Early response to nanoparticles in the Arabidopsis transcriptome compromises plant defence and root-hair development through salicylic acid signalling

Background: The impact of nano-scaled materials on photosynthetic organisms needs to be evaluated. Plants represent the largest interface between the environment and biosphere, so understanding how nanoparticles affect them is especially relevant for environmental assessments. Nanotoxicology studies in plants allude to quantum size effects and other properties specific of the nano-stage to explain increased toxicity respect to bulk compounds. However, gene expression profiles after exposure to nanoparticles and other sources of environmental stress have not been compared and the impact on plant defence has not been analysed. Results: Arabidopsis plants were exposed to TiO2-nanoparticles, Ag-nanoparticles, and multi-walled carbon nanotubes as well as different sources of biotic (microbial pathogens) or abiotic (saline, drought, or wounding) stresses. Changes in gene expression profiles and plant phenotypic responses were evaluated. Transcriptome analysis shows similarity of expression patterns for all plants exposed to nanoparticles and a low impact on gene expression compared to other stress inducers. Nanoparticle exposure repressed transcriptional responses to microbial pathogens, resulting in increased bacterial colonization during an experimental infection. Inhibition of root hair development and transcriptional patterns characteristic of phosphate starvation response were also observed. The exogenous addition of salicylic acid prevented some nano-specific transcriptional and phenotypic effects, including the reduction in root hair formation and the colonization of distal leaves by bacteria. Conclusions: This study integrates the effect of nanoparticles on gene expression with plant responses to major sources of environmental stress and paves the way to remediate the impact of these potentially damaging compounds through hormonal priming.

Genetic analysis of immunological traits in tilapia

The immunological response to handling stress of four tilapia species is evaluated.Polymorphism is examined in genes known to influence immune response in fish.

Structure-function analysis of USP1: insights into the role of Ser313 phosphorylation site and the effect of cancer-associated mutations on autocleavage

Background: In complex with its cofactor UAF1, the USP1 deubiquitinase plays an important role in cellular processes related to cancer, including the response to DNA damage. The USP1/UAF1 complex is emerging as a novel target in cancer therapy, but several aspects of its function and regulation remain to be further clarified. These include the role of the serine 313 phosphorylation site, the relative contribution of different USP1 sequence motifs to UAF1 binding, and the potential effect of cancer-associated mutations on USP1 regulation by autocleavage. Methods: We have generated a large set of USP1 structural variants, including a catalytically inactive form (C90S), non-phosphorylatable (S313A) and phosphomimetic (S313D) mutants, deletion mutants lacking potential UAF1 binding sites, a mutant (GG/AA) unable to undergo autocleavage at the well-characterized G670/G671 diglycine motif, and four USP1 mutants identified in tumor samples that cluster around this cleavage site (G667A, L669P, K673T and A676T). Using cell-based assays, we have determined the ability of these mutants to bind UAF1, to reverse DNA damage-induced monoubiquitination of PCNA, and to undergo autocleavage. Results: A non-phosphorylatable S313A mutant of USP1 retained the ability to bind UAF1 and to reverse PCNA ubiquitination in cell-based assays. Regardless of the presence of a phosphomimetic S313D mutation, deletion of USP1 fragment 420-520 disrupted UAF1 binding, as determined using a nuclear relocation assay. The UAF1 binding site in a second UAF1-interacting DUB, USP46, was mapped to a region homologous to USP1(420-520). Regarding USP1 autocleavage, co-expression of the C90S and GG/AA mutants did not result in cleavage, while the cancer-associated mutation L669P was found to reduce cleavage efficiency. Conclusions: USP1 phosphorylation at S313 is not critical for PCNA deubiquitination, neither for binding to UAF1 in a cellular environment. In this context, USP1 amino acid motif 420-520 is necessary and sufficient for UAF1 binding. This motif, and a homologous amino acid segment that mediates USP46 binding to UAF1, map to the Fingers sub-domain of these DUBs. On the other hand, our results support the view that USP1 autocleavage may occur in cis, and can be altered by a cancer-associated mutation.

Investigation of damping effects on statistical energy analysis of coupled structures

The effects of damping on energy sharing in coupled systems are investigated. The approach taken is to compute the forced response patterns of various idealised systems, and from these to calculate the parameters of Statistical Energy Analysis model for the systems using the matrix inversion approach [1]. It is shown that when SEA models are fitted by this procedure, the values of the coupling loss factors are significantly dependent on damping except when it is sufficiently high. For very lightly damped coupled systems, varying the damping causes the values of the coupling loss factor to vary in direct proportion to the internal loss factor. In the limit of zero damping, the coupling loss factors tend to zero. This is a view which contrasts strongly with 'classical' SEA, in which coupling loss factors are determined by the nature of the coupling between subsystems, independent of subsystem damping. One implication of the strong damping dependency is that equipartition of modal energy under low damping does not in general occur. This is contrary to the classical SEA prediction that equipartition of modal energy always occurs if the damping can be reduced to a sufficiently small value. It is demonstrated that the use of this classical assumption can lead to gross overestimates of subsystem energy ratios, especially in multi-subsystem structures. © 1996 Academic Press Limited.

Global analysis of mRNA half-lives and de novo transcription in a dinoflagellate, Karenia brevis

Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into the roles of differential mRNA stability and de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed and pre-existing RNA pools in Karenia brevis. These isolated fractions were then used for analysis of global mRNA stability and de novo transcription by hybridization to a K. brevis microarray. Global K. brevis mRNA half-lives were calculated from the ratio of newly transcribed to pre-existing RNA for 7086 array features using the online software HALO (Half-life Organizer). Overall, mRNA half-lives were substantially longer than reported in other organisms studied at the global level, ranging from 42 minutes to greater than 144 h, with a median of 33 hours. Consistent with well-documented trends observed in other organisms, housekeeping processes, including energy metabolism and transport, were significantly enriched in the most highly stable messages. Shorter-lived transcripts included a higher proportion of transcriptional regulation, stress response, and other response/regulatory processes. One such family of proteins involved in post-transcriptional regulation in chloroplasts and mitochondria, the pentatricopeptide repeat (PPR) proteins, had dramatically shorter half-lives when compared to the arrayed transcriptome. As transcript abundances for PPR proteins were previously observed to rapidly increase in response to nutrient addition, we queried the newly synthesized RNA pools at 1 and 4 h following nitrate addition to N-depleted cultures. Transcriptome-wide there was little evidence of increases in the rate of de novo transcription during the first 4 h, relative to that in N-depleted cells, and no evidence for increased PPR protein transcription. These results lend support to the growing consensus of post-transcriptional control of gene expression in dinoflagellates.

Liver genomic responses to ciguatoxin: evidence for activation of Phase I and Phase II detoxification pathways following an acute hypothermic response in mice

Ciguatoxins (CTX) are polyether neurotoxins that target voltage-gated sodium channels and are responsible for ciguatera, the most common fish-borne food poisoning in humans. This study characterizes the global transcriptional response of mouse liver to a symptomatic dose (0.26 ng/g) of the highly potent Pacific ciguatoxin-1 (P-CTX-1). At 1 h post-exposure 2.4% of features on a 44K whole genome array were differentially expressed (p ≤ 0.0001), increasing to 5.2% at 4 h and decreasing to 1.4% by 24 h post-CTX exposure. Data were filtered (|fold change| ≥ 1.5 and p ≤ 0.0001 in at least one time point) and a trend set of 1550 genes were used for further analysis. Early gene expression was likely influenced prominently by an acute 4°C decline in core body temperature by 1 h, which resolved by 8 h following exposure. An initial downregulation of 32 different solute carriers, many involved in sodium transport, was observed. Differential gene expression in pathways involving eicosanoid biosynthesis and cholesterol homeostasis was also noted. Cytochrome P450s (Cyps) were of particular interest due to their role in xenobiotic metabolism. Twenty-seven genes, mostly members of Cyp2 and Cyp4 families, showed significant changes in expression. Many Cyps underwent an initial downregulation at 1 h but were quickly and strongly upregulated at 4 and 24 h post-exposure. In addition to Cyps, increases in several glutathione S-transferases were observed, an indication that both phase I and phase II metabolic reactions are involved in the hepatic response to CTX in mice.

Characterizing Jobos Bay, Puerto Rico: a watershed modeling analysis and monitoring plan

Land-based pollution is commonly identified as a major contributor to the observed deterioration of shallow-water coral reef ecosystem health. Human activity on the coastal landscape often induces nutrient enrichment, hypoxia, harmful algal blooms, toxic contamination and other stressors that have degraded the quality of coastal waters. Coral reef ecosystems throughout Puerto Rico, including Jobos Bay, are under threat from coastal land uses such as urban development, industry and agriculture. The objectives of this report were two-fold: 1. To identify potentially harmful land use activities to the benthic habitats of Jobos Bay, and 2. To describe a monitoring plan for Jobos Bay designed to assess the impacts of conservation practices implemented on the watershed. This characterization is a component of the partnership between the U.S. Department of Agriculture (USDA) and the National Oceanic and Atmospheric Administration (NOAA) established by the Conservation Effects Assessment Project (CEAP) in Jobos Bay. CEAP is a multi-agency effort to quantify the environmental benefits of conservation practices used by private landowners participating in USDA programs. The Jobos Bay watershed, located in southeastern Puerto Rico, was selected as the first tropical CEAP Special Emphasis Watershed (SEW). Both USDA and NOAA use their respective expertise in terrestrial and marine environments to model and monitor Jobos Bay resources. This report documents NOAA activities conducted in the first year of the three-year CEAP effort in Jobos Bay. Chapter 1 provides a brief overview of the project and background information on Jobos Bay and its watershed. Chapter 2 implements NOAA’s Summit to Sea approach to summarize the existing resource conditions on the watershed and in the estuary. Summit to Sea uses a GIS-based procedure that links patterns of land use in coastal watersheds to sediment and pollutant loading predictions at the interface between terrestrial and marine environments. The outcome of Summit to Sea analysis is an inventory of coastal land use and predicted pollution threats, consisting of spatial data and descriptive statistics, which allows for better management of coral reef ecosystems. Chapters 3 and 4 describe the monitoring plan to assess the ecological response to conservation practices established by USDA on the watershed. Jobos Bay is the second largest estuary in Puerto Rico, but has more than three times the shoreline of any other estuarine area on the island. It is a natural harbor protected from offshore wind and waves by a series of mangrove islands and the Punta Pozuelo peninsula. The Jobos Bay marine ecosystem includes 48 km² of mangrove, seagrass, coral reef and other habitat types that span both intertidal and subtidal areas. Mapping of Jobos Bay revealed 10 different benthic habitats of varying prevalence, and a large area of unknown bottom type covering 38% of the entire bay. Of the known benthic habitats, submerged aquatic vegetation, primarily seagrass, is the most common bottom type, covering slightly less than 30% of the bay. Mangroves are the dominant shoreline feature, while coral reefs comprise only 4% of the total benthic habitat. However, coral reefs are some of the most productive habitats found in Jobos Bay, and provide important habitat and nursery grounds for fish and invertebrates of commercial and recreational value.

Geographic patterns in the lag of temperature response to insolation for El Niño vs. La Niña conditions [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): The most important control on the annual cycle of temperature is insolation, with secondary influences from terms related to moisture, yet direct statistical analysis of the moisture-driven modulations (such as El Niño) of the response of temperature to insolation are not available. We have examined one aspect of the relationship between insolation and the instrumental record of maximum daily temperature - the lag between the two - at 252 stations in the western United States.

River salinity variations in response to discharge: examples from the western United States during the early 1900s

Major controls on river salinity (total dissolved solids) in the western United States are climate, geology, and human activity. Climate, in general, influences soil-river salinity via salt-balance variations. When climate becomes wetter, river discharge increases and soil-river salinity decreases; when climate becomes drier river discharge decreases and soil-river salinity increases. This study characterizes the river salinity response to discharge using statistical-dynamic methods. An exploratory analysis of river salinity, using early 1900s water quality surveys in the western United States, shows much river salinity variability is in response to storm and annual discharge. Presumably this is because river discharge is largely supported by surface flow.

THEORETICAL ROAD DAMAGE DUE TO DYNAMIC TYRE FORCES OF HEAVY VEHICLES. PART 1: DYNAMIC ANALYSIS OF VEHICLES AND ROAD SURFACES.

Theory is presented for simulating the dynamic wheel forces generated by heavy road vehicles and the resulting dynamic response of road surfaces to these loads. Sample calculations are provided and the vehicle simulation is validated with data from full-scale tests. The methods are used in the accompanying paper to simulate the road damage done by a tandem-axle vehicle.

A comparison of methods for the coupled analysis of floating structures

The dynamic analysis of a deepwater floating platform and the associated mooring/riser system should ideally be fully coupled to ensure a reliable response prediction. It is generally held that a time domain analysis is the only means of capturing the various coupling and nonlinear effects accurately. However, in recent work it has been found that for an ultra-deepwater floating system (2000m water depth), the highly efficient frequency domain approach can provide highly accurate response predictions. One reason for this is the accuracy of the drag linearization procedure over both first and second order motions, another reason is the minimal geometric nonlinearity displayed by the mooring lines in deepwater. In this paper, the aim is to develop an efficient analysis method for intermediate water depths, where both mooring/vessel coupling and geometric nonlinearity are of importance. It is found that the standard frequency domain approach is not so accurate for this case and two alternative methods are investigated. In the first, an enhanced frequency domain approach is adopted, in which line nonlinearities are linearized in a systematic way. In the second, a hybrid approach is adopted in which the low frequency motion is solved in the time domain while the high frequency motion is solved in the frequency domain; the two analyses are coupled by the fact that (i) the low frequency motion affects the mooring line geometry for the high frequency motion, and (ii) the high frequency motion affects the drag forces which damp the low frequency motion. The accuracy and efficiency of each of the methods are systematically compared. Copyright © 2007 by ASME.

Transient thermal analysis of power devices based on Fourier-series thermal model

A new thermal model based on Fourier series expansion method has been presented for dynamic thermal analysis on power devices. The thermal model based on the Fourier series method has been programmed in MATLAB SIMULINK and integrated with a physics-based electrical model previously reported. The model was verified for accuracy using a two-dimensional Fourier model and a two-dimensional finite difference model for comparison. To validate this thermal model, experiments using a 600V 50A IGBT module switching an inductive load, has been completed under high frequency operation. The result of the thermal measurement shows an excellent match with the simulated temperature variations and temperature time-response within the power module. ©2008 IEEE.

Vibration and stress analysis in the presence of structural uncertainty

At medium to high frequencies the dynamic response of a built-up engineering system, such as an automobile, can be sensitive to small random manufacturing imperfections. Ideally the statistics of the system response in the presence of these uncertainties should be computed at the design stage, but in practice this is an extremely difficult task. In this paper a brief review of the methods available for the analysis of systems with uncertainty is presented, and attention is then focused on two particular "non- parametric" methods: statistical energy analysis (SEA), and the hybrid method. The main governing equations are presented, and a number of example applications are considered, ranging from academic benchmark studies to industrial design studies. © 2009 IOP Publishing Ltd.

Predicting shock response in uncertain structures using the Hybrid method

Using the Hybrid method (FE + SEA) it is possible to estimate the frequency response of an uncertain structure. The current work develops the Hybrid method to allow for time domain analysis of the shock response of a structure. Problems to be overcome when taking Hybrid method results into the time domain are a) the Hybrid method frequency response has no phase information, and b) the Hybrid method frequency response is smoothed in frequency and shows no modal peaks. In this paper the first problem has been overcome, using minimum phase reconstruction. Explanation of minimum phase reconstruction and its limitations are described, and application to shock problems described. © 2009 IOP Publishing Ltd.

An analysis of the cooperative mechano-sensitive feedback between intracellular signaling, focal adhesion development, and stress fiber contractility

Cells communicate with their external environment via focal adhesions and generate activation signals that in turn trigger the activity of the intracellular contractile machinery. These signals can be triggered by mechanical loading that gives rise to a cooperative feedback loop among signaling, focal adhesion formation, and cytoskeletal contractility, which in turn equilibrates with the applied mechanical loads. We devise a signaling model that couples stress fiber contractility and mechano-sensitive focal adhesion models to complete this above mentioned feedback loop. The signaling model is based on a biochemical pathway where IP3 molecules are generated when focal adhesions grow. These IP3 molecules diffuse through the cytosol leading to the opening of ion channels that disgorge Ca2+ from the endoplasmic reticulum leading to the activation of the actin/myosin contractile machinery. A simple numerical example is presented where a one-dimensional cell adhered to a rigid substrate is pulled at one end, and the evolution of the stress fiber activation signal, stress fiber concentrations, and focal adhesion distributions are investigated. We demonstrate that while it is sufficient to approximate the activation signal as spatially uniform due to the rapid diffusion of the IP3 through the cytosol, the level of the activation signal is sensitive to the rate of application of the mechanical loads. This suggests that ad hoc signaling models may not be able to capture the mechanical response of cells to a wide range of mechanical loading events. © 2011 American Society of Mechanical Engineers.