Altered dynamics upon oligomerization corresponds to key functional sites

It is known that over half of the proteins encoded by most organisms function as oligomeric complexes. Oligomerization confers structural stability and dynamics changes in proteins. We investigate the effects of oligomerization on protein dynamics and its functional significance for a set of 145 multimeric proteins. Using coarse‐grained elastic network models, we inspect the changes in residue fluctuations upon oligomerization and then compare with residue conservation scores to identify the functional significance of these changes. Our study reveals conservation of about ½ of the fluctuations, with ¼ of the residues increasing in their mobilities and ¼ having reduced fluctuations. The residues with dampened fluctuations are evolutionarily more conserved and can serve as orthosteric binding sites, indicating their importance. We also use triosephosphate isomerase as a test case to understand why certain enzymes function only in their oligomeric forms despite the monomer including all required catalytic residues. To this end, we compare the residue communities (groups of residues which are highly correlated in their fluctuations) in the monomeric and dimeric forms of the enzyme. We observe significant changes to the dynamical community architecture of the catalytic core of this enzyme. This relates to its functional mechanism and is seen only in the oligomeric form of the protein, answering why proteins are oligomeric structures. Proteins 2017; 85:1422–1434. © 2017 Wiley Periodicals, Inc.     

长白山针阔混交林不同演替阶段群落系统发育和功能性状结构

群落构建一直是生态学研究的热点,基于系统发育和功能性状量化生境过滤、竞争排斥以及随机过程在群落构建中的作用,能够深入理解群落构建机制。本研究以长白山针阔混交林不同演替阶段的3个5.2 hm~2样地(次生杨桦林、次生针阔混交林、原始椴树红松林)为平台,基于被子植物分类系统Ⅲ(Angiosperm Classification System,APGⅢ)构建的系统发育树和7个关键功能性状(叶面积、比叶面积、叶片厚度、叶片氮含量、叶片磷含量、氮磷比、最大树高),结合环境数据,分析不同演替阶段群落系统发育和功能性状结构。研究表明:(1)各演替阶段7个植物功能性状都表现出显著的系统发育信号,表明植物功能性状受系统发育历史影响;(2)系统发育和功能性状结构在不同演替阶段和不同径级均为非随机状态。随着演替的推进群落系统发育和功能性状结构由聚集走向发散;随着径级的增加,系统发育和功能性状结构的聚集程度减小,表明随着演替阶段的进行和径级增大,竞争性排斥的作用逐渐明显;(3)各演替阶段系统发育和功能性状的周转都为非随机且不同因子对两者的解释力度存在差异。演替早期空间距离的解释力度小于环境距离,说明生境过滤在群落构建中的重要性,而在演替后期空间距离的解释力度大于环境距离,验证了扩散限制在群落构建中的重要性。     

An annotated checklist of the fish fauna of the river systems draining the Kahuzi-Biega National Park (Upper Congo: Eastern DR Congo)

The Kahuzi-Biega National Park (KBNP), situated mainly in the Eastern Highlands Ecoregion of the Upper Congo basin, is drained by the Lowa and Ulindi rivers, and some western affluents of Lake Kivu. In this study, the first list of the fish diversity of these systems is provided based on museum collections and complemented, for the Lowa River system and the western Lake Kivu affluents, with recently collected specimens (2013–2017). A total of 118 species are reported from the Lowa basin, 22 from the Ulindi basin and seven from these Lake Kivu affluents. Within the Lowa and Ulindi, respectively, five and one species, all cichlids, have been introduced. Currently, 51 species are reported from within the park, only two of which have been reported from the highlands, i.e., Amphilius kivuensis from the Luha, the source of the Luka River, and Clarias liocephalus from the headwaters of the Lake Kivu’ affluents. With a total of 30 species, Cyprinidae is by far the largest family, representing 25% of the total species diversity of the Lowa basin. It is followed by Mormyridae with 13 species (11%), Alestidae and Mochokidae with 10 species each (8%), Clariidae and Amphiliidae with eight species (7%), and Distichodontidae with six species (5%). Seven new species for science were discovered and 11 species were found to be endemic to the Lowa system. Although further exploration is needed, this underscores the importance of the KBNP in protecting the fish fauna of the Lowa basin but also highlights the park's limited coverage of the fish fauna of the Lowa basin.     

Long‐term temporal and spatial trends in eutrophication status of the Baltic Sea

Much of the Baltic Sea is currently classified as ‘affected by eutrophication’. The causes for this are twofold. First, current levels of nutrient inputs (nitrogen and phosphorus) from human activities exceed the natural processing capacity with an accumulation of nutrients in the Baltic Sea over the last 50–100 years. Secondly, the Baltic Sea is naturally susceptible to nutrient enrichment due to a combination of long retention times and stratification restricting ventilation of deep waters. Here, based on a unique data set collated from research activities and long‐term monitoring programs, we report on the temporal and spatial trends of eutrophication status for the open Baltic Sea over a 112‐year period using the HELCOM Eutrophication Assessment Tool (HEAT 3.0). Further, we analyse variation in the confidence of the eutrophication status assessment based on a systematic quantitative approach using coefficients of variation in the observations. The classifications in our assessment indicate that the first signs of eutrophication emerged in the mid‐1950s and the central parts of the Baltic Sea changed from being unaffected by eutrophication to being affected. We document improvements in eutrophication status that are direct consequences of long‐term efforts to reduce the inputs of nutrients. The reductions in both nitrogen and phosphorus loads have led to large‐scale alleviation of eutrophication and to a healthier Baltic Sea. Reduced confidence in our assessment is seen more recently due to reductions in the scope of monitoring programs. Our study sets a baseline for implementation of the ecosystem‐based management strategies and policies currently in place including the EU Marine Strategy Framework Directives and the HELCOM Baltic Sea Action Plan.     

Microbial biofilm inoculants benefit growth and yield of chrysanthemum varieties under protected cultivation through enhanced nutrient availability

Protected cultivation of ornamental flowers, as a commercial venture, becomes less profitable with excessive use of fertilizers. The present study examined the influence of microbial biofilm inoculants (Anabaena–Azotobacter, Anabaena–Trichoderma and Trichoderma–Azotobacter) on the availability of soil nutrients and structure of rhizosphere microbial communities in three varieties of chrysanthemum (var. White Star, Thai Chen Queen and Zembla). Varietal-specific responses in growth, enzyme activities, flower yield of plants and availability of soil nutrients were recorded. Dehydrogenase activity was highest in var. White Star treated with the Anabaena–Trichoderma biofilm inoculants. The Anabaena–Azotobacter inoculant enhanced the availability of nitrogen, phosphorus and micronutrients in the soil, besides 40–50% increase in soil organic carbon, as compared to carrier alone or no inoculation. PCR-DGGE profiling of the cyanobacterial communities and qPCR quantification of 16S rRNA abundance of bacteria, archaea and cyanobacteria in the rhizosphere soils, revealed the stronger influences of these inoculants, especially in var. Zembla. Principal Component Analysis (PCA) helped to illustrate that the enhanced microbe-mediated availability of soil macro-and micronutrients, except iron content (Fe), was the most influential factor facilitating improved plant growth and yield parameters. The Anabaena–Azotobacter, and Anabaena–Trichoderma biofilm inoculants, proved superior in all three chrysanthemum varieties.     

福建平潭岛海岸不同演化阶段草丛沙堆表面老鼠艻叶水势日变化特征

以福建省平潭岛海岸不同演化阶段草丛沙堆表面典型沙生植物老鼠艻为对象,研究其叶水势日变化特征及其影响因素.结果表明: 老鼠艻叶水势日变化以“W”型为主,午间出现短暂升高现象.发育阶段沙堆表面老鼠艻叶水势日均值较稳定阶段高,且夜间水分恢复能力更强;老鼠艻叶水势与大气水势和相对湿度呈显著正相关,与气温呈显著负相关,但与不同深度土壤水势无显著相关性;发育阶段沙堆丘间地老鼠艻叶水势在10:00—16:00皆高于迎风坡和背风坡,迎风坡除10:00和12:00外皆低于背风坡.不同坡位叶水势日变异程度表现为背风坡>迎风坡>丘间地,但无显著差异.沙堆迎风坡老鼠艻叶水势与大气水势和相对湿度呈显著正相关,与气温呈显著负相关;沙堆背风坡和丘间地老鼠艻叶水势与气象因子有一定相关性,但不显著.     

The influence of ants on patterns of colonization and establishment within a set of coexisting lycaenid butterflies in a south-east Asian tropical rain forest

In Peninsular Malaysia ten species of lycaenid butterflies use leaf flushes or inflorescences of the legume tree Saraca thaipingensis as larval hostplant. Resource partitioning among these species is regulated by a complex mixture of patterns of interaction with ants. Females of obligately myrmecophilous species lay their eggs exclusively on trees colonized by their specific host ants. On trees colonized by weaver ants, only specialist mutualists adapted to these territorial ants are able to survive, while larvae of other species are killed. The formicine ant Cladomyrma petalae, which inhabits hollow twigs of the myrmecophytic hostplant, likewise precludes oviposition by female butterflies. Lycaenid larvae confronted with this ant species never survive, but one concealed feeding species (Jamides caeruleus) escapes removal due to the cryptic life-habits of the larvae. Two facultative myrmecophiles associate in a mutualistic way with a wide and largely overlapping range of ant genera which forage at the extrafloral nectaries of leaf flushes. One species (Cheritra freja) is not myrmecophilous, but is tolerated by all but the most territorial ants. Ant-dependent hostplant selection and egg-clustering characterize the obligate mutualists, whereas facultative myrmecophiles and the non-myrmecophile distribute their eggs singly over appropriate hostplants. Signals mediating caterpillar-ant communication are highly specialized in one obligate myrmecophile (Drupadia theda), but rather unspecific in four other species tested. Altogether our observations indicate that colonization and establishment of lycaenid butterflies on S. thaipingensis trees are governed by specializations as well as opportunistic use of resources (ants and hostplant parts). Therefore, the diversity of this species assemblage is maintained by deterministic as well as stochastic factors.