The Stem Region of Premembrane Protein Plays an Important Role in the Virus Surface Protein Rearrangement during Dengue Maturation

Newly assembled dengue viruses (DENV) undergo maturation to become infectious particles. The maturation process involves major rearrangement of virus surface premembrane (prM) and envelope (E) proteins. The prM-E complexes on immature viruses are first assembled as trimeric spikes in the neutral pH environment of the endoplasmic reticulum. When the virus is transported to the low pH environment of the exosomes, these spikes rearrange into dimeric structures, which lie parallel to the virus lipid envelope. The proteins involved in driving this process are unknown. Previous cryoelectron microscopy studies of the mature DENV showed that the prM-stem region (residues 111–131) is membrane-associated and may interact with the E proteins. Here we investigated the prM-stem region in modulating the virus maturation process. The binding of the prM-stem region to the E protein was shown to increase significantly at low pH compared with neutral pH in ELISAs and surface plasmon resonance studies. In addition, the affinity of the prM-stem region for the liposome, as measured by fluorescence correlation spectroscopy, was also increased when pH is lowered. These results suggest that the prM-stem region forms a tight association with the virus membrane and attracts the associated E protein in the low pH environment of exosomes. This will lead to the surface protein rearrangement observed during maturation.     

Engineering microbial systems to explore ecological and evolutionary dynamics

A major goal of biological research is to provide a mechanistic understanding of diverse biological processes. To this end, synthetic biology offers a powerful approach, whereby biological questions can be addressed in a well-defined framework. By constructing simple gene circuits, such studies have generated new insights into the design principles of gene regulatory networks. Recently, this strategy has been applied to analyze ecological and evolutionary questions, where population-level interactions are critical. Here, we highlight recent development of such systems and discuss how they were used to address problems in ecology and evolutionary biology. As illustrated by these examples, synthetic ecosystems provide a unique platform to study ecological and evolutionary phenomena that are challenging to study in their natural contexts.     

不同干扰背景下景观指数与物种多样性的多尺度效应——以巩义市为例

以黄河中下游山地丘陵区的巩义市为研究区,采用典型样地法对灌草丛、人工林和农田边缘3种不同干扰背景下的自然、半自然生境内的植物进行调查。基于景观生态学原理,在地理信息系统技术支持下,借助于Fragstatta3.3软件,以调查样地为中心,计算了150、250、500、750、1000、1250、1500m不同半径缓冲区内表征景观形状(Edge and patch shape)、边缘对照(Edge contrast)、相似度和邻近度(Proximity and similarity)、景观多样性(Diversity)、基质(Texture)、斑块大小和密度(Patch size and patch density)共6类52个指数,运用冗余分析(RDA)筛选出不同尺度下对该区农业景观中植物多样性有显著影响的景观指数。结果表明:不同尺度,景观指数对物种多样性的影响变化显著。灌草丛生境,在500—750m范围内,SHAPE_AM指数和PARA_AM指数能够很好的解释物种多样性,解释量为33.6%;人工林生境,SHAPE_AM指数、AREA_CV指数、SIMI指数和PAFRAC指数在1000—1250m范围内对物种多样性的解释量达到48.1%;农田边缘生境,GYRATE_CV指数、ENN_CV指数、PARA_MN指数和FRAC_AM指数在750—1250m范围内对物种多样性影响显著,解释量为32%。其中,辛普森多样性指数(SIDI)与灌草丛物种多样性在750—1250m范围内作用显著,ENN_CV指数仅对农田边缘物种多样性影响较大。景观指数对物种多样性的影响具有尺度依赖性,未来应全面综合探讨这些指数的尺度效应及在景观生态学中的应用。     

岭南垛基果林湿地土壤碳组分特征

岭南垛基果林湿地是珠三角地区典型的湿地类型之一,其对土壤碳汇的贡献值得关注。为探讨果林种植类型对土壤有机碳的影响,对广州垛基果林湿地内种植黄皮(Clausenalansium)(HP),龙眼(Dimocarpuslongan)(LY)、杨桃(Averrhoa carambola)(YT),龙眼和黄皮间种(LH),杨桃、龙眼和黄皮间种(YLH)共5种种植类型下的表层(0～20 cm)土壤碳组分进行研究。结果表明,不同的植被类型对土壤的总有机碳(SOC)、可溶性有机碳(DOC)、微生物生物量碳(MBC)、易氧化有机碳(ROC)、惰性碳(NLC)含量都有影响,LY的SOC含量最高(22.6 g/kg),显著高于YLH (P<0.05),且NLC含量显著高于LH和YLH (P<0.05)。NLC含量与土壤养分呈正相关,与土壤容重呈负相关。YT的MBC含量显著高于LY、HP、LH (P<0.05),且MBC/SOC显著高于HP、LY(P<0.05)。YLH模式下,土壤DOC含量和DOC/SOC显著高于其他植被类型(P<0.05)。LH的ROC/SOC显著高于HP和L...     

Competition and habitat filtering jointly explain phylogenetic structure of soil bacterial communities across elevational gradients

The importance of assembly processes in shaping biological communities is poorly understood, especially for microbes. Here, we report on the forces that structure soil bacterial communities along a 2000 m elevational gradient. We characterized the relative importance of habitat filtering and competition on phylogenetic structure and turnover in bacterial communities. Bacterial communities exhibited a phylogenetically clustered pattern and were more clustered with increasing elevation. Biotic factors (i.e., relative abundance of dominant bacterial lineages) appeared to be most important to the degree of clustering, evidencing the role of the competitive ability of entire clades in shaping the communities. Phylogenetic turnover showed the greatest correlation to elevation. After controlling the elevation, biotic factors showed greater correlation to phylogenetic turnover than all the habitat variables (i.e., climate, soil and vegetation). Structural equation modelling also identified that elevation and soil organic matter exerted indirect effects on phylogenetic diversity and turnover by determining the dominance of microbial competitors. Our results suggest that competition among bacterial taxa induced by soil carbon contributes to the phylogenetic pattern across elevational gradient in the Tibetan Plateau. This highlights the importance of considering not only abiotic filtering but also biotic interactions in soil bacterial communities across stressful elevational gradients.     

春兰和蕙兰菌根真菌rDNA ITS序列及共生专一性分析

春兰(Cymbidium goeringii)和蕙兰(Cymbidium faberi)是我国较为广泛分布的地生类型兰属植物,具有悠久的栽培历史和很高的经济价值.菌根真菌与兰科植物专一性关系一直是兰科茵根研究中的热点.该文对35株分离自浙江天目山野生春兰和蕙兰的菌根真菌进行了rDNA ITS序列分析,并在此基础上初步探讨了菌根真菌与春兰、蕙兰之间的专一性关系.结果表明,分离获得的菌根真菌与其共生兰属植物在种的层面具显著专一性,即物种是影响或决定浙江天目山地区春兰、蕙兰与共生菌根真菌专一性的重要因素;研究同时发现,自蕙兰同一条根分离获得的菌根真菌菌株间亦表现丰富的多样性差异.     

Changes of soil organic and inorganic carbon in relation to grassland degradation in Northern Tibet

The effect of livestock grazing on grassland degradation and the resulting impact on soil carbon concentration is an important factor in carbon estimation. We addressed this issue using field observations and laboratory analysis of samples from Tibetan grassland. Based on the field measurements, we investigated the soil organic carbon (SOC) and soil inorganic carbon (SIC) under two contrasting degradation states: lightly or non-degraded grasslands (LDG) and heavily degraded grasslands (HDG). We assessed their relationships with environmental factors using data collected from 99 sites across Northern Tibet during 2011–2012. Data were analyzed using a linear mixed-effects model and one-way ANOVA. The results showed that: (1) SOC concentration decreased and SIC concentration increased following grassland degradation, especially at soil depths in the range of 0–10 cm (P < 0.05); (2) the major environmental factors affecting SOC and SIC were soil pH and plant biomass; (3) spatially, the SOC density increased with the mean annual temperature and mean annual precipitation, whereas SIC exhibited the opposite trend; (4) the SOC density increased at first and then decreased with increasing grazing intensity, with an opposite trend in SIC; and (5) soil carbon storage in this region was 0.14 Pg smaller in the HDG than in the LDG. This study suggests that grassland degradation can significantly affect the vertical distribution and storage of SOC and SIC. The carbon sequestration capacity of the top 100 cm of soil in Northern Tibet was estimated as 0.14 Pg.     

Detection of a Bocavirus Circular Genome in Fecal Specimens from Children with Acute Diarrhea in Beijing,China

To determine if human bocavirus 2 (HBoV2) has a circular genome similar to the head-to-tail sequence of HBoV1 and the episomal form of HBoV3, 15 HBoV2 positive samples identified from 553 stool specimens from children with acute diarrhea were tested for a head-to-tail sequence using TaqMan-based real-time PCR. A circular genome with a head-to-tail sequence was identified in one (BJQ435) out of 15 samples tested by nested PCR. The complete circular genome of HBoV2-C1 (BJQ435) was 5307 nt in length and was flanked with a 520 nt-long terminal non-coding region (NCR). The secondary structure of HBoV2 -C1 had some differences compared to HBoV3-E1 ({"type":"entrez-nucleotide","attrs":{"text":"JN086998","term_id":"340746301","term_text":"JN086998"}}JN086998). Our study indicates that the HBoV genome exists in the form of a head-to-tail monomer and provides more information for understanding the HBoV replication mechanism.