The Alarmone (p)ppGpp Regulates Primer Extension by Bacterial Primase

Primase is an essential component of the DNA replication machinery, responsible for synthesizing RNA primers that initiate leading and lagging strand DNA synthesis. Bacterial primase activity can be regulated by the starvation-inducible nucleotide (p)ppGpp. This regulation contributes to a timely inhibition of DNA replication upon amino acid starvation in the Gram-positive bacterium Bacillus subtilis. Here, we characterize the effect of (p)ppGpp on B. subtilis DnaG primase activity in vitro. Using a single-nucleotide resolution primase assay, we dissected the effect of ppGpp on the initiation, extension, and fidelity of B. subtilis primase. We found that ppGpp has a mild effect on initiation, but strongly inhibits primer extension and reduces primase processivity, promoting termination of primer extension. High (p)ppGpp concentration, together with low GTP concentration, additively inhibit primase activity. This explains the strong inhibition of replication elongation during starvation which induces high levels of (p)ppGpp and depletion of GTP in B. subtilis. Finally, we found that lowering GTP concentration results in mismatches in primer base pairing that allow priming readthrough, and that ppGpp reduces readthrough to protect priming fidelity. These results highlight the importance of (p)ppGpp in protecting replisome integrity and genome stability in fluctuating nucleotide concentrations upon onset of environmental stress.     

Immunoregulatory effect of mesenchymal stem cell via mitochondria signaling pathways in allergic asthma

Asthma is a complicated lung disease, which has increased morbidity and mortality rates in worldwide. There is an overlap between asthma pathophysiology and mitochondrial dysfunction and MSCs may have regulatory effect on mitochondrial dysfunction and treats asthma. Therefore, immune-modulatory effect of MSCs and mitochondrial signaling pathways in asthma was studied.After culturing of MSCs and producing asthma animal model, the mice were treated with MSCs via IV via IT. BALf's eosinophil Counting, The levels of IL-4, −5, −13, −25, –33, INF-γ, Cys-LT, LTB4, LTC4, mitochondria genes expression of COX-1, COX-2, ND1, Nrf2, Cytb were measured and lung histopathological study were done.BALf's eosinophils, the levels of IL-4, −5, −13, −25, –33, LTB4, LTC4, Cys-LT, the mitochondria genes expression (COX-1, COX-2, Cytb and ND-1), perivascular and peribronchial inflammation, mucus hyper-production and hyperplasia of the goblet cell in pathological study were significantly decreased in MSCs-treated asthma mice and reverse trend was found about Nrf-2 gene expression, IFN-γ level and ratio of the INF-γ/IL-4.MSC therapy can control inflammation, immune-inflammatory factors in asthma and mitochondrial related genes, and prevent asthma immune-pathology.     

Establishment and growth of hawthorn in floodplains in the Netherlands

Dendrochronology was used to assess the influence of soil conditions, elevation and related inundation, climate fluctuations and vegetation cover on the establishment and growth of hawthorn in non-grazed river floodplains. Presence of forest influences the discharge capacity of the floodplain, therefore forest development needs to be considered in management plans. Although ring detection in hawthorn is difficult, clear dynamics in establishment and growth of this shrub species were found. Establishment was mainly influenced by inundation (length and height). The effect of inundation on establishment is location dependent; positive due to transport and deposition of seeds in higher areas, and negative due to drowning of young plants in lower locations. Extreme climatic events were found to influence establishment including a drought in 2003 and relatively low and high precipitation in 2004–2006 and 2007 respectively. These events combined with almost no inundation caused some anomalies in the time series for hawthorn establishment. Once above a certain height, hawthorn is able to withstand various abiotic disturbances occurring in these dynamic river floodplains. Excavated areas are enhancing forest development following hawthorn establishment and therefore these areas should be limited in size (e.g. by deeper and narrower excavations and thus a steeper transition towards the grasslands).     

The method matters: A guide for indicator aggregation in ecological assessments

Ecological assessment requires the integration of many physical, chemical, and/or biological quality elements. The choice of the aggregation method of such partial assessments into an overall assessment can considerably affect the assessment outcome – an issue that has been controversially discussed within the scientific community for the last decade. Current practice often considers only two different aggregation methods, the weighted arithmetic mean (additive aggregation) and the one-out, all-out method (minimum aggregation). However, both have important drawbacks. Additive aggregation compensates a bad status of one quality element by a number of elements featuring good status. Minimum aggregation can lead to overly pessimistic assessment results, since only the quality element in the worst status is considered. Here, we introduce a toolbox containing current and new aggregation methods, demonstrate and discuss their properties with simple, didactical examples, and suggest in which situations best to use them. Then, we illustrate the consequences of selected aggregation schemes for ecological river assessment with the case study of the Swiss Modular Concept of stream assessment (SMC), which we apply to ten river reaches in the Mönchaltdorfer Aa catchment in Switzerland. To be able to do so, we used multi-criteria decision analysis, i.e., multi-attribute value theory, to arrange the SMC quality elements into an objectives hierarchy, and to translate their individual assessments into value functions. Our case study revealed that choosing the most appropriate aggregation method particularly matters, if objectives with significantly different qualities are aggregated. We argue that redundant objectives (i.e., quality elements), often found at the lower levels of the objectives hierarchy, should best be aggregated additively allowing for compensation to increase the statistical significance of the results. Further, we suggest that complementary sub-objectives that often occur at higher levels may be optimally aggregated with a mixture of additive and minimum aggregation. Such a mixed method will allow some compensation, but nevertheless penalize for very bad states. Since here we compare commonly used aggregation methods with some which we believe have never been discussed in an assessment context before, our study concurrently informs ecological assessment in theory and in practice.     

Structural Basis of DEPTOR to Recognize Phosphatidic Acid Using its Tandem DEP Domains

DEP domain containing mTOR-interacting protein (DEPTOR) plays pivotal roles in regulating metabolism, growth, autophagy and apoptosis by functions as an endogenous inhibitor of mTOR signaling pathway. Activated by phosphatidic acid, a second messenger in mTOR signaling, DEPTOR dissociates from mTORC1 complex with unknown mechanism. Here, we present a 1.5 Å resolution crystal structure, which shows that the N-terminal two tandem DEP domains of hDEPTOR fold into a dumbbell-shaped structure, protruding the characteristic β-hairpin arms of DEP domains on each side. An 18 amino acids DDEX motif at the end of DEP2 interacts with DEP1 and stabilizes the structure. Biochemical studies showed that the tandem DEP domains directly interact with phosphatidic acid using two distinct positively charged patches. These results provide insights into mTOR activation upon phosphatidic acid stimulation.     

Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction

Traditional sequence analysis algorithms fail to identify distant homologies when they lie beyond a detection horizon. In this review, we discuss how co-evolution-based contact and distance prediction methods are pushing back this homology detection horizon, thereby yielding new functional insights and experimentally testable hypotheses. Based on correlated substitutions, these methods divine three-dimensional constraints among amino acids in protein sequences that were previously devoid of all annotated domains and repeats. The new algorithms discern hidden structure in an otherwise featureless sequence landscape. Their revelatory impact promises to be as profound as the use, by archaeologists, of ground-penetrating radar to discern long-hidden, subterranean structures. As examples of this, we describe how triplicated structures reflecting longin domains in MON1A-like proteins, or UVR-like repeats in DISC1, emerge from their predicted contact and distance maps. These methods also help to resolve structures that do not conform to a “beads-on-a-string” model of protein domains. In one such example, we describe CFAP298 whose ubiquitin-like domain was previously challenging to perceive owing to a large sequence insertion within it. More generally, the new algorithms permit an easier appreciation of domain families and folds whose evolution involved structural insertion or rearrangement. As we exemplify with α1-antitrypsin, coevolution-based predicted contacts may also yield insights into protein dynamics and conformational change. This new combination of structure prediction (using innovative co-evolution based methods) and homology inference (using more traditional sequence analysis approaches) shows great promise for bringing into view a sea of evolutionary relationships that had hitherto lain far beyond the horizon of homology detection.     

基于InVEST模型的疏勒河流域碳储量时空变化研究

研究区域土地利用方式与生态系统服务碳储量的关系，对于区域生态系统保护及经济社会可持续发展具有重要意义。利用InVEST模型碳储量模块和CA-Markov模型，探究并预测疏勒河流域1990-2015及2015-2040年流域生态系统碳储量时空变化特征及其与土地利用方式之间的关系。结果表明：疏勒河流域1990、1995、2000、2005、2010、2015年碳储量分别为7.994×10⁸、7.996×10⁸、7.998×10⁸、8.038×10⁸、8.064×10⁸、8.071×10⁸t，呈逐年增加趋势，累计增加7.7×10⁶t。土地利用类型变化是导致生态系统碳储量变化的主要因素，未利用地向耕地和草地转化有利于碳储量增加，而草地向耕地和未利用地的转化则导致碳储量减少。疏勒河流域碳储量存在显著的空间格局，碳储量较高区域呈现"北部点状-中部带状-南部点状片状"特征，这种分布格局与流域土地利用类型紧密联系。预测表明至2040年疏勒河流域碳储量为9.128×10⁸t，较2015年增加13.1%，主要原因是草地、耕地和林地面积较大幅度增长，提高了流域内的碳储量。     

Method for the appraisal of anthropogenic disturbance of macrozoobenthic communities of soft substrata

A method for quantitative appraisal of disturbances of macrobenthic communities of soft substrata caused by anthropogenic pollution is proposed. This method is based on the establishment of the dependence of various parameters characterizing the abundance and structure of communities (biomass, population density, number of species, Shannon-Weaver and Pielou indices, etc.) on the level of total contamination of bottom sediments. Using the percentage of deviation of abundance parameters and ecological indices from the norm (the initial horizontal segment of model curves), as well as ERL _q and ERM _q values, which limit the area of progressive degradation of bottom communities (an almost linear drop in abundance and structure characters), is suggested as a numerical characteristic of such deformations. Mapping of aqueous areas on the basis of these characteristics enabled us to obtain a synoptic view of the extent and spatial scale of anthropogenic impacts. An example of the application of this method for assessment of the state of benthic communities in the Peter the Great Bay (Sea of Japan) is shown for the end of the 1980s. The method is verified on the basis of comparison with the results obtained by standard methods of appraisal of the ecological status of macrozoobenthic communities.