Ectomycorrhizal fungal diversity and saprotrophic fungal diversity are linked to different tree community attributes in a field‐based tree experiment

Exploring the link between above‐ and belowground biodiversity has been a major theme of recent ecological research, due in large part to the increasingly well‐recognized role that soil microorganisms play in driving plant community processes. In this study, we utilized a field‐based tree experiment in Minnesota, USA, to assess the effect of changes in plant species richness and phylogenetic diversity on the richness and composition of both ectomycorrhizal and saprotrophic fungal communities. We found that ectomycorrhizal fungal species richness was significantly positively influenced by increasing plant phylogenetic diversity, while saprotrophic fungal species richness was significantly affected by plant leaf nitrogen content, specific root length and standing biomass. The increasing ectomycorrhizal fungal richness associated with increasing plant phylogenetic diversity was driven by the combined presence of ectomycorrhizal fungal specialists in plots with both gymnosperm and angiosperm hosts. Although the species composition of both the ectomycorrhizal and saprotrophic fungal communities changed significantly in response to changes in plant species composition, the effect was much greater for ectomycorrhizal fungi. In addition, ectomycorrhizal but not saprotrophic fungal species composition was significantly influenced by both plant phylum (angiosperm, gymnosperm, both) and origin (Europe, America, both). The phylum effect was caused by differences in ectomycorrhizal fungal community composition, while the origin effect was attributable to differences in community heterogeneity. Taken together, this study emphasizes that plant‐associated effects on soil fungal communities are largely guild‐specific and provides a mechanistic basis for the positive link between plant phylogenetic diversity and ectomycorrhizal fungal richness.     

Features and influencing factors of carbon emissions indicators in the perspective of residential consumption: Evidence from Beijing,China

This research establishes a residential indirect carbon emissions model through input–output structure decomposition analysis (IO-SDA) and LMDI, analyses the influencing factors affecting urban and rural residential carbon emissions indicators in Beijing through input–output tables from 2000 to 2010, and calculates the direct carbon emissions from residential consumption. As the results suggest, the total carbon emissions from residential consumption in Beijing showed volatility. Growing rural and urban differences in direct emissions, and for indirect emissions, mean that urban greatly exceeds rural in this regard. Rising per capita GDP and population, as well as intermediate demand and sectoral emissions intensity change induce growth in indirect emissions in both urban and rural settings: of which, per capita GDP contributes the most. Declining energy intensity contributes the most to emission reductions, followed by residential consumption rates, the rural to urban consumption ratio and consumption structure effects are much smaller.     

Advancing understanding of the complex nature of urban systems

Cities and urbanized regions are complex, dynamic, and highly integrated systems linking social, ecological, and technical infrastructure domains in ways that create deep challenges for good governance, policymaking, and planning. The combination of impacts from climate change in cities, air pollution, rapid population growth, multiple sources of development pressure and overall urban system complexity make it difficult for decision-makers to develop and guide development trajectories along more livable, equitable, and at the same time, more resilient pathways. Advancing urban sustainability and resilience agendas requires expanding the scope of inter- and trans-disciplinarity approaches, moving beyond the historically separate social–ecological and socio-technical approaches to jointly study social–ecological–technical infrastructure systems in cities. We take urban complexity as a given and suggest that in both research and practice we need to better capture and understand feedbacks, interdependencies, and non-linearities which create uncertainties and challenge the efficacy of governance practices to achieve normative goals for society. Here, we explore new methods, tools, and approaches to advance our understanding of urban system complexity through a series of journal special issue articles that examine urban structure–function relationships, urban sustainability transitions, green space availability, social–ecological memory, functional traits, and urban land use scenarios.     

Fitness, genetic load and purging in experimental populations of the housefly

The relative effects of purging of the genetic load versus thefixation of deleterious alleles, under inbreeding, will influencea population's probability of extinction. The relative contributionof these two phenomena is expected to depend upon the rate ofinbreeding. A further complication is due to the fact that a purgingof the genetic load in one environment does not necessarily implya purging of the genetic load in other environments. To addressthese two issues, we compare fitness and genetic load in populationsexperiencing similar levels of inbreeding, but occurring as either ashort-term bottleneck or as a consequence of long-term reducedpopulation size, over a range of environments. Inbred populationshave consistently lower fitness than outbred populations acrossall environments tested. However, the bottlenecked populationssuffer less inbreeding depression for a given level of inbreeding,whether or not challenged by novel environments, than populationskept at a constant small size. The results of this study demonstratethat populations initiated from a small number of founders are ableto recover fitness and survive novel environmental challenges,provided that habitat is available for rapid population growth.     

Different strategies of energy storage in cultured and freshly isolated Symbiodinium sp.

The endosymbiotic relationship between cnidarians and Symbiodinium is critical for the survival of coral reefs. In this study, we developed a protocol to rapidly and freshly separate Symbiodinium from corals and sea anemones. Furthermore, we compared these freshly‐isolated Symbiodinium with cultured Symbiodinium to investigate host and Symbiodinium interaction. Clade B Symbiodinium had higher starch content and lower lipid content than those of clades C and D in both freshly isolated and cultured forms. Clade C had the highest lipid content, particularly when associated with corals. Moreover, the coral‐associated Symbiodinium had higher protein content than did cultured and sea anemone‐associated Symbiodinium. Regarding fatty acid composition, cultured Symbiodinium and clades B, C, and D shared similar patterns, whereas sea anemone‐associated Symbiodinium had a distinct pattern compared coral‐associated Symbiodinium. Specifically, the levels of monounsaturated fatty acids were lower than those of the saturated fatty acids, and the level of polyunsaturated fatty acids (PUFAs) were the highest in all examined Symbiodinium. Furthermore, PUFAs levels were higher in coral‐associated Symbiodinium than in cultured Symbiodinium. These results altogether indicated that different Symbiodinium clades used different energy storage strategies, which might be modified by hosts.     

Cues used in host‐seeking behavior by frog‐biting midges (Corethrella spp. Coquillet)

We investigated the role of carbon dioxide and host temperature in host attraction in frog‐biting midges (Corethrella spp). In these midges, females are known to use frog calls to localize their host, but the role of other host‐emitted cues has yet not been investigated. We hypothesized that carbon dioxide acts as a supplemental cue to frog calls. To test this hypothesis, we determined the responses of the midges to carbon dioxide, frog calls, and both cues. A significantly lower number of midges are attracted to carbon dioxide and silent traps than to traps broadcasting frog calls. Adding carbon dioxide to the calls does not increase the attractiveness to the midges. Instead, carbon dioxide can have deterrent effects on frog‐biting midges. Temperature of calling frogs is not a cue potentially available to the midges. Contrary to our hypothesis, there was no supplemental effect of carbon dioxide when presented in conjunction to calls. Midge host‐seeking behavior strongly depends on the mating calls emitted by their anuran host. Overall, non‐acoustic cues such as host body temperature and carbon dioxide are not important in long‐distance host location by frog‐biting midges.     

Genotype by environment interaction for livability of dairy calves from first parity cows

Death of calves around parturition is a matter of concern for dairy farmers. Relatively high stillbirth rates and unfavourable trends have been reported for Holstein heifers in the Netherlands and several other countries. In our study, we investigated herd differences, genetic parameters and genotype by environment interaction for heifer calf livability. A large dataset with data from calvings between 1993 and 2012 of Dutch dairy farms was used. There were considerable differences between herds in livability of calves from heifers, with averages ranging from 74% to 95%. Both herds with relatively high and low averages showed the same negative trend between 1993 and 2012, with largest declines in herds with the lowest averages. We found that heritability and genetic variation of first parity livability were substantially larger in herd environments where the likelihood of stillbirth was high v. environments where stillbirth was at a low level. The genetic correlations between herd environment levels were all very close to unity, indicating that ranking of sires was similar for all environments. However, for herds with a relatively high stillbirth incidence selecting sires with favourable breeding values is expected to be twice as profitable as in herds with a relatively low stillbirth incidence.     

癌症相关microRNA与靶基因的生物信息学分析

MicroRNAs(miRNAs)是一类长度约为22nt的内源性非编码RNA,通过与靶基因转录本互补结合调控基因的表达。近年来,研究发现miRNA与癌症发生密切相关,miRNA可以直接充当癌基因或者抑癌基因而影响肿瘤的发生和生长。为更进一步揭示癌症相关miRNA的特征及靶基因的功能,文章通过数据库搜索及文献检索,在人类基因组中发现了475个癌症相关miRNA,系统地比较了癌症相关miRNA与非癌症miRNA以及基因内和基因间区癌症相关miRNA在保守性、SNP位点分布、癌谱及转录调控等特性。研究发现,癌症相关miRNA比非癌症miRNA保守性要强,发生SNP概率比较低,同时发现miRNA所涉及癌症数目与保守性成正相关。基因组定位分析发现,癌症相关miRNA比非癌症miRNA更倾向于成簇存在。进一步对宿主基因、癌症相关miRNA及作用的靶基因与癌症发生进行关联分析,发现一些非癌症miRNA的宿主基因倾向于被癌症miRNA作用。本研究结果为深入理解miRNA与癌症之间的关系,以及进一步为miRNA作为癌症诊断指示物提供理论依据。     

Role of inter-domain cavity in the attachment of the orange carotenoid protein to the phycobilisome core and to the fluorescence recovery protein

Using molecular modeling and known spatial structure of proteins, we have derived a universal 3D model of the orange carotenoid protein (OCP) and phycobilisome (PBS) interaction in the process of non-photochemical PBS quenching. The characteristic tip of the phycobilin domain of the core-membrane linker polypeptide (L_CM) forms the attachment site on the PBS core surface for interaction with the central inter-domain cavity of the OCP molecule. This spatial arrangement has to be the most advantageous one because the L_CM, as the major terminal PBS-fluorescence emitter, accumulates energy from the most other phycobiliproteins within the PBS before quenching by OCP. In agreement with the constructed model, in cyanobacteria, the small fluorescence recovery protein is wedged in the OCP’s central cavity, weakening the PBS and OCP interaction. The presence of another one protein, the red carotenoid protein, in some cyanobacterial species, which also can interact with the PBS, also corresponds to this model.     

Structural modeling of HLA-B*1502/peptide/carbamazepine/T-cell receptor complex architecture: implication for the molecular mechanism of carbamazepine-induced Stevens-Johnson syndrome/toxic epidermal necrolysis

Drug-induced adverse reactions are a significant problem in healthcare worldwide and are estimated to cost billions of dollars annually in the United States. A portion of such reactions is observed to strongly associate with certain human leukocyte antigen (HLA) alleles; one of the strongest associations is the HLA-B*1502 protein with carbamazepine (CBZ)-induced Stevens–Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) – the odds ratio value can even be higher than one thousand. The particularly strong association in CBZ-induced SJS/TEN suggests that the HLA-B*1502 is not only a genetic marker but also a participant in the pathogenesis of the disease. In the current study, we attempt to computationally model the atomic-level structure of the complete HLA-B*1502/peptide/CBZ/T-cell receptor (TCR) complex architecture based on prior knowledge obtained from epidemiological investigations as well as in vitro and in vivo assays. The model tells a different story about the molecular mechanism of CBZ-induced SJS/TEN from that previously reported for abacavir (ABC)-induced hypersensitivity (HSR); the CBZ molecule is located at the interface between HLA-B*1502/peptide and TCR, directly contacts the P3–P6 residues of antigen peptide, and bound within a pocket region encompassed by two TCR CDR3 fingers. Molecular dynamics simulation and binding energy analysis further reveal that the CBZ shows considerably high affinity to TCR over HLA-B*1502/peptide, which can tightly interact with the former rather than the latter. From the model, two hypotheses are proposed that can well explain most previous observations and are expected to guide next wet-lab experiments. This study could help to promote our understanding of the molecular mechanism and pathological implication underlying CBZ-induced SJS/TEN.