A versatile approach to multiple gene RNA interference using microRNA-based short hairpin RNAs

Background: Effective and stable knockdown of multiple gene targets by RNA interference is often necessary to overcome isoform redundancy, but it remains a technical challenge when working with intractable cell systems. Results: We have developed a flexible platform using RNA polymerase II promoter-driven expression of microRNA-like short hairpin RNAs which permits robust depletion of multiple target genes from a single transcript. Recombination-based subcloning permits expression of multi-shRNA transcripts from a comprehensive range of plasmid or viral vectors. Retroviral delivery of transcripts targeting isoforms of cAMP-dependent protein kinase in the RAW264.7 murine macrophage cell line emphasizes the utility of this approach and provides insight to cAMP-dependent transcription. Conclusion: We demonstrate functional consequences of depleting multiple endogenous target genes using miR-shRNAs, and highlight the versatility of the described vector platform for multiple target gene knockdown in mammalian cells

The Alliance for Cellular Signaling Plasmid Collection: A Flexible Resource for Protein Localization Studies and Signaling Pathway Analysis

Cellular responses to inputs that vary both temporally and spatially are determined by complex relationships between the components of cell signaling networks. Analysis of these relationships requires access to a wide range of experimental reagents and techniques, including the ability to express the protein components of the model cells in a variety of contexts. As part of the Alliance for Cellular Signaling, we developed a robust method for cloning large numbers of signaling ORFs into Gateway® entry vectors, and we created a wide range of compatible expression platforms for proteomics applications. To date, we have generated over 3000 plasmids that are available to the scientific community via the American Type Culture Collection. We have established a website at www.signaling-gateway.org/data/plasmid/ that allows users to browse, search, and blast Alliance for Cellular Signaling plasmids. The collection primarily contains murine signaling ORFs with an emphasis on kinases and G protein signaling genes. Here we describe the cloning, databasing, and application of this proteomics resource for large scale subcellular localization screens in mammalian cell lines

Data from: Investigation of nitrogen and phosphorus contents in water in the tributaries of Danjiangkou Reservoir

.As part of the efforts to ensure adequate supply of quality water from Danjiangkou Reservoir to Beijing, surface water were sampled from the tributaries of Danjiangkou Reservoir in normal (May), flood (August) and dry (December) seasons of 2014, and characterized for nitrogen and phosphorus contents as specified in the applicable standards. Test results indicated that 1)the organic pollutions in Sihe and Shendinghe rivers were more serious than those in other tributaries, and the concentrations of nitrogen and phosphorus favoured the growth of most algae; 2) total phosphorus (TP), total nitrogen (TN) and dissolved inorganic nitrogen (DIN) were in the forms of dissolved phosphorus (DTP), dissolved nitrogen (DTN) and nitrate nitrogen (NO3-N) in these seasons, respectively; 3) compared with nitrogen, phosphorus was more likely to block phytoplankton overrunning; 4)TN, TP, permanganate index (CODMn) and other ions were positively correlated. These findings provided an important basis for the effective measures taken later on as appropriate to ensure adequate supply of quality water from Danjiangkou Reservoir to Beijing

Supercavitating flow around high-speed underwater projectile near free surface induced by air entrainment

Cavitating flow near free surface is a complicated issue and may provide new inspiration on high-speed surface cruising. This study observes stable supercavitating flow as a new phenomenon in a launch experiment of axisymmetric projectile when the upper side of the projectile coincides with the free surface. A numerical approach is established using large eddy-simulation and volume-of-fluid methods, and good agreements are achieved between numerical and experimental results. Supercavity formation mechanism is revealed by analyzing the experiment photographs and the iso-surface of 90% water volume fraction in numerical results. The entrainment of a large amount of air into the cavity can cause the pressure inside the cavity to similarly increase with the pressure outside the cavity, which makes the actual cavitation number close to zero and is similar to supercavitation. Cases with various headforms of the projectile and cavitation numbers on the cavitating flow, as well as the drag reduction effects are further examined. Results indicate that the present strategy near the free surface could possibly be a new effective approach for high-speed cruising after vigorous design optimization in the future

Assessing variability of optimum air temperature for photosynthesis across site-years, sites and biomes and their effects on photosynthesis estimation

Gross primary productivity (GPP) of vegetation is affected by air temperature. Biogeochemical models use the optimum air temperature (Topt) parameter, which comes from biome-specific look-up tables (Topt−b−LT). Many studies have shown that plants have the capacity to adapt to changes in environmental conditions over time, which suggests that the static Topt−b−LT parameters in the biogeochemical models may poorly represent actual Topt and induce uncertainty in GPP estimates. Here, we estimated biome-specific, site-year-specific, and site-specific optimum air temperature using GPP data from eddy covariance (EC) flux tower sites (GPPEC) (Topt−b−EC, Topt−sy−EC, Topt−s−EC), the Enhanced Vegetation Index (EVI) from MODIS images (Topt−b−EVI, Topt−sy−EVI, Topt−s−EVI), and mean daytime air temperature (TDT). We evaluated the consistency among the four Topt parameters (Topt−b, Topt−sy, Topt−s and Topt−b−LT), and assessed how they affect satellite-based GPP estimates. We find that Topt parameters from MODIS EVI agree well with those from GPPEC, which indicates that EVI can be used as a variable to estimate Topt at individual pixels over large spatial domains. Topt−b, Topt−sy, and Topt−s differed significantly from Topt−b−LT. GPP estimates using Topt−b and Topt−sy were more consistent with GPPEC than when using Topt−b−LT for all the land cover types. Our use of Topt−sy substantially improved 8-day and annual GPP estimates across biomess (from 1% to 34%), especially for cropland, grassland, and open shrubland. Our simple calculation shows that global GPP estimates differ by up to 10 Pg C/yr when using our suggested Topt−sy−EVI instead of using the static Topt−b−LT. Our new approach on estimating Topt has the potential to improve estimates of GPP from satellite-based models, which could lead to better understanding of carbon-climate interactions

Estimating site-specific optimum air temperature and assessing its effect on the photosynthesis of grasslands in mid- to high-latitudes

The effect of air temperature on photosynthesis is important for the terrestrial carbon cycle. The optimum air temperature for photosynthesis is one of the major parameters in data-driven and process-based photosynthesis models that estimate the gross primary production (GPP) of vegetation under a changing climate. To date, most models use the biome-specific optimum air temperature ( ${T}_{{\rm{o}}{\rm{p}}{\rm{t}}-{\rm{b}}}$ ) parameter. To what degree will the site-specific optimum air temperature ( ${T}_{{\rm{o}}{\rm{p}}{\rm{t}}-{\rm{s}}}$ ) affect GPP simulation results remains unclear. In this study, we estimated ${T}_{{\rm{o}}{\rm{p}}{\rm{t}}-{\rm{s}}}$ by using GPP data from 11 grassland eddy flux tower sites (GPP _EC ) and satellite vegetation indices (NDVI and EVI). We found that T _opt-s parameter values estimated from EVI have good consistency with those from GPP _EC at individual sites. We also evaluated the effects of site-specific and biome-specific optimum air temperature parameters on grassland photosynthesis. The results showed that the use of ${T}_{{\rm{o}}{\rm{p}}{\rm{t}}-{\rm{s}}}$ in the Vegetation Photosynthesis Model improved to various degrees in both daily and annual GPP estimates in those grassland flux tower sites. Our results highlight the necessity and potential for the use of ${T}_{{\rm{o}}{\rm{p}}{\rm{t}}-{\rm{s}}}$ in terrestrial GPP models, especially in those situations with large temperature variation (heatwave and cold spill events)

Protective Effects of α-Lipoic Acid and Chlorogenic Acid on Cadmium-Induced Liver Injury in Three-Yellow Chickens

Cadmium (Cd) is a type of noxious heavy metal that is distributed widely. It can severely injure the hepatocytes and cause liver dysfunction by inducing oxidative stress and mitochondrial damage. We evaluated the protective effects of α-lipoic acid (α-LA) or chlorogenic acid (CGA) and their combination on counteracting cadmium toxicity in vivo in three-yellow chickens. For three months, CdCl2 (50 mg/L) was administrated through their drinking water, α-LA (400 mg/kg) was added to feed and CGA (45 mg/kg) was employed by gavage. The administration of Cd led to variations in growth performance, biochemical markers (of the liver, kidney and heart), hematological parameters, liver histopathology (which suggested hepatic injury) and ultrastructure of hepatocytes. Some antioxidant enzymes and oxidative stress parameters showed significant differences in the Cd-exposure group when compared with the control group. The groups treated with Cd and administrated α-LA or CGA showed significant amelioration with inhibited mitochondrial pathway-induced apoptosis. Combining both drugs was the most effective in reducing Cd toxicity in the liver. In summary, the results demonstrated that α-LA and CGA may be beneficial in alleviating oxidative stress induced by oxygen free radicals and tissue injury resulting from Cd-triggered hepatotoxicity

Supporting data

There are two files in the data package. One file gives the geographic information about the research area and sampling points, the other supplies all the experimental data used in the manuscript