability, referred to as crowding. Animals are able to adapt to resource shortages by exhibiting a repertoire of life history and physiological plasticities. In addition to resource-related plasticity, crowding might lead to reduced fitness, with consequences for individual life history. We explored how different mechanisms behind resource-related plasticity and crowding-related fitness act independently or together, using the water flea Daphnia magna as a case study. For testing hypotheses related to mechanisms of plasticity and crowding stress across different biological levels, we used an individual-based population model that is based on dynamic energy budget theory. Each of the hypotheses, represented by a sub-model, is based on specific assumptions on how the uptake and allocation of energy are altered under conditions of resource shortage or crowding. For cross-level testing of different hypotheses, we explored how well the sub-models fit individual level data and also how well they predict population dynamics under different conditions of resource availability. Only operating resource-related and crowding-related hypotheses together enabled accurate model predictions of D. magna population dynamics and size structure. Whereas this study showed that various mechanisms might play a role in the negative feedback between population density and individual life history, it also indicated that different density levels might instigate the onset of the different mechanisms. This study provides an example of how the integration of dynamic energy budget theory and individual-based modelling can facilitate the exploration of mechanisms behind the regulation of population size. Such understanding is important for assessment, management and the conservation of populations and thereby biodiversity in ecosystems

A framework for evolutionary systems biology

<p>Abstract</p> <p>Background</p> <p>Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects.</p> <p>Results</p> <p>Here I propose a novel framework that brings together evolutionary theory and current systems biology approaches in order to quantify small effects of mutations and their epistatic interactions <it>in silico</it>. Central to this approach is the definition of fitness correlates that can be computed in some current systems biology models employing the rigorous algorithms that are at the core of much work in computational systems biology. The framework exploits synergies between the realism of such models and the need to understand real systems in evolutionary theory. This framework can address many longstanding topics in evolutionary biology by defining various 'levels' of the adaptive landscape. Addressed topics include the distribution of mutational effects on fitness, as well as the nature of advantageous mutations, epistasis and robustness. Combining corresponding parameter estimates with population genetics models raises the possibility of testing evolutionary hypotheses at a new level of realism.</p> <p>Conclusion</p> <p>EvoSysBio is expected to lead to a more detailed understanding of the fundamental principles of life by combining knowledge about well-known biological systems from several disciplines. This will benefit both evolutionary theory and current systems biology. Understanding robustness by analysing distributions of mutational effects and epistasis is pivotal for drug design, cancer research, responsible genetic engineering in synthetic biology and many other practical applications.</p

Učinki plazemske obdelave na sorpcijo vode v viskoznih vlaknih

We investigated water sorption in viscose nonwoven fibres manufactured by Tosama d.d. with the surface density of 175 g/m2. A comparison between untreated fibres and by oxygen plasma treated fibres was made using optical polarization microscopy. Plasma treatment was done for 10 minutes at pressure of 75 Pa at current of 250 mA at the power of 500 W. Swelling was characterized by measurements of fibre diameter. Modifications of intensity of the polarized light transmitted through the fibre were measured as a function of time of exposure to water. Characteristic swelling and intensity modification times were resolved for untreated and oxygen plasma treated fibres. The swelling time of oxygen plasma in comparison to untreated plasma is reduced by the factor of 0.54 and intensity change time by the factor of 0.4. From the characteristic swelling and intensity change times it was concluded that oxygen plasma treatment of viscose increases the speed of water sorption.Proučevali smo sorpcijo vode pri vlaknih v viskozni kopreni, ki jo proizvaja podjetje Tosama d.d., s površinsko gostoto 175 g/m2. Primerjali smo neobdelana in s kisikovo plazmo obdelana vlakna z uporabo optično-polarizacijske mikroskopije. Plazemska obdelava je trajala 10 minut pri tlaku 75 Pa, toku 250 mA in pri moči 500 W. Nabrekanje viskoznih vlaken smo opazovali preko sprememb premera vlakna. Z optično polarizacijsko mikroskopijo smo merili spremembe intenzitete polarizirane svetlobe, ki potuje skozi vlakno med močenjem. Iz meritev na neobdelanih in s plazmo obdelanih vlaknih smo ocenili karakteristične čase nabrekanj vlaken in spremembe intenzitete polarizirane svetlobe, ki potuje skozi vlakna. Pri s plazmo obdelanih vlaknih se časi nabrekanja zmanjšajo za faktor 0.54 in čas spremembe intenzitete za 0.4. Iz meritev smo zaključili, da obdelava s kisikovo plazmo pohitri proces sorpcije vode