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1.
Kyung Suk Lee Amanda B. Marciel Alexander G. Kozlov Charles M. Schroeder Timothy M. Lohman Taekjip Ha 《Journal of molecular biology》2014
Single-stranded DNA binding proteins (SSBs) selectively bind single-stranded DNA (ssDNA) and facilitate recruitment of additional proteins and enzymes to their sites of action on DNA. SSB can also locally diffuse on ssDNA, which allows it to quickly reposition itself while remaining bound to ssDNA. In this work, we used a hybrid instrument that combines single-molecule fluorescence and force spectroscopy to directly visualize the movement of Escherichia coli SSB on long polymeric ssDNA. Long ssDNA was synthesized without secondary structure that can hinder quantitative analysis of SSB movement. The apparent diffusion coefficient of E. coli SSB thus determined ranged from 70,000 to 170,000 nt2/s, which is at least 600 times higher than that determined from SSB diffusion on short ssDNA oligomers, and is within the range of values reported for protein diffusion on double-stranded DNA. Our work suggests that SSB can also migrate via a long-range intersegment transfer on long ssDNA. The force dependence of SSB movement on ssDNA further supports this interpretation. 相似文献
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Nitrogen yield advantage from grass–legume mixtures is robust over a wide range of legume proportions and environmental conditions 下载免费PDF全文
Matthias Suter John Connolly John A. Finn Ralf Loges Laura Kirwan Maria‐Teresa Sebastià Andreas Lüscher 《Global Change Biology》2015,21(6):2424-2438
Current challenges to global food security require sustainable intensification of agriculture through initiatives that include more efficient use of nitrogen (N), increased protein self‐sufficiency through homegrown crops, and reduced N losses to the environment. Such challenges were addressed in a continental‐scale field experiment conducted over 3 years, in which the amount of total nitrogen yield (Ntot) and the gain of N yield in mixtures as compared to grass monocultures (Ngainmix) was quantified from four‐species grass–legume stands with greatly varying legume proportions. Stands consisted of monocultures and mixtures of two N2‐fixing legumes and two nonfixing grasses. The amount of Ntot of mixtures was significantly greater (P ≤ 0.05) than that of grass monocultures at the majority of evaluated sites in all 3 years. Ntot and thus Ngainmix increased with increasing legume proportion up to one‐third of legumes. With higher legume percentages, Ntot and Ngainmix did not continue to increase. Thus, across sites and years, mixtures with one‐third proportion of legumes attained ~95% of the maximum Ntot acquired by any stand and had 57% higher Ntot than grass monocultures. Realized legume proportion in stands and the relative N gain in mixture (Ngainmix/Ntot in mixture) were most severely impaired by minimum site temperature (R = 0.70, P = 0.003 for legume proportion; R = 0.64, P = 0.010 for Ngainmix/Ntot in mixture). Nevertheless, the relative N gain in mixture was not correlated to site productivity (P = 0.500), suggesting that, within climatic restrictions, balanced grass–legume mixtures can benefit from comparable relative gains in N yield across largely differing productivity levels. We conclude that the use of grass–legume mixtures can substantially contribute to resource‐efficient agricultural grassland systems over a wide range of productivity levels, implying important savings in N fertilizers and thus greenhouse gas emissions and a considerable potential for climate change mitigation. 相似文献
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Ji Guo Su Xiao Ming Han Xiao Zhang Yan Xue Hou Jian Zhuo Zhu Yi Dong Wu 《Journal of biomolecular structure & dynamics》2016,34(3):560-571
Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK2) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified. 相似文献
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Phosphorus release from resuspended sediment in the shallow and wind-exposed Lake Arresø, Denmark 总被引:13,自引:10,他引:3
Wind-induced sediment resuspension occurs frequently in the shallow and eutrophic Lake Arresø, Denmark. The impact of resuspension on internal phosphorus loading was investigated by laboratory experiments studying P-release from the undisturbed sediment surface and by experiments simulating resuspension events.Phosphorus release from undisturbed sediment sampled in May and August was 12 mg and 4 mg m–2 d–1, respectively. During experimental simulation of resuspension, soluble reactive phosphate (SRP) increased by 20–80 µg l–1, which indicates that a typical resuspension event in the lake would be accompanied by the release of 150 mg SRP m–2. The internal P loading induced by resuspension is estimated to be 60–70 mg m–2 d–1, or 20–30 times greater than the release from undisturbed sediment.SRP release during simulation of resuspension was mainly dependent on the equilibrium conditions in the water column and was basically independent of the increase in suspended solids and the duration of resuspension. A second simulation of resuspension conducted 26 hours later, did not result in any further release of SRP from sediment sampled in May. In contrast, there was an additional SRP release from sediment sampled in August, indicating that an exchangable P pool, capable of altering equilibrium conditions, is built up between resuspension events.It is concluded that resuspension, by increasing the P flux between sediment and water, plays a major role in the maintenance of the high nutrient level in Lake Arresø. A relatively high release rate is maintained during resuspension because of the low Fe:P ratio and the high concentration of NH4Cl-extractable P in the sediment. 相似文献
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The utilization of some amino acids, added at 1 mM and 10 mM concentrations, as the sole combined nitrogen sources by Frankia sp. strain CpI1, has been investigated. Glutamine, like NH
4
+
, provided rapid growth without N2 fixation. Histidine at 1 mM yielded poor N2-fixing activity but better cell growth than N2. Aspartate, glutamate, alanine, proline, each at 1 mM concentration, supported similar levels of N2 fixation and growth. Growth on 10 mM glutamate, proline, or histidine resulted in poor N2-fixing activity and poor cell growth. Cells grown on 10 mM alanine had about half the N2-fixing activity of cells grown on N2 but growth was good. Aspartate at 10 mM concentration, however, stimulated N2-fixing activity dramatically and promoted faster growth. Enzyme analysis suggested that asparate is catabolized by glutamate-oxaloacetate transaminase (GOT), since GOT specific activity was induced, and aspartase activity was not detected, in cells grown on aspartate as the sole combined nitrogen source. Thinlayer chromatography (TLC) of metabolites extracted from N2-grown cells fed with [14C]-aspartate showed that label was rapidly accumulated mainly on aspartate and/or glutamate, depending on the cells' physiological state, without detectable labeling on fumarate or oxaloacetate (OAA). These findings provide evidence that aspartate is catabolized by GOT to OAA which, in turn, is rapidly converted to -ketoglutarate through the TCA cycle and then to glutamate by GOT or by glutamate synthase (GOGAT). The stimulation of N2 fixation and growth by aspartate is probably caused by an increased intracellular glutamate pool. 相似文献
9.
A. Rigotto S.R. Cotta A.C.F. Dias J.L.N. Carvalho F.D. Andreote 《Letters in applied microbiology》2020,71(5):444-450
Sugarcane cultivation supports Brazil as one of the largest world sugar and ethanol producer. In order to understand the impact of changing sugarcane harvest from manual to mechanized harvest, we studied the effect of machinery traffic on soil and consequently soil compaction upon soil microbial communities involved in nitrogen cycling. The impact of sugarcane harvest was dependent on soil depth and texture. At deeper soil layers, mechanized harvesting increases the abundance of nitrogen fixers and denitrifying communities (specifically nosZ clade I and II) while manual harvesting increases the abundance of ammonia oxidizers (specifically AOA) and increases denitrifying communities (nosZ clade I and II) on top and at intermediate depth. The effect of change on the harvest system is more evident on sandy soil than on clay soil, where soil indicators of compaction (bulk density and penetration resistance) were negatively correlated with soil microorganisms associated with the nitrogen cycle. Our results point to connections between soil compaction and N transformations in sugarcane fields, besides naming biological variables to be used as proxies for alterations in soil structure. 相似文献
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应用CITYGREEN模型评估深圳市绿地净化空气与固碳释氧效益 总被引:13,自引:1,他引:12
基于深圳市1990、1995、2000、2005年4a解译、分类的遥感影像,以ARCVIEW软件为平台,利用CITYGREEN模型中的净化空气和固碳释氧模块,计算深圳市1990、1995、2000、2005年4a的各景观生态功能区绿地系统的生态服务价值.研究表明:在净化空气方面,四年的生态服务价值依次为2039.42万元、3325.79万元、2025.2万元、2980.61万元,生态敏感型支持功能亚区的生态服务价值最高,依次为214.83万元、167.55万元、217.57万元、174.19万元,;在固碳释氧方面,4a的生态服务价值依次为446916万元、454994万元、447135万元、407771万元,生态协调区中的西部沿海农工协调亚区的生态服务价值最低,依次为556.85万元、951.59万元、535.21万元、690.53万元.反应出绿地系统是城市中重要的生态系统,具有显著的生态服务价值.深圳市各景观生态功能区绿地的生态服务价值的不平衡性与城市化进程相关. 相似文献