Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization

The success of medical threatments with DNA and silencing interference RNA is strongly related to the design of efficient delivery technologies. Cationic polymers represent an attractive strategy to serve as nucleic-acid carriers with the envisioned advantages of efficient complexation, low cost, ease of production, well-defined size, and low polydispersity index. However, the balance between efficacy and toxicity (safety) of these polymers is a challenge and in need of improvement. With the aim of designing more effective polycationic-based gene carriers, many parameters such as carrier morphology, size, molecular weight, surface chemistry, and flexibility/rigidity ratio need to be taken into consideration. In the present work, the binding mechanism of three cationic polymers (polyarginine, polylysine and polyethyleneimine) to a model siRNA target is computationally investigated at the atomistic level. In order to better understand the polycationic carrier-siRNA interactions, replica exchange molecular dynamic simulations were carried out to provide an exhaustive exploration of all the possible binding sites, taking fully into account the siRNA flexibility together with the presence of explicit solvent and ions. Moreover, well-tempered metadynamics simulations were employed to elucidate how molecular geometry, polycation flexibility, and charge neutralization affect the siRNA-polycations free energy landscape in term of low-energy binding modes and unbinding free energy barriers. Significant differences among polymer binding modes have been detected, revealing the advantageous binding properties of polyarginine and polylysine compared to polyethyleneimine

Acidification increases microbial polysaccharide degradation in the ocean

© The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution 3.0 License. The definitive version was published in Biogeosciences 7 (2010): 1615–1624, doi:10.5194/bg-7-1615-2010.With the accumulation of anthropogenic carbon dioxide (CO2), a proceeding decline in seawater pH has been induced that is referred to as ocean acidification. The ocean's capacity for CO2 storage is strongly affected by biological processes, whose feedback potential is difficult to evaluate. The main source of CO2 in the ocean is the decomposition and subsequent respiration of organic molecules by heterotrophic bacteria. However, very little is known about potential effects of ocean acidification on bacterial degradation activity. This study reveals that the degradation of polysaccharides, a major component of marine organic matter, by bacterial extracellular enzymes was significantly accelerated during experimental simulation of ocean acidification. Results were obtained from pH perturbation experiments, where rates of extracellular α- and β-glucosidase were measured and the loss of neutral and acidic sugars from phytoplankton-derived polysaccharides was determined. Our study suggests that a faster bacterial turnover of polysaccharides at lowered ocean pH has the potential to reduce carbon export and to enhance the respiratory CO2 production in the future ocean.This study was supported by the Helmholtz Association (HZ-NG-102) and the Belgian Science Policy (SD/CS/03)

Bulldozers and Blueberries: Managing Fence Damage by Bare-Nosed Wombats at the Agricultural–Riparian Interface

Fence damage by bare-nosed wombats (Vombatus ursinus) can be a serious problem for farmers wishing to reduce herbivory by other herbivores on valuable crops. We investigated the effectiveness of exclusion fencing to prevent the incursion of unwanted native and feral herbivores and the use of swinging gates designed to allow wombats to pass through the fence without having to damage it. We also examined the temporal response of animals toward exclusion fencing and wombat gates. The 10-month study took place on the interface between natural riparian vegetation and a 22-ha blueberry (Vaccinium corymbosum) orchard in southeastern Australia. Following the testing of exclusion fencing (i.e., footing wire and flexible fence), we installed 6 swinging wombat gates at existing breach points within the exclusion fencing. Wombat gates were 0.6 m high × 0.5 m wide and constructed of 200 × 100 × 6 mm galvanized steel. We continually observed the response of wombats and other animals to both exclusion fencing and wombat gates using heat- and motion-sensing digital cameras. We made a total of 1,480 detections of the 3 target species—wombats, red foxes (Vulpes vulpes), and swamp wallabies (Wallabia bicolor)—in the study area between August 2007 and June 2008. Most were wombat detections (79%), followed by detections of swamp wallabies (12%) and foxes (8%). Wombats became accustomed to using the gates within 1 month, with an average exclusion rate of 48% in the first month after their installation. For the final 6 months of the project, the number of wombat detections showed an exclusion rate of approximately 25%. The swinging gates were equally consistent in excluding foxes and wallabies. The results of this study showed that swinging wombat gates were effective in regulating access by wombats while excluding other unwanted animals

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Faculty authors explore Spanish vanguard poetry, fatherhood, multi-modal learning, and more

Changing nutrient stoichiometry affects phytoplankton production, DOP accumulation and dinitrogen fixation – a mesocosm experiment in the eastern tropical North Atlantic

Ocean deoxygenation due to climate change may alter redox-sensitive nutrient cycles in the marine environment. The productive eastern tropical North Atlantic (ETNA) upwelling region may be particularly affected when the relatively moderate oxygen minimum zone (OMZ) deoxygenates further and microbially driven nitrogen (N) loss processes are promoted. Consequently, water masses with a low nitrogen to phosphorus (N : P) ratio could reach the euphotic layer, possibly influencing primary production in those waters. Previous mesocosm studies in the oligotrophic Atlantic Ocean identified nitrate availability as a control of primary production, while a possible co-limitation of nitrate and phosphate could not be ruled out. To better understand the impact of changing N : P ratios on primary production and N2 fixation in the ETNA surface ocean, we conducted land-based mesocosm experiments with natural plankton communities and applied a broad range of N : P ratios (2.67–48). Silicic acid was supplied at 15 µmol L−1 in all mesocosms. We monitored nutrient drawdown, biomass accumulation and nitrogen fixation in response to variable nutrient stoichiometry. Our results confirmed nitrate to be the key factor determining primary production. We found that excess phosphate was channeled through particulate organic matter (POP) into the dissolved organic matter (DOP) pool. In mesocosms with low inorganic phosphate availability, DOP was utilized while N2 fixation increased, suggesting a link between those two processes. Interestingly this observation was most pronounced in mesocosms where nitrate was still available, indicating that bioavailable N does not necessarily suppress N2 fixation. We observed a shift from a mixed cyanobacteria–proteobacteria dominated active diazotrophic community towards a diatom-diazotrophic association of the Richelia-Rhizosolenia symbiosis. We hypothesize that a potential change in nutrient stoichiometry in the ETNA might lead to a general shift within the diazotrophic community, potentially influencing primary productivity and carbon export

New Tropical Peatland Gas and Particulate Emissions Factors Indicate 2015 Indonesian Fires Released Far More Particulate Matter (but Less Methane) than Current Inventories Imply

Deforestation and draining of the peatlands in equatorial SE Asia has greatly increased their flammability, and in September-October 2015 a strong El Niño-related drought led to further drying and to widespread burning across parts of Indonesia, primarily on Kalimantan and Sumatra. These fires resulted in some of the worst sustained outdoor air pollution ever recorded, with atmospheric particulate matter (PM) concentrations exceeding those considered "extremely hazardous to health" by up to an order of magnitude. Here we report unique in situ air quality data and tropical peatland fire emissions factors (EFs) for key carbonaceous trace gases (CO2, CH4 and CO) and PM2.5 and black carbon (BC) particulates, based on measurements conducted on Kalimantan at the height of the 2015 fires, both at locations of "pure" sub-surface peat burning and spreading vegetation fires atop burning peat. PM2.5 are the most significant smoke constituent in terms of human health impacts, and we find in situ PM2.5 emissions factors for pure peat burning to be 17.8 to 22.3 g·kg-1, and for spreading vegetation fires atop burning peat 44 to 61 g·kg-1, both far higher than past laboratory burning of tropical peat has suggested. The latter are some of the highest PM2.5 emissions factors measured worldwide. Using our peatland CO2, CH4 and CO emissions factors (1779 ± 55 g·kg-1, 238 ± 36 g·kg-1, and 7.8 ± 2.3 g·kg-1 respectively) alongside in situ measured peat carbon content (610 ± 47 g-C·kg-1) we provide a new 358 Tg (± 30%) fuel consumption estimate for the 2015 Indonesian fires, which is less than that provided by the GFEDv4.1s and GFASv1.2 global fire emissions inventories by 23% and 34% respectively, and which due to our lower EFCH4 produces far less (~3×) methane. However, our mean in situ derived EFPM2.5 for these extreme tropical peatland fires (28 ± 6 g·kg-1) is far higher than current emissions inventories assume, resulting in our total PM2.5 emissions estimate (9.1 ± 3.5 Tg) being many times higher than GFEDv4.1s, GFASv1.2 and FINNv2, despite our lower fuel consumption. We find that two thirds of the emitted PM2.5 come from Kalimantan, one third from Sumatra, and 95% from burning peatlands. Using new geostationary fire radiative power (FRP) data we map the fire emissions' spatio-temporal variations in far greater detail than ever before (hourly, 0.05°), identifying a tropical peatland fire diurnal cycle twice as wide as in neighboring non-peat areas and peaking much later in the day. Our data show that a combination of greatly elevated PM2.5 emissions factors, large areas of simultaneous, long-duration burning, and very high peat fuel consumption per unit area made these Sept to Oct tropical peatland fires the greatest wildfire source of particulate matter globally in 2015, furthering evidence for a regional atmospheric pollution impact whose particulate matter component in particular led to millions of citizens being exposed to extremely poor levels of air quality for substantial periods. © 2018 by the authors

Biochar research activities and their relation to development and environmental quality. A meta-analysis

Biochar is the solid product that results from pyrolysis of organic materials. Its addition to highly weathered soils changes physico-chemical soil properties, improves soil functions and enhances crop yields. Highly weathered soils are typical of humid tropics where agricultural productivity is low and needs to be raised to reduce human hunger and poverty. However, impact of biochar research on scientists, politicians and end-users in poor tropical countries remains unknown; assessing needs and interests on biochar is essential to develop reliable knowledge transfer/translation mechanisms. The aim of this publication is to present results of a meta-analysis conducted to (1) survey global biochar research published between 2010 and 2014 to assess its relation to human development and environmental quality, and (2) deduce, based on the results of this analysis, priorities required to assess and promote the role of biochar in the development of adapted and sustainable agronomic methods. Our main findings reveal for the very first time that: (1) biochar research associated with less developed countries focused on biochar production technologies (26.5 ± 0.7%), then on biochars’ impact on chemical soil properties (18.7 ± 1.2%), and on plant productivity (17.1 ± 2.6%); (2) China dominated biochar research activities among the medium developed countries focusing on biochar production technologies (26.8 ± 0.5%) and on use of biochar as sorbent for organic and inorganic compounds (29.1 ± 0.4%); and (3) the majority of biochar research (69.0±2.9%) was associated with highly developed countries that are able to address a higher diversity of questions. Evidently, less developed countries are eager to improve soil fertility and agricultural productivity, which requires transfer and/or translation of biochar knowledge acquired in highly developed countries. Yet, improving local research capacities and encouraging synergies across scientific disciplines and countries are crucial to foster development of sustainable agronomy in less developed countries. © 2017, The Author(s)

Biochar reduces the efficiency of nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) mitigating N2O emissions

Among strategies suggested to decrease agricultural soil N2O losses, the use of nitrification inhibitors such as DMPP (3,4-dimethylpyrazole phosphate) has been proposed. However, the efficiency of DMPP might be affected by soil amendments, such as biochar, which has been shown to reduce N2O emissions. This study evaluated the synergic effect of a woody biochar applied with DMPP on soil N2O emissions. A incubation study was conducted with a silt loam soil and a biochar obtained from Pinus taeda at 500 degrees C. Two biochar rates (0 and 2% (w/w)) and three different nitrogen treatments (unfertilized, fertilized and fertilized + DMPP) were assayed under two contrasting soil water content levels (40% and 80% of water filled pore space (WFPS)) over a 163 day incubation period. Results showed that DMPP reduced N2O emissions by reducing ammonia-oxidizing bacteria (AOB) populations and promoting the last step of denitrification (measured by the ratio nosZI + nosZII/nirS + nirK genes). Biochar mitigated N2O emissions only at 40% WFPS due to a reduction in AOB population. However, when DMPP was applied to the biochar amended soil, a counteracting effect was observed, since the N2O mitigation induced by DMPP was lower than in control soil, demonstrating that this biochar diminishes the efficiency of the DMPP both at low and high soil water contents.This work was funded by the Spanish Government (AGL2015-64582-C3-2-R MINECO/FEDER), by the Basque Government (IT-932-16) and by the European Union (FACCE-CSA no 276610/MIT04-DESIGN-UPVASC, FACCE-CSA no 2814ERA01A and 2814ERA02A). This work is also supported by the USDA/NIFA Interagency Climate Change Grant Proposal number 2014-02114 [Project number 6657-12130-002-08I, Accession number 1003011] under the Multi-Partner Call on Agricultural Greenhouse Gas Research of the FACCE-Joint Program Initiative. Any opinions, findings, or recommendation expressed in this publication are those of the authors and do not necessarily reflect the view of the USDA. MLC was supported by a Ramon y Cajal contract from the Spanish Ministry of Economy and Competitiveness and thanks Fundacion Seneca for financing the project 19281/PI/14

Kinetic study of time-dependent fixation of UVI on biochar

Biochar, a by-product from the production of biofuel and syngas by gasification, was tested as a material for adsorption and fixation of UVI from aqueous solutions. A batch experiment was conducted to study the factors that influence the adsorption and time-dependent fixation on biochar at 20oC, including pH, initial concentration of UVI and contact time. Uranium (UVI) adsorption was highly dependent on pH but adsorption on biochar was high over a wide range of pH values, from 4.5 to 9.0, and adsorption strength was time-dependent over several days. The experimental data for pH > 7 were most effectively modelled using a Freundlich adsorption isotherm coupled to a reversible first order kinetic equation to describe the time-dependent fixation of UVI within the biochar structure. Desorption experiments showed that UVI was only sparingly desorbable from the biochar with time and isotopic dilution with 233UVI confirmed the low, or time-dependent, lability of adsorbed 238UVI. Below pH 7 the adsorption isotherm trend suggested precipitation, rather than true adsorption, may occur. However, across all pH values (4.5–9) measured saturation indices suggested precipitation was possible: autunite below pH 6.5 and either swartzite, liebigite or bayleyite above pH 6.5