Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics,possible effects on chromatin structure

The intrinsically disordered, positively charged H4 histone tail is important for chromatin structure and function. We have explored conformational ensembles of human H4 tail in solution, with varying levels of charge neutralization via acetylation or amino-acid substitutions such as $K\to Q$. We have employed an explicit water model shown recently to be well suited for simulations of intrinsically disordered proteins.Upon progressive neutralization of the H4, its radius of gyration decreases linearly with the tail charge q, the trend is explained using a simple polymer model. While the wild type state ($q=+8$) is essentially a random coil, hyper-acetylated H4 ($q=+3$) is virtually as compact and stable as a globular protein of the same number of amino-acids.Conformational ensembles of acetylated H4 match the corresponding $K\to X$ substitutions only approximately: based on the ensemble similarity, we propose $K\to M$ as a possible alternative to the commonly used $K\to Q$.Possible effects of the H4 tail compaction on chromatin structure are discussed within a qualitative model in which the chromatin is highly heterogeneous, easily inter-converting between various structural forms. We predict that upon progressive charge neutralization of the H4 tail, the least compact sub-states of chromatin de-condense first, followed by de-condensation of more compact structures, e.g. those that harbor a high fraction of stacked di-nucleosomes. The predicted hierarchy of DNA accessibility increase upon progressive acetylation of H4 might be utilized by the cell for selective DNA accessibility control.     

Interconnecting solvent quality,transcription, and chromosome folding in Escherichia coli

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Seasonal variation in N2O emissions from urine patches: Effects of urine concentration, soil compaction and dung

Urine patches in pastures rank among the highest sources of the greenhouse gas nitrous oxide (N₂O) from animal production systems. Previous laboratory studies indicate that N₂O emissions for urine-N in pastures may increase with a factor five or eight in combination with soil compaction and dung, respectively. These combinations of urine, compaction and dung occur regularly in pastures, especially in so-called camping areas. The aims of this study were (i) to experimentally quantify the effect of compaction and dung on emission factors of N₂O from urine patches under field conditions; (ii) to detect any seasonal changes in emission from urine patches; and (iii) to quantify possible effects of urine concentration and -volume. A series of experiments on the effects of compaction, dung, urine-N concentration and urine volume was set up at a pasture on a sandy soil (typic Endoaquoll) in Wageningen, the Netherlands. Artificial urine was applied 8 times in the period August 2000–November 2001, and N₂O emissions were monitored for a minimum of 1 month after each application. The average emission factor for urine-only treatments was 1.55%. Over the whole period, only soil compaction had a clear significant effect, raising the average N₂O emissions from urine patches from 1.30% to 2.92% of the applied N. Dung had no consistent effect; although it increased the average emissions from 1.60% to 2.82%, this was clearly significant (P< 0.01) for only one application date and marginally significant (P=0.054) for the whole experiment. Both compaction and dung increased water-filled pore space (WFPS) of the topsoil for a more prolonged time than high urine volumes. No effect of amount of urine-N or urine volume on N₂O emissions relative to added N was detected for the whole experiment. There were clear differences between application dates, with highest emissions for urine-only treatments of 4.25% in October, 2000, and lowest of –0.11% in June, 2001. Emissions peaked at 60–70% WFPS, and decreased rapidly with both higher and lower WFPS. We conclude that compaction leads to a considerable increase in the N₂O emissions under field conditions, mainly through higher WFPS. Dung addition may have the same effect, although this was not consistent throughout our experiment. Seasonal variations seemed mainly driven by differences in WFPS. Based on this study, mitigation strategies should focus on minimizing the grazing period with wet conditions leading to WFPS > 50%, avoiding camping areas in pastures, and on avoiding grazing under moist soil conditions. Greenhouse gas budgets for grazing conditions should include the effects of soil compaction and dung to represent actual emissions.     

Structural changes in S. epidermidis biofilms after transmission between stainless steel surfaces

Transmission is a main route for bacterial contamination, involving bacterial detachment from a donor and adhesion to receiver surfaces. This work aimed to compare transmission of an extracellular polymeric substance (EPS) producing and a non-EPS producing Staphylococcus epidermidis strain from biofilms on stainless steel. After transmission, donor surfaces remained fully covered with biofilm, indicating transmission through cohesive failure in the biofilm. Counter to the numbers of biofilm bacteria, the donor and receiver biofilm thicknesses did not add up to the pre-transmission donor biofilm thickness, suggesting more compact biofilms after transmission, especially for non-EPS producing staphylococci. Accordingly, staphylococcal density per unit biofilm volume had increased from 0.20 to 0.52 μm^–3 for transmission of the non-EPS producing strain under high contact pressure. The EPS producing strain had similar densities before and after transmission (0.17 μm^–3). This suggests three phases in biofilm transmission: (1) compression, (2) separation and (3) relaxation of biofilm structure to its pre-transmission density in EPS-rich biofilms.     

Investigation of the Variability of NIR In-line Monitoring of Roller Compaction Process by Using Fast Fourier Transform (FFT) Analysis

The purpose of this research was to investigate the variability of the roller compaction process while monitoring in-line with near-infrared (NIR) spectroscopy. In this paper, a pragmatic method in determining this variability of in-line NIR monitoring roller compaction process was developed and the variability limits were established. Fast Fourier Transform (FFT) analysis was used to study the source of the systematic fluctuations of the NIR spectra. An off-line variability analysis method was developed as well to simulate the in-line monitoring process in order to determine the variability limits of the roller compaction process. For this study, a binary formulation was prepared composed of acetaminophen and microcrystalline cellulose. Different roller compaction parameters such as roll speed and feeding rates were investigated to understand the variability of the process. The best-fit line slope of NIR spectra exhibited frequency dependence only on the roll speed regardless of the feeding rates. The eccentricity of the rolling motion of rollers was identified as the major source of variability and correlated with the fluctuations of the slopes of NIR spectra. The off-line static and dynamic analyses of the compacts defined two different variability of the roller compaction; the variability limits were established. These findings were proved critical in the optimization of the experimental setup of the roller compaction process by minimizing the variability of NIR in-line monitoring.     

Evaluating spatial within plot crop variability for different management practices with an optical sensor?

Subsoil constraints to root growth exacerbate frequent water and nutrient limitations to crop yields in Mediterranean-type environments. Amelioration of subsoil constraints can relieve these limitations by opening root-access to subsoil water and nutrients. However, decisions in subsoil amelioration are hampered by seasonally variable yield responses in these environments. We used the APSIM model to analyse the impact of subsoil constraints on yield and yield variability. The simulated yield data were used to calculate the financial benefits of subsoil amelioration across several scenarios. There was a strong yield-dependence on accessible soil water governed by root depth. Root depth development was limited to a minimum of either the effect of subsoil constraints or the weather-dependent depth of the soil wetting front. Insufficient rainfall in dry years or in a drier region often resulted in shallow soil wetting fronts and correspondingly shallow roots even in the absence of subsoil compaction. In these situations, there is little response to subsoil amelioration. Positive yield responses and positive financial returns to subsoil amelioration are therefore greater in good rainfall years and are more likely in a wetter region. A yield response to amelioration is also greater in coarser textured sand than finer textured sandy loam in an average rainfall season because the same amount of rainfall results in a deeper wetting front in sand than in sandy loam. Hence, roots in a sand are required to grow deeper compared to a sandy loam to access the same amount of water and therefore benefited more from subsoil amelioration in an average rainfall year. In wet years, sands leach more nitrate than sandy loam, which decreases yields and the response to subsoil amelioration in sands is more than in the sandy loam. Environmental threats occur along with yield loss when roots cannot access subsoil water. These include increased nitrate leaching and deep drainage due to unused water remaining in the soil profile. By allowing roots to access deep soil water, ameliorating subsoil is expected to yield financial gains in average to good rainfall seasons and decrease the environmental risk of drainage and leaching loss. The financial gains are expected to offset potential financial losses in dry and dry finish seasons especially in coarser textured soils and wetter environment. Responsible Editor: Jan Vos.     

土壤压实胁迫下丛枝菌根真菌对高羊茅生理生态的影响

该试验设计4种土壤压实处理[土壤容重分别为1.2(CK_1)、1.3、1.4和1.5 g·cm~(-3)],并与压实处理前分别接种2种丛枝菌根真菌(arbuscular mycorrhizal fungi,AMF)——摩西斗管囊霉(Funneliformis mosseae,Fm)和根内根孢囊霉(Rhizophagus intraradices,Ri)组成的4个接种处理[Fm、Ri、Fm+Ri和不接种(CK_2)],共组成16个处理,分析不同处理对高羊茅(Festuca elata)品种‘艾瑞3号’的生理生态指标的影响,为AMF在压实土壤中的应用提供理论基础。结果表明:(1)高羊茅根系的菌根侵染率和菌丝密度均随土壤容重的增加而逐渐降低;与CK_1相比,在土壤容重1.5 g·cm~(-3)处理下接种Fm、Ri、Fm+Ri的高羊茅根系菌根侵染率分别显著降低了27.8%、39.8%和30.0%,菌丝密度分别显著降低43.8%、42.1%和43.8%,且在1.5 g·cm~(-3)土壤容重下,接种Fm+Ri处理的菌根侵染率和菌丝密度比单接种Fm分别提高17.3%和25.2%,比单接种Ri处理分别提高53.0%和36.3%。(2)接种AMF能有效增加土壤压实胁迫下高羊茅植株的株高、分蘖数和干物质质量,显著提高高羊茅耐受力,接种Fm+Ri处理的株高、分蘖数及干物质质量在1.5 g·cm~(-3)土壤容重下分别比未接种(CK_2)显著增加36.1%、39.5%和144.0%。(3)接种AMF能显著提高土壤压实胁迫下高羊茅根系活力以及过氧化氢酶(CAT)活性,接种Fm+Ri处理的根系活力以及CAT活性在1.5 g·cm~(-3)土壤容重下分别是对照(CK_2)的1.4和1.5倍。(4)接种AMF能显著提高土壤压实胁迫下高羊茅叶绿素a、b以及总叶绿素含量,接种Fm+Ri处理在1.5 g·cm~(-3)土壤容重下比对照(CK_2)的上升幅度分别提高43.1%、100.0%和59.3%。(5)接种AMF能显著提高土壤压实胁迫下高羊茅叶片净光合速率(P_n)、蒸腾速率(T_r)以及气孔导度(G_s),显著降低其叶片胞间CO_2浓度(C_i),接种Fm+Ri处理在1.5 g·cm~(-3)土壤容重下比对照(CK_2)的升降幅度分别为52.5%、33.3%、181.1%和-32.9%。综上所述,土壤压实胁迫显著抑制AMF的侵染,而共同接种Fm+Ri能显著促进AMF对根系的侵染,且共同接种处理的效果明显优于单一接种;AMF可通过增强高羊茅根系活力、降低氧化胁迫造成的伤害、提高植物叶绿素含量与光合作用来增强自身的抗土壤压实能力。     

Nutrient uptake and growth of barley as affected by soil compaction

A field experiment with different levels of compaction was carried out on a mouldboard ploughed silty clay, with the objective of studying the effects on plant nutrient uptake and growth. Soil from the field was also used in laboratory studies of carbon and nitrogen mineralization, and plant uptake of water and nutrients. In the field, low as well as high bulk densities reduced biomass production and nutrient uptake of barley (Hordeum vulgare L.) compared to intermediate bulk densities, where grain yield was approximately 20% higher. In the beginning of the growing season, the concentration of phosphorus and potassium was lowest in plants grown in the loosest and in the most compacted soil, and suboptimal for plant growth. The uptake of nutrients transported by diffusion was more affected by compaction than for nutrients transported by mass flow. The reasons for lowered uptake in loose compared to moderately compacted soil could be reduced root-to-soil contact, a low diffusion coefficient for nutrients and/or reduced mass transport of water to seed and roots. Differences in plant nutrient concentrations between treatments gradually declined until harvest. Immediately after compaction there was probably oxygen deficiency in the compacted soil since the air-filled porosity was critically low, but as the soil dried out, mechanical resistance to root growth may have become a more important growth-limiting factor. In the laboratory study, severe compaction reduced carbon mineralization and uptake of water and nutrients by roots, and caused denitrification. There were only small differences between loose and moderately compacted soil in carbon mineralization, nitrogen concentration in the soil, uptake of water and nutrients and dry matter yield. The large yield increase due to recompaction in the field was not reproduced in the laboratory. Possible reasons are differences in soil temperature between the field and laboratory, in the sowing and fertilizing methods, the pretreatment of the soil and in the spatial variability of bulk density. It is possible that recompaction is needed only in the uppermost part of the soil, which is the loosest, dries out first, and is where the seed as well as the fertilizer are placed. This revised version was published online in July 2006 with corrections to the Cover Date.