Regional Contingencies in the Relationship between Aboveground Biomass and Litter in the World’s Grasslands

Based on regional-scale studies, aboveground production and litter decomposition are thought to positively covary, because they are driven by shared biotic and climatic factors. Until now we have been unable to test whether production and decomposition are generally coupled across climatically dissimilar regions, because we lacked replicated data collected within a single vegetation type across multiple regions, obfuscating the drivers and generality of the association between production and decomposition. Furthermore, our understanding of the relationships between production and decomposition rests heavily on separate meta-analyses of each response, because no studies have simultaneously measured production and the accumulation or decomposition of litter using consistent methods at globally relevant scales. Here, we use a multi-country grassland dataset collected using a standardized protocol to show that live plant biomass (an estimate of aboveground net primary production) and litter disappearance (represented by mass loss of aboveground litter) do not strongly covary. Live biomass and litter disappearance varied at different spatial scales. There was substantial variation in live biomass among continents, sites and plots whereas among continent differences accounted for most of the variation in litter disappearance rates. Although there were strong associations among aboveground biomass, litter disappearance and climatic factors in some regions (e.g. U.S. Great Plains), these relationships were inconsistent within and among the regions represented by this study. These results highlight the importance of replication among regions and continents when characterizing the correlations between ecosystem processes and interpreting their global-scale implications for carbon flux. We must exercise caution in parameterizing litter decomposition and aboveground production in future regional and global carbon models as their relationship is complex.     

Cellular Chaperonin CCTγ Contributes to Rabies Virus Replication during Infection

Rabies, as the oldest known infectious disease, remains a serious threat to public health worldwide. The eukaryotic cytosolic chaperonin TRiC/CCT complex facilitates the folding of proteins through ATP hydrolysis. Here, we investigated the expression, cellular localization, and function of neuronal CCTγ during neurotropic rabies virus (RABV) infection using mouse N2a cells as a model. Following RABV infection, 24 altered proteins were identified by using two-dimensional electrophoresis and mass spectrometry, including 20 upregulated proteins and 4 downregulated proteins. In mouse N2a cells infected with RABV or cotransfected with RABV genes encoding nucleoprotein (N) and phosphoprotein (P), confocal microscopy demonstrated that upregulated cellular CCTγ was colocalized with viral proteins N and P, which formed a hollow cricoid inclusion within the region around the nucleus. These inclusions, which correspond to Negri bodies (NBs), did not form in mouse N2a cells only expressing the viral protein N or P. Knockdown of CCTγ by lentivirus-mediated RNA interference led to significant inhibition of RABV replication. These results demonstrate that the complex consisting of viral proteins N and P recruits CCTγ to NBs and identify the chaperonin CCTγ as a host factor that facilitates intracellular RABV replication. This work illustrates how viruses can utilize cellular chaperonins and compartmentalization for their own benefit.     

A new Cre driver mouse line, Tcf21/Pod1-Cre, targets metanephric mesenchyme

Conditional gene targeting in mice has provided great insight into the role of gene function in kidney development and disease. Although a number of Cre-driver mouse strains already exist for the kidney, development of additional strains with unique expression patterns is needed. Here we report the generation and validation of a Tcf21/Pod1-Cre driver strain that expresses Cre recombinase throughout the condensing and stromal mesenchyme of developing kidneys and in their derivatives including epithelial components of the nephron and interstitial cells. To test the efficiency of this line, we crossed it to mice transgenic for either loss or gain of function β-catenin conditional alleles. Mice with deletion of β-catenin from Tcf21-expressing cells are born with hypoplastic kidneys, hydroureters and hydronephrosis. By contrast, Tcf21-Cre driven gain of function for β-catenin in mice results in fused midline kidneys and hypoplastic kidneys. Finally, we report the first renal mesenchymal deletion of Patched1 (Ptch1), the receptor for sonic hedgehog (Shh), which results in renal cysts demonstrating a functional role of Shh signaling pathway in renal cystogensis. In summary, we report the generation and validation of a new Cre driver strain that provides robust excision in metanephric mesenchyme.     

The effects of fertilization on the trait-abundance relationships in a Tibetan alpine meadow community

Aims Comparisons of the trait–abundance relationships from various habitat types are critical for community ecology, which can offer us insights about the mechanisms underlying the local community assembly, such as the relative role of neutral vs. niche processes in shaping community structure. Here, we explored the responses of trait–abundance relationships to nitrogen (N), phosphorus (P) and potassium (K) fertilization in an alpine meadow.Methods Five fertilization treatments (an unfertilized control and additions of N, P, K and NPK respectively) were implemented using randomized block design in an alpine Tibetan meadow. Species relative abundance (SRA), plant above-ground biomass and species richness were measured in each plot. For 24 common species, we measured species functional traits: saturated height, specific leaf area (SLA) and leaf dry matter content (LDMC) in each treatment but seed size only in the unfertilized control. Standard major axis (SMA) regression and phylogenetically independent contrasts (PICs) analysis were used to analyse species trait–abundance relationships in response to different fertilization treatments.Important findings Positive correlations between SRA and saturated height were raised following N, P and NPK fertilizations, which indicated an increase in light competition in these plots. In P fertilized plots, SRA was also positively correlated with LDMC because tall grasses with a nutrients conservation strategy often have a relative competitive advantage in capturing limited light and soil nutrients. In K fertilized plots, neither the trait–abundance relationships nor above-ground biomass or species richness significantly differed from that in the control, which suggests that K was not a limiting resource in our study site. These significant correlations between species traits and relative abundance in fertilized treatment suggest that trait-based selection plays an important role in determining species abundance within local communities in alpine meadows.     

Spatial Structures of the Environment and of Dispersal Impact Species Distribution in Competitive Metacommunities

The correspondence between species distribution and the environment depends on species’ ability to track favorable environmental conditions (via dispersal) and to maintain competitive hierarchy against the constant influx of migrants (mass effect) and demographic stochasticity (ecological drift). Here we report a simulation study of the influence of landscape structure on species distribution. We consider lottery competition for space in a spatially heterogeneous environment, where the landscape is represented as a network of localities connected by dispersal. We quantified the contribution of neutrality and species sorting to their spatial distribution. We found that neutrality increases and the strength of species-sorting decreases with the centrality of a community in the landscape when the average dispersal among communities is low, whereas the opposite was found at elevated dispersal. We also found that the strength of species-sorting increases with environmental heterogeneity. Our results illustrate that spatial structure of the environment and of dispersal must be taken into account for understanding species distribution. We stress the importance of spatial geographic structure on the relative importance of niche vs. neutral processes in controlling community dynamics.     

拟南芥乙酰羟酸合成酶(AHAS)点突变原核表达与活性测定

拟南芥乙酰羟酸合成酶(AHAS)参与支链氨基酸合成。为考察AHAS不同结构域对支链氨基酸合成的影响,分别对其大小亚基上特定位点进行点突变后进行原核表达,体外重组后对其全酶活性进行测定,并对其终端产物之一——缬氨酸对AHAS全酶活性的影响进行探讨。结果显示:AHAS小亚基G88D突变将解除其终端产物的反馈抑制作用,而大亚基E305D与E482D的突变降低AHAS全酶活性,且2种不同突变大亚基对AHAS全酶活性影响存在差异。AHAS大亚基E482D突变较E305D突变影响更大。研究结果表明:AHAS大小亚基间存在着相互作用,且大小亚基不同结构域突变对AHAS全酶活性具有不同的影响。     

An Ensemble Method with Hybrid Features to Identify Extracellular Matrix Proteins

The extracellular matrix (ECM) is a dynamic composite of secreted proteins that play important roles in numerous biological processes such as tissue morphogenesis, differentiation and homeostasis. Furthermore, various diseases are caused by the dysfunction of ECM proteins. Therefore, identifying these important ECM proteins may assist in understanding related biological processes and drug development. In view of the serious imbalance in the training dataset, a Random Forest-based ensemble method with hybrid features is developed in this paper to identify ECM proteins. Hybrid features are employed by incorporating sequence composition, physicochemical properties, evolutionary and structural information. The Information Gain Ratio and Incremental Feature Selection (IGR-IFS) methods are adopted to select the optimal features. Finally, the resulting predictor termed IECMP (Identify ECM Proteins) achieves an balanced accuracy of 86.4% using the 10-fold cross-validation on the training dataset, which is much higher than results obtained by other methods (ECMPRED: 71.0%, ECMPP: 77.8%). Moreover, when tested on a common independent dataset, our method also achieves significantly improved performance over ECMPP and ECMPRED. These results indicate that IECMP is an effective method for ECM protein prediction, which has a more balanced prediction capability for positive and negative samples. It is anticipated that the proposed method will provide significant information to fully decipher the molecular mechanisms of ECM-related biological processes and discover candidate drug targets. For public access, we develop a user-friendly web server for ECM protein identification that is freely accessible at http://iecmp.weka.cc.     

Effects of traits,species identity and local environmental conditions on the assessment of interactions: insights from an alpine meadow community

Aims The prediction that facilitation is the dominant interaction in physically stressful conditions has been supported by many but not all field studies. In the present paper, we tested the effects of the identity of species, the local environmental conditions and the currencies of performance measurement on such variation.Methods Using contrasting two plots, six species, and up to five multiple traits, we comprehensively explored the effects of the above factors on the assessment of plant interactions in an alpine meadow of the Qing-Hai Tibetan Plateau. Additionally, we attempted to figure out the possible mechanisms underlying the responses observed. The data were analysed by both standard ANOVAs and multivariate statistics.Important findings Our results demonstrated that the response to the removal of neighbours was both species and trait specific, and the effect of the local environmental conditions was dependent on the species involved. The contrast between plots had crucial influence on the net interactions of Kobresia macrantha, but little effect on Elymus nutans. Regarding the abiotic conditions, neighbours had significant impact on soil temperature, moist and solar radiation. The results contribute to advance our knowledge on the potential underlying factors influencing the assessment of facilitation.