The microbiota protects against Pseudomonas aeruginosa pneumonia via γδ T cell-neutrophil axis in mice

Exposure to antimicrobials leading to microbiota dysbiosis has been found to be an independent risk factor for extensively drug-resistant Pseudomonas aeruginosa acquisition. Microbiota dysbiosis may induce imbalanced immune responses and can affect disease susceptibility. However, the potential role of commensal microbiota in bacterial pneumonia is poorly defined. The aim of this study was to investigate the mechanistic basis for the defective host defenses against P. aeruginosa pneumonia induced by antibiotic pretreatment perturbing microbiota. We found that antibiotic pretreatment significantly perturbed the composition of intestinal microbiota. The microbiota dysbiosis impaired host defenses against P. aeruginosa pneumonia, as reflected by the increased bacterial burden and dissemination, compromised local inflammatory responses and shortened survival time in microbiota-depleted mice compared with controls. This impairment correlated with a defective γδ T17 cell and downstream neutrophil responses. Anti-TCRγδ-treated mice had changes similar to those in the microbiota-depleted mice. Overall, our results suggest the importance of microbiota in supporting the host defense against pneumonia, define a crucial role for the γδ T cell-neutrophil axis in the potential mechanism, and delineate the deleterious effects of antibiotic treatment on antibacterial defenses.     

Structure of monoubiquitinated PCNA

Ubiquitination of proliferating cell nuclear antigen (PCNA) to ub-PCNA is essential for DNA replication across bulky template lesions caused by UV radiation and alkylating agents, as ub-PCNA orchestrates the recruitment and switching of translesion synthesis (TLS) polymerases with replication polymerases. This allows replication to proceed, leaving the DNA to be repaired subsequently. Defects in a TLS polymerase, Pol η, lead to a form of Xeroderma pigmentosum, a disease characterized by severe skin sensitivity to sunlight damage and an increased incidence of skin cancer. Structurally, however, information on how ub-PCNA orchestrates the switching of these two classes of polymerases is lacking. We have solved the structure of ub-PCNA and demonstrate that the ubiquitin molecules in ub-PCNA are radially extended away from the PCNA without structural contact aside from the isopeptide bond linkage. This unique orientation provides an open platform for the recruitment of TLS polymerases through ubiquitin-interacting domains. However, the ubiquitin moieties, to the side of the equatorial PCNA plane, can place spatial constraints on the conformational flexibility of proteins bound to ub-PCNA. We show that ub-PCNA is impaired in its ability to support the coordinated actions of Fen1 and Pol δ in assays mimicking Okazaki fragment processing. This provides evidence for the novel concept that ub-PCNA may modulate additional DNA transactions other than TLS polymerase recruitment and switching.     

The organic content of the surficial sediment: a method for the study of ecosystems development in abandoned river channels

To characterise different abandoned river channels, a simple index of the surface sediment was developed i.e. the content of organic matter (expressed as C × N) plotted in relation to that of CaCO₃. The age of the channels studied ranges from 20 to 300 years. Some of them still contain water; others are silted up. Two types are distinguished. The ecosystems of the first one are closed and show a slow rate of development governed by autogenous processes. Those of the second type are more open and show a fast rate of development mainly controlled by allogenous processes. These distinctions are used in a diagrammatic model of the dynamics of Rhône River alluvial plain to be used in fundamental or applied future research.     

Effects of different nitrogen forms and combination with foliar spraying with 6-benzylaminopurine on growth,transpiration, and water and potassium uptake and flow in tobacco

NH₄ ⁺-N can have inhibitory effects on plant growth. However, the mechanisms of these inhibitory effects are still poorly understood. In this study, effects of different N forms and a combination of ammonium + 6-benzylaminopurine (6-BA, a synthetic cytokinin) on growth, transpiration, uptake and flow of water and potassium in 88-days-old tobacco (Nicotiana tabacum L. K 326) plants were studied over a period of 12 days. Plants were supplied with equal amounts of N in different forms: NO₃ ^–, NH₄NO₃, NH₄ ⁺ or NH₄ ⁺+6-BA (foliar spraying every 2 days after onset of the treatments). For determining flows and partitioning upper, middle and lower strata of three leaves each were analysed. During the 12 days study period, 50% replacement of NO₃ ^–-N by NH₄ ⁺-N (NH₄NO₃) did not change growth, transpiration, uptake and flow of water and K⁺ compared with the NO₃ ^–-N treatment. However, NH₄ ⁺-N as the sole N-source caused: (i) a substantial decrease in dry weight gain to 42% and 46% of the NO₃ ^–-N and NH₄NO₃ treatments, respectively; (ii) a marked reduction in transpiration rate, due to reduced stomatal conductance, illustrated by more negative leaf carbon-isotope discrimination (¹³C) compared with the NO₃ ^– treatment, especially in upper leaves; (iii) a strong reduction both in total water uptake, and in the rate of water uptake by roots, likely due to a decrease in root hydraulic conductivity; (iv) a marked reduction of K⁺ uptake to 10%. Under NH₄ ⁺ nutrition the middle leaves accumulated 143%, and together with upper leaves 206% and the stem 227% of the K⁺ currently taken up, indicating massive mobilisation of K⁺ from lower leaves and even the roots. Phloem retranslocation of K⁺ from the shoot and cycling through the root contributed 67% to the xylem transport of K⁺, and this was 2.2 times more than concurrent uptake. Foliar 6-BA application could not suppress or reverse the inhibitory effects on growth, transpiration, uptake and flow of water and ions (K⁺) caused by NH₄ ⁺-N treatment, although positive effects by 6-BA application were observed, even when 6-BA (10^–8 M) was supplied in nutrient solution daily with watering. Possible roles of cytokinin to regulate growth and development of NH₄ ⁺-fed plants are discussed.     

黑河中游湿地景观破碎化过程及其驱动力分析

在遥感和GIS技术支持下,基于1975-2010年长时间序列遥感影像,选取斑块密度指数(PD)、景观内部生境面积指数(IA)、斑块平均面积指数(MPS)、斑块形状破碎化指数(FS1、FS2)等具有典型生态意义的景观指数模型,系统分析了黑河中游湿地景观的破碎化过程,并结合灰色关联分析、主成分分析等方法,探讨了影响研究区湿地景观破碎化过程的各驱动因子.结果表明:近35年来,研究区湿地景观破碎化主要表现为斑块平均面积的萎缩,斑块密度的上升以及斑块形状破碎化指数的增大.整个研究时段内,研究区湿地斑块平均面积减少了48.95hm2,斑块密度的上升0.006个/hm2;导致黑河中游湿地景观破碎化发生和发展的驱动力包含自然和人文两个方面.自然因子对湿地景观破碎化进程的影响则主要体现在气温和降水上,而且气温对湿地景观破碎化进程的影响程度明显大于降水.但在1975-2010年间的这一较小时间尺度上,人类活动对湿地景观破碎化的贡献率明显高于自然因子,人类活动能力的增强以及影响范围的不断扩大是引发黑河中游湿地景观破碎化的主因.     

A comprehensive examination of the network position hypothesis across multiple river metacommunities

The hierarchical branching nature of river networks can have a strong influence on the assembly of freshwater communities. This unique structure has spurred the development of the network position hypothesis (NPH), which states that the strength of different assembly processes depends on the community position in the river network. Specifically, it predicts that 1) headwater communities should be exclusively controlled by the local environment given that they are more isolated and environmentally heterogeneous relative to downstream reaches. In contrast, 2) downstream communities should be regulated by both environmental and dispersal processes due to increased connectivity given their central position in the riverscape. Although intuitive, the NPH has only been evaluated on a few catchments and it is not yet clear whether its predictions are generalizable. To fill this gap, we tested the NPH on river dwelling fishes using an extensive dataset from 28 French catchments. Stream and climatic variables were assembled to characterize environmental conditions and graph theory was applied on river networks to create spatial variables. We tested both predictions using variation partitioning analyses separately for headwater and downstream sites in each catchment. Only 10 catchments supported both predictions, 11 failed to support at least one of them, while in 7 the NPH was partially supported given that spatial variables were also significant for headwater communities. We then assembled a dataset at the catchment scale (e.g. topography, environmental heterogeneity, network connectivity) and applied a classification tree analysis (CTA) to determine which regional property could explain these results. The CTA showed that the NPH was not supported in catchments with high heterogeneity in connectivity among sites. In more homogeneously connected catchments, the NPH was only supported when headwaters were more environmentally heterogeneous than downstream sites. We conclude that the NPH is context dependent even for taxa dispersing exclusively within streams.     

三峡工程运行后对洞庭湖湿地的影响

长江三峡工程建成运行后,其下游第一个大型通江湖泊——洞庭湖的水文、水质以及湿地环境等均发生了很大变化。三峡工程已经开始影响到洞庭湖的泥沙淤积、水位波动、水质以及植被演替等。以三峡水库调度运行方案、河湖交互作用和洞庭湖湿地植被分布格局为基础,从长江三峡工程对洞庭湖水文、水质以及湿地植被演替等方面综述了三峡工程对洞庭湖湿地的综合影响。三峡工程减缓了长江输入洞庭湖泥沙的淤积速率,对短期内增加洞庭湖区调蓄空间、延长洞庭湖寿命有利。总体上减少了洞庭湖上游的来水量,改变了洞庭湖原来的水位/量变化规律。给洞庭湖水环境质量造成了直接或间接的影响,对其水质改变尚存一定争议,但至少在局部地区加剧了污染。水位变化和泥沙淤积趋缓协同改变了洞庭湖湿地原有植被演替方式,改以慢速方式演替,即群落演替的主要模式为:水生植物—虉草或苔草—芦苇—木本植物。展望了今后的研究趋势与方向,为三峡工程与洞庭湖关系的进一步研究提供参考。     

A comparison of the accuracy and precision of several open-water oxygen productivity techniques

Several methods for the estimation of the reaeration coefficient were compared by determining the ability of the methods to recover the correct K value from a computer-simulated stream oxygen record affected by a variety of non-ideal conditions. Noisy data and long observation intervals were not a serious problem for most methods. Saturating photosynthesis, fluctuating light intensity, afternoon depression and temperature variation caused failures by some methods but were well handled by others. Serious impairment of all methods occurred with low productivity or high K. In general, the best-performing methods were the modified hysteresis, nighttime regression, daytime regression, Odum and Hornberger-Kelly daytime methods.     

IRBAS: An online database to collate,analyze, and synthesize data on the biodiversity and ecology of intermittent rivers worldwide

Key questions dominating contemporary ecological research and management concern interactions between biodiversity, ecosystem processes, and ecosystem services provision in the face of global change. This is particularly salient for freshwater biodiversity and in the context of river drying and flow‐regime change. Rivers that stop flowing and dry, herein intermittent rivers, are globally prevalent and dynamic ecosystems on which the body of research is expanding rapidly, consistent with the era of big data. However, the data encapsulated by this work remain largely fragmented, limiting our ability to answer the key questions beyond a case‐by‐case basis. To this end, the Intermittent River Biodiversity Analysis and Synthesis (IRBAS; http://irbas.cesab.org ) project has collated, analyzed, and synthesized data from across the world on the biodiversity and environmental characteristics of intermittent rivers. The IRBAS database integrates and provides free access to these data, contributing to the growing, and global, knowledge base on these ubiquitous and important river systems, for both theoretical and applied advancement. The IRBAS database currently houses over 2000 data samples collected from six countries across three continents, primarily describing aquatic invertebrate taxa inhabiting intermittent rivers during flowing hydrological phases. As such, there is room to expand the biogeographic and taxonomic coverage, for example, through addition of data collected during nonflowing and dry hydrological phases. We encourage contributions and provide guidance on how to contribute and access data. Ultimately, the IRBAS database serves as a portal, storage, standardization, and discovery tool, enabling collation, synthesis, and analysis of data to elucidate patterns in river biodiversity and guide management. Contribution creates high visibility for datasets, facilitating collaboration. The IRBAS database will grow in content as the study of intermittent rivers continues and data retrieval will allow for networking, meta‐analyses, and testing of generalizations across multiple systems, regions, and taxa.