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1.

Background

Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm.

Results

NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms’ niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds.

Conclusions

The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.  相似文献   
2.
Small nucleolar RNAs (snoRNAs) guide nucleotide modifications of cellular RNAs in the nucleus. We previously showed that box C/D snoRNAs from the Rpl13a locus are unexpected mediators of physiologic oxidative stress, independent of their predicted ribosomal RNA modifications. Here we demonstrate that oxidative stress induced by doxorubicin causes rapid cytoplasmic accumulation of the Rpl13a snoRNAs through a mechanism that requires superoxide and a nuclear splice variant of NADPH oxidase. RNA-sequencing analysis reveals that box C/D snoRNAs as a class are present in the cytoplasm, where their levels are dynamically regulated by NADPH oxidase. These findings suggest that snoRNAs may orchestrate the response to environmental stress through molecular interactions outside of the nucleus.  相似文献   
3.
The spread of competitive grasses, changes in species composition and vegetation structure are direct consequences of grassland and heathland abandonment. As an alternative to more costly management measures such as traditional pastoralism, year-round low-intensity grazing with large herbivores is increasingly used to restore and maintain semi-open habitats. However, the suitability of this grazing regime has not yet been investigated for long-abandoned, highly degraded but nutrient-poor sandy grassland and heathland communities. In particular, it is unclear if year-round grazing is suitable for preventing the further spread of highly competitive grasses such as Calamagrostis epigejos while simultaneously maintaining or improving characteristic species richness and vegetation structure. Hence, we conducted a comprehensive field study on two spatial scales (plot-level: 25 m2, macroplot-level: 1 ha) to analyse the impacts of year-round low-intensity cattle and horse grazing on the development of the highly competitive grass Calamagrostis epigejos, as well as the vegetation structure and plant species richness of long-abandoned but nutrient-poor dry sandy grassland and heathland communities, their mosaics and Calamagrostis stands within an 800 ha heathland between 2008 and 2015. Finally, we assessed the local conservation status of the habitat types after seven years of grazing in comparison to long-abandoned sites.Grazing successfully reduced the coverage of Calamagrostis epigejos, whereby Calamagrostis stands developed towards species-rich sandy grasslands after seven years of grazing. In addition, the quality of the vegetation structure was improved by enhancing the proportion of bare soil, while litter and grass cover, litter thickness and height of the field layer as well as the coverage of ruderal indicators were significantly reduced on grazed sites in comparison to ungrazed sites in 2015. Moreover, we found an overall positive grazing effect on species richness: Total species number, number of target species as well as subordinated target species significantly increased within the vegetation types over time.Thus, year-round low-intensity cattle and horse grazing is a suitable management tool for restoring, maintaining and even improving long-abandoned, nutrient-poor sandy grassland and heathland communities, and thus to enhance the local conservation status of the habitat types. However, if there is a high initial cover of woody species (e.g. shrubs, tree rejuvenation), then an extensive shrub and tree clearance will be necessary, with manual shrub cutting being crucial to reduce the heavy regrowth of the woody species. In addition, a one-time mowing should be implemented in highly degraded heaths to facilitate the vegetative rejuvenation of degenerate stands of Calluna vulgaris, thus improving its attractiveness for the grazing animals.  相似文献   
4.
中国奥甲螨科3新种(甲螨亚目:奥甲螨科)   总被引:2,自引:1,他引:1  
王慧芙 《蛛形学报》1993,2(2):97-103
记述采自我国南方的奥甲螨科3新种:鞭毛奧甲螨Oppia flagellifera sp.nov.、雕纹大奥甲螨Lasiobelba sculpta sp.nov.和闽越奥甲螨Vietoppia fujianensis sp.nov,。  相似文献   
5.
The present study was conducted to elaborate vegetation composition structure to analyze role of edaphic and topographic factors on plant species distribution and community formation during 2013–14. A mixture of quadrat and transect methods were used. The size of quadrat for trees shrubs and herbs were 10 × 5, 5 × 2, 1 × 1 meter square respectively. Different phytosociological attribute were measured at each station. Primary results reported 123 plant species belong to 46 families. Asteraceae and Lamiaceae were dominant families with 8 species each. PCORD version 5 were used for Cluster and Two Way Cluster Analyses that initiated 4 plant communities within elevation range of 529–700 m from sea level. Indicator species analyses (ISA) were used to identify indicator species of each community. CANOCO Software (version 4.5) was used to measure the influence of edaphic and topographic variables on species composition, diversity and community formation. Whereas Canonical Correspondence Analysis (CCA) was used to measure the effect of environmental variables which showed elevation and aspect were the stronger environmental variable among topographic and CaCO3 contents, electric conductivity, soil pH were the stronger edaphic factors in determination of vegetation and communities of the Bheer Hills. Grazing pressure was one of the main anthropogenic factors in this regard.  相似文献   
6.
一株海洋放线菌的鉴定及其促生作用机理   总被引:2,自引:2,他引:0  
【背景】海洋放线菌BM-2是本实验室从连云港海域分离得到的一株具有抗菌和促生作用的优良菌株,具有良好的开发应用前景。【目的】明确海洋放线菌BM-2的分类地位,揭示该菌株的促生作用机理,为菌株的开发应用提供理论依据。【方法】通过形态观察、生理生化特性和16S rRNA基因序列分析,对海洋放线菌BM-2菌株进行种属鉴定;采用透明圈法、平板划线法测定BM-2菌株解磷、解钾作用、固氮作用和产植酸酶、1-氨基环丙烷-1-羧基(1-aminocyclopropane-1-carboxylate,ACC)脱氨酶的能力;运用沙尔科夫斯基反应(Salkowski法)和铬天青(chromeazurol S,CAS)法分别测定菌株产吲哚乙酸(indole acetic acid,IAA)和产铁载体的能力。【结果】培养特征、菌落形态观察及生理生化试验结果表明,BM-2菌株符合链霉菌属(Streptomyces)的特征,16S rRNA基因序列与GenBank中栗褐链霉菌(Streptomyces badius)的序列相似性为99.72%;BM-2菌株具有固氮和解有机磷活性,能够产生ACC脱氨酶、铁载体和IAA。【结论】BM-2菌株为栗褐连霉菌(Streptomyces badius),固氮、解有机磷作用以及产生ACC脱氨酶、IAA可能是该菌株的促生作用机制。  相似文献   
7.
Cancer cells are characterized by elevated levels of reactive oxygen species, which are produced mainly by the mitochondria. The dismutase SOD2 localizes in the matrix and is a major antioxidant. The activity of SOD2 is regulated by the deacetylase SIRT3. Recent studies indicated that SIRT3 is decreased in 87% of breast cancers, implying that the activity of SOD2 is compromised. The resulting elevation in reactive oxygen species was shown to be essential for the metabolic reprograming toward glycolysis. Here, we show that SOD2 itself is down-regulated in breast cancer cell lines. Further, activation of oncogenes, such as Ras, promotes the rapid down-regulation of SOD2. Because in the absence of SOD2, superoxide levels are elevated in the matrix, we reasoned that mechanisms must exist to retain low levels of superoxide in other cellular compartments especially in the intermembrane space of the mitochondrial to avoid irreversible damage. The dismutase SOD1 also acts as an antioxidant, but it localizes to the cytoplasm and the intermembrane space of the mitochondria. We report here that loss of SOD2 correlates with the overexpression of SOD1. Further, we show that mitochondrial SOD1 is the main dismutase activity in breast cancer cells but not in non-transformed cells. In addition, we show that the SOD1 inhibitor LCS-1 leads to a drastic fragmentation and swelling of the matrix, suggesting that in the absence of SOD2, SOD1 is required to maintain the integrity of the organelle. We propose that by analogy to the cadherin switch during epithelial-mesenchymal transition, cancer cells also undergo a SOD switch during transformation.  相似文献   
8.
Dinitrosyliron complexes (DNIC) have been found in a variety of pathological settings associated with NO. However, the iron source of cellular DNIC is unknown. Previous studies on this question using prolonged NO exposure could be misleading due to the movement of intracellular iron among different sources. We here report that brief NO exposure results in only barely detectable DNIC, but levels increase dramatically after 1–2 h of anoxia. This increase is similar quantitatively and temporally with increases in the chelatable iron, and brief NO treatment prevents detection of this anoxia-induced increased chelatable iron by deferoxamine. DNIC formation is so rapid that it is limited by the availability of NO and chelatable iron. We utilize this ability to selectively manipulate cellular chelatable iron levels and provide evidence for two cellular functions of endogenous DNIC formation, protection against anoxia-induced reactive oxygen chemistry from the Fenton reaction and formation by transnitrosation of protein nitrosothiols (RSNO). The levels of RSNO under these high chelatable iron levels are comparable with DNIC levels and suggest that under these conditions, both DNIC and RSNO are the most abundant cellular adducts of NO.  相似文献   
9.
Mitochondria frequently change their shape through fission and fusion in response to physiological stimuli as well as pathological insults. Disrupted mitochondrial morphology has been observed in cholestatic liver disease. However, the role of mitochondrial shape change in cholestasis is not defined. In this study, using in vitro and in vivo models of bile acid-induced liver injury, we investigated the contribution of mitochondrial morphology to the pathogenesis of cholestatic liver disease. We found that the toxic bile salt glycochenodeoxycholate (GCDC) rapidly fragmented mitochondria, both in primary mouse hepatocytes and in the bile transporter-expressing hepatic cell line McNtcp.24, leading to a significant increase in cell death. GCDC-induced mitochondrial fragmentation was associated with an increase in reactive oxygen species (ROS) levels. We found that preventing mitochondrial fragmentation in GCDC by inhibiting mitochondrial fission significantly decreased not only ROS levels but also cell death. We also induced cholestasis in mouse livers via common bile duct ligation. Using a transgenic mouse model inducibly expressing a dominant-negative fission mutant specifically in the liver, we demonstrated that decreasing mitochondrial fission substantially diminished ROS levels, liver injury, and fibrosis under cholestatic conditions. Taken together, our results provide new evidence that controlling mitochondrial fission is an effective strategy for ameliorating cholestatic liver injury.  相似文献   
10.
Species distribution models (SDMs) are increasingly used to predict species ranges and their shifts under future scenarios of global environmental change (GEC). SDMs are thus incorporating key drivers of GEC (e.g. climate, land use) to improve predictions of species’ habitat suitability (i.e. as an indicator of species occurrence). Yet, most SDMs incorporating land use only consider dominant land cover types, largely ignoring other key aspects of land use such as land management intensity and livestock. We developed SDMs including main land use components (i.e. land cover, livestock and its management intensity) to assess their relative importance in shaping habitat suitability for the Egyptian vulture, an endangered raptor linked to livestock presence. We modelled current and future (2020 and 2050) habitat suitability for this vulture using an organism-centred approach. This allowed us to account for basic species’ habitat needs (i.e. nesting cliff) while gaining insight into our variables of interest (i.e. livestock and land cover). Once nest-site requirements were fulfilled, land use variables (i.e. openland and sheep and goat density) were the main factors determining species’ habitat suitability. Current suitable area could decrease by up to 6.81% by 2050 under scenarios with rapid economic growth but no focus on environmental conservation and rural development. Local solutions to environmental sustainability and rural development could double current habitat suitability by 2050. Land use is expected to play a key role in determining Egyptian vulture's distribution through land cover change but also through changes in livestock management (i.e. species and stocking density). Change in stocking densities (sheep and goats/km2) becomes thus an indicator of habitat suitability for this vulture in our study area. Abandonment of agro-pastoral practises (i.e. below ∼15–20 sheep and goats/km2) will negatively influence the species distribution. Nonetheless, livestock densities above these values will not further increase habitat suitability. Given the widespread impacts of livestock on ecosystems, the role of livestock and its management intensity in SDMs for other (non-livestock-related) species should be further explored.  相似文献   
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