蚯蚓在生态系统中的作用

蚯蚓能够对许多决定土壤肥力的过程产生重要影响, 被称为“生态系统工程师”。它通过取食、消化、排泄和掘穴等活动在其体内外形成众多的反应圈, 从而对生态系统的生物、化学和物理过程产生影响。蚯蚓在生态系统中既是消费者、分解者, 又是调节者, 它在生态系统中的功能具体表现在: (1) 对土壤中有机质分解和养分循环等关键过程的影响; (2) 对土壤理化性质的影响; (3) 与植物、微生物及其他动物的相互作用。蚯蚓活动及其在生态系统中的功能受蚯蚓生态类群、种群大小、植被、母岩、气候、时间尺度以及土地利用历史的综合控制。蚯蚓外来种入侵与生态系统的关系以及蚯蚓对全球变化的响应和影响是两个值得关注的问题。土壤本身的复杂性, 蚯蚓自然历史和生物地理学知识的缺乏, 野外控制蚯蚓群落方法的滞后等都限制了蚯蚓生态学的发展。其他新技术如研究养分循环的碳氮同位素分析和揭示土壤微结构的图像分析等技术的应用是蚯蚓生态功能研究的迫切需要。     

Discovery and optimization of potent broad-spectrum arenavirus inhibitors derived from benzimidazole and related heterocycles

A series of potent arenavirus inhibitors sharing a benzimidazole core were previously reported by our group. SAR studies were expanded beyond the previous analysis, which involved the attached phenyl rings and methylamino linker portion, to include modifications focused on the benzimidazole core. These changes included the introduction of various substituents to the bicyclic benzimidazole ring system along with alternate core heterocycles. Many of the analogs containing alternate nitrogen-based bicyclic ring systems were found to retain antiviral potency compared to the benzimidazole series from which we derived our lead compound, ST-193. In fact, 21h, built on an imidazopyridine core, possessed a near tenfold increase in potency against Lassa virus pseudotypes compared to ST-193. As found with the benzimidazole series, broad-spectrum arenavirus activity was also observed for a number of the analogs discovered during this study.     

Mapping the glycoxidation product Nε-carboxymethyllysine in the milk proteome

Milk processing leads to severe protein damage caused by the formation of nonenzymatic posttranslational modifications (nePTMs), such as glycation and glycoxidation. As a result, the technological and nutritional function of milk proteins can be critically altered. The present study investigated the protein-specific distribution of the glycoxidation product N(ε) -carboxymethyllysine (CML) in the proteome of processed milk. For this purpose, raw milk and heated milk were separated by 1-D or 2-DE. The distribution of CML in the milk proteome was examined by immunoblotting. The changes in the protein composition that occurred during heating were monitored by Coomassie staining. Relative modification rates were measured for the major milk protein fractions after 30 and 60 min of heating at 120°C and normalized to the content of the respective protein fraction in the samples. The highest glycoxidation rates were detected in the high molecular weight aggregates that are generated during heating. The casein fraction and the whey protein β-lactoglobulin were affected in a similar manner. The relevance of the results for industrial milk processing was confirmed by analyzing several commercial milk products accordingly. The presented approach allows nonenzymatic posttranslational modification mapping of the entire milk proteome.     

Structure of Three-Way DNA Junctions 1. Non-Planar DNA Geometry

Abstract

Three-way junctions were obtained by annealing two synthetic DNA-oligomers. One of the strands contains a short palindrome sequence, leading to the formation of a hairpin with four base pairs in the stem and four bases in the loop. Another strand is complementary to the linear arms of the first hairpin-containing strand. Both strands were annealed to form a three-way branched structure with sticky ends on the linear arms. The branched molecules were ligated, and the ligation mixture was analysed on a two-dimensional gel in conditions which separated linear and circular molecules. Analysis of 2D-electrophoresis data shows that circular molecules with high mobility are formed. Formation of circular molecules is indicative of bends between linear arms. We estimate the magnitude of the angle between linear arms from the predominant size of the circular molecules formed. When the junction-to-junction distance is 20–21 bp, trimers and tetramers are formed predominately, giving an angle between linear arms as small as 60–90°. Rotation of the hairpin position in the three- way junction allowed us to measure angles between other arms, yielding similar values. These results led us to conclude that the three-way DNA junction possesses a non-planar pyramidal geometry with 60–90° between the arms. Computer modeling of the three-way junction with 60° pyramidal geometry showed a predominantly B-form structure with local distortions at the junction points that diminish towards the ends of the helices. The size distributions of circular molecules are rather broad indicating a dynamic flexibility of three-way DNA junctions.     

Sampling and scoring: A marriage made in heaven

Most structure prediction algorithms consist of initial sampling of the conformational space, followed by rescoring and possibly refinement of a number of selected structures. Here we focus on protein docking, and show that while decoupling sampling and scoring facilitates method development, integration of the two steps can lead to substantial improvements in docking results. Since decoupling is usually achieved by generating a decoy set containing both non‐native and near‐native docked structures, which can be then used for scoring function construction, we first review the roles and potential pitfalls of decoys in protein–protein docking, and show that some type of decoys are better than others for method development. We then describe three case studies showing that complete decoupling of scoring from sampling is not the best choice for solving realistic docking problems. Although some of the examples are based on our own experience, the results of the CAPRI docking and scoring experiments also show that performing both sampling and scoring generally yields better results than scoring the structures generated by all predictors. Next we investigate how the selection of training and decoy sets affects the performance of the scoring functions obtained. Finally, we discuss pathways to better alignment of the two steps, and show some algorithms that achieve a certain level of integration. Although we focus on protein–protein docking, our observations most likely also apply to other conformational search problems, including protein structure prediction and the docking of small molecules to proteins.Proteins 2013; 81:1874–1884. © 2013 Wiley Periodicals, Inc.     

Deepened winter snow cover enhances net ecosystem exchange and stabilizes plant community composition and productivity in a temperate grassland

Global warming has greatly altered winter snowfall patterns, and there is a trend towards increasing winter snow in semi‐arid regions in China. Winter snowfall is an important source of water during early spring in these water‐limited ecosystems, and it can also affect nutrient supply. However, we know little about how changes in winter snowfall will affect ecosystem productivity and plant community structure during the growing season. Here, we conducted a 5‐year winter snow manipulation experiment in a temperate grassland in Inner Mongolia. We measured ecosystem carbon flux from 2014 to 2018 and plant biomass and species composition from 2015 to 2018. We found that soil moisture increased under deepened winter snow in early growing season, particularly in deeper soil layers. Deepened snow increased the net ecosystem exchange of CO₂ (NEE) and reduced intra‐ and inter‐annual variation in NEE. Deepened snow did not affect aboveground plant biomass (AGB) but significantly increased root biomass. This suggested that the enhanced NEE was allocated to the belowground, which improved water acquisition and thus contributed to greater stability in NEE in deep‐snow plots. Interestingly, the AGB of grasses in the control plots declined over time, resulting in a shift towards a forb‐dominated system. Similar declines in grass AGB were also observed at three other locations in the region over the same time frame and are attributed to 4 years of below‐average precipitation during the growing season. By contrast, grass AGB was stabilized under deepened winter snow and plant community composition remained unchanged. Hence, our study demonstrates that increased winter snowfall may stabilize arid grassland systems by reducing resource competition, promoting coexistence between plant functional groups, which ultimately mitigates the impacts of chronic drought during the growing season.     

Soil acidification reduces the effects of short‐term nutrient enrichment on plant and soil biota and their interactions in grasslands

Soil nitrogen (N) and phosphorus (P) contents, and soil acidification have greatly increased in grassland ecosystems due to increased industrial and agricultural activities. As major environmental and economic concerns worldwide, nutrient enrichment and soil acidification can lead to substantial changes in the diversity and structure of plant and soil communities. Although the separate effects of N and P enrichment on soil food webs have been assessed across different ecosystems, the combined effects of N and P enrichment on multiple trophic levels in soil food webs have not been studied in semiarid grasslands experiencing soil acidification. Here we conducted a short‐term N and P enrichment experiment in non‐acidified and acidified soil in a semiarid grassland on the Mongolian Plateau. We found that net primary productivity was not affected by N or P enrichment alone in either non‐acidified or acidified soil, but was increased by combined N and P enrichment in both non‐acidified and acidified soil. Nutrient enrichment decreased the biomass of most microbial groups in non‐acidified soil (the decrease tended to be greatest with combined N and P enrichment) but not in acidified soil, and did not affect most soil nematode variables in non‐acidified or acidified soil. Nutrient enrichment also changed plant and microbial community structure in non‐acidified but not in acidified soil, and had no effect on nematode community structure in non‐acidified or acidified soil. These results indicate that the responses to short‐term nutrient enrichment were weaker for higher trophic groups (nematodes) than for lower trophic groups (microorganisms) and primary producers (plants). The findings increase our understanding of the effects of nutrient enrichment on multiple trophic levels of soil food webs, and highlight that soil acidification, as an anthropogenic stressor, reduced the responses of plants and soil food webs to nutrient enrichment and weakened plant–soil interactions.