Hierarchical saturation of soil carbon pools near a natural CO2 spring

Soil has been identified as a possible carbon (C) sink to mitigate increasing atmospheric CO₂ concentration. However, several recent studies have suggested that the potential of soil to sequester C is limited and that soil may become saturated with C under increasing CO₂ levels. To test this concept of soil C saturation, we studied a gley and organic soil at a grassland site near a natural CO₂ spring. Total and aggregate‐associated soil organic C (SOC) concentration showed a significant increase with atmospheric CO₂ concentration. An asymptotic function showed a better fit of SOC and aggregation with CO₂ level than a linear model. There was a shift in allocation of total C from smaller size fractions to the largest aggregate fraction with increasing CO₂ concentration. Litter inputs appeared to be positively related to CO₂ concentration. Based on modeled function parameters and the observed shift in the allocation of the soil C from small to large aggregate‐size classes, we postulate that there is a hierarchy in C saturation across different SOC pools. We conclude that the asymptotic response of SOC concentration at higher CO₂ levels indicates saturation of soil C pools, likely because of a limit to physical protection of SOC.     

Reliability and stability of dream recall frequency.

Although a large number of studies investigating factors affecting dream recall frequency (DRF) have been carried out, research investigating the reliability and stability of DRF is scarce. Dream diaries of 196 participants kept over at least 28 days were analyzed. The results of the present study indicate that a time period of 2 weeks was sufficient to obtain reliable measurements of interindividual differences in DRF. Despite the high day-to-day fluctuations of dream recall, the stability of this variable was very high. Studies that investigate the stability of DRF by means of other methodological approaches (e.g., questionnaire scales, laboratory awakenings) and over longer time periods (e.g., 1 year) should be carried out to complement the present findings. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The Antibody Light-Chain Linker Regulates Domain Orientation and Amyloidogenicity

The antibody light chain (LC) consists of two domains and is essential for antigen binding in mature immunoglobulins. The two domains are connected by a highly conserved linker that comprises the structurally important Arg108 residue. In antibody light chain (AL) amyloidosis, a severe protein amyloid disease, the LC and its N-terminal variable domain (V_L) convert to fibrils deposited in the tissues causing organ failure. Understanding the factors shaping the architecture of the LC is important for basic science, biotechnology and for deciphering the principles that lead to fibril formation. In this study, we examined the structure and properties of LC variants with a mutated or extended linker. We show that under destabilizing conditions, the linker modulates the amyloidogenicity of the LC. The fibril formation propensity of LC linker variants and their susceptibility to proteolysis directly correlate implying an interplay between the two LC domains. Using NMR and residual dipolar coupling-based simulations, we found that the linker residue Arg108 is a key factor regulating the relative orientation of the V_L and C_L domains, keeping them in a bent and dense, but still flexible conformation. Thus, inter-domain contacts and the relative orientation of V_L and C_L to each other are of major importance for maintaining the structural integrity of the full-length LC.     

定点突变提高苯丙氨酸羟化酶的热稳定性

嗜热菌中,蛋白质存在Ala替换Gly以及Arg替换Lys的趋势。为了提高紫色色杆菌来源的苯丙氨酸羟化酶的热稳定性,将该酶中所有Gly突变成Ala,Lys突变成Arg,筛选获得热稳定性提高的突变体,并进行组合突变,对突变酶的酶学性质进行研究。结果表明,突变酶K94R和G221A在50℃的半衰期分别为26.2 min、16.8 min,比原始酶(9.0 min)分别提高了1.9倍、0.9倍,同时组合突变酶K94R/G221A在50℃处理1 h后仍保留65.6%的酶活,比原始酶(8.6%)高出6.6倍。圆二色谱结果显示原始酶和突变酶K94R、G221A及K94R/G221A的T_m值分别为51.5℃、53.8℃、53.1℃和54.8℃。蛋白三维结构模拟推测突变体热稳定性提高机理为:突变体K94R中Arg94与Ile95之间形成额外氢键,稳定其所在的柔性区域;突变体G221A中Ala221与Leu281产生疏水作用,稳定酶分子C-端柔性区。该研究结果为蛋白质热稳定性改造提供了参考,也为苯丙氨酸羟化酶在功能性食品领域的应用奠定了基础。     

产酸克雷伯氏菌赖氨酸脱羧酶的异源表达及粗酶性质

赖氨酸脱羧酶,可以催化赖氨酸脱羧生成戊二胺。戊二胺是重要的平台化合物,可以合成新型聚酰胺材料、脂肪族异氰酸酯等新材料。本研究对来自于产酸克雷伯氏菌的赖氨酸脱羧酶进行异源表达。以pUC18质粒为载体,将来源于产酸克雷伯氏菌的赖氨酸脱羧酶基因ldc克隆到大肠杆菌,得到菌株LN18。在添加0.5 mmol/L IPTG的LB培养基中,对LN18进行摇瓶培养,发酵液酶活可达到35 U/g发酵液,从发酵液制备的赖氨酸脱羧酶粗酶蛋白的酶活可以达到30 000 U/g粗蛋白。产酸克雷伯氏菌赖氨酸脱羧粗酶蛋白大小约80 kDa,粗酶的最适温度和pH值分别为55℃和5.5,与文献中报道的大肠杆菌的赖氨酸脱羧酶Cad A在pH 8.0几乎没有酶活不同,产酸克雷伯氏菌的赖氨酸脱羧酶在pH 8.0的酶活达到最优pH下酶活的30%以上。金属离子对酶活有一定的影响,Mg~(2+)对酶活有促进作用,Fe~(2+)、Zn~(2+)、Ca~(2+)有一定的抑制作用。     

长白山白桦林不同演替阶段土壤有机碳组分的变化

为了解长白山天然针阔混交林群落恢复演替土壤碳储量的变化,采用空间代替时间的方法,选取白桦幼龄林、白桦中龄林、白桦成熟林、阔叶红松成熟林和阔叶红松过熟林5个不同演替序列,研究其土壤总有机碳(SOC)、易氧化有机碳(ROC)、微生物生物量碳(MBC)及颗粒有机碳(POC)含量。结果表明:随着白桦林从早期到晚期的演替,SOC、MBC、ROC、POC以及土壤全氮、全磷和碳氮比(C/N)均呈现先逐渐增加后保持稳定的规律。随着土层深度的增加,SOC、MBC、ROC和POC含量均显著降低(P0.05),5个演替序列内ROC/SOC和POC/SOC的变化范围分别为12.91%~47.95%和14.21%~69.46%。相关分析表明:MBC、ROC和POC含量与土壤总有机碳(SOC)含量呈极显著正相关(P0.01),SOC、MBC、ROC和POC含量与全氮、全磷及碳氮比呈极显著正相关(P0.01)。研究结果为了解白桦林在演替过程中土壤有机碳的稳定性变化和固碳潜力提供数据支持。     

A short motif in Arabidopsis CDK inhibitor ICK1 decreases the protein level,probably through a ubiquitin‐independent mechanism

The ICK/KRP family of cyclin‐dependent kinase (CDK) inhibitors modulates the activity of plant CDKs through protein binding. Previous work has shown that changing the levels of ICK/KRP proteins by overexpression or downregulation affects cell proliferation and plant growth, and also that the ubiquitin proteasome system is involved in degradation of ICK/KRPs. We show in this study that the region encompassing amino acids 21 to 40 is critical for ICK1 levels in both Arabidopsis and yeast. To determine how degradation of ICK1 is controlled, we analyzed the accumulation of hemagglutinin (HA) epitope‐tagged ICK1 proteins in yeast mutants defective for two ubiquitin E3 ligases. The highest level of HA‐ICK1 protein was observed when both the N‐terminal 1–40 sequence was removed and the SCF (SKP1–Cullin1–F‐box complex) function disrupted, suggesting the involvement of both SCF‐dependent and SCF‐independent mechanisms in the degradation of ICK1 in yeast. A short motif consisting of residues 21–30 is sufficient to render green fluorescent protein (GFP) unstable in plants and had a similar effect in plants regardless of whether it was fused to the N‐terminus or C‐terminus of GFP. Furthermore, results from a yeast ubiquitin receptor mutant rpn10Δ indicate that protein ubiquitination is not critical in the degradation of GFP‐ICK1^1–40 in yeast. These results thus identify a protein‐destabilizing sequence motif that does not contain a typical ubiquitination residue, suggesting that it probably functions through an SCF‐independent mechanism.     

Boosting protein stability with the computational design of β‐sheet surfaces

β‐sheets often have one face packed against the core of the protein and the other facing solvent. Mutational studies have indicated that the solvent‐facing residues can contribute significantly to protein stability, and that the preferred amino acid at each sequence position is dependent on the precise structure of the protein backbone and the identity of the neighboring amino acids. This suggests that the most advantageous methods for designing β‐sheet surfaces will be approaches that take into account the multiple energetic factors at play including side chain rotamer preferences, van der Waals forces, electrostatics, and desolvation effects. Here, we show that the protein design software Rosetta, which models these energetic factors, can be used to dramatically increase protein stability by optimizing interactions on the surfaces of small β‐sheet proteins. Two design variants of the β‐sandwich protein from tenascin were made with 7 and 14 mutations respectively on its β‐sheet surfaces. These changes raised the thermal midpoint for unfolding from 45°C to 64°C and 74°C. Additionally, we tested an empirical approach based on increasing the number of potential salt bridges on the surfaces of the β‐sheets. This was not a robust strategy for increasing stability, as three of the four variants tested were unfolded.