黄土高原次生林演替对团聚体有机碳含量及化学稳定性的影响

次生林演替过程中土壤团聚体有机碳的积累机制和化学稳定性研究较少。为探明次生林演替对土壤团聚体有机碳含量及其化学组成稳定性的影响,选取黄土高原次生白桦林(演替初期),山杨辽东栎混交林(演替中期)和辽东栎林(演替后期)为研究对象,分析演替过程中不同粒径土壤团聚体有机碳含量变化特征。采用傅里叶红外光谱技术(FTRI)测定活性(AC)和非活性(IC)有机碳化学组成,以(IC/AC)作为有机碳化学组成稳定性指标,并分析其影响因素。结果表明:次生林演替过程中土壤团聚体有机碳含量表现出逐渐增加的趋势且各群落间差异显著(P<0.05),以演替后期的中等粒径团聚体为最高(37.63 g/kg)。土壤团聚体AC中多糖体有机碳含量最高(55.87%),而IC中芳香族有机碳含量最高(94.45%),演替过程中IC与AC总体变化趋势均呈现先降后增。IC/AC随着演替的进行呈先降低后升高的趋势,其中演替后期微团聚体有机碳化学组成稳定性最强达到了3.95。微团聚体含量(WM)与土壤全氮、全磷、全钾一起,显著促进了团聚体有机碳化学组成稳定性(P<0.05)。综上,次生林演替有利于促进土壤团聚体有机碳的积累以及有机碳化学稳定,其中微团聚体起到了关键性作用。     

Triple helical structure and stabilization of collagen-like molecules with 4(R)-hydroxyproline in the Xaa position

In this study, we examine the relationships between the structure and stability of five related collagen-like molecules that have hydroxyproline residues occupying positions not observed in vertebrate collagen. Two of the molecules contain valine or threonine and form stable triple helices in water. Three of the molecules contain allo-threonine (an enantiomer of threonine), serine, or alanine, and are not stable. Using molecular dynamics simulation methods, we examine possible explanations for the stability difference, including considering the possibility that differences in solvent shielding of the essential interchain hydrogen bonds may result in differences in stability. By comparing the structures of threonine- and allo-threonine-containing molecules in six polar and nonpolar solvation conditions, we find that solvent shielding is not an adequate explanation for the stability difference. A closer examination of the peptides shows that the structures of the unstable molecules are looser, having weaker intermolecular hydrogen bonds. The weakened hydrogen bonds result from extended Yaa residue Psi-angles that prevent optimal geometry. The Phi-Psi-maps of the relevant residues suggest that each residue's most favorable Psi-angle determines the corresponding collagen-like molecule's stability. Additionally, we propose that these molecules illustrate a more general feature of triple-helical structures: interchain hydrogen bonds are always longer and weaker than ideal, so they are sensitive to relatively small changes in molecular structure. This sensitivity to small changes may explain why large stability differences often result from seemingly small changes in residue sequence.     

土壤团聚体的稳定机制及人类活动的影响

土壤团聚体是土壤结构的基本单位,它的形成不仅是自然的过程,而且受到人类活动的严重影响,即土地利用变化,耕作干扰,有机肥施用以及种植制度和轮作方式等人类活动的影响。土壤结构的改善不仅决定于输入有机碳的总量,而且与有机质的组成和特征有关,因有机质的组成和特征不同,使微团聚体和大团聚体的稳定作用具有不同的机制。     

蚂蚁扰动对土壤有机碳循环过程的影响研究进展

蚂蚁作为生态系统的消费者和分解者,其对土壤有机碳库的影响一直是学术界研究的热点。目前研究主要从蚂蚁对土壤宏量元素储量、理化性质、微生物群落活动等方面探究蚂蚁对土壤有机碳库的影响。本文综述了蚂蚁扰动对土壤有机碳循环过程特征的影响。蚂蚁筑巢改变了蚁穴土壤的微生境、微气候与土壤理化性质,并通过重构土壤微生物群落结构特征、调控地表植被演替过程与格局等方式,直接或间接的影响蚁巢中土壤有机碳来源、碳库分配过程、有机碳库稳定性、有机质微观分子特征等,在微域、局地乃至景观尺度上影响土壤有机碳的循环过程。未来研究应着重从量化蚂蚁扰动及其导致的环境因子波动对土壤碳通量变化的贡献、建立定量模型联系并统一蚂蚁影响下土壤碳循环过程、厘清蚂蚁影响土壤有机碳库稳定性的机制等方面开展深入研究,揭示蚂蚁作为“生态工程师”在调控土壤碳循环过程中的作用机制。     

林火干扰对森林生态系统土壤有机碳的影响研究进展

林火干扰是森林生态系统特殊而重要的生态因子,可改变生态系统的养分循环与能量传递。研究林火干扰对森林生态系统土壤有机碳的影响,有助于理解森林生态系统中土壤碳固持和碳循环过程,为制定科学合理的旨在减缓全球变化的林火管理策略具有重要意义。从4个方面阐述了林火干扰对森林生态系统土壤有机碳的影响及内在机制:分别从大尺度和小尺度两个方面阐述了林火干扰对土壤有机碳的影响及对森林生态系统碳循环与碳平衡的作用机制;探讨了不同林火干扰类型和林火干扰强度下,土壤活性有机碳对林火干扰的响应机制;阐明了林火干扰对土壤惰性有机碳的影响及作用机制;论述了林火干扰主要通过改变土壤有机碳的输入和输出过程进而影响土壤有机碳的稳定性及内在机制。最后提出了提高林火干扰对森林生态系统土壤有机碳影响定量化研究的4种路径选择:(1)全面比较研究不同林火干扰类型对土壤有机碳循环及其碳素再分配过程的功能特征;(2)进一步阐明林火干扰通过改变植被结构进而影响土壤生物群落结构,剖析土壤碳库循环的内在机制;(3)完善不同时空尺度下林火干扰对森林生态系统土壤碳库周转过程的定量化研究;(4)加强不同林火干扰类型土壤碳库稳定性差异的研究。     

Positive contribution of hydration structure on the surface of human lysozyme to the conformational stability

Water molecules make a hydration structure with the network of hydrogen bonds, covering on the surface of proteins. To quantitatively estimate the contribution of the hydration structure to protein stability, a series of hydrophilic mutant human lysozymes (Val to Ser, Tyr, Asp, Asn, and Arg) modified at three different positions on the surface, which are located in the alpha-helix (Val-110), the beta-sheet (Val-2), and the loop (Val-74), were constructed. Their thermodynamic parameters of denaturation and crystal structures were examined by calorimetry and by x-ray crystallography at 100 K, respectively. The introduced polar residues made hydrogen bonds with protein atoms and/or water molecules, sometimes changing the hydration structure around the mutation site. Changes in the stability of the mutant proteins can be evaluated by a unique equation that considers the conformational changes resulting from the substitutions. Using this analysis, the relationship between the changes in the stabilities and the hydration structures for mutant human lysozymes substituted on the surface could be quantitatively estimated. The analysis indicated that the hydration structure on protein surface plays an important role in determining the conformational stability of the protein.     

Molecular mechanisms of Fe2+-induced beta-lactoglobulin cold gelation

To get more insight into the mechanisms of cold gelation of beta-lactoglobulin (beta-lg), macroscopic and molecular structural changes during Fe(2+)-induced gelation of beta-lg were investigated using Fourier transform-infrared (FTIR) spectroscopy and rheological methods. The FTIR spectroscopy results show that, upon the preheating treatment (first step of gel process), native globular proteins are denatured and aggregated molecules are found in solution. The spectra are similar to those of gels obtained in the second step of the process upon incorporation of Fe, which suggests that aggregated molecules formed during the preheating treatment constitute the structural basis of the aggregation. However, the rheological data show that the aggregation is achieved via two molecular mechanisms, both of which are modulated by the iron concentration. At 30 mM of iron, gel formation is essentially controlled by van der Waals interactions, while at 10 mM of iron, hydrophobic interactions predominate. At the two concentrations, disulfide bonds contribute to gel consolidation, the effect being more pronounced at 10 mM of iron. These mechanisms lead to the formation of gels of different microstructures. At the highest iron concentration, a strong and rapid decrease in the repulsion forces is produced, resulting in random aggregation. At the lowest iron concentration, the iron diminishes the superficial charge of both molecules and aggregated molecules, facilitating the interaction among hydrophobic regions and leading to the growth of the aggregation in the preferential direction and to filamentous gel formation. This study provides a comprehensive view of the different modes of gelation.     

Utilization of fertilizer nitrogen by plants in soils of different structure

Summary A pot experiment was performed to study the influence of soil aggregation on wheat growth and consumption of nitrogen. Three aggregate size classes of a loess soil were prepared and were fertilized on four levels of nitrogen in two forms (mineral and organic).Potassium and phosphorus were added equally to all treatments.The original, poorly aggregated soil was streated with a soil conditioner and crushed subsequently to obtain the three aggregate size classes.The coarsely aggregated soil produced higher yields than the finely aggregated one. However, additions of mineral nitrogen tended to eliminate the yield differences. Additions of organic nitrogen, on the other hand, rather enlarged the yield differences between the coarsely and finely aggregated soils.     

G3 domains of aggrecan and PG-M/versican form intermolecular disulfide bonds that stabilize cell-matrix interaction

The extracellular matrix plays a critical role in maintaining tissue integrity. Among the matrix molecules, the large aggregating chondroitin sulfate proteoglycans are the major structural molecules and are the primary contributors to the stability for some tissues such as cartilage. The notable exceptions are nanomelic cartilage and arthritic cartilage: the former contains a point mutation leading to a stop codon before translating to the C-terminal G3 domain; the latter contains a large proportion of aggrecan from which the G3 domain has been cleaved. These phenomena suggest that the G3 domain may be important in cartilage stability. Here, we demonstrated for the first time that the G3 domains of aggrecan and another proteoglycan, PG-M/versican, formed intermolecular disulfide bonds, and all subdomains were involved. Further studies indicated that each of the 10 cysteine residues of the aggrecan G3 domain could potentially form intermolecular disulfide bonds in vitro. The disulfide bonds were disrupted in the presence of reducing reagent beta-mercaptoethanol and dithiothreitol. As a result, normal chondrocyte-matrix interaction was disrupted, and the structure of the extracellular matrix was altered. Furthermore, disruption of disulfide bonds also reduced the role of PG-M/versican G3 domain in mediating cell adhesion. Our study provides strong evidence of the importance of proteoglycan interactions through intermolecular disulfide bonds in cartilage firmness and cell-matrix stability.     

The effects of stubble retention and tillage practices on surface soil structure and hydraulic conductivity of a loess soil

The current cropping system of excessive tillage and stubble removal in the northwestern Loess Plateau of China is clearly unsustainable. A better understanding of tillage and stubble management on surface soil structure is vital for the development of effective soil conservation practices in the long term. Changes in surface soil structure and hydraulic properties were measured after 4 years of stubble management (stubble retained vs. stubble removed) under contrasting tillage practices (no-tillage vs. conventional tillage) in a silt loam soil (Los Orthic Entisol) in Dingxi, Gansu, the northwestern Loess Plateau, China. Our results indicated that after 4 years small but significant changes in soil properties were observed amongst the different tillage and stubble treatments. Surface soil (0–5 cm) under no-tillage with stubble retention had the highest water stability of macroaggregates (>250 μm), soil organic carbon (SOC) and saturated hydraulic conductivity. Significant correlation was found between water stable macro-aggregates and soil organic carbon content, indicating the importance of the latter on soil structural stability. The improvement in soil structure and stability was confirmed by higher soil hydraulic conductivity measurements. Consistently higher K_sat was detected in the no tillage with stubble retained soil compared to other treatments. Therefore, no-tillage with stubble retention practice is an effective management technique for improving physical quality of this fragile soil in the long term.     

NMR as a tool for elucidating the structures of circular and knotted proteins

Cyclotides are a recently discovered family of mini-proteins that have a head-to-tail cyclised backbone stabilized by a knotted arrangement of three disulfide bonds. They have a wide range of biological activities, including uterotonic, anti-bacterial, anti-HIV, and anti-tumour activity but their insecticidal activities suggest that their natural function is in plant defense. They are exceptionally resistant to chemical, enzymatic and thermal treatments because of their unique structural scaffold. This stability and resistance to proteolysis makes them a potentially valuable protein engineering tool at the interface of chemistry and biology: they have the structure of proteins but the stability and biophysical properties of organic molecules. In this review the role of NMR in defining the structures of cyclotides is described.     

Endocytosis and breakdown of ribonuclease oligomers by sinusoidal rat liver cells in vivo. I. Effect of size.

Aspects of protein structure determining endocytosis of proteins by sinusoidal rat liver cells in vivo have been studied, using cross-linked or aggregated derivatives of bovine pancreatic ribonuclease A (labelled with 125I) as probes. Ribonuclease was cross-linked by reaction with dimethylsuberimidate, a way of modification that does not change the charge of the protein. Monomer, dimer and polymer fractions were isolated by gel filtration and characterized in respect of size and number of amino groups modified. Maintenance of enzyme activity, stability of disulfide bonds, and lack of susceptibility to endoproteases showed that the cross-linking procedure did not result in gross conformational changes of the ribonuclease molecules. Monomer, dimer and polymer fractions were injected into nephrectomized rats and plasma clearance and uptake in liver and spleen were determined. About 30% of the injected polymer fraction was found in liver 15 min after injection; for dimer and monomer fractions values of 6% and 2% of the dose were found. Similar differences were found in spleen. Autoradiography, cell isolation, and subcellular fractionation showed that in liver the radioactive proteins were taken up in lysosomes of sinusoidal cells. Similar results were obtained with fractions of aggregated ribonuclease prepared by freeze-drying the protein from 50% acetic acid. Our results demonstrate that the rate of uptake of the ribonuclease derivatives is positively correlated with the size of the molecules. Similarity of the results obtained with cross-linked and aggregated fractions suggests that the number of ribonuclease 'subunits'/molecule, rather than the procedures used to prepare the polymers, determine the rate of uptake by liver and spleen.     

The effect of additional disulfide bonds on the stability and folding of ribonuclease A

The significant contribution of disulfide bonds to the conformational stability of proteins is generally considered to result from an entropic destabilization of the unfolded state causing a faster escape of the molecules to the native state. However, the introduction of extra disulfide bonds into proteins as a general approach to protein stabilization yields rather inconsistent results. By modeling studies, we selected positions to introduce additional disulfide bonds into ribonuclease A at regions that had proven to be crucial for the initiation of the folding or unfolding process, respectively. However, only two out of the six variants proved to be more stable than unmodified ribonuclease A. The comparison of the thermodynamic and kinetic data disclosed a more pronounced effect on the unfolding reaction for all variants regardless of the position of the extra disulfide bond. Native-state proteolysis indicated a perturbation of the native state of the destabilized variants that obviously counterbalances the stability gain by the extra disulfide bond.     

Mechanical stability of helical beta-peptides and a comparison of explicit and implicit solvent models

Synthetic β-peptide oligomers have been shown to form stable folded structures analogous to those encountered in naturally occurring proteins. Literature studies have speculated that the conformational stability of β-peptides is greater than that of α-peptides. Direct measurements of that stability, however, are not available. Molecular simulations are used in this work to quantify the mechanical stability of four helical β-peptides. This is achieved by subjecting the molecules to tension. The potential of mean force associated with the resulting unfolding process is determined using both an implicit and an explicit solvent model. It is found that all four molecules exhibit a highly stable helical structure. It is also found that the energetic contributions to the potential of mean force do not change appreciably when the molecules are stretched in explicit water. In contrast, the entropic contributions decrease significantly. As the peptides unfold, a loss of intramolecular energy is compensated by the formation of additional water-peptide hydrogen bonds. These entropic effects lead in some cases to a loss of stability upon cooling the peptides, a phenomenon akin to the cold denaturing of some proteins. While the location of the free energy minimum and the structural helicity of the peptides are comparable in the implicit-solvent and explicit-water cases, it is found that, in general, the helical structure of the molecules is more stable in the implicit solvent model than in explicit water.     

稻草覆盖和香根草篱对红壤水稳性团聚体组成及有机碳含量的影响

基于植物篱和秸秆覆盖控制红壤坡耕地水土流失的长期定位试验,研究香根草篱(H)、稻草覆盖(M)、香根草篱+稻草覆盖(HM)水保措施下红壤水稳性团聚体组成及有机碳分布特征。结果表明:与常规等高农作模式(CK)相比,草篱、稻草覆盖、草篱+稻草覆盖模式下土壤总有机碳含量提高0.07—2.42 g/kg。草篱对土壤团聚体组成及其结合有机碳的影响在篱内效果显著,随着与草篱距离增大影响减弱。草篱和稻草覆盖对土壤团聚体组成和结合有机碳含量的影响不同,草篱主要增加2 mm水稳性团聚体含量及其结合有机碳含量,稻草覆盖增加0.25 mm水稳性团聚体含量及其结合有机碳含量。综合来看,草篱和稻草覆盖相结合对改善坡面土壤结构作用稳定。土壤有机碳含量较高时,土壤总有机碳含量与粒径2mm的大团聚体有机碳含量呈显著正相关(r=0.659);随着有机碳含量降低,土壤总有机碳含量与土壤0.25—0.053 mm和0.053 mm微小团聚体碳含量相关性逐渐增大。     

Old and stable soil organic matter is not necessarily chemically recalcitrant: implications for modeling concepts and temperature sensitivity

Soil carbon turnover models generally divide soil carbon into pools with varying intrinsic decomposition rates. Although these decomposition rates are modified by factors such as temperature, texture, and moisture, they are rationalized by assuming chemical structure is a primary controller of decomposition. In the current work, we use near edge X‐ray absorption fine structure (NEXAFS) spectroscopy in combination with differential scanning calorimetry (DSC) and alkaline cupric oxide (CuO) oxidation to explore this assumption. Specifically, we examined material from the 2.3–2.6 kg L^?1 density fraction of three soils of different type (Oxisol, Alfisol, Inceptisol). The density fraction with the youngest ¹⁴C age (Oxisol, 107 years) showed the highest relative abundance of aromatic groups and the lowest O‐alkyl C/aromatic C ratio as determined by NEXAFS. Conversely, the fraction with the oldest C (Inceptisol, 680 years) had the lowest relative abundance of aromatic groups and highest O‐alkyl C/aromatic C ratio. This sample also had the highest proportion of thermally labile materials as measured by DSC, and the highest ratio of substituted fatty acids to lignin phenols as indicated by CuO oxidation. Therefore, the organic matter of the Inceptisol sample, with a ¹⁴C age associated with ‘passive’ pools of carbon (680 years), had the largest proportion of easily metabolizable organic molecules with low thermodynamic stability, whereas the organic matter of the much younger Oxisol sample (107 years) had the highest proportion of supposedly stable organic structures considered more difficult to metabolize. Our results demonstrate that C age is not necessarily related to molecular structure or thermodynamic stability, and we suggest that soil carbon models would benefit from viewing turnover rate as codetermined by the interaction between substrates, microbial actors, and abiotic driving variables. Furthermore, assuming that old carbon is composed of complex or ‘recalcitrant’ compounds will erroneously attribute a greater temperature sensitivity to those materials than they may actually possess.     

陇东雨养苹果覆膜对土壤团聚体结构稳定性与细根分布的影响

不同的果园管理方式可影响果树根系生长、分布与土壤团聚体稳定性、有机碳固存,进而改变“根-土”复合体响应关系。对西北陇东旱塬不同覆膜年限(2 a、4 a和6 a)苹果园表层土壤(0—20 cm)细根生长进行调查,并采用干筛法和湿筛法相结合的方式对土壤团聚体进行分级(>2 mm, 0.5—2 mm, 0.25—0.5 mm和<0.25 mm)。计算团聚体稳定性参数[> 0.25 mm机械稳定性团聚体含量(DR_0.25)、> 0.25 mm水稳性团聚体含量(WR_0.25)、平均重量直径(MWD)、平均几何直径(GMD)、团聚体破坏率(PAD)、水稳系数(WSC)]和团聚体有机碳含量。分析细根生长与土壤物理结构对长期覆膜的响应,探明土壤团聚体稳定性与有机碳固持关系,揭示黄绵土物理结构稳定机制。结果表明：6 a处理通过增加表层土壤黏粒和物理性黏粒比例,改变孔隙结构,抑制细根生长,其根量、根长和根表面积仅为对照(CK)的20.97%、24.66%和41.25%;降低表层土壤团聚体力稳性,其DR_0.25、机械稳...     

The interplay between soil structure,roots, and microbiota as a determinant of plant–soil feedback

Plant–soil feedback (PSF) can influence plant community structure via changes in the soil microbiome. However, how these feedbacks depend on the soil environment remains poorly understood. We hypothesized that disintegrating a naturally aggregated soil may influence the outcome of PSF by affecting microbial communities. Furthermore, we expected plants to differentially interact with soil structure and the microbial communities due to varying root morphology. We carried out a feedback experiment with nine plant species (five forbs and four grasses) where the “training phase” consisted of aggregated versus disintegrated soil. In the feedback phase, a uniform soil was inoculated in a fully factorial design with soil washings from conspecific‐ versus heterospecific‐trained soil that had been either disintegrated or aggregated. This way, the effects of prior soil structure on plant performance in terms of biomass production and allocation were examined. In the training phase, soil structure did not affect plant biomass. But on disintegrated soil, plants with lower specific root length (SRL) allocated more biomass aboveground. PSF in the feedback phase was negative overall. With training on disintegrated soil, conspecific feedback was positively correlated with SRL and significantly differed between grasses and forbs. Plants with higher SRL were likely able to easily explore the disintegrated soil with smaller pores, while plants with lower SRL invested in belowground biomass for soil exploration and seemed to be more susceptible to fungal pathogens. This suggests that plants with low SRL could be more limited by PSF on disintegrated soils of early successional stages. This study is the first to examine the influence of soil structure on PSF. Our results suggest that soil structure determines the outcome of PSF mediated by SRL. We recommend to further explore the effects of soil structure and propose to include root performance when working with PSF.     

A comparative study on the stability and structure of two different green fluorescent proteins in organic co-solvent systems

Green fluorescent protein (GFP) has been used as a reporter marker in a wide range of biological and bioengineering studies. The expanded use of GFP in the field of biosensors, biochips and bio-conjugations requires the stability of GFP in organic co-solvent systems. This prompted us to examine the kinetic stability of two different GFP sequences, n-GFP and s-GFP, showing different folding robustness and thermodynamic stability, under a range of organic co-solvent systems. n-GFP and s-GFP are variants whose biophysical properties are comparable to wild type and super folder GFPs, respectively. The stability of n-GFP and s-GFP in 50% water-miscible organic solvents showed that s-GFP with higher thermodynamic stability exhibited much higher stability against organic solvents than n-GFP, which has lower thermodynamic stability. s-GFP was quite stable even in 90% organic solvents. Circular dichroism analysis confirmed that s-GFP maintained its native structure in organic co-solvent systems, whereas n-GFP showed structural variations under these conditions. Four highly fluctuating loop regions were identified from molecular dynamic simulations under the organic cosolvent conditions. A structural comparison of n-GFP and s-GFP suggested that the improved kinetic stability of s-GFP was due to its larger number of hydrogen bonds and salt-bridges that were present in four loop regions. This study suggests that thermodynamically stable s-GFP can be a good choice for use under harsh organic co-solvent conditions.