Search

Chronic obstructive pulmonary disease (COPD) is characterized by expiratory airflow limitation and symptoms such as shortness of breath. Although many studies have demonstrated dysregulated microRNA (miRNA) and gene (mRNA) expression in the pathogenesis of COPD, how miRNAs and mRNAs systematically interact and contribute to COPD development is still not clear. To gain a deeper understanding of the gene regulatory network underlying COPD pathogenesis, we used Sparse Multiple Canonical Correlation Network (SmCCNet) to integrate whole blood miRNA and RNA-sequencing data from 404 participants in the COPDGene study to identify novel miRNA–mRNA networks associated with COPD-related phenotypes including lung function and emphysema. We hypothesized that phenotype-directed interpretable miRNA–mRNA networks from SmCCNet would assist in the discovery of novel biomarkers that traditional single biomarker discovery methods (such as differential expression) might fail to discover. Additionally, we investigated whether adjusting -omics and clinical phenotypes data for covariates prior to integration would increase the statistical power for network identification. Our study demonstrated that partial covariate adjustment for age, sex, race, and CT scanner model (in the quantitative emphysema networks) improved network identification when compared with no covariate adjustment. However, further adjustment for current smoking status and relative white blood cell (WBC) proportions sometimes weakened the power for identifying lung function and emphysema networks, a phenomenon which may be due to the correlation of smoking status and WBC counts with the COPD-related phenotypes. With partial covariate adjustment, we found six miRNA–mRNA networks associated with COPD-related phenotypes. One network consists of 2 miRNAs and 28 mRNAs which had a 0.33 correlation (p = 5.40E-12) to forced expiratory volume in 1 s (FEV1) percent predicted. We also found a network of 5 miRNAs and 81 mRNAs that had a 0.45 correlation (p = 8.80E-22) to percent emphysema. The miRNA–mRNA networks associated with COPD traits provide a systems view of COPD pathogenesis and complements biomarker identification with individual miRNA or mRNA expression data.

Expression quantitative trait loci (eQTL) analyses detect genetic variants (SNPs) associated with RNA expression levels of genes. The conventional eQTL analysis is to perform individual tests for each gene-SNP pair using simple linear regression and to perform the test on each tissue separately ignoring the extensive information known about RNA expression in other tissue(s). Although Bayesian models have been recently developed to improve eQTL prediction on multiple tissues, they are often based on uninformative priors or treat all tissues equally. In this study, we develop a novel tissue augmented Bayesian model for eQTL analysis (TA-eQTL), which takes prior eQTL information from a different tissue into account to better predict eQTL for another tissue. We demonstrate that our modified Bayesian model has comparable performance to several existing methods in terms of sensitivity and specificity using allele-specific expression (ASE) as the gold standard. Furthermore, the tissue augmented Bayesian model improves the power and accuracy for local-eQTL prediction especially when the sample size is small. In summary, TA-eQTL's performance is comparable to existing methods but has additional flexibility to evaluate data from different platforms, can focus prediction on one tissue using only summary statistics from the secondary tissue(s), and provides a closed form solution for estimation.

Background: Exploring microorganisms especially bacteria associated with the degradation of lignocellulosic biomass shows great potentials in biofuels production. The rice endophytic bacterium Pantoea ananatis Sd-1 with strong lignocellulose degradation capacity has been reported in our previous study. However, a comprehensive analysis of its corresponding degradative system has not yet been conducted. The aim of this work is to identify and characterize the lignocellulolytic enzymes of the bacterium to understand its mechanism of lignocellulose degradation and facilitate its application in sustainable energy production. Results: The genomic analysis revealed that there are 154 genes encoding putative carbohydrate-active enzymes (CAZy) in P. ananatis Sd-1. This number is higher than that of compared cellulolytic and ligninolytic bacteria as well as other eight P. ananatis strains. The CAZy in P. ananatis Sd-1 contains a complete repertoire of enzymes required for cellulose and hemicellulose degradation. In addition, P. ananatis Sd-1 also possesses plenty of genes encoding potential ligninolytic relevant enzymes, such as multicopper oxidase, catalase/hydroperoxidase, glutathione S-transferase, and quinone oxidoreductase. Quantitative real-time PCR analysis of parts of genes encoding lignocellulolytic enzymes revealed that they were significantly up-regulated (at least P < 0.05) in presence of rice straw. Further identification of secretome of P. ananatis Sd-1 by nano liquid chromatography-tandem mass spectrometry confirmed that considerable amounts of proteins involved in lignocellulose degradation were only detected in rice straw cultures. Rice straw saccharification levels by the secretome of P. ananatis Sd-1 reached 129.11 ± 2.7 mg/gds. Correspondingly, the assay of several lignocellulolytic enzymes including endoglucanase, exoglucanase, â-glucosidase, xylanase-like, lignin peroxidase-like, and laccase-like activities showed that these enzymes were more active in rice straw relative to glucose substrates. The high enzymes activities were not attributed to bacterial cell densities but to the difference of secreted protein contents. Conclusion: Our results indicate that P. ananatis Sd-1 can produce considerable lignocellulolytic enzymes including cellulases, hemicellulases, and ligninolytic relevant enzymes. The high activities of those enzymes could be efficiently induced by lignocellulosic biomass. This identified degradative system is valuable for the lignocellulosic bioenergy industry. [ABSTRACT FROM AUTHOR]

In this paper, the generalized likelihood uncertainty estimation (GLUE) methodology, which is widely applied in the field of hydrology, is used for testing and predictive uncertainty estimation in the application of the Xinanjiang rainfall-runoff (XAJ-RR) model for estimating monthly stream flow (Nangao reservoir) catchment in China. However, one of the drawbacks of using the GLUE method is the definition of the likelihood function, which reflects the behavior of the hydrological model. Although there are different formulations of likelihood functions in the literature, most previous research focused on the application of the GLUE method with the likelihood function of Nash-Sutcliffe (NS) efficiency. In this respect, to illustrate the impact of the selection of likelihood functions on the results of the GLUE method, the authors adopted four likelihood functions: NS, normalized absolute error (NAE), index of agreement (IoA), and Chiew and McMahon (CM). The main findings of the study are that (1) the parameter uncertainty is more sensitive to the choice of the likelihood functions than the uncertainty in the model prediction by the GLUE method; (2) the parameters of the XAJ-RR model with NS had less uncertainty compared to those of NAE, IoA, and CM; (3) the uncertainty bounds showed slight differences from various likelihood functions; and (4) the computational efficiency of the GLUE method based on likelihood function IoA was much better because the IoA likelihood function corresponded to narrower uncertainty bounds, higher bracketing of observations, and the best maximum value of likelihood functions. Thus, this study confirms the importance of the likelihood function selection in the application of GLUE to the uncertainty assessment of the XAJ-RR model. [ABSTRACT FROM AUTHOR]

Chronic Obstructive Pulmonary Disease (COPD) is the third leading cause of mortality in the United States; however, COPD has heterogeneous clinical phenotypes. This is the first large scale attempt which uses transcriptomics, proteomics, and metabolomics (multi-omics) to determine whether there are molecularly defined clusters with distinct clinical phenotypes that may underlie the clinical heterogeneity. Subjects included 3,278 subjects from the COPDGene cohort with at least one of the following profiles: whole blood transcriptomes (2,650 subjects); plasma proteomes (1,013 subjects); and plasma metabolomes (1,136 subjects). 489 subjects had all three contemporaneous -omics profiles. Autoencoder embeddings were performed individually for each -omics dataset. Embeddings underwent subspace clustering using MineClus, either individually by -omics or combined, followed by recursive feature selection based on Support Vector Machines. Clusters were tested for associations with clinical variables. Optimal single -omics clustering typically resulted in two clusters. Although there was overlap for individual -omics cluster membership, each -omics cluster tended to be defined by unique molecular pathways. For example, prominent molecular features of the metabolome-based clustering included sphingomyelin, while key molecular features of the transcriptome-based clusters were related to immune and bacterial responses. We also found that when we integrated the -omics data at a later stage, we identified subtypes that varied based on age, severity of disease, in addition to diffusing capacity of the lungs for carbon monoxide, and precent on atrial fibrillation. In contrast, when we integrated the -omics data at an earlier stage by treating all data sets equally, there were no clinical differences between subtypes. Similar to clinical clustering, which has revealed multiple heterogenous clinical phenotypes, we show that transcriptomics, proteomics, and metabolomics tend to define clusters of COPD patients with different clinical characteristics. Thus, integrating these different -omics data sets affords additional insight into the molecular nature of COPD and its heterogeneity.

In lower organisms, NADP(H)-dependent glutamate dehydrogenases (GDHs) have high affinities to ammonium and play important roles in nitrogen assimilation. Glutamate dehydrogenases in higher plants have lower affinities for ammonium so their nitrogen is mainly assimilated as ammonium by the glutamine synthetase (GS)/glutamate synthase (GOGAT) pathway. In present study, an NADP(H)-dependent glutamate dehydrogenase gene (CeGDH) was cloned from the fungus Cylindrocarpon ehrenbergii (Ce) and ectopically expressed in rice (Oryza sativa L. 'Kitaake'). Meanwhile, the enzyme activity of CeGDH was detected and the effects of CeGDH in transgenic rice were analyzed. The determination of enzymatic activity in vitro showed that CeGDH's aminating activity is higher than its deaminating activity, which was also confirmed by the results of enzymatic activity in vivo in CeGDH transgenic rice. These results suggested that the CeGDH is inclined to convert 2-Oxoglutarate to glutamate. Additionally, the nitrogen assimilation ability and grain yield were analyzed in CeGDH transgenic plants. The hydroponic experiments revealed that the shoot and root lengths and nitrogen contents were improved obviously in transgenic plants compared with the wild-type under low-nitrogen conditions at seedling stage. In field conditions, the agronomic traits analysis showed that panicle numbers and grain yields of the transgenic plants also increased significantly under low-nitrogen conditions. These results demonstrated that the introduction of CeGDH into rice could enhance nitrogen utilization, improve growth, and increase grain yields, especially in low nitrogen fertility. [ABSTRACT FROM AUTHOR]

In the Huaibei Plain basin, China, soybean is a main crop. During the soybean growth period, rainfall can vary largely and depth to watertable can also vary largely. The amount of water supplied to the soybean rootzone by groundwater affects soybean growth and yield. Accurate simulation of groundwater contributions to soybean rootzone soil moisture (groundwater contribution) can be important for determining irrigation to and drainage from soybean fields. Based on field observations and local weather data of 2005, HYDRUS-1D was validated by comparing simulated and measured rootzone soil water contents. The validated model was used to estimate the daily groundwater contributions for three different soybean hydrological growing seasons, i.e., an average year (1997), a wet year (2005), and a dry year (2004) with soybean growth at its optimal state. The main results were: (1) seasonal groundwater contribution was 157 mm in the experimental field, and the estimated groundwater contributions were 158, 222, and 387 mm in the wet, average, and dry seasons, respectively; (2) the groundwater contribution was about 63% of the total seasonal transpiration in the experimental field, and those were about 142, 80, and 66% of the total seasonal transpiration in dry, average, and wet seasons, respectively. [ABSTRACT FROM AUTHOR]

Vegetation and land-surface hydrology are intrinsically linked under long-term climate change. This paper aims to evaluate the dynamics of potential natural vegetation arising from 21st century climate change and its possible impact on the water budget of the Hanjiang River basin in China. Based on predictions of the Intergovernmental Panel on Climate Change Special Report on Emissions Scenarios (IPCC-SRES) A1 scenario from the PRECIS (Providing Regional Climates for Impact Studies) regional climate model, changes in plant functional types (PFTs) and leaf area index (LAI) were simulated via the Lund-Potsdam-Jena dynamic global vegetation model. Subsequently, predicted PFTs and LAIs were employed in the Xinanjiang vegetation-hydrology model for rainfall-runoff simulations. Results reveal that future long-term changes in precipitation, air temperature and atmospheric CO2 concentration would remarkably affect the spatiotemporal distribution of PFTS and LAIS. These climate-driven vegetation changes would further influence regional water balance. With the decrease in forest cover in the 21st century, plant transpiration and evaporative loss of intercepted canopy water will tend to fall while soil evaporation may rise considerably. As a result, total evapotranspiration may increase moderately with a slight increase in annual runoff depth. This indicates that, for long-term hydrological prediction, climate-induced changes in terrestrial vegetation cannot be neglected as the terrestrial biosphere plays an important role in land-surface hydrological responses. [ABSTRACT FROM AUTHOR]

With overly-rapid socio-economic development and population increases, water abstraction for agricultural, industrial and municipal use increases rapidly, while the water left for ecological maintenance decreases greatly. At the same time, large amounts of polluted water are discharged into rivers because purification plants are inadequate or not built in time, causing serious eco-environmental problems in the Haihe river basins which make regional development unsustainable. Estimating eco-environmental carrying capacity related to water is a key to curbing overuse of water and resolving eco-environmental problems. Because of different trends in water resources development and resultant eco-environmental problems in different sub-basins of the Haihe river, there are different water-related eco-environmental carrying capacities (EECCs) in these sub-basins. Time-series and multi-objective optimization methods are used to determine the EECC in various eco-environmental regions of the Haihe river basins, China. The results show that the entirety of the Haihe river basins will not reach a stable, sustainable state until about 2033, through gradual amelioration of eco-environmental problems. The various eco-regions of the sub-basins will need different lengths of time to reach their own stable states because of different available water resources, eco-environmental problems and social and economic development. [ABSTRACT FROM AUTHOR]

The article presents a study which analyzes the groundwater movement into the root zone and the groundwater uptake of a 10-year-old Populus euphratica woodland using the HYDRUS-ID software package in Ejina Basin, Northwest China. It compares the predicted soil moisture contents during the growing season of P. euphratica with field measured values. The simulation results showed that P. euphratica obtained about 53% of its water from groundwater with an average table depth of 2.64 m.

Glycosylphosphatidylinositol (GPI) anchors of mammals as well as yeast contain ethanolaminephosphate side chains on the α1–4- and the α1∼6-linked mannoses of the anchor core structure (protein-CO-NH-(CH2)2-PO4-6Manα1-2Manα1-6Manα1-4GlcNH2-inositol-PO4-lipid). In yeast, the ethanolaminephosphate on the α1–4-linked mannose is added during the biosynthesis of the GPI lipid by Mcd4p. MCD4 is essential because Gpi10p, the mannosyltransferase adding the subsequent αl–2-linked mannose, requires substrates with an ethanolaminephosphate on the α1–4-linked mannose. The Gpi10p ortholog of Trypanosoma brucei has no such requirement. Here we show that the overexpression of this ortholog rescues mcd4Δ cells. Phenotypic analysis of the rescued mcd4Δ cells leads to the conclusion that the ethanolaminephosphate on the α1–4-linked mannose, beyond being an essential determinant for Gpi10p, is necessary for an efficient recognition of GPI lipids and GPI proteins by the GPI transamidase for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to Golgi and for the physiological incorporation of ceramides into GPI anchors by lipid remodeling. Furthermore, mcd4Δ cells have a marked defect in axial bud site selection, whereas this process is normal in gpi7Δ and gpi1. This also suggests that axial bud site selection specifically depends on the presence of the ethanolaminephosphate on the α1–4-linked mannose. [ABSTRACT FROM AUTHOR]

Groundwater plays a critical role in arid West China where water is the limiting factor for development. This paper first describes groundwater characteristics in a region of four arid inland river watersheds and the problems associated with groundwater consumption. This region exhibits a unique alternating pattern of high mountains and depressions, which results in extensive interactions of surface water and groundwater. Then the authors propose six strategies to support adequate exploitation and use of groundwater in the region. These strategies are: 1) setting up a groundwater monitoring system; 2) forming a unified watershed authority, 3) protecting mountain ecology; 4) increasing the efficiency of groundwater usage; 5) protecting groundwater; and 6) supporting advanced research. The implementation of these strategies should be built upon the promotion of sustainable economic development and broad public support. [ABSTRACT FROM AUTHOR]

Osteopontin (OPN) is a secreted phosphoglycoprotein that has been linked to tumor progression and survival in several solid tumors, including head and neck cancers. Previous studies showed that OPN expression is induced by tumor hypoxia, and its plasma levels can serve as a surrogate marker for tumor hypoxia and treatment outcome in head and neck cancer patients. In this study, we investigate the transcriptional mechanism by which hypoxia enhances OPN expression. We found that OPN is induced in head and neck squamous cell carcinoma (HNSCC) cell lines and in NIH3T3 cells by hypoxia at both mRNA and protein levels in a time-dependent manner. Actinomycin D chase experiments showed that hypoxic induction of OPN was not due to increased mRNA stability. Deletion analyses of the mouse OPN promoter regions indicated that a ras-activated enhancer (RAE) located at −731 to −712 relative to the transcription start site was essential for hypoxia-enhanced OPN transcription. Using electrophoretic mobility shift assays with the RAE DNA sequence, we found that hypoxia induced sequence-specific DNA-binding complexes. Furthermore, hypoxia and ras exposure resulted in an additive induction of OPN protein and mRNA levels that appeared to be mediated by the RAE. Induction of OPN through the RAE element by hypoxia is mediated by an Akt-kinase signaled pathway as decreasing Akt levels with dominant negative constructs resulted in inhibition of OPN induction by hypoxia. Taken together, these results have identified a new hypoxia responsive transcriptional enhancer that is regulated by Akt signaling.Oncogene (2005) 24, 6555–6563. doi:10.1038/sj.onc.1208800; published online 20 June 2005 [ABSTRACT FROM AUTHOR]

Vascular endothelial growth factor (VEGF) is an angiogenic protein with neurotrophic and neuroprotective effects. Because VEGF promotes the proliferation of vascular endothelial cells, we examined the possibility that it also stimulates the proliferation of neuronal precursors in murine cerebral cortical cultures and in adult rat brain in vivo. VFGF (>10 ng/ml) stimulated 5-bromo-2'deoxyuridine (BrdUrd) incorporation into cells that expressed immature neuronal marker proteins and increased cell number in cultures by 20-30%. Cultured cells labeled by BrdUrd expressed VEGFR2/FIk-1, but not VEGFR1/FIt-1 receptors, and the effect of VEGF was blocked by the VEGFR2/FIk-1 receptor tyrosine kinase inhibitor SU1498. Intracerebroventricular administration of VEGF into rat brain increased BrdUrd labeling of cells in the subventricular zone (SVZ) and the subgranular zone (SGZ) of the hippocampal dentate gyrus (DG), where VEGFR2/FIk-1 was colocalized with the immature neuronal marker, doublecortin (Dcx). The increase in BrdUrd labeling after the administration of VFGF was caused by an increase in cell proliferation, rather than a decrease in cell death, because VEGF did not reduce caspase-3 cleavage in SVZ or SGZ. Ceils labeled with BrdUrd after VEGF treatment in vivo include immature and mature neurons, astroglia, and endothelial cells. These findings implicate the angiogenesis factor VEGF in neurogenesis as well. [ABSTRACT FROM AUTHOR]

Investigates the role of neuroglobin (Ngb) in neuronal responses to hypoxia or ischemia. Expression of Ngb in cerebral neurons; Increase in Ngb expression by neuronal hypoxia and focal cerebral ischemia; Effect of hypoxia-inducible Ngb expression on the promotion of neuronal survival from hypoxic-ischemic insults.

Chronic obstructive pulmonary disease (COPD) is a disease in which airflow obstruction in the lung makes it difficult for patients to breathe. Although COPD occurs predominantly in smokers, there are still deficits in our understanding of the additional risk factors in smokers. To gain a deeper understanding of the COPD molecular signatures, we used Sparse Multiple Canonical Correlation Network (SmCCNet), a recently developed tool that uses sparse multiple canonical correlation analysis, to integrate proteomic and metabolomic data from the blood of 1008 participants of the COPDGene study to identify novel protein−metabolite networks associated with lung function and emphysema. Our aim was to integrate -omic data through SmCCNet to build interpretable networks that could assist in the discovery of novel biomarkers that may have been overlooked in alternative biomarker discovery methods. We found a protein−metabolite network consisting of 13 proteins and 7 metabolites which had a -0.34 correlation (p-value = 2.5 × 10−28) to lung function. We also found a network of 13 proteins and 10 metabolites that had a -0.27 correlation (p-value = 2.6 × 10−17) to percent emphysema. Protein−metabolite networks can provide additional information on the progression of COPD that complements single biomarker or single -omic analyses.

Smoking causes chronic obstructive pulmonary disease (COPD). Though recent studies identified a COPD metabolomic signature in blood, no large studies examine the metabolome in bronchoalveolar lavage (BAL) fluid, a more direct representation of lung cell metabolism. We performed untargeted liquid chromatography−mass spectrometry (LC−MS) on BAL and matched plasma from 115 subjects from the SPIROMICS cohort. Regression was performed with COPD phenotypes as the outcome and metabolites as the predictor, adjusted for clinical covariates and false discovery rate. Weighted gene co-expression network analysis (WGCNA) grouped metabolites into modules which were then associated with phenotypes. K-means clustering grouped similar subjects. We detected 7939 and 10,561 compounds in BAL and paired plasma samples, respectively. FEV1/FVC (Forced Expiratory Volume in One Second/Forced Vital Capacity) ratio, emphysema, FEV1 % predicted, and COPD exacerbations associated with 1230, 792, eight, and one BAL compounds, respectively. Only two plasma compounds associated with a COPD phenotype (emphysema). Three BAL co-expression modules associated with FEV1/FVC and emphysema. K-means BAL metabolomic signature clustering identified two groups, one with more airway obstruction (34% of subjects, median FEV1/FVC 0.67), one with less (66% of subjects, median FEV1/FVC 0.77; p < 2 × 10−4). Associations between metabolites and COPD phenotypes are more robustly represented in BAL compared to plasma.

For winter wheat (Triticum aestivum L.) that grows during the rainless season, the contribution of groundwater to the root zone (CGWR) is an important water source for growth. Accurately estimating the CGWR is important for making decisions on irrigation and discharge for winter wheat fields and preventing water pollution. Because winter wheat slows and even stops root growth over winter, so the fixed root density distribution function that is suitable for soybean [Glycine max (L.) Merr.] may not suit winter wheat calculations. Therefore, when estimating the CGWR of winter wheat with the numerical model HYDRUS-1D, the root density distribution function should first be determined from two types: fixed or piecewise root density distribution functions. Based on field observations and local weather data for 2004-2005 and 2005-2006, HYDRUS-1D was evaluated with different root density distribution functions by comparing simulated and measured root zone soil water contents. The evaluated model with the most suitable distribution function was used to estimate the daily CGWR for six winter wheat hydrological growth seasons. For all seasons, winter wheat growth was assumed to be at its optimal state. The main results were: (i) a piecewise root density distribution function was the most suitable for winter wheat; (ii) simulated seasonal CGWRs were 154, 128, and 136 mm in the dry, normal, and wet seasons, respectively; and (iii) the CGWR for winter wheat transpiration was about 58, 47, and 69% of the total in dry, normal, and wet seasons, respectively. Overall, we concluded that accurate description of the root density distribution was helpful to estimate the CGWR. [ABSTRACT FROM AUTHOR]

Mechanically strengthened, highly cube textured Ni-7 at.%W/Ni-12 at.%W multi-layer substrates developed for coated conductors have been prepared by the advanced spark plasma sintering technique. The key innovation for developing this weakly magnetic and reinforced substrate was to use a new powder metallurgy and sintering route to bond multi-layers of Ni7W/Ni12W/Ni7W together in order to get an initial ingot, followed by the optimized cold working and annealing. Particular efforts were made in view of the optimization of the design, pressing as well as the heat treatment processes of the starting ingots to obtain a chemically gradient composite bulk, thus ensuring the subsequent cold deformation. The produced composite substrates have a strong \langle 001\rangle {100} texture on Ni7W outer layers. The percentage of the biaxially orientated grains within a misorientation angle of 10° is as high as 97.5%, while the length percentage of low-angle grain boundaries ranging from 2° to 10° in the composite substrate reaches 87.2%. Moreover, the yield strength s0.2 of the tape approaches 333 MPa, and the saturation magnetization is substantially reduced by 81.6% at 77 K when compared to that of a commercial used Ni5W substrate. [ABSTRACT FROM AUTHOR]

We report on the development of mechanically strengthened, highly textured Ni-5 at.%W/Ni-12 at.%W composite materials prepared by a powder metallurgical approach as promising weakly magnetic substrates for coated superconductors. The key configuration of this composite substrate consists of a thin, sharp cubic textured Ni-5 at.%W layer on a Ni-12 at.%W alloy core, thus providing a mechanical reinforcement while decreasing the saturation magnetization of the whole substrate. The composite substrates have a sharp cubic texture at the top Ni-5 at.%W outer layer and their yield strength reaches 272 MPa, exceeding that of the commercially used Ni5W substrates by a factor of 1.6. The saturation magnetization of the composite substrate Ni5W/Ni12W/Ni5W is substantially reduced when compared to that of pure Ni and Ni-5 at.%W substrates, respectively. [ABSTRACT FROM AUTHOR]

Drought and salinity are major environmental stresses that impair crop growth and productivity worldwide. Improving drought and salt tolerance of crops with microbial mutualists is an effective and environmentally sound strategy to meet the demands of the ever-growing world population. In the present study, we found that the Streptomyces albidoflavus OsiLf-2, a moderately salt-tolerant endophytic actinomycete, produced abundant osmolytes, including proline, polysaccharides, and ectoine. Inoculation with OsiLf-2 increased the osmotic-adjustment ability of the rice host by increasing the proline content (by 250.3% and 49.4%) and soluble sugar (by 20.9% and 49.4%) in rice under drought and salt conditions, relative to the uninoculated control. OsiLf-2 increased stress responses in the rice host at the physiological and biochemical levels (photosynthesis efficiency, osmolytes and antioxidant content), and the gene level (osmolytes synthesis, stress-responsive and ion-transport related genes), raising rice yields under both greenhouse and saline–alkaline soil conditions. The use of endophytic actinomycetes offers a promising biotechnological approach to developing stress-tolerant plants. [ABSTRACT FROM AUTHOR]

The CRISPR-Cas9 system is a powerful and revolutionary genome-editing tool for eukaryotic genomes, but its use in bacterial genomes is very limited. Here, we investigated the use of the Streptococcus pyogenes CRISPR-Cas9 system in editing the genome of Clostridium cellulolyticum, a model microorganism for bioenergy research. Wild-type Cas9-induced double-strand breaks were lethal to C. cellulolyticum due to the minimal expression of nonhomologous end joining (NHEJ) components in this strain. To circumvent this lethality, Cas9 nickase was applied to develop a single-nick-triggered homologous recombination strategy, which allows precise one-step editing at intended genomic loci by transforming a single vector. This strategy has a high editing efficiency (>95%) even using short homologous arms (0.2 kb), is able to deliver foreign genes into the genome in a single step without a marker, enables precise editing even at two very similar target sites differing by two bases preceding the seed region, and has a very high target site density (median interval distance of 9 bp and 95.7% gene coverage in C. cellulolyticum). Together, these results establish a simple and robust methodology for genome editing in NHEJ-ineffective prokaryotes. [ABSTRACT FROM AUTHOR]