Author: naturehydro

To test whether this difference is due to an artifact of our extraction procedure, we have tried to denature both extracts with a number of techniques; however, leaf polypeptides never broke down to such small components. This result, although preliminary, is the first evidence of a difference in DNA associated proteins from two plant organs and as such, is worth further investigation. Our technical approach is to isolate proteins which bind specifically with the T-DNA regulatory sequences of the root-specific and the leaf-specific T-DNA genes. First, proteins are isolated on the basis of their general DNA-binding capacity. To this effect, protein extracts from each plant organ are run on DNA-cellulose affinity columns to fractionate proteins which show general DNA-binding capacities. The test we use for visualizing DNA-binding proteins is a modified version of the technique published by Bowen et al., 1980: proteins are transferred to nitrocellulose filters and probed with nick-translated labelled DNA. The DNA sequences we are using for these experiments are sub-clones containing the leaf-specific and the root- specific promoters of the pRiA4 T -DNA. The goal is to show that there is indeed a specificity in the recognition of each of these sequences by the two types of extracts and to identify what proteins are’ involved. The difficulty that will be encountered in this part of the project is in defining conditions that will enhance the sequence specificity of the DNA-binding proteins. This has been a major difficulty in the identification of sequence-specific recognition factors. Retarded electrophoretic migration of DNA complexed to proteins has proven to be a useful method in detecting specific over non-specific binding of proteins to isolated sequences: it has recently been used to identify specific transcription factors in SV 40 infected cells, and in O2 induced cytochrome expression in yeast. We are now testing several approaches in order to determine the general and sequence specific DNA-binding properties of the Tobacco root and leaf proteins.

These include investigating factors influencing the formation of DNA-protein complexes in solution,ebb flow tray such as salt conditions, length of reaction and subsequent washes, and competition experiments with random sequence DNA such as calf-thymus DNA. If necessary, the DNA-cellulose column fractionation will be more elaborate to yield protein species in significantly purified form so as to reduce the background of non-specific binding. DNA-protein complex formation will also. be tested using smaller probes i.e purified promoter sequences from the plasmid that bear the leaf and root pRi T-DNA regulated genes. We hope thus to discriminate between sequence specificity and general binding affinities of the proteins now being isolated. This approach will focus on the other aspect of tissue-specificity i.e a study of the DNA sequences that interact with cellular factors to control the activity of specialized genes. It is also the most straightforward part of the project proposed. We would like to define what the DNA sequences are that interact with the proteins that are being isolated-in 1-. This we will determine by DNA foot-printing experiments: DNA-protein complexes will be formed -using purified protein fractions from the root or leaf extracts and purified restriction fragments containing sequences of the pRiA4 T-DNA for the root and leaf-specific promoters. It will thus be possible to identify the precise positions of the binding-sites of the tissue-specific proteins in the 5’upstream regions of the two genes under consideration. . Foot printing experiments are difficult if the proteins required to complex with the DNA are in low abundance. Hence, this experiment depends on previous work to attain a semi-purification of the proteins required. The initial aim of this work will be to introduce the plasmids we have from the Ri TDNA which contain genes expressed preferentially in different tissues, into protoplasts from these tissues. We will study the expression of the genes on these plasmids at the RNA and protein level.· The DNA will be introduced into the protoplasts either by transfection or by electroporation, both techniques are presently being used in our lab. The assays in this case will be short term expression assays in which the RNA from the protoplasts which carry the plasmids ,. will be isolated within 48 hr of introduction of the DNA.

The RNA encoded by the gene driven from the plasmid promoter will be quantified. To study expression at the level of protein the promoters will be isolated and linked to in vitro to the gene coding for the chloramphenicol acetyltransferase enzyme . CAT activity will be measured after introducing the DNA into protoplasts. A large part of this work will be directed at maintaining the tissue specific expression of the rotoplast by adjusting the growth conditions during the course of the experiment. We will modulate the culture media by adjusting the ratio of auxin to cytokinin and determine the effect on tissue specific expression. Also, we will investigate the involvement of oligosaccharins in determining the tissue specific expression of these plasmids. After the transient expression experiments are underway, plants will be regenerated containing these modified Ri T-DNAs. Protoplasts will be isolated from root and leaf tissues of these plants, and nuclei will immediately be tested for transcriptional activity, using the technique of Ackerman et al., CAT activity will be measured in parallel, as it is easily detectable in small amounts of material. By addition to root-nuclei of extracts from leaf tissues and harvesting of the subequent transcription complexes, it is hoped that it will be possible to activate the silent root-specific promoter . This assay will be used to test the factors isolated in the DNA binding work described above for tissue-specific activators. The overall goal of this program is to develop an understanding of the processes involved in hydrocarbon production in plants. Specifically, we are interested in the mechanisms and control of isoprenoid biosynthesis. Acquiring this basic information will be necessary before we can genetically manipulate plants to increase hydrocarbon yields. We use the latex isolated from laticifer cells of the Euphorbia lathyris plant for our biosynthetic studies. These cells are the site of both the biosynthesis and the storage of large quantities of sterols . We are currently examining the final steps of sterol synthesis, the epoxidation and cyclization of squalene, to determine if more than one squalene cyclase is ,.- involved in sterol synthesis. We are also attempting to identify the organelle involved in the conversion of mevalonic acid to sterols. A secondary interest is the’ synthesis of sesquiterpenes which are a better candidate for direct use as fuel than are the triterpenoids.

The manipulation of a plant towards increased sesquiterpene production at the expense of sterol product is thus a long-term goal of our research. This requires an understanding of the processes involved, specifically the initial cyclization of farnesyl pyrophosphate ,flood and drain tray the branch point at which sesquiterpene synthesis diverts from the general isoprenoid biosynthetic pathway. It may be possible to increase the hydrocarbon content of plants by changing the environment around these plants. We have found that by increasing the day length from about 12 hours to 16. hours and by maintaining a constant day/night temperature region, we observed about a 9-fold increase in the activity of 3-hydrox-3-methyglutaryl-Coenzyme A Reductase . Since this enzyme plays a key role in the synthesis of isoprenoids, it is possible that hydrocarbon production is sensitive to environmental controls. Controlled changes in environmental conditions could restrict growth while having only small effects on the photosynthetic rate . If applied when the plant approached maturity, this could result in an increase in assimilates available for partitioning into isoprenoid biosynthesis. We also hope to identify the internal controls of carbon allocation, since they also could be manipulated to increase plant hydrocarbon production. To investigate these posiblities we are observing the effects of three different environmental variables on hydrocarbon production: salinity stress, water stress .and nitrogen deficiency. After establishing the growth conditions necessary to grow E. lathyris hydroponically, we completed the preliminary study of salinity stress. Extractions of the hydrocarbons and sugars will be performed on the water-stressed plants. However, experiments utilizing nutrient stress have not been successful to this point as low levels of nitrogen cause rapid senescence and death. The effects of salinity on growth were determined from changes in shoot length, total fresh weight and root and shoot dry weights. Changes in the photosynthetic apparatus were determined from chlorophyll content, thylakoid proton gradient formation~ and in vivo fluorescnece patterns. Changes in the levels of energy-rich compounds were determined by heptane and methanol extractions of the dried plant. Only the shoot portion of the plant was used for this extraction as this is what would be available for harvest. The preliminary results indicate that salinities of 50 mM NaCI and greater affect both growth and photosynthesis, though the reduction in growth is sharper than the reduction in photosynthesis. Results of extraction experiments with plant components also indicate that increased salinity causes an increase in carbon allocation to the heptane and methanol fractions, with most of the increase occurring in the carbohydrate-rich methanol fraction. Salinization also caused a 3-fold increase in HMGR activity. To obtain a more comprehensive understanding of carbon flow through E. [athyris, we performed some preliminary carbon-labeling experiments. Now that we have established that it is possible to use isotope labeling to monitor latex production and follow carbon translocation in E. [athyris, this technique will be used further in stress experiments. trlterpenols, and their fatty acid esters.

To understand the bio-synthetic processes involved in the production of sterols. it is necessary to elucidate the structures of these compounds. We have previously identified four of the six major triterpenols as cyloartenol, 24-methylenecyc1oartenol, lanosterol and 24-methylenelanosterol. With the results obtained from 3H-NMR, chemical shift reagents, 13C-NMR and optical rotation we have identified the fifth compound as eupha-7,24- dienol. Wehav~ made a preliminary identification of the sixth compound as euphol on the basis of its behavior in gas chromatography. In most plant systems the initial product of squalene cyclization is cycloartenol and not lanosterol as found in animals and fungi.’ However, since lanosterol is a major component of E. [athyris latex, we are attempting to determine if lanosterol is a product of cyc1oartenol, produced via separate, parallel pathway, or is a precursor of cyc1oartenol. To determine if one of the first two mechanisms is responsible for squalene cyclization, we have synthesized deuterium-labeled MVA to be used as a susbtrate to follow its latex-catalyzed conversion to lanosterol. . One of the major difficulties in this analysis is the high level of endogenous sterols .present in the latex. These make the small amount of newly synthesized deuterated compounds difficult to detect by gas chromatography-mass spectrometry. Attempts at delipidation by extraction with organic solvents such as butanol and diisopI:opyl ether greatly reduced the level of triterpenols but also. destroyed all bioysnthetic activity. Purification by rate sedimentation and isopycnic centrifugation has reduced the lipid level to some extent, but we are still trying to find the proper analytical conditions that will allow us to employ the GC-MS to observe the deuterium label. By choosing special sequences for synthetic DNA oligomers we have been able to form stable “sticky end” dimers in solution from DNA hairpin with dangling ends. The sequences are chosen with a central section which is not complementary to any other in the molecule, which is flanked by a self-complementary sequence. Such sequences have been shown previously to lead to hairpin formation. We have modified these sequences to include a self complementary dangling tail, which allows two such molecules to associate in solution. We have observed the imino proton spectra from these molecules to confirm that such a dimer is indeed the stable form in solution. The imino protons have been assigned using nuclear Overhauser effect difference spectra, and confirm that the dimer is essentially a single continuous double helix in solution. On each of the backbone strands, however, there is a break and a missing phosphate. We have now collected complete two dimensional NOE data sets of two different sequences. In these spectra, when collected at sufficiently short mixing times, the cross peak intensities reflect the inverse sixth power of distances between protons.

The desire to increase detector count by up to two orders of magnitude requires a fresh approach. We identified components in current detector systems that are currently not scalable, and proposed to improve their scalability. The five areas that we have chosen to focus on are: Monolithic fabrication of inductors and capacitors for frequency-multiplexed readout, monolithic fabrication of a silicon lenslet array for optical coupling of the detectors, spray application of anti-reflection coatings for silicon lenslet arrays, fully automated wire bonding to the a detector array, and automated electrical inspection of detector array. Current CMB experiments using frequency-domain multiplexing use printed circuit boards with thousands of hand-soldered capacitors in the cryogenic readout electronics. We have developed a monolithic technology at LBNL Micro Systems Lab to fabricate superconducting inductors and capacitors on silicon wafers. We achieved resonances with high quality factor, predictable resonance peak location, and high yield. Using lithographic fabrication greatly reduces cost and gives a scalable technology with an order of magnitude increase in multiplexing factor. We have successfully machined monolithic silicon lenslet arrays from single crystal silicon., which can replace hand-assembed arrays. We have also developed a plasma sprayed ceramic anti-reflection coatings that can replace our current hand-molded coatings. We have also succeeded in wire bonding to our detector wafers with an automatic wire bonder at LBNL. We are bonding at a 100 micron pitch wire bond, which gives higher connection density and lower cost than the manual wire bonding in current use. Finally, we have developed automated electrical inspection that can characterize thousands of detectors per wafer automatically and rapidly. Previously each detector was hand tested for electrical continuity. New telescope techniques that can explore objects in deep space with high resolution and sensitivity in near-IR region are highly demanded for the study of properties of dark energy and dark matter over time. However,rolling benches near-IR observations from the Earth’s surface are extremely challenging because of the bright background emitted from the atmosphere.

Fortunately, these 300+ OH emission lines are intrinsically very narrow, covering only a small fraction of the total spectrum, and the continuum between the lines is typically as dark as zodiacal light, the background level directly observed from space. Therefore, selectively filtering the OH emission light will enable high sensitive deep space near-IR measurements from the ground. We are developing an innovative optical filter system for highly sensitive near-IR observation by effectively removing the OH emission lines from the Earth’s atmosphere. Different from natural materials, the physical properties of a metamaterial is not primarily dependent on its chemical constituents, but rather upon the structures of the building blocks which are much smaller than light wavelengths. The IR filter design is investigated through numerical simulations and we are exploring effective thin film deposition strategies for large number of layers with controlled roughness and stress. The metamaterial near-IR filter system will be fully compatible with existing telescopes and other instruments because of the large acceptance angle, moderate diameter, and thin filter thickness. By tailoring effective optical properties of the nanoscale layered structures, our metamaterial filter system can provide sharp spectral filtering line-width and high transmission of residual signals, which will be otherwise impossible for traditional techniques based on natural materials. Through the design of the nanoscale structures of the filter system and the development of related nanofabrication techniques, we have developed a multilayer algorithm to realize the desired performance. We have also investigated the fabrication process. Our most significant accomplishment is the design of an integral multilayer-filter system. The system can eliminate a large number of OH emission lines in the spectrum from 1.5~1.8 µm where most of skyline noise comes from. Our approach combines the Needle Optimization and the Tunneling method to search for the global minimum of the merit function. We adopt the scheme of distributed IR filters, and different sub-units are assembled to form an integral filter system with a figure of merit around three. Our method can be generally applicable to a broader bandwidth. We have also explored proper fabrication process of growing multilayer thin films with controlled thicknesses and surface roughness. Although we have achieved more than 30 layers of Silica and TiO2 thin films with the thickness of each layer monitored in situ, we realized that it is very challenging to fabricate the full structure with current state-of-art thin film technologies, which requires the deposition of over 1000 layers with total thickness in the order of millimeters and the roughness of each layer less than 1% of its thickness.

We believe this difficulty is resulted from the mathematical limitations of Needle Optimization approach we employed, and a much better mathematical tool must be developed. We are exploring a better design in collaboration with Prof. James A. Sethian, a mathematician to optimize the astrofilter structure with less number of layers and less sensitive to the fabrication errors of surface morphology. Compost is one of the main organic fertilizers. For optimum growth and balanced nutrition, plants need to be fertilized, because Turkish soils are very low in plant nutrients, especially in phosphorus and zinc. With rising environmental concerns about heavy fertilization polluting the soil and water, it is very important to produce mycorrhizal inoculation in order to reduce the amount of chemical fertilizers. Also very recently there has been a great demand for organic production. Since plants are strongly mycorrhiza-dependent, it is meaningful to produce mycorrhiza-inoculated seedlings. Mycorrhizal fungi are the most common symbiotic organisms, occurring on nearly 90% of plant species. Most horticultural plants are colonized by arbuscular mycorrhizal fungi , whose presence can enhance the growth of the host plant . Mycorrhizal fungi can expand effectiveness of root surface area for better nutrient and water uptake. Also it has been reported by Douds et al. that mycorrhizal fungi seem to be stimulated in cropping systems which incorporate crop rotations, green manures, reduced tillage and minimize pesticides and chemical fertilizers while utilizing organic amendments. Since the last century human population has risen. Accordingly, there is a huge demand for food. In order to have sufficient food, more chemical input has been used in agriculture in the last 40 years. Consequently, soil quality and plant health decreased. Soil biological fertility and ecological balance have been damaged. Once soil fertility is damaged, it is rather difficult to recover soil sustainability. Therefore, there is a great demand for rehabilitation of soil by adding organic amendments. It is possible to protect the soil environment by using organic sources, such as compost and mycorrhizal applications. Perner et al. reported that the addition of compost in combination with mycorrhizal inoculation can improve nutrient status and flower development of plants grown on peat-based substrates. Labidi et al. studied the influence of added compost and arbuscular mycorrhiza on production of extra-radical mycelia in Acacia cyanophylla, finding that compost addition enhanced the production of AM mycelia in all treatments in Saharan ecosystems. Since there is compost material in natural ecosystem,ebb and flow bench and in the same environment mycorrhiza exists, it was hypothesized that different compost materials have different effects on mycorrhizal inoculation. The role of mycorrhiza in ecological systems still needs to be studied. In forest ecosystems, there is a large amount of compost, and plant roots get benefit from mycorrhiza.

It is important to do research on the role of several composting materials on horticultural plant seedling quality and growth. The experiment was carried out in a greenhouse at Çukurova University, Faculty of Agriculture, Department of Soil Science, Adana, Turkey. 14 different compost materials were produced. Tomato and pepper plants were inoculated with G. caledonium. A level of 1000- spores per pot was placed 3 cm below the seeds. Non-mycorrhizal plants also received the same amount of mycorrhizal spore free medium. The experiment was arranged in a randomized complete block design in three replications. Plants were fertilized with a mixture of 70% compost, 18% ground basaltic tuff, 10% andesitic tuff and 2% rock phosphate. Seedlings were then produced in two growth media, consisting of organic fertilizer, soil and sand and andesitic tuff, soil and organic fertilizer . Plants were then inoculated with G. caledonium, while control plants received the same amount of growth medium free from mycorrhizal spores. Roots were stained and analyzed for mycorrhizal fungal root colonization based on the gridline intersection method. At harvest time, plant length, stem diameter, shoot and root dry matter, nutrient content and root colonization were determined. The results showed that the mycorrhizal inoculation significantly increased tomato and pepper plant length and that plant diameter depended on compost materials. The efficiency of mycorrhiza, growth media and compost applications were different. The results showed that the mycorrhizal inoculation significantly increased pepper plant length and diameter . In both growth media, animal manure , chicken manure, plant material, straw, and different plant material were determined as the best compost material for tomato growth . 6:3:1 mixed growth media was better than 1:1:1 . In the two growth media, domestic waste, animal fertilizers , plant material and sewage sludge were determined to be the best compost material for pepper plant growth . 6:3:1 mixed growth media was better than 1:1:1 . Pepper and tomato plants grown in 1:1:1 growth medium showed a high response to mycorrhizal inoculum. Mycorrhizal colonization was investigated and it was found that mycorrhizal colonization levels differed by compost materials. As shown previously, mycorrhizal fungi can improve the performance of seedling quality by stimulating nutrient uptake . In the present experiment, effects of different compost materials on plant parameters were more pronounced than the effects of mycorrhizal inoculation. This may be directly related to the nutrient content of compost materials. Soil biological properties, such as useful microorganism, are important for soil quality. Also the interactions between micro organisms, such as mycorrhiza, soil-borne fungi and nematodes are important for sustainable agriculture.In exchange for plant carbohydrates they increase the uptake of immobile nutrients, such as P, Zn, and Cu, and also NH4 + -N, K and Mn . Horticultural cultivation is becoming widespread in the Mediterranean coasts of Turkey. Soils in this region have high levels of clay and lime, which cause P, Zn, Fe and Mn deficiency; consequently, the major problem in the region is nutrient deficiency in several plant species . Cakmak et al. reported that zinc deficiency is a critical nutritional problem for plants and humans in Turkey. Since the Zn is an essential element for several enzymes in plants, Zn deficiency reduces the plant growth dramatically. Zn deficiency can be alleviated by fertilization. However the recent rise in the use of fertilizers has affected both human health and ecosystems. In the last few decades, it has been observed that a reduction of fertilizer input resulted in the improvement of soil quality. We tested whether mycorrhizal inoculation of seedlings could completely or partially substitute fertilizer application. In general, horticultural plants are mycorrhizal dependent. Our earlier results showed that mycorrhizal seedlings are more resistant to environmental stress factors, such as water deficiency and hot temperature. Under field conditions, the effect of mycorrhizal inoculation on the mortality of seedling was tested and it was found that inoculated seedlings had a greater survival rate than non inoculated plants . It is essential to screen efficient AM fungi in order to get the maximum benefit from mycorrhiza for a particular host. Lee and George have shown that G. mosseae inoculated cucumber plants had increased P, Zn, and Cu concentrations, and mycorrhizal hyphae transported those nutrients to the plants. Since most horticultural crops are grown under controlled nursery conditions before being transplanted to the greenhouse or open field, it is possible to inoculate the seedlings in the nursery. The effect of inoculation with several mycorrhizal species on seedling survival and plant growth nutrient uptake and root infection of cucumbers, melons, watermelons and marrows were studied. Several field experiments were carried out on an Arik clay-loam soil, which was classified as an Entic Chromoxerert in the Agricultural Experimental Station of Çukurova University, Adana, in southern Turkey, whose prevailing climate is Mediterranean. Soil is calcareous and pH is 7.7 and organic matter content is 1.46 %. Honey melon , watermelon , cucumber , and marrow seeds were sown in a sand: soil: organic matter growth medium.

The double-curvature geometry of the system was optimized using a Genetic Algorithm, with experiments being performed in three stages: Stage 1 – Radiance only ; Stage 2 – Radiance + BSDF material ; Stage 3 – BSDF + Radiance 3-Phased Method. The second round of experiments focused on Stage 2 and Stage 3 only. Main conclusions drawn were: under direct beam radiation, the difference between the two methods is significant, with the 3-Phase Method performing up to 34% better in simulating the direct solar component. Without a strong direct solar component, the two methods have a closer performance, simulating diffuse light within a closer range, but Radiance+BSDF still has a significant error rate of up to 10%, thus proving unacceptable for this end. Rapid Prototyping was done initially done using 3D printing, with white plastic coated with 97% reflectance film, and its light transmission measured with the Integrating Sphere at LBNL. A final, industry-grade prototype was designed and budgeted, with an extra thin aluminum profile, 0.020 inches thick, built with 6063 Alloy, T6 temper, and coated with 3M D50A Specular Film Protected, with 98.5% visible light reflectance. A prototype sized for Flexlab, including casting dies, was budgeted at only $1200 by SAPA, but construction was not authorized. Final validation of simulation methods developed against physical measurements was thus not possible. Conclusions regarding product development: for optically complex systems, typical Rapid Prototyping methods do not display the necessary optical accuracy; however, measurements with the goniophotometer require uniform samples, and no larger than one square inch. Thus,hydroponic bucket for optically complex systems with non-uniform geometry, the only current option is building a full-scale prototype for physical testing.

If product development is to be made a priority, new alternatives should be developed to bridge between computer simulations and full scale, expensive and difficult to build prototypes. Whole Building Analysis with 3D Pareto Multi-criteria optimization: building variables under study were: floor stacking patterns, glazing and shading systems characteristics, and shading panes offset, for each orientation, and skylight dimensions. The multi-Objective Metrics and Goals applied were: illuminance levels , Cooling Energy Use Intensity and Heating Energy Use Intensity . Results suggested that Whole Building Multi-criteria Analysis is a fast and effective way of testing complex building alternatives at early design stages, providing useful, operative information for decision making in very short amounts of time, in comparison to standard parametric simulation. The large penetration of renewable energy sources requires flexible resources to manage the variability in generation and demand. Increased observability, improved modeling, and more detailed simulation algorithms are necessary to quantify the impact of intermittent generation to the power network, and – at the same time – efficiently plan the operation of the flexible resources. In order to study the interactions of such complex systems, co-simulation platforms are deemed necessary. The Virtual Grid Integration Laboratory is a modular co-simulation platform designed to study interactions between demand response strategies, building comfort, communication networks, and power system operation. It combines three different simulation tools and incorporates functions for the optimal management of both the grid and the flexible resources. First, research was conducted to determine the appropriate simulation tools for VirGIL and the interfaces to couple them. The Functional Mockup Interface has been selected for coupling the simulation tools. FMI provides a standardized interface, which allows for a very modular co-simulation architecture, where several different modules can be added, exchanged, and tested. FMI enables battery modeling, Electric Vehicle simulation, and advanced optimization functions to be coupled in the future.

DIgSILENT Power factory has been selected as the power system simulator. Using a widely used commercial power system simulation platform will help reduce the barriers to the industry for adopting such platforms, investigate and subsequently deploy demand response strategies in their daily operation. Modelica has been selected as the building modeling language. Modelica is an acausal modeling language, which allows for efficient simulation. Given the complexity of the building models and controls, simulation speed and accuracy are important factors. OMNET++, an established open-source network simulator, has been selected as the communication networks simulation tool. An FMI wrapper was developed for Power factory and OMNET++. VirGIL is the first tool worldwide that will connect Power factory, and OMNET in a co-simulation environment over FMI. Detailed Energy Plus models for existing buildings in LBNL campus were converted to RC models through the BRCM toolbox, and then converted to the Modelica language. Model reduction algorithms were used to reduce the model complexity but maintain the accuracy as much as possible. Studies to compare the accuracy have been carried out. All simulation tools are coupled through FMI to a master algorithm, which is implemented in Ptolemy II. To increase VirGIL’s simulation speed, novel simulation algorithms, notably the Quantized State Simulation algorithm, have been developed in Ptolemy. The first case study of VirGIL was on the LBNL distribution grid. Real data have been used for the power network and the modeling of Building 71. In the second year, we plan to simulate more complex systems, and extend VirGIL by adding advanced optimization algorithms for power system planning and building operation. Research shows that electricity sub-metering can lead to a 10%-30% reduction in electricity use in commercial buildings, and it is likely these savings are available in residential and industrial facilities too. The cost to install available electricity metering technology is very high resulting in virtually no market penetration and an inability to achieve the available savings. We aim to demonstrate the core technologies needed for electricity metering technology that has one-tenth the installed cost of today’s solutions. This new solution will provide sufficient accuracy and time resolution to enabling the retro- and continuous commissioning as well as distributed resource grid integration activities needed for a low carbon society. The core technologies behind power meter are voltage and current measurement, and we will demonstrate non-contact measurement of both quantities.

A suite of sensors will be installed on the surface of circuit breakers in electrical panels, and this installation can be done with minimal training and without an electrician. The sensors will measure the magnetic and electric fields passing through the face of the breaker thousands of times per second, and a set of inverse electromagnetic algorithms will estimate voltage and current in real-time. Each sensor unit will accurately estimate power under a variety of conditions and also compensate for external error sources automatically and without user driven calibration. Our most significant accomplishment is the successful demonstration of accurate voltage, current, and power measurement using a combination of commercially available sensors, custom electronics, and custom electromagnetic and statistical auto-calibration algorithms. We built a proof-of-concept sensor, installed it on various circuit breakers, and demonstrated measurement of voltage, current, and power under laboratory and real-world conditions. We also demonstrated the ability to reliably mitigate the impact of interfering fields from nearby currents. We have also designed an advanced sensor capable of measuring magnetic field in multiple locations and in multiple directions. This technology is critical for reducing the complexity of the installation, improving interference mitigation,stackable planters and enabling improved auto-calibration algorithms. The vector fields that are now measurable are useful for key aspects of advanced auto-calibration algorithms that require no reference information. We are currently applying these results to the design of new sensors and auto-calibration algorithms. The new sensors use a combination of commercially available components and CMOS multi-axis magnetic field sensors. The new algorithms utilize newly identified statistical properties of the primary and interfering signals as well as new inverse electromagnetic analysis techniques. The goal of the first year of this 2-year LDRD was to construct a mass spectrometer that will allow quantitative analysis of gas consumption and gas evolution from electrochemical or chemical systems. This spectrometer is envisioned to become a critical component of a comprehensive and systematic approach designed to understand fundamental reactions occurring in metal-air batteries, Li-ion batteries, CO2 reduction catalysis, oxygen reduction catalysis, and other systems where gas evolution occurs. The differential electrochemical mass spectrometer was constructed over the first 9 months of FY2014 and is now fully operational. The DEMS was custom-built to provide many unique features that allow in-situ, real-time quantitative analysis of gas consumption/evolution in electrochemical cells, which can then be related to Coulometry to more clearly understand electrochemical processes. This technique is extraordinarily powerful and sensitive and provides the capability to assign electrochemical currents to specific reactions. By combining this information with that provided by other spectroscopic and classic electrochemical characterization techniques, complex electrochemical processes can be clearly understood and more readily controlled. Construction and calibration of the DEMS was completed in June 2014, allowing it to have all of the useful features necessary to quantify gas consumption and evolution from electrochemical systems. We are currently exploring three avenues of research with this capability: new electrolyte systems for Li-air batteries , outgassing of Li-ion battery materials at high voltages, and magnesium corrosion in aqueous electrolyte systems to understand limitations of aqueous Mg-air batteries. Proposals have been submitted to the NSF and JCAP II in an attempt to secure funding for aqueous electrocatalysis research . Among the interesting scientific outcomes of our endeavors, we have identified that oxygen out gassing of high voltage non-stoichiometric, Li Li-ion battery cathode materials occurs above 4.6 V and continuously occurs if the electrode is held above that potential, implying that O2 evolution is a parasitic process that should be avoided. Furthermore, CO2 evolution at potentials much lower than 4.6V occurs in this system, implying that the electrode catalyzes an unwanted side reaction.

We have also quantified H2 evolution from Mg electrodes immersed in various aqueous electrolytes as a function of anodic and cathodic currents, providing useful insight into the currently poorly understood Mg-corrosion reaction. Vehicle-grid integration can simultaneously transform the electricity market and the automotive market. For the automotive market, VGI can: 1) allow vehicles to meet all corporate average fuel economy requirements and increasingly stringent emissions regulations, 2) move harmful vehicle emissions away from densely populated areas, and 3) provide revenue to offset the capital cost of vehicle electrification. For the electricity market, VGI can: 4) provide a distributed and growing source of grid energy storage, 5) provide better renewables integration, 6) provide a rapidly ramping resource for many electricity markets, and 7) encourage consumers to more closely scrutinize their home electricity bills just like with gasoline or diesel fuel prices. Despite these benefits, the widespread deployment of VGI faces many uncertainties and barriers within both the electricity market and the automotive market. This LDRD project has created the Vehicle-to-Grid Simulator to provide systematic quantitative methods to develop solutions to the electricity market and automotive market barriers to VGI. This LDRD is developing two versions of V2G-Sim, 1) V2G-Sim Analysis, and 2) V2G-Sim Operations. The V2G-Sim Analysis model couples sub-models for: a) driver behavior, b) automated generation of trip-specific drive cycles , c) vehicle power train models of energy usage during a trip, d) vehicle charging, and e) vehicle response to managed charging or V2G algorithms. V2G-Sim Analysis predicts the behavior for individual vehicles/drivers, and then aggregates individual vehicle profiles to generate grid impacts predictions for large numbers of plug-in vehicles . With these coupled sub-models, V2GSim Analysis provides a platform for scenario analysis of PEV deployment for transmission and distribution infrastructure planning, impacts analysis from various PEV managed charging or V2G algorithms, design of market and pricing structures, etc. V2G-Sim Operations builds upon V2G-Sim Analysis to provide temporally- and spatially-resolved forecasting of PEV charging demands and V2G opportunities allowing an aggregator or integrator to bid PEV services onto an electricity market and operate an electricity grid having many PEVs as a resource within the grid while ensuring each vehicle is sufficiently charged when it needs to be. An underappreciated aspect of climate change is how uncertainty about expected changes affects climate mitigation and adaptation measures. In the past, energy and water planners counted on a relatively stable assessment of climate, infrastructure and policy baselines. With climate change, planners face new uncertainties and forecasts of greater variability. Infrastructure plans must be revised which might include a new peripheral canal or a more decentralized electricity grid, mitigation measures might be considered, such as incorporating bio-fuels and improved batteries, and the valuation of water, as a product or as an energy commodity, must be reconsidered.

We have shown that when values from the literature are used for the model-insensitive parameters, the number of calibrated parameters can be reduced for Model A from four to two, for Model C from four to one, for Model B from six to four, and for Model D from six to three. The reduced number of calibrated parameters leads to a reduced complexity of the calibration task and a reduced uncertainty in optimized parameters, especially in connection with the HYDRUS programs. The small number of additional calibration parameters makes the modeling approach of temperature-dependent root growth a convenient add-on to the HYDRUS models. However, the implementation of the influence of other stress factors on the vertical root penetration, as well as on the root length density distribution, into the HYDRUS models still needs to be validated against experimental data.The purpose of this project is to develop the technology necessary for a fiber based laser plasma accelerator to be used for electronic brachytherapy treatment of prostate cancer. Such a device would deliver MeV electrons suitable for medical applications in a small form factor machine. The laser pulse is transported through a hollow core fiber optic that terminates at an embedded gas target where ionization and acceleration occurs. LPAs operate with energy gradients 1000 times larger than conventional accelerators allowing for the energy gain to occur within a millimeter of the treatment area, increasing the therapeutic dose to the tumor site while minimizing collateral irradiance of adjacent healthy tissue. These milestones include, design of a gas jet capable of providing 1-10 MeV electrons, development of a hollow core fiber suitable for transporting the necessary laser energy,ebb and flow trays and establishing a program to evaluate the efficacy of LPA produced electrons as a radiation source. The gas jet target uses a gas profile featuring a sharp density transition to reduce the laser energy needed for electron injection.

Laser plasma simulations will be conducted to establish the gas parameters and physical dimensions necessary to produce MeV electrons. This will be followed by design and fabrication of a gas jet able to deliver the requisite profile. Accomplishments Simulations have successfully shown 1-10 MeV electron beam generation with about 10 mJ of laser energy. This is achieved by relying on breaking of a laser excited plasma wave at a sharp density transition. To realize this density profile with step, a special gas jet has been developed with two distinct gas regions. The second gas region has half the electron density of the first region, and the density transition occurs in a few 10’s of µm that, according to the simulations, is expected to allow electron injection with small amounts of laser energy. The total length of the gas cell is 350 µm, sufficiently small to act as an internal target during treatment. Guided by the simulation results, a design was developed to physically achieve such a density profile. This jet design uses two converging diverging nozzles that are pressure matched at the nozzles’ exit. The resulting flow is known as a slip line where two regions of disparate density can exist in steady state. In order to demonstrate the initial design, the gas jet was constructed at a scale that is fourteen times larger than the original design. This enables easier manufacturing and a rather straightforward measurement of the density drop. Furthermore, the enlarged device would act as an initial laser target for comparison to simulation. A provisional patent was submitted for this novel two-stream gas jet technique. Currently, we are in the process of integrating the target into an existing target chamber that is powered by an existing10 TW laser system. This includes modifying several components of the system to accommodate the new target. In initial experiments, high power laser beams have been focused on the gas target with the longitudinal profile of plasma recombination light showing evidence of a density drop. Quantifying the longitudinal gas density and studies to establish the minimum amount of laser energy that is needed to generate e-beams are scheduled for FY15. Additionally, a second round of simulations that includes ionization effects for the scaled up target is being performed to benchmark experimental results.This proposal is laying the groundwork for the development of computer codes that will be ultimately capable of virtual prototyping and virtual computer experiments on the next generation of supercomputers. The advanced design of future particle accelerators requires consideration of a variety of physical processes that are not appropriately modeled with current techniques and computational power.

We are pursuing the development of a new, highly accurate and scalable solver combining the accuracy of spectral methods with the scalability of finite-difference methods. We propose a crucial change to the scalable algorithm, namely changing the solver portion from FDTD to PSATD solver, to mitigate significant unphysical effects from discretization errors. Traditionally, such a move would compromise the scalability of the PIC method and render the calculation intractable for the required accuracy and spatial resolution. Key to our approach is the design and high-performance implementation of a new solver to take advantage of multilevel parallelism in emerging systems by naturally subdividing the computational domain and workload in a way that is optimally assigned to the heterogeneous computational resources. Our algorithmic research will provide high numerical accuracy and stability. One of our most significant accomplishments is the development of a novel method for highfidelity modeling of the propagation of electromagnetic waves on a supercomputer. The unprecedented level of flexibility in the tuning of accuracy and locality of our method enables very high accuracy while preserving scalability to a very large number of computer cores. Our new solver also offers larger time steps than conventional solvers by removing the standard limitations due to the well-known Courant-Friedrich-Levy condition. Another significant accomplishment is the analysis of the so-called “numerical Cherenkov” instability for our solver in various modes that has lead to the successful development of novel methods that mitigate the instability. The mitigation method has been automated in our ParticleIn-Cell code Warp and is now successfully used by collaborators at other institutions. Strong scaling of the new method was demonstrated on NERSC’s supercomputers Hopper and Edison, yielding near-linear scaling up-to 50,000 cores. During the scalability studies, we also worked to analyze the performance variability of Edison at larger core counts and developed methods to ascertain scalability in the time-sharing environment with the newer Cray Aries interconnect with Dragonfly topology. The scalability of our solver was also contrasted to the scaling of standard global FFTs. The results were presented at the international SC’14 conference and will be documented in a journal publication. We are beginning to develop and study the scalability of the solver on test-bed next generation computers through portable implementations of the solvers, via heterogeneous and emerging programing models. The solver is critical to the further development of the Warp code, which has been selected in a highly competitive competition as a first tier NERSC NESAP application. We are also in the process of extending our methods to three dimensions and applying them to large-scale simulations of laser plasma accelerators.

The goal of this proposal is to develop the scientific user community for the next generation soft x-ray spectro-microscopy and tomography based on x-ray ptychography. X-ray ptychography is a robust diffraction imaging method that can take full advantage of the high brightness of the ALS and which is not limited in resolution by the x-ray optics. The technique we have developed enhances the already high resolution scanning transmission x-ray microscope with the addition of diffraction data and is able to probe chemical species, molecular orientation, magnetization,4×8 flood tray and structural morphology at <10 nm resolution. We will apply this method to difficult problems in the material sciences with a focus on materials for energy and carbon cycle research. In particular, we will study chemical phase transformations in nano-crystals of active battery electrodes, hydration reactions in calcium silicate hydrate, pore evolution in sintered zirconia, and magnetic domain structure in thin magnetic films. Finally, we will further develop in situ methods for high resolution microscopy of electrochemical and hydration reactions in these materials. These studies require the ability to visualize 10 nm scale features embedded in a micron-scale matrix with sensitivity to the chemical species however there currently is no imaging technique with such capabilities. We will develop soft x-ray scanning diffraction microscopy with the study of these systems and provide a microscopy program that will directly and efficiently benefit from the very high brightness of the new COSMIC beamline at the ALS and future beamlines at the ALS-U. This program will readily be extended to other problems in the materials sciences such as the study of porous zeolites for carbon capture and catalysis and the characterization of materials by design like self-assembled nanoparticle aggregates for replacement of non-renewable resources in batteries and solid state devices. Finally, this project will leverage the computational resources at NERSC for the reconstruction of Giga-element datasets and potentially provide experimental feedback to material computation efforts. Using the unique spatial resolution and chemical sensitivity of our imaging method we have directly visualized a two phase chemical transformation and the complicated chemical domain pattern present in the smallest available nano-crystals of LiFePO4. Our measurements were also correlated with high resolution transmission electron microscope images of many such particles to show that these small particles do not suffer from material fracture but still display a complicated domain pattern which does not correlate with the material crystallographic axes as was expected. These results seem to indicate that the superior electrochemical performance of the small particles is due primarily to mechanical issues rather than the fundamental character of the phase transformation itself and provides critical insight into how to engineer higher performing batteries. We have also used our high resolution imaging technique to measure the magnetic domain wall width distribution in a thin film of CoPd, the pore size distribution in sintered Yttria stabilized zirconia, and the x-ray magnetic circular dichroism spectrum in magnetotactic bacteria all with spatial resolutions which are not achievable at any other x-ray facility worldwide.

Storage ring based light sources have been extremely successful over the years, enabling forefront science in many areas. Recent developments in accelerator technology and lattice design open the door for very large further increases in brightness – more than 100 times, particularly by reducing the horizontal emittance. This can greatly enhance the capability of light sources for imaging and spectroscopy. While there are no showstoppers, work was necessary to reduce risk and cost, enable a timely execution, and optimize the properties of the source to the needs of the science case and prospective user community. The goal of this project was to investigate, demonstrate and improve critical technologies necessary for diffraction limited storage ring light sources at the subsystem level. At a later stage, tests will be carried out with some of those new systems using beams in existing light sources. roject Description There is a great need in advanced diffraction gratings at the ALS and other synchrotron facilities. To provide high spectral resolution and high diffraction efficiency the gratings are required to have a variable line spacing , perfect blazed grooves, and smooth groove surface. For Reflective Zone Plates elliptical lines are required to provide two dimensional focusing. Due to limitations of conventional techniques one can only design gratings within a very limited set of variables. New approaches for fabrication of high quality grating in a cost effective manner should be found to make advanced diffraction gratings available. This work aims development of a new grating fabrication process based on Direct Write Lithography technique which is used in semiconductor industry for making high resolution MEMS structures, nanostructures, and consumer microelectronics. A grating pattern can be written by scanning a focused laser or electron beam over a substrate surface coated with a photoresist. The DWL technology will be used as a pattering technique for making diffraction gratings of arbitrary groove density variation and groove shape complexity. The best available DWL systems will be used for making grating prototypes which will be characterized in terms of groove position accuracy, imaging performances, and diffraction efficiency. DWL process will be optimized and eventually combined with wet anisotropic etch technique for making highly efficient blazed gratings.

Therefore, leaf and other vegetative litter should be considered as potential sources of Phytophthora, including pathogenic species, whether they are found in natural streams or other surface waters. Alternatively, the suitability of local vegetation may be a determinant of what Phytophthora species become established or prominent in streams.Current farming and food systems confront and are implicated in multiple challenges and unsustainable changes, including biophysical dimensions such as climate change , environmental pollution, escalating losses of biodiversity, and deteriorating ecosystem services . Social forces and structures as well as unsustainable socioeconomic processes also strain present capacities to manage growing population pressure, unplanned urbanization, food and nutrition insecurity, dietary shifts, and health disparities associated with poverty, and growing inequality among multiple stakeholders, including women, youth, migratory workers, and indigenous peoples . Both urban and rural actors are impacted in relation to land ownership and land use change issues and drivers underpinning global industrial agriculture and connected food systems. Human activity has approached critical limits over an increasing number of the so-called Planetary Boundaries , beyond which the functioning of ecosystem services may be substantially altered, increasing the risk of destabilizing life on our planet . Agriculture and food systems are both a villain and a victim in approaching or breaching PBs, and this is already impacting the ability to farm and produce food. How can humanity sustainably grow nutritious food and return to a safe operating space within the PBs? As an alternative to this scenario,hydroponic growing supplies a growing number of studies and reports indicate significant potential gains from transitioning toward agroecological agriculture as a way of nourishing current populations sustainably while allowing for future generations to support their livelihoods .

One core quality of transitioning to agroecological farming systems is the regenerative trend of increased “outputs” per unit “input” for a more efficient agriculture for using and conserving diversity on a long-term basis, through the use and combination of different agricultural techniques in ways which restore and nourish the soil and enhance the local environment, instead of continuously degrading it. In addition, the diversification strategy makes food producing systems resilient to external shocks and influences, such as floods or droughts, using, for example, approaches built on the principles and science of agroecology . There is growing evidence that such production systems allow for lower cost and more diverse fruit and vegetable supply . Furthermore, conventional thinking about food is increasingly being challenged, shifting from being regardedonly as a commodity toward becoming acknowledged for its nourishment, social and cultural values, the links it creates between people, and its deep connectedness with ecosystems, ecosystem services, and natural resources . The current globalized industrial food system exhibits the same drivers which impact and shape farming industries and food production, and underscores the importance of focusing on how food flows into food systems, and which structures and related policies are shaped to support and reinforce current farming as well as food systems . It is not only conventional and industrial production of animal feed, genetic material, or major commodities such as wheat, rice, coffee, sugar, maize, and chicken which are controlled and shipped across continents by large trans-national corporations. Our globalized industrial food systems sometimes also include food which originates from farming systems based on organic farming regulations and principles like the IFOAM principles, calling for more coherent, equitable and holistic food systems, and applying agroecological farming methods. In other words, the intentions behind such farming systems and their contributions to agricultural and environmental sustainability are not always extended to food systems, which generally contribute to out-competing local produce, distorting prices and producing huge amounts of food waste and other waste.

This can be seen as a contradiction and emphasizes the importance of thinking of not only organic and agroecological production, but also has consequences for thinking the principles into the entire food systems. At the same time, there are many examples of organic farming and food as well as agroecology presenting alternatives to the industrial farming and food systems , and by increasing and emphasizing this, we can move toward a food system that falls within the PBs. This calls for profound analyses of how agroecological food systems function, and how they can contribute to coherent, resilient and equitable production and exchange of food, while human and social capitals are built up throughout the food systems, and resources are cycled rather than transported through, from or to disconnected parts of the systems. How can such food systems meet challenges such as losses of complex and system-oriented, context-relevant knowledge about farming and food, and how can they contribute to re-connect consumers and the food that they eat across urban-rural settings in city-region food systems? An increasing number of papers and reports link agroecology and food systems , referring to the fact that agriculture and food systems are intricately linked, and to a large extent driven by the same global structures. Given the intricate and mutually-reinforcing relations between agriculture, food, and socioeconomic systems, the present article aims to characterize and explore how the concept of agroecology stimulates the conceptualization of agroecological food systems, or perhaps even a more inclusive term like “socio-agroecological food systems.” Food systems following the principles of agroecology calling for resilience, multi-functionality , equity, and recycling of resources face particular challenges and have significant options for impacting sustainable development in city regions . This needs to be seen in a light where an increasing amount of the global population lives in urban areas, from smaller towns with a few thousand inhabitants, to mega-cities of millions of people. Urbanization has changed diets and nutrition, while food consumption has become detached from food production worldwide . Taking a systems approach to reconnecting these gaps requires major changes in consumption patterns, resource management and social responsibility, if everybody is to be nourished in agroecological food systems.

We aim to explore the connections and linkages between the concepts of agroecology and food systems, and focus particularly on how the food system framework can locate and ground the concept of agroecology within a rural– urban landscape setting. This exercise requires us to critically examine the reciprocal flows and the multiple environmental, social, and governance related connections needed for an agroecological food system transformation.A food system is a system that involves activities, social and institutional structures, and processes related to the production, distribution, exchange, and consumption of food . Agricultural systems are part of food systems, integrated in ecosystems, and constituted socioecological systems . Over the past few decades, the understanding of food systems has clearly developed as result of the development of a more and more globalized food system . Ericksen compared some features of “traditional” versus “modern” food systems, and addressed the governance of different food systems, with or without support for local production, and Foran and co-authors point to the existence of different concepts of how food systems are constructed, with examples from so-called developing countries. The structure and governance of the food system clearly influences consumption patterns by providing both producers and non-food-producing consumers with options of availability. The range of social and environmental welfare outcomes stemming from food system activities were also discussed and visualized in Ericksen ,flood table and Jennings and co-authors analyzed how planned and well governed city-region food systems could contribute to different aspects of food security for different groups of citizens, stable incomes, circular economies, and resilience at various levels. Characterizing a food system can follow through its different social aspects and arrangements, like the type and degree of contact between those who grow and produce food and those who receive and eat the food without participating in the production of it, or who and how many people are involved in the cycle between the soil and the plate. Where local food systems with short supply chains have potential for involving resource feedback loops, raising collective awareness among different actors within the food system, and give possibilities for mutual learning , a larger and decoupled food system lacks the direct interaction and feedback, reduces exchange of experiences and knowledge, or the embeddedness inherent in a localized food system. A decade of research on New York’s Chinatown produce economy gives an example of the importance of this connectedness: the studies revealed that 80-plus produce markets offered an incredibly diverse assortment of lower-cost produce because they are connected to a web of nearby, independently-run small farms and wholesalers . In a food chain , a product flows through different steps, where various forms of transformation may occur, and connection and feedback loops between these different steps may not necessarily exist. In such systems, farmers or industrial food producers can risk becoming producers of “food from nowhere,” as expressed by Bové and Dufour , and later unfolded by Campbell , and “consumers” can become reduced to a non-informed and non-responsible person, only “consuming food no matter of origin,” as a contrast to so-called “food citizens” defined as a consumer who makes decisions that support a democratic, economically just and environmentally sustainable food system, with a possibility of being actively involved in the food system at different levels . The call and practice of re-localizing of food systems is similarly seen as a harbinger of rural– urban reciprocity as consumers and producers are re-embedded physically and socially in the food system while raising awareness of their respective impacts on one another .Agroecology is widely acknowledged equally as a science, a practice and a movement . Its academic roots go back nearly 100 years, drawing on the fields of agronomy, horticulture, and ecology.

Through the view of agricultural systems as ecosystems, agroecology combines these disciplines and has subsequently incorporated further disciplines of cultural, human, and social sciences in a wider systems approach. It has existed as an explicit concept since the 1930s, evolving through the 1970s by increasing awareness of practices, focusing on indigenous knowledge and emerging social movements. These tenets position agroecological paradigms as both an alternative to chemical, mono-cultural or industrial farming, and as a catalyst for conventional agriculture to adopt more sustainable approaches. Agroecological systems are considered to be built on the principles of natural ecosystems and are seen as multifunctional and functionally integrated systems of complementary and dynamic relations between living organisms and their environments. In Table 1, some well-explored key characteristics related to agroecology are listed. The functions of natural ecosystems, in terms of energy and nutrient flow, as well as the dynamics of adjusting and being resilient to constantly changing surroundings and regulating populations, clearly are different from an agroecosystem. The latter are altered by and reacting to human dominance, or at a more extreme end, are disconnected or isolated from pre-existing energy and nutrient flows . Over the past decades, many academic agroecologists have increasingly stressed the importance of considering the human and social systems as integrated parts of the agroecological system. Building complex systems involves extensive human knowledge, experience, and community collaboration. Blay-Palmer and co-authors point to how the benefits of sharing place-based knowledge and good practices can help in joining forces for transforming food systems at a wider scale. The scale of an agroecological system can be large or small, but the scope of agroecological farming activities is wide; the majority of the population of smaller-scale family farmers are often considered to be applying agroecological farming approaches, and are currently estimated to produce food nourishing 50–70% of the global population, and supply up to 80% of the food in Sub-saharan Africa and Asia . With regard to human livelihood and scale related to agroecological systems, Walter Goldschmidt found that rural communities with more, smaller farms saw higher human well being than those with fewer, larger farms in settings of North-American farming in the middle of last century. This has been questioned by modernist scholars, but has also seen numerous studies supporting its conclusions over time, and it certainly has never been strongly refuted . As the example above on research in New York’s Chinatown produce economy showed, the diversity of production was found directly related to the proximity of supply and lower cost of healthy food. Another argument for how the resilience of an agroecosystem includes environmental elements as well as social and institutional elements is raised by Gonzales De Molina who refers to Holling, Berkes, and Folke and Holt-Giménez : “The resilience of an agroecosystem does not depend solely on its productive arrangements.

Collections also have been useful in determining whether the establishment and early stages of invasion are linked to single or multiple introductions. For example, Russello et al. used genetic evidence obtained from natural history specimens to infer the origin of monk parakeet populations in the USA and to link the invasion success of this species to propagule pressure exerted by the pet trade industry. Voucher specimens are useful for testing evolutionary hypotheses through data gathered from examination of trait and molecular variation. Molecular methods can be used to examine genetic variation of introduced populations and to reconstruct patterns of genetic change over time. For example, Hartley et al. used DNA extracted from vouchers to determine that blow flies were preadapted to rapid evolution in response to organophosphate insecticides. Also, phenotypic changes that occur during the different stages of invasions can be examined using natural history collections. Zangerl and Berenbaum used herbarium specimens to examine changes in phytochemistry of an invasive plant over a 152-year time period after introduction. In accordance with the enemy release hypothesis , they found that insect damage was nonexistent during the establishment phase of this species, and in accordance with the evolution of increased competitive ability hypothesis , they found that defense compounds of plants from the introduced range were significantly lower than those of plants from the native range. Further, defense compounds increased after the accidental introduction of a specialist insect herbivore from the native range. Another approach to examine factors that contribute to invasion success is to study a group of introduced species, both invasive and noninvasive. For example, Suarez et al. examined unintentionally introduced ant species from port-of-entry samples stored at the National Museum of Natural History. They found that 12% of 232 introduced species have become established in the USA, and that the probability of establishment was influenced by propagule pressure and nesting habit of ant species. Similar investigations of intentional introductions,hydroponics growing system such as bio-control agents and horticultural plants , also may provide important information on species-level ecological traits as well as phylogenetic patterns and evolutionary processes related to invasion success.

Natural history collection data are not quantitative and include species occurrences only . In addition, especially when dealing with few samples, there is a concern about how representative the samples are of the introduced populations. In some cases, these concerns can be alleviated and relative abundances of invaders can be determined from passive sampling techniques that indiscriminately collect specimens . Also, relative abundances may be inferred using specimens as a random sample of the associated community. For example, changes in the composition of pollen loads collected from bumble bee specimens reflected changes in abundance of an invasive weed in northwestern Europe . Similarly, insect and other animal specimens could be used to examine invasive parasitoids, parasites, and pathogens, and plant specimens could be used to examine invasive herbivores and pathogens. Despite the limitations of natural history collections, numerous studies have demonstrated the utility of these collections in the study of invasion biology.Natural history collections from museums and herbaria contain a wealth of data that may be used in the study of biological invasions. For example, Suarez and Tsutsui estimated that more than 100 million insect specimens are contained in just 11 entomological collections in the United States. Worldwide, natural history collections contain billions of specimens that have been collected over hundreds of years and these collections are continuing to grow . Natural history collections provide a valuable source of preserved biological materials ranging from whole organisms to DNA libraries and cell lines. Collection specimens are associated with, at minimum, information on the date and locality of collection, and often have additional information, including associated observational data and physical samples derived from specimens, such as frozen tissues and DNA extracts. Furthermore, much of the data housed in natural history collections recently has been digitized and is available through a number of searchable databases and online resources. Biodiversity informatics is an emerging field of science, and great strides have been made to link available genetic, species, and ecosystem level data, and make these data available electronically to users worldwide . The Invaders Database System , National Biological Information Infrastructure , Global Biodiversity Information Facility are just a few examples of online data portals and resources that provide access to a global network of biodiversity information, including data on voucher specimens located in natural history collections found throughout the world .

The Invaders Database System is focused on the Pacific Northwest region of the USA and combines manually entered herbarium records dating back to 1877 with records from regional literature, extension agents, and state agriculture departments, providing presence data that allow researchers to examine historical spread.For example, GBIF provides access to 285 data providers, 7445 datasets, and nearly 175 million searchable records. Some online data sources, such as Lifemapper and the Ocean Bio-geographic Information System provide links to data from a number of collections as well as tools for mapping and predicting species distributions using linked data. Such online resources will only continue to enhance the accessibility of data; however, many natural history collections are still making efforts to digitize available data. Thus, invasive species researchers should be aware that there may be a number of local, regional, and taxon- specific collections containing voucher specimens with potentially important data that are not yet summarized electronically.Improvements to natural history collection data accessibility are well underway, as many curated collections are being digitized and made available on the internet. Digitization of collection data is important for invasive species researchers who may want to use these collections, and the linking of many collections through a data portal or centralized database increases the power of available data. To facilitate the study of early-stage invasions, we recommend that researchers and field collectors, who often are very familiar with the flora or fauna within the regions they study, collect and deposit voucher specimens in the appropriate natural history collection when new or rare species are detected, in particular those species of foreign origin. Further, if an introduced species is observed in a new habitat, it would be especially useful to collect multiple individuals and to record the number of individuals observed in the population. Also voucher specimens for biological control introductions and new horticultural introductions should be deposited in the appropriate natural history collection with pertinent data, including geographic source of origin. In particular, we recommend that natural resource managers and researchers introducing bio-control agents deposit voucher specimens with data including the number of individuals introduced, the original source population of agents, the laboratory where they were reared, and the location of introduction. Because substantial efforts are being made to digitize and link data from natural history collections through centralized data portals and databases, these vouchers may be especially useful for future investigations.

Considering the potential benefits of UA for improved ecosystem functioning, in this review we discuss the ability of UA to support local and landscape level biodiversity, the role of UA in providing ecosystem services,mobile vertical grow tables and the agenda for future UA research.Urban agriculture activities are diverse and can include the cultivation of vegetables, medicinal plants, spices, mushrooms, fruit trees, ornamental plants, and other productive plants, as well as the keeping of livestock for eggs, milk, meat, wool, and other products. This definition points to the fact that UA is not solely for food production, but for a wide range of needs of the local community, including medicinal and ornamental plants. The different types of UA allow for a diverse set of vegetation structures to contribute to the edible landscape in a range of community types, and this wide range of products means that UA systems are highly heterogeneous in size, form, and function. A description of different types of UA can be found in Table 1, with associated images in Fig. 1. Community or allotment gardens often represent small-scale, highly-patchy, and qualitatively rich semi-natural ecosystems and are usually located in urban or semi-urban areas for food production . Private gardens are primarily located in suburban areas and may be the most prevalent form of urban agriculture in cities. Privately owned gardens cover an estimated 22–27% of the total urban area in the UK , 36% of urban area in New Zealand , and 19.5% of the urban area in Dayton, Ohio, USA . Easement gardens are located within private/community properties, but are often regulated by the local government. Urban easements are established with the purpose of improving water quality and erosion control , but they can include a wide array of biodiversity, depending on management type . Roof-top gardens are any garden established on the roof of a building and can be both decorative and used for agriculture. Urban orchards are tree-based food production systems that can be owned and run privately or by the community. Increasingly, schools and hospitals are establishing fruit trees that provide crops, erosion control,shade, and wild life habitat, while producing food for the local community . Many UA systems may fit into more than one category. For example, both private gardens and community gardens may exist as rooftop gardens, and community orchards may exist within community gardens.Urban landscapes are typically highly simplified, intensively developed ecosystems with low levels of native biodiversity . However, urban green spaces such as UA can bring diverse green infrastructure back into the urban system, providing vegetative structure and biodiversity for ecosystem function and services across fragmented habitats and spatial scales . UA may be especially important for biodiversity conservation in cities because vegetative structural complexity in simplified landscapes contributes disproportionately more to conservation than in more natural landscapes . Just as in agricultural systems where more complex agri-environment management can have a larger effect on biodiversity when implemented in simple agricultural landscapes than more complex landscapes , UA provides many opportunities for re-vegetating the landscape at the local scale within a vegetatively depauperate urbanized landscape. Urban agriculture has the potential to support biodiversity not only within UA sites, but also nearby due to a landscape-mediated ‘spill over’ of energy, resources, and organisms across habitats. Such spill over may be an important process for the persistence of wildlife populations in human-dominated landscapes because it allows for resource acquisition and re-colonization events . At the same time, chemical, water, and animal movement is bi-directional, and intensified management implemented in backyards, such as pesticide application, extensive pruning, frequent mowing and other disturbances, can limit the capacity of gardens to maintain rare or sensitive insect species . Thus, it is important to understand that not all biodiversity is necessarily “good” biodiversity, and there may be a number of disservices that come from UA as well . Here, we examine the ability of UA systems to support vegetative, insect, and vertebrate biodiversity .The wide variety of UA types in practice allow for considerable variation in vegetative complexity and diversity. Domestic gardens vary widely in features that may promote plant biodiversity,such as ponds,moss, ground cover, and varied vascular vegetative structures . For example, tropical home gardens have stratified vegetation similar to those seen in multi-stratified agroforestry systems and can thus provide a large amount of planned and associated biodiversity . The diversity of vegetation types within home gardens has been documented in Santarem, Brazil, where 98 plant species were identified in 21 urban gardens and included a large diversity of fruit trees and shrubs , ornamental plants , vegetable/herb plants , and medicinal plants . In Leon, Nicaragua, 293 plant species belonging to 88 families were recorded across 96 surveyed home gardens, ranging in habit and taxonomic origin . In Hobart, Australia, 12 distinctly different garden types with different species, habits, and canopy heights were documented in front and backyard gardens , and a similar survey conducted in Toronto found 25 woody plant species and 17 different herbaceous plant species per backyard garden . In an example from five UK cities, more than 1000 species were recorded in 267 gardens, exceeding that recorded in all other local urban and semi-natural habitats .In Stockholm, allotment gardens are older than many backyard gardens, often representing lush, well-managed flower-filled areas ranging in size . Such areas are often extremely rich in plant diversity, with more than 440 different plant species recorded in a single 400 m2 allotment garden .

Human pathogen contamination of produce was the leading cause of food borne illnesses and outbreaks associated with a single-ingredient commodity between 2004 and 2013 . Lack of visual evidence that indicates the presence of contamination on produce contributes to the estimated 9.4 million cases of food borne illness in the United States annually . Various pathogen groups and toxins can be causal agents of food borne illness associated with produce; however, non-typhoidal Salmonella ranks as the second leading cause of all illnesses associated with consumption of produce . In a pre-harvest setting, enteric pathogenic bacteria are introduced to fresh produce through many routes, including low quality irrigation water, use of contaminated organic fertilizers, close proximity to livestock operations, wildlife intrusions, improper worker hygiene, or contaminated equipment . Once on the leaf surface, bacteria are faced with harsh conditions, such as UV irradiation, low nutrient and water availability, and unfavorable weather . Bacteria may escape these conditions by attaching to the leaf surface and forming bio-films or by transitioning to an endophytic lifestyle through internalization into the leaf extracellular space via natural pores or wounds . While leaf internalization is likely to confer some protection to the bacteria, it is not without some disadvantages. Plants can detect endophytic bacteria in the apoplast through pattern recognition receptors localized at the cell membrane that perceive conserved microbial molecules known as pathogen- or microbe-associated molecular patterns . PRR-PAMP binding leads to initiation of PAMP-triggered immunity , which functions to prevent further internalization of bacteria and to eradicate those that have already entered the apoplast . This suggests that internalization trades one challenge for another ,black plastic planting pots and only bacteria that can cope with these challenges will be able to colonize leaves successfully.

Previous studies have shown that Salmonella spp. interact with plants in a sophisticated manner, although the exact mechanisms are not fully understood . For instance, similar to some plant pathogens, Salmonella enterica serovar Typhimurium SL1344 can modulate stomatal movement in Arabidopsis leaves, where it induces a transient stomatal closure and re-opening at 4 h post incubation . Stomatal closure can diminish bacterial internalization and subsequent contamination of internal leaf tissues. The mechanism for stomatal re-opening by the phytopathogen Pseudomonas syringae pv. tomato is through the action of coronatine , a polyketide phytotoxin . However, the genomes of STm strains LT2 and 14028s do not encode genes for coronatine synthesis . Furthermore, stomatal re-opening is not a ubiquitous response to human pathogens. For instance, Escherichia coli O157:H7 induces a lasting stomatal closure in lettuce and Arabidopsis for at least 4 and 8 h, respectively . Beyond the ability to modulate stomatal movement, STm SL1344 can survive at a higher titer within the apoplast of Arabidopsis leaves than O157:H7 after surface-inoculation and S. enterica serovar Thompson strain RM1987 can survive at high titers on the surface of romaine lettuce leaves . Therefore, S. enterica may either induce a weak plant immune response or can counteract plant immunity and consequently persist on and in leaves . Internalization and persistence within the apoplast are arguably the most important targets for managing contamination of produce by Salmonella, as endophytic populations cannot be removed through typical washing tactics . Here, we provide details of multiple genomic regions required for internalization and persistence of STm 14028s into lettuce leaves. These genomic regions were identified with a genetic screen of multi-gene deletion mutants of STm 14028s to pinpoint proteins and metabolic pathways responsible for stomatal re-opening and apoplastic persistence. Selected MGD mutants were further characterized regarding their ability to survive in the apoplast, induce hallmark plant defenses, and replicate in apoplastic wash fluid. While all mutants induced a prolonged stomatal closure when applied to the leaf surface, the mutants were found to vary in other aspects of phyllosphere survival. Five-mL of LSLB bacterial cultures were grown in 14.0 mL culture tubes on a rotary shaker to an OD600 of 0.8–1.0. Cells were harvested by centrifugation and resuspended in water to an OD600 of 0.002 . Inoculum was infiltrated with a needleless syringe into leaves of 5-week-old lettuce plants that were kept under the same environmental conditions used for plant growth. Stomatal bioassay was conducted as previously described at 2 and 4 hpi. Mean stomatal aperture widths from three independent leaves and SE were calculated. The difference between the means was compared by Student’s t-test to determine statistical significance.

Apoplastic wash fluid was extracted from 5-week-old lettuce leaves, omitting the cotyledons, using an infiltration centrifugation method as previously described . To ensure that plant cellular contamination did not occur during extraction, AWF was evaluated for cellular contaminants using the Sigma-Aldrich RGlucose-6-Phosphate Dehydrogenase Assay Kit . None of the AWF used exhibited detectable levels of G6PDH . AWF was saved in aliquots to limit freeze-thaw cycles and stored at −20◦C and filter sterilized at the time of use. Bacterial cultures were grown in LSLB liquid medium on an orbital shaker to an OD600 of 0.8–0.1. Cells were harvested by centrifugation and resuspended in water to an OD600 of 0.2 . An aliquot of this inoculum was added to each medium to achieve an initial bacterial culture concentration of 5 × 106 CFU/mL in a 96-well plate format. Growth curves were obtained by growing cultures stationary, except for a 30-s rotation prior to each OD600 reading using a BioTek EPOCH 2 Microplate Spectrophotometer . OD600 readings were obtained every 30 min throughout a 24-h period and blanks were included as a control. This experiment was performed three times with three technical replicates each time. Mean OD600 for each time point of the growth curve was calculated after subtracting the mean blank value and subsequently converted to bacterial cell number per mL of culture. Growth rates in the log-phase of growth were determined using the formula N0 x 2 n = Nf where N0 is the number of bacteria at the first time point of interest, Nf is the number of bacteria at the final time point of interest, and n is the number of generations.We utilized a collection of MGD bacterial mutants derived from STm strain 14028s . We first confirmed that this strain induces a similar stomatal response to that of STm strain SL1344 . We evaluated changes in the stomatal aperture width in leaves of young lettuce plants by floating leaf pieces onto bacterial inoculum as previously reported . Both STm strains induced an initial stomatal closure at 2 h post inoculation followed by re-opening at 4 hpi , suggesting that the MGD library could be useful to identify STm genomic regions required for successful stomatal re-opening at 4 hpi. Second, to ensure that lack of re-opening was due to deletion of genes required for stomatal re-opening by STm 14028s rather than temporal factors, the circadian movement of lettuce stomata was determined. This analysis indicated that the stomatal aperture was widest at 6 h after first light . We therefore, chose to start the stomatal bioassay at 2 hafl to ensure that the 4 hpi time point corresponded to a time with maximum expected stomatal aperture width. A primary screen of 303 MGD strains with a single biological replicate indicated that 177 mutants were unable to re-open stomata, suggesting a high rate of false-positives. Thus, we functionally annotated the predicted deleted genes in these 177 mutants .

Considering the current knowledge of STm epiphytic behavior , we reasoned that genes involved in secretion,black plastic pots for plants perception of environmental signals, signaling, and regulatory functions could be involved in opening of the stomatal pore. Thus, we selected 51 MGD mutants based on their functional annotation for retesting with at least three biological replicates. The primary functional units missing in these 51 mutants are described in Supplementary Table S2. From this confirmation screen, only eight mutants were unable to reopen lettuce stomata consistently and they were selected for further characterization. Furthermore, previous results indicated that mutants for the Salmonella Pathogenicity Island 1 and 2 were unable to open lettuce stomatal pores . Thus, we also analyzed two MGD strains from our collection that have a predicted deletion of these regions in addition to a few adjacent genes . To confirm that the lack of stomatal re-opening using leaf pieces floating on bacterial inoculum was a reproducible response that can also be observed in leaves still attached to the plant, we designed a stomatal bio-assay that included infiltration of mature lettuce leaves with STm 14028s, Mut3, or Mut9 bacterium suspensions. In this assay, bacteria are placed in the leaf apoplast, including the sub-stomatal chamber, where they can be in contact with the guard cells. All three strains induced a strong stomatal closure at 2 hpi , similar to observations made using surface inoculation of mature, whole plants . Furthermore, the wild type strain STm 14028s, but not the mutant strains, induced stomatal reopening at 4 hpi , suggesting that this response is robust. To rule out the possibility that the infiltration procedure induced an unpredictable stomatal movement, we assessed the circadian stomatal movement in untreated lettuce leaves as well as leaves infiltrated with water , STm 14028s,or Mut9. Mock-treated and untreated leaves showed an almost identical movement pattern, stomata of Mut9-infifiltrated leaves remained closed throughout the daylight period, and STm 14028s-infiltrated leaves showed a transient reduction in stomatal aperture width at 2 hpi that corresponded to 4 hafl. Upon completion of this screening procedure, the genome position of the deleted region for each mutant was identified at the nucleotide level by whole genome sequencing of the mutant strains. This procedure, which was readily available in a time and cost-effective matter, allowed us to predict the genotype and the functional units missing in each mutant using the available STm 14028s and LT2 genome annotations . Furthermore, each mutant, except Mut5, was able to swim and swarm , confirming the predicted genotype of Mut5 is missing genes involved in flagellar biosynthesis and chemotaxis . Movement and chemotaxis have previously been associated with STm SL1344 internalization through the stomatal pore . Thus, the identification of Mut5 during the Salmonella genetic screening validates our procedure, which identified known and novel features associated with bacterial epiphytic behavior. The 10MGD strains were further tested for phenotypic traits required for colonization of leaves as described below. As all selected mutants were unable to stimulate stomatal re-opening at 4 hpi , we sought to determine whether each mutation also affected the population dynamics in the lettuce leaf apoplast. To characterize each mutant’s ability to survive within the apoplast, leaves were infiltrated with bacterial inoculum. This allowed for direct analysis of population titer changes due to apoplastic interactions and eliminated confounding factors, such as failure to survive on the leaf surface and/or lack of internalization through stomata.The wild type bacterium STm 14028s population declined significantly in lettuce leaves , while variable population titers were observed among the mutants . For instance, seven mutants, Mut1/2/4/5/7/8/10, had significantly greater population titers than that of the wild type bacterium at 21 dpi, whereas Mut3 and Mut6 apoplastic persistence did not differ from that of the wild type at 21 dpi . Interestingly, only Mut9 showed significantly impaired endophytic survival . This finding indicates that genes missing in this mutant, including the SPI-2 and the suf, ynh, lpp, and ttr operons , may be required for the bacterium to cope with or overcome plant defenses and/or the ability of the bacterium to obtain nutrients from the apoplastic environment necessary to maintain its population. To test for these possibilities, we performed a callose deposit assay and a bacterial growth rate assay using lettuce apoplastic wash fluid . Callose deposition is a hallmark plant defense response that is induced upon biotic stress . Thus, we determined the average number of callose deposits in lettuce leaves inoculated with STm 14028s, Mut3, and Mut9. We observed that all three bacteria induced similar numbers of callose deposits that were significantly higher than those seen in the water control . Because all three STm strains induced a relatively low number of callose deposits , we also inoculated Arabidopsis with the virulent phytopathogen Pst DC3000 for comparison with this well-established system.

A corollary goal is to provide the nursery industry with a source of new and interesting, economically advantageous and environmentally sound plant revenue. With increasing pressure from state and regional waterquality control boards for zero runoff in the nursery industry , plants requiring fewer inputs will be a welcome addition.A field was prepared to test 240 plants on a UC Davis research farm in USDA Zone 9 . Plants were placed 2 yards apart along rows that were 2 yards apart, with 20 plants per row in each of 12 rows. This allowed the simultaneous testing of six individual plants on each of four different water treatments for each of the 10 species. The rows were covered with 3 to 4 inches of bark mulch, and two 2-gallon-perhour drippers were buried beneath the mulch in the root zone of each plant. The plants were placed according to a randomized complete block pattern in three blocks throughout the field. Each row was furnished with four water lines to deliver one of the water treatments to each plant after they were established. It is important that even drought-tolerant plants be given supplemental water until well established, because the development of an adequate root system is a key component of drought-tolerance . The 10 species were planted in fall 2004, and frost-killed specimens of creeping sage were replaced in spring 2005. Likewise, the plants were also watered during long, rain-free periods in the winter of 2005 to 2006. Experimental irrigation treatments were carried out during the 2006 growing season. The four irrigation levels were based on percentages of reference evapotranspiration as described in Water Use Classification of Landscape Species III . ETo was defined as the amount of water evaporated from a 4- to 7-inch-tall, cool-season grass in open field conditions. WUCOLS classifies landscape plants according to how much water they need compared to cool-season turfgrass,drainage planter pot which is high water-use and needs 80% of ETo to look green and healthy in the summer growing season.

In our trial, we used the following percentages of ETo: 20% , 40% , 60% and 80% . We wanted to assess not only if these plants were truly drought-tolerant, but also if they could survive under garden conditions where they might be combined with higher water-use species or adjacent to a high water-use lawn. The average water-holding capacity of the soil was determined from soil samples collected at field capacity along a transect across the field. Irrigation was measured to replace half of the soil’s water-holding capacity in the root zone of each treatment to a depth of 1.5 feet. Since some of the moisture in the soil is held too tightly to soil particles for plant uptake, plant water stress is usually avoided by providing an irrigation when 50% of field capacity has been depleted. This amounted to 21.2 gallons of water per plant delivered over a period of approximately 5.25 hours. We used ETo values calculated by the California Irrigation Management Information System , which comprises data collection stations in various locations throughout the state that measure precipitation, relative humidity, solar radiation, temperature and wind speed. The California Department of Water Resources provides values daily for ETo online for the public . During the May to October 2006 irrigated growing season, the Davis CIMIS station was accessed daily via the Internet, and the ETo values were placed into a water budget worksheet to calculate the four percentages of accumulated water deficit. From this data, the subsequent need for irrigation in any one of the water-use treatments could be determined. In brief, all the plants received the same amount of water at each irrigation, but how often they received it was determined by their water-use percentage of ETo treatment . This low water-tolerance screening is somewhat unique to the needs of a California introduction program, since most states do not deal with complete drought from May to November each year.After the first summer of regular irrigation followed by wintering over in open field conditions, four species had suffered 50% or greater mortality, leaving six species in sufficient numbers to collect data . The species that did not survive the first year were coast gum plant, California beach aster, seaside daisy and creeping sage. The species that did survive were Apache plume, California lilac ‘Valley Violet’, serpentine columbine, rosy coral bells, eyelash grass and San Diego sedge. The first three species that did not survive are native to warm coastal areas, as reflected by their common names. Although they had grown well in the UC Davis Arboretum for years, the unmitigated summer heat and cooler winter temperatures of our field-trial site proved too inhospitable for them.

The fourth species that did not survive, creeping sage, was bitten back by frost in winter 2005 and did not transplant well into the clay-loam field soil in spring. However, the few creeping sage plants that did survive spread up to 9 feet in two directions across bare paths where the soil did not stay moist. It is native to well-drained slopes and is probably a good choice for restoration in its native range in the coastal and Sierra foothills, but was not deemed a good selection for most Central Valley gardens with space restrictions and heavier soils.One of the six species that survived in the UC Davis open field, Apache plume, did not advance to the next stage of zone garden trials. It is a woody shrub with small, dissected leaves and a profusion of pink staminate flowers that lend it a fuzzy appearance when in bloom. While the September 2006 plant growth index was higher with moderate levels of irrigation than with either low or high levels , this difference was statistically insignificant . This species bloomed heavily over a long period of time, and showed no signs of disease or pest damage. However, Apache plume also had some undesirable characteristics. Large branches tended to flop over, yielding an untidy, open habit as the season progressed, and the abundant seeds selfsowed rather freely in dry paths and mulched beds.The second woody shrub was a UC Davis Arboretum selection of California lilac that has become our banner species, ‘Valley Violet’. This California lilac performed beautifully at any watering level,plant pot with drainage which was unexpected since so many other species of this genus will not tolerate summer water. It should be noted that July 2006 was exceptionally hot, even for Davis , and yet the lilac’s appearance was unaffected even at the lowest level of summer water. Steady increases in relative plant growth index over the season from 1.15 to 1.45 were observed for all irrigation levels, with no significant difference between the treatments . In the spring, this plant bloomed in profusion from the base of its branches to the tips and was unbothered by pests or disease. This California lilac, with its yearlong deep green color and staggering spring floral display, was eagerly accepted by all the demonstration gardens involved in the next phase of the trial.Two of our herbaceous species, serpentine columbine and rosy coral bells, are naturally found in shady woodland locations. Consequently, they all showed a loss in plant growth index at all irrigation levels during the hottest part of the growing season in our exposed site, with values between 0.7 and 0.9 .

However, there were no statistically significant differences between the irrigation treatments, leading us to conclude that during the hottest months, protection from the sun was more critical to the success of these species than the availability of water. Interestingly, under the highest watering regimen, two of the six columbines died by the end of July and two more died by the end of August, possibly showing an intolerance of wet soil during the hot season. However, the remaining two columbines were already beginning to recover by September when temperatures began to drop, and all irrigation levels for both of these woodland herbaceous species showed dramatic recovery by the following June. Noteworthy in both species was the prolific flower display, far beyond what was observable with specimens in shady locations in the nearby Arboretum during the same year. While both the coral bells and columbine leaves showed signs of sunburn and necrosis during the summer, their flowering seemed to benefit from the availability of light during the winter and spring months. Both were attractive to bees and syrphid flies, but were unbothered by pests or diseases. So, even though our test site’s exposure was damaging to foliage, their mere survival under these conditions, combined with their spring beauty and attraction of beneficial insects, caused us to advance them to the next phase of the trial with a recommendation for planting sites with at least afternoon shade during the summer. Plants suited to dry shade are sorely lacking in the nursery trade, making serpentine columbine and rosy coral bells good introduction candidates.Also called blue grama grass, eyelash grass is a bunchtype grass with a wide native range in prairies throughout North America. The amount of water it received in our trial made no significant difference in the amount of summer growth, with a September relative plant growth index of 1.9 to 2.0 . Regardless of the amount of water, this species maintained a neat, fountain-form habit desirable for an ornamental grass, and had no pest or disease problems. For these reasons, we advanced eyelash grass to the zone garden trials.San Diego sedge showed an unexpected toughness and drought tolerance for a plant that grows along streams in the wild. It sent up handsome flower spikes that matured to an attractive, buff-colored seed head held above sword-shaped leaves. None of these seeds has been observed to self-sow in the field, making it unlikely to be invasive in dry areas. At all irrigation levels, the plants showed consistent, positive changes in plant growth indices until the end of August, when growth leveled off, presumably in favor of seed production . San Diego sedge plants irrigated at the two lowest water levels did show slightly lower relative growth indices as the season progressed, with those given the second lowest water level inexplicably displaying the lowest relative plant growth index. However, the only statistically significant differences were between the low-medium and high-medium treatments in September . Plants at all irrigation levels became more attractive as the season progressed, and they were pest-free and disease-free. There was no consistent pattern to which watering level the plants preferred, making San Diego sedge a good candidate for a strong structural element in a variety of garden situations.The key to the next stage of this endeavor was the Master Gardener Program, which is coordinated by UC Cooperative Extension. Because these programs are located in most counties throughout the state, they are uniquely situated to grow and collect data on the plants that are advanced from the first phase of the trials. Many counties have demonstration gardens, which make perfect sites for both data collection and exposure to the public. The counties currently participating in the second phase of the native plant trials are Shasta , Placer/Nevada , Alameda , Santa Clara , Mariposa , Fresno and San Diego . The sites include coastal, inland valley and low mountain gardens, but all are within the boundaries of the climate zones recognized as “Mediterranean.” As plants became available beginning in fall 2006 through fall 2007, each site was provided with six plants each of several prospective species advanced from the irrigation trial. Master Gardeners in these areas have planted, tended and collected data on the plants provided. They are taking monthly measurements using the same protocol as the plant growth index used in the field trial. Soil types have been noted, irrigation frequency is being tracked and any unusual weather events noted. In addition, each garden is supplied with data sheets that allow them to rate each plant on a scale of 1 to 5 each month infive categories: foliage, flowering, pest resistance, disease resistance and overall vigor. Table 3 and figure 4 provide examples of the first year’s compiled observations for rosy coral bells.

However, as pH decreased, Cd removal efficiency in tests without nitrate addition was relatively higher than in tests with nitrate addition, especially at low pH conditions. This indicates that the removal capacity of iron hydroxide or iron oxide derived from the reaction between nZVI and nitrate is much lower than that of pristine nZVI. As seen in Fig. 3, the removal efficiency in both reaction systems increased by more than 20% when pH increased from 7.5 to 8.0, and 15% as pH increased from 8.0 to 8.5. Meanwhile, in a control test a significant increase in Cd removal efficiency was observed at pH 8.5 , although Cd started to precipitate out from water at pH
8.0 . This meant the increase in Cd removal efficiency was mainly due to the presence of nZVI. The sharp increase in removal efficiency and capacity may be due to three main reasons: the critical pH value for Cd hydrolysis þ and Cd23 þ) and precipitation 2) is 8.0 , which may have contributed to the increased removal rate through electrostatic interaction and deposition; the isoelectric point of nZVI is around 8.1 , below which nZVI particles are positively charged and above which they are negatively charged. The negatively charged surface at pH > IEP favors Cd adsorption due to strong electrostatic attraction. Thus, the change of surface charge of nZVI may also have contributed to the increased removal of Cd; and high pH, especially above 7, could also improve Cd adsorption on iron oxide . Comparing the results of these two series of experiments, the enhanced Cd removal capacity in the presence of nitrate most likely resulted from elevated solution pH. Specific sorption may have also contributed to Cd removal because of the relatively high removal efficiency observed around pH 6 .Under global warming and climate change,25 liter pot cultivated plants are encountering increased biotic and abiotic stresses, which lead to reductions of plant growth and reproduction and consequently economic losses. The use of plant endophytic bacteria to promote plant growth and increase tolerance of environmental stresses has provided an alternative to standard agricultural practices that has fewer safety concerns.

Endophytic bacteria can be defined as non-pathogenic bacteria that colonize the interior of host plants and can be isolated from surface-sterilized plant tissues. These bacteria can obtain a constant nutrient supply from host plants by living inside the plants and having close contact with plant cells. The endophytic bacteria colonization process is usually initiated at wounds and cracks in the roots by a rhizospheric population of the bacteria in the soil. After entering the plant roots, endophytic bacteria can systemically colonize the above ground parts of plants, including stems and leaves.Endophytic bacteria communities include five main phyla. Proteobacteria is the most dominant phylum isolated from host plants, which includes α-, β-, and γ-Proteobacteria. Actinobacteria, Planctomycetes, Verrucomicrobia, and Acidobacteria are also commonly identified. The most frequently isolated bacteria genera are Bacillus, Burkholderia, Microbacterium, Micrococcus, Pantoea, Pseudomonas, and Stenotrophomonas, with the two major genera being Bacillus and Pseudomonas. Several factors affect the composition of endophytic bacteria populations, including plant growth conditions, plant age, types of analyzed plant tissues, soil contents, and other environmental factors. Endophytic bacteria can have several beneficial effects on host plants, such as promotion of plant growth and yield, increased resistance to plant pathogens , enhanced tolerance to abiotic stresses, elimination of soil pollutants through the facilitation of phytoremediation, and production of various metabolites with potential applications in agriculture, medicine, and industry. Some endophytic bacteria help host plants acquire increased amounts of limited resources from the environment. This can include enhancing the uptake of nitrogen, phosphorous, or iron by expressing nitrogenase, solubilizing precipitated phosphates, or producing iron-chelating agents in bacteria, respectively. Some endophytic plant-growth-promoting bacteria can increase host plants’ metabolism and nutrient accumulation by providing or regulating various plant hormones, including auxin, cytokinin, gibberellins, or ethylene.

Auxin and ethylene are the two major hormones that affect plant growth and development and that are involved in plant-endophytic bacteria interactions. In addition to these four hormones, several endophytes can utilize signaling pathways mediated by salicylic acid, jasmonic acid, and ethylene to initiate induced systemic resistance and protect host plants from phytopathogen infection. A number of endophytic bacteria can also produce various antibiotics, toxins, hydrolytic enzymes, and antimicrobial volatile organic compounds to limit pathogen infection. We previously isolated a plant endophytic bacterium, Burkholderia sp. strain 869T2, from surface-sterilized root tissues of vetiver grass. Strain 869T2 can also live within banana plants, in which it promoted growth and reduced Fusarium wilt disease occurrence. Genomic sequences of the strain 869T2 contain the gene for 1-aminocyclopropane-1-carboxylate deaminase, which may modulate host plant ethylene levels. Strain 869T2 also has genes related to the synthesis of pyrrolnitrin, which may function as a broad-spectrum anti-fungal agent, as well as dioxin-degradation-related genes. Furthermore, strain 869T2 can degrade the toxic dioxin congener 2,3,7,8-tetrachlorinated dibenzo-p-dioxin , mainly via its 2-haloacid dehalogenase. A recent study compared the genome sequences of 31 Burkholderia spp. and reclassified Burkholderia cenocepacia strain 869T2 as Burkholderia seminalis. We also compared the genome sequences of the strain 869T2 with those of five published B. seminalis strains: FL-5-4-10-S1-D7, FL-5-5-10-S1-D0, Bp9022, Bp8988, and TC3.4.2R3. The strain 869T2 shared 93–95% of its genome with the other five B. seminalis strains. Furthermore, strain 869T2 lacked several genetic loci that are important for human virulence. Based on the results of our analysis of the core genome phylogeny and whole-genome average nucleotide identity , strain 869T2 was classified as B. seminalis. B. seminalis is a member of the Burkholderia cepacia complex , which is a group of Gram-negative, aerobic, non-sporulating, rod-shaped bacteria. Bcc consists of opportunistic human pathogens that exist in patients suffering from cystic fibrosis as well as pathogens of many vegetables and fruits,25 liter plant pot such as onion and banana . Contrary to the pathogenic traits that led to their original discovery, some Bcc bacteria have ecologically beneficial interactions with host plants.

The plant endophytic bacterium B. seminalis strain TC3.4.2R3, isolated from sugarcane, can serve as a bio-control agent to reduce infections with Fusarium oxysporum and the cacao pathogens Moniliophthora perniciosa , Phytophthora citrophtora, P. capsici, and P. palmivoraas well as orchid necrosiscaused by Burkholderia gladioli through the production of pyochelin, a rhamnolipid, and other unidentified diffusible metabolites. Another strain of Burkholderia seminalis, strain R456 isolated from rice rhizosphere soils, decreased the occurrence of rice sheath blight disease caused by Rhizoctonia solani. Furthermore, Burkholderia seminalis strain ASB21 was found to be able to produce the plant hormone auxin, promote rice seedling growth, and reduce aluminum toxicity symptoms in host plants. Similarly, a Burkholderia seminalis strain isolated from Bangalore, India can produce indole acetic acid and enhance tomato seedling growth. Although it is known that Burkholderia seminalis belongs to the plant-growth-promoting rhizobacteria , only limited strains and their promoting abilities are well characterized. In this study, we examined the amounts of IAA produced by B. seminalis strain 869T2 in various growth conditions, detected the strain’s siderophore synthesis and phosphate solubilization abilities, and demonstrated its growth-promoting abilities in several leafy vegetables, including pak choi, lettuce, and amaranth. Indole acetic acid production was determined as described previously, with minor modifications. Bacterial cultures were grown on LB media containing 100 µg mL−1 of tryptophan with different pH levels and appropriate antibiotic for 48 h at selected temperatures . Bacteria were also cultured on M9 salt media at 30 ◦C for 48 h with 100 µg mL−1 of tryptophan and 2% of different kinds of sugar: glucose, fructose, or sucrose. Fully grown bacteria cultures were then centrifuged at 5000 rpm for 10 min, and the supernatant was passed through a syringe filter with a pore size of 0.2 µm to remove bacteria. The 500 µL of supernatant was mixed with 1 mL of the Salkowski reagent and incubated at room temperature for 25 min. Finally, the concentrations of IAA in the supernatants were determined by comparison of the absorbance measured at 530 nm with a standard curve of 0–100 µg mL−1 IAA.Various growth parameters of different plant species were measured at selected days, ranging from 14 to 80 days, after inoculation with strain 869T2. The fresh weight, dry weight, and length of leaves and roots as well as the width, number, and surface area of leaves were measured in harvested pak choi, lettuce, and Chinese amaranth as described previously. The fresh weight, length, number, and color of fruits of hot pepper and okra were recorded following previously described methods. The chlorophyll content of the lettuce leaves was measured using a previously published protocol. Chlorophyll was extracted from the leaves with N, N-Dimethylformamide for 1 hour in the dark, and chlorophyll a and b concentrations were calculated from the absorbance of the crude extract at 647 and 664 nm. Anthocyanin concentrations were determined using a published acidified methanol method. Hot pepper fruits were first ground with liquid nitrogen. Acidified methanol was then mixed with the ground materials for 10 min in darkness with shaking. These crude extracts were subsequently mixed with an extraction solvent containing 1:1 chloroform:water to isolate anthocyanins. After centrifugation, the absorbance of the supernatant was read at 530 and 657 nm by the spectrophotometer, and anthocyanin contents were calculated from these values. The effects of pH were also examined by culturing strain 869T2 in LB media at 30 ◦C over a pH range of 4 to 9. Strain 869T2 was able to grow over this entire pH range . The results shown in Figure 1D demonstrate that IAA production was at a similar level when bacteria were grown at pH 6 to 9, whereas the IAA amount decreased 44.0% when bacteria were grown at pH 4. Additionally, three different sugars, glucose, fructose, and sucrose, were used in the minimal medium to examine the effects of different carbon sources on IAA production.

Strain 869T2 grew similarly in the M9 salt media with different kinds of sugars . The results shown in Figure 1F indicate that when strain 869T2 was grown in the media with two kinds of monosaccharide, glucose and fructose, the IAA amounts were higher than for the bacteria grown in the media with sucrose. We further investigated whether strain 869T2 had other plant-growth-promoting traits, including siderophore production and phosphate solubilization abilities, with agar plate assays. Supplementary Materials Figure S1A shows that the strain 869T2 colonies exposed to CAS agarose turned yellow, indicating the siderophore production ability of strain 869T2. Furthermore, Figure S1B reveals that the formation of halos around the strain 869T2 colonies grown in Pikovskaya’s agar medium with 0.5% tricalcium phosphate suggests that strain 869T2 may have the ability to solubilize phosphate.A previous study by Ho et al. demonstrated that strain 869T2 promoted plant growth in banana, a monocot. Here, the growth promotion ability of strain 869T2 was tested in three different eudicot plants from the Brassicaceae family, namely Arabidopsis thaliana, ching chiang pak choi, and pak choi. Because strain 869T2 produced relatively higher amounts of IAA at 25 ◦C to 37 ◦C , we cultured strain 869T2 at three different temperatures, 25 ◦C, 30 ◦C, and 37 ◦C. Subsequently Arabidopsis thaliana ecotype Columbia was inoculated with these strains to determine which strain had the best plant growth promotion ability. We confirmed the endophytic colonization of the Arabidopsis plants by strain 869T2 by reisolating the bacteria from surface-sterilized inoculated plant tissues. The identities of the isolated bacteria were determined via sequencing and phylogenetic analysis of the 16S ribosomal RNA gene. Subsequently, different plant growth parameters were examined in Arabidopsis plants inoculated with strain 869T2 and in mockinoculated controls. Two weeks after inoculation, the presence of strain 869T2 increased the average fresh weight , rosette diameter , root length , number of leaves , total leaf area per plant , leaf area per leaf , number of inflorescences , and number of siliques of Arabidopsis plants more than 1.5- to 2.1-fold compared with mock-inoculated controls. As shown in Figure 2I–K, the overall size and number of leaves of plants inoculated with strain 869T2 were greater than those of control plants, indicating that strain 869T2 promoted Arabidopsis plant growth. Furthermore, when the plants were inoculated with strain 869T2 grown at 30 ◦C, the average root length and average total leaf area per plant were slightly higher than for the strains grown at 25 ◦C and 37 ◦C.

This branch of the immune system known as pathogen-triggered immunity is the first line of active defense against infection. Human pathogen on plants is an emerging field that only recently has caught the attention of plant biologists and phytopathologists. A few studies have been reported in the last 5–10 years, which focused on the most well studied PAMPs, flagellin and lipopolysaccharide , in the interaction of human pathogens with plants. Table 1 lists the plants, bacterial strains, and method details for such studies.Flagellin, the structural component of flagellum in bacteria, is involved in bacterial attachment and motility on the plant , is recognized by plant through the FLS2 receptor , and induces plant defenses . Similar to the well-studied PTI elicitor flg22 , the flg22 epitope of S. enterica serovar Typhimurium 14028 is also an effective PAMP and elicitor of downstream immune responses in Arabidopsis , tobacco, and tomato plants . Flagellum-deficient mutants of S. enterica serovar Typhimurium 14028 are better colonizers of wheat, alfalfa, and Arabidopsis roots as compared to the wild type bacterium further suggesting that the Salmonella flagellum induces plant defenses that may restrict bacterial colonization of several plant organs. However, the Salmonella flg22 peptide is not the only PAMP for elicitation of plant immune response as fls2mutant of Arabidopsis still shows a low level of PTI activation in response to this PAMP . Purified flagellin or derived epitopes of E. coli O157:H7 has not been used to induce plant defenses. However, flagellum-deficient mutant of this strain does not activate the SA-dependent BGL2 gene promoter as much as the wild type strain and shows larger population in Arabidopsis than the wild type strain further suggesting that surface structures in the bacterial cell are perceived by plants. The differences in responses observed could be attributed to the presence of other microbial signatures eliciting plant defense.Although flagellin sequences from S. enterica strains and other bacteria are highly conserved,best vertical garden system even a minor change of five amino acids in the flg22 epitope leads to reduced activation of PTI in Arabidopsis, tobacco, and tomato plants .

Adding to the specificity, it has also been shown that Brassicaceae and Solanocecae plants recognize specific flagellin . Hence, evolving variations in flagellin sequences could be a strategy employed by the pathogens to avoid plant recognition, which in turn leads to the development of pathogen- specific immune responses in the plant. Flagella also play an important role in bacterial behavior on the plant. Several studies have pointed out to the usefulness of flagella for attachment to leaf surfaces and movement on plant surfaces .Lipopolysaccharide is a component of the cell wall of Gram-negative bacterial pathogens of animals and plants. In the animal host, LPS is a well-characterized PAMP that is recognized by host Toll-like receptor 4 . In plants however, receptors for LPS have not been discovered yet. Nonetheless, current evidence suggests that human pathogen-derived LPS can be perceived by plants resulting in PTI activation. For instance, on the leaf surface, purified LPS from Pseudomonas aeruginosa, S. Minnesota R595, and E. coli O55:B5 induces strong stomatal closure in Arabidopsis . Purified LPS from Salmonella triggers of ROS production and extracellular alkalinization in tobacco cell suspension but not on tomato leaves suggesting that LPS recognition may be either dependent on experimental conditions or variable among plant species. Genetic evidence suggests that the high activity of SA dependent BGL2 gene promoter in Arabidopsis is dependent on the presence of LPS in E. coli O157:H7 as higher activity of this promoter was observed in the wild type bacterial as compared to its LPS mutant . However, LPS-dependent responses seem not to be sufficient to restrict bacterial survival on plants as the population titer of E. coli O157:H7 LPS mutant or wild type in plant is essentially the same . Additionally, live S. Typhimurium cells do not induce ROS in epidermal tissue of tobacco suggesting that, at least Salmonella, can suppress LPS-induced ROS and extracellular alkalinization. Similar to flagellin, the O-antigen moiety of LPS is not only important for plant perception of bacterial cells, but also for bacterial attachment, fitness, and survival on plants .

One of the earliest PTI responses in plants is stomatal closure that greatly decreases the rate of pathogen entry into plant’s internal tissues. This response requires molecular components of PTI including such as flagellin and LPS perception and hormone perception and signaling . Stomatal immunity is also triggered by the presence of human pathogens S. enterica serovar Typhimurium SL1344 and E. coli O157:H7 , albeit at various levels. For instance, E. coli O157:H7 induces a strong stomatal immunity and Salmonella SL1344 elicits only a transient stomatal closure in both Arabidopsis and lettuce suggesting that the bacterial strain SL1344 can either induce weaker or subvert stomata-based defense. Active suppression of stomatal closure by SL1344 may be unlikely because it cannot re-open dark-closed stomata . However, it is possible that signaling pathways underlying bacterium-triggered and dark-induced stomatal closure are not entirely overlapping and SL1344 acts on immunity- specific signaling to subvert stomatal closure.Recognition of PAMPs by PRRs leads to several hallmark cellular defense responses that are categorized based on the timing of response. Zipfel and Robatzek have discussed that early responses occur within seconds to minutes of recognition including ion fluxes, extracellular alkalinization, and oxidative burst. Intermediate responses occur within minutes to hours including stomatal closure, ethylene production, mitogen-activated protein kinase signaling, and transcriptional reprogramming. Late responses occur from hours to days and involve callose deposition, salicylic acid accumulation, and defense gene transcription. These hallmark plant cellular defenses have also been tested for both E. coli and S. enterica . In particular, S. enterica infection results in the induction of MPK3/MPK6 kinase activity and plant defense-associated genes PDF1.2, PR1, and PR2 in Arabidopsis leaves as well as PR1, PR4, and PR5 in lettuce . MPK6 activation in Arabidopsis is independent of FLS2 , indicating that flagellin is not the only active PAMP of Salmonella and plant response to other PAMPs may converge at MAPK signaling.

Direct comparison of the PR1 gene expression in Arabidopsis indicated that both E. coli O157:H7 and Salmonella SL1344 are able to induce this defense marker gene, however at difference levels . The PR1 gene induction is low in SL1344-infected plants indicating that immune responses are either weaker or are suppressed by Salmonella.The ethylene-insensitive mutant of Arabidopsis, ein2, supports higher Salmonella 14028 inside whole seedlings as compared to the wild type Col-0 plants . Furthermore, addition of a specific inhibitor of ethylene mediated signaling, 1- methylcyclopropene , to the growth medium resulted in increased S. enterica 14028 endophytic colonization of Medicago truncatula, but not M. sativum, roots and hypocotyls suggesting that the role of endogenous ethylene signaling maybe be specific to each plant-bacterium interaction. However, ethylene signaling may play a contrasting role during fruit contamination. Tomato mutants with defects in ethylene synthesis, perception, and signal transduction show significantly reduced Salmonella proliferation within their fruits as compared to the wild type control .Similar to the ein2 mutant, the coronatine-insensitive mutant of Arabidopsis, coi1-16, also supports high Salmonella 14028 inside whole seedlings . Along with the induction of the jasmonate-responsive gene PDF1.2 addressed in the same study and mentioned above, it seems that jasmonate signaling isalso an important component to restrict Salmonella infection in, at least, Arabidopsis. These results are surprising as coi1 mutants are well known to have increased resistant to various bacterial pathogen of plants, such as P. syringae, but not to fungal or viral pathogens .Two genetic lines of Arabidopsis has been extensively used to determine the role of salicylic acid in plant defenses against phytopathogens,frambuesa cultivo the transgenic nahG plant that cannot accumulate SA and the null mutant npr1 that is disrupted in both SA-dependent and -independent defense responses . Both of these plant lines support higher populations of Salmonella 14028 inside their roots and seedlings as compared to the wild type plant. NPR1-dependent signaling is important reduce the population of the curli-negative strain of E. coli O157:H7 43895 but not for the curli-positive strain 86-24 in Arabidopsis leaves . Although only a few strains of Salmonella and E. coli have been used, there is an emerging patterns suggesting that SA itself and activation of SA-signaling can potentially restrict HPOP. In attempts to understand the overall cellular transcriptional response to human bacterial pathogens, global transcriptomic analyses have been used. Thilmony et al. showed that E. coli O157:H7 regulates PTI-associated genes in Arabidopsis leaves, albeit in a flagellin-independent manner. A similar transcriptomic analysis with medium-grown Arabidopsis seedlings 2h after inoculation with S. enterica serovar Typhimurium 14028, E. coli K-12, and P. syringae pv. tomato DC3000 showed a strong overlap among genes responsive to each bacterial infection suggesting a common mechanism of plant basal response toward bacteria . Gene expression analysis of Medicago truncatula seedlings root-inoculated with only two bacterial cells per plant indicated that 83 gene probes were commonly regulated in response to S. enterica and E. coli O157:H7 . All together, these studies indicate that each human pathogenic bacterium can modulate specific plant genes beyond a basal defense response; however the mechanisms for plant-bacterium specificity are largely unknown.Successful virulent pathogens of plants are able to defeat this army plant defense by employing its own set of artillery and cause disease in the host plant .

In incompatible interactions , the host plant already has pre-evolved molecules that recognize these effectors and cause a specific defense response to this pathogen. This specific response is called effector-triggered immunity . Because the type 3-secretion system is important for the virulence of both animal and plant pathogenic bacteria on their natural hosts as evidenced by the use of bacterial mutants, it is reasonable to expect that T3SS would be important for HPOP as well. However, animal and plant cell surfaces are structurally different; the plant cells wall seems to be impenetrable by the secretion needle of the extracellular animal pathogens as discussed by He et al. raising the question of how these effectors can reach the plant cytoplasm and interfere with plant defenses. To date, there is no evidence for the ability of human pathogens to inject T3SS effectors inside plant cells. It is possible that the T3SS is still active on the plant cell surface and the effectors are secreted into the plant apoplast. If that is the case, however, plant membrane receptors would be necessary to recognize the effectors and trigger plant cellular responses. Nevertheless, it has been observed that the T3SS mutant of E. coli O157:H7, escN, has reduced ability to attach to and colonize baby spinach leaves similar to the fliC mutant . Furthermore, apoplastic population of T3SS structural mutants of S. enterica serovar Typhimurium 14028 is smaller than that of the wild type bacterium in Arabidopsis leaves and plant defense-associated genes are up-regulated for longer time by the prgH mutant than wild type Salmonella in Arabidopsis seedlings . Contrary to these findings, Iniguez et al. reported that two Salmonella 14028 T3SS-SPI1, the structural mutant spaS and the effector mutant sipB, hypercolonize roots and hypocotyls of M. sativum and fail to induce SA-dependent PR1 promoter in Arabidopsis leaves. More studies need to be conducted to conclude whether T3SS of Salmonella acts as “recognizable” surface structure similar to flagellum and/or as a conduit to deliver effectors in plant tissues and trigger ETI. It is worth mentioning that T3SS and effectors of the phytopathogen P. syringae pv. syringae have functions on ETI as well as bacterial fitness on plant surface and the filamentous T3SS protein EspA is required for E. coli O157:H7 attachment to arugula leaves . The invA structural mutant, that is defective in all T3SS-1 system-associated phenotypes, induces high ROS and extracellular alkalinizing in tobacco BY-2 cell suspension and hypersensitive reaction in tobacco leaves as compared to the wild type strain suggesting that T3SS is important for this suppression of immunity. However, Shirron and Yaron also reported that plant response to the regulatory mutant phoP that modulates the expression of many effector proteins and membrane components , is no different to that of the wild type bacterium. These findings raised the question whether the phenotypes observed are due to the T3SS structure itself or due to the translocated effectors.